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env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_glm/__init__.py
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# License: BSD 3 clause
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from .glm import (
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GammaRegressor,
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PoissonRegressor,
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TweedieRegressor,
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_GeneralizedLinearRegressor,
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)
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__all__ = [
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"_GeneralizedLinearRegressor",
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"PoissonRegressor",
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"GammaRegressor",
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"TweedieRegressor",
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]
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"""
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Newton solver for Generalized Linear Models
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"""
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# Author: Christian Lorentzen <[email protected]>
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# License: BSD 3 clause
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|
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import warnings
|
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from abc import ABC, abstractmethod
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import numpy as np
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import scipy.linalg
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import scipy.optimize
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from ..._loss.loss import HalfSquaredError
|
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from ...exceptions import ConvergenceWarning
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from ...utils.optimize import _check_optimize_result
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from .._linear_loss import LinearModelLoss
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class NewtonSolver(ABC):
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"""Newton solver for GLMs.
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This class implements Newton/2nd-order optimization routines for GLMs. Each Newton
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iteration aims at finding the Newton step which is done by the inner solver. With
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Hessian H, gradient g and coefficients coef, one step solves:
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H @ coef_newton = -g
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For our GLM / LinearModelLoss, we have gradient g and Hessian H:
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g = X.T @ loss.gradient + l2_reg_strength * coef
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H = X.T @ diag(loss.hessian) @ X + l2_reg_strength * identity
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Backtracking line search updates coef = coef_old + t * coef_newton for some t in
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(0, 1].
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This is a base class, actual implementations (child classes) may deviate from the
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above pattern and use structure specific tricks.
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Usage pattern:
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- initialize solver: sol = NewtonSolver(...)
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- solve the problem: sol.solve(X, y, sample_weight)
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References
|
46 |
+
----------
|
47 |
+
- Jorge Nocedal, Stephen J. Wright. (2006) "Numerical Optimization"
|
48 |
+
2nd edition
|
49 |
+
https://doi.org/10.1007/978-0-387-40065-5
|
50 |
+
|
51 |
+
- Stephen P. Boyd, Lieven Vandenberghe. (2004) "Convex Optimization."
|
52 |
+
Cambridge University Press, 2004.
|
53 |
+
https://web.stanford.edu/~boyd/cvxbook/bv_cvxbook.pdf
|
54 |
+
|
55 |
+
Parameters
|
56 |
+
----------
|
57 |
+
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
|
58 |
+
Initial coefficients of a linear model.
|
59 |
+
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
|
60 |
+
i.e. one reconstructs the 2d-array via
|
61 |
+
coef.reshape((n_classes, -1), order="F").
|
62 |
+
|
63 |
+
linear_loss : LinearModelLoss
|
64 |
+
The loss to be minimized.
|
65 |
+
|
66 |
+
l2_reg_strength : float, default=0.0
|
67 |
+
L2 regularization strength.
|
68 |
+
|
69 |
+
tol : float, default=1e-4
|
70 |
+
The optimization problem is solved when each of the following condition is
|
71 |
+
fulfilled:
|
72 |
+
1. maximum |gradient| <= tol
|
73 |
+
2. Newton decrement d: 1/2 * d^2 <= tol
|
74 |
+
|
75 |
+
max_iter : int, default=100
|
76 |
+
Maximum number of Newton steps allowed.
|
77 |
+
|
78 |
+
n_threads : int, default=1
|
79 |
+
Number of OpenMP threads to use for the computation of the Hessian and gradient
|
80 |
+
of the loss function.
|
81 |
+
|
82 |
+
Attributes
|
83 |
+
----------
|
84 |
+
coef_old : ndarray of shape coef.shape
|
85 |
+
Coefficient of previous iteration.
|
86 |
+
|
87 |
+
coef_newton : ndarray of shape coef.shape
|
88 |
+
Newton step.
|
89 |
+
|
90 |
+
gradient : ndarray of shape coef.shape
|
91 |
+
Gradient of the loss w.r.t. the coefficients.
|
92 |
+
|
93 |
+
gradient_old : ndarray of shape coef.shape
|
94 |
+
Gradient of previous iteration.
|
95 |
+
|
96 |
+
loss_value : float
|
97 |
+
Value of objective function = loss + penalty.
|
98 |
+
|
99 |
+
loss_value_old : float
|
100 |
+
Value of objective function of previous itertion.
|
101 |
+
|
102 |
+
raw_prediction : ndarray of shape (n_samples,) or (n_samples, n_classes)
|
103 |
+
|
104 |
+
converged : bool
|
105 |
+
Indicator for convergence of the solver.
|
106 |
+
|
107 |
+
iteration : int
|
108 |
+
Number of Newton steps, i.e. calls to inner_solve
|
109 |
+
|
110 |
+
use_fallback_lbfgs_solve : bool
|
111 |
+
If set to True, the solver will resort to call LBFGS to finish the optimisation
|
112 |
+
procedure in case of convergence issues.
|
113 |
+
|
114 |
+
gradient_times_newton : float
|
115 |
+
gradient @ coef_newton, set in inner_solve and used by line_search. If the
|
116 |
+
Newton step is a descent direction, this is negative.
|
117 |
+
"""
|
118 |
+
|
119 |
+
def __init__(
|
120 |
+
self,
|
121 |
+
*,
|
122 |
+
coef,
|
123 |
+
linear_loss=LinearModelLoss(base_loss=HalfSquaredError(), fit_intercept=True),
|
124 |
+
l2_reg_strength=0.0,
|
125 |
+
tol=1e-4,
|
126 |
+
max_iter=100,
|
127 |
+
n_threads=1,
|
128 |
+
verbose=0,
|
129 |
+
):
|
130 |
+
self.coef = coef
|
131 |
+
self.linear_loss = linear_loss
|
132 |
+
self.l2_reg_strength = l2_reg_strength
|
133 |
+
self.tol = tol
|
134 |
+
self.max_iter = max_iter
|
135 |
+
self.n_threads = n_threads
|
136 |
+
self.verbose = verbose
|
137 |
+
|
138 |
+
def setup(self, X, y, sample_weight):
|
139 |
+
"""Precomputations
|
140 |
+
|
141 |
+
If None, initializes:
|
142 |
+
- self.coef
|
143 |
+
Sets:
|
144 |
+
- self.raw_prediction
|
145 |
+
- self.loss_value
|
146 |
+
"""
|
147 |
+
_, _, self.raw_prediction = self.linear_loss.weight_intercept_raw(self.coef, X)
|
148 |
+
self.loss_value = self.linear_loss.loss(
|
149 |
+
coef=self.coef,
|
150 |
+
X=X,
|
151 |
+
y=y,
|
152 |
+
sample_weight=sample_weight,
|
153 |
+
l2_reg_strength=self.l2_reg_strength,
|
154 |
+
n_threads=self.n_threads,
|
155 |
+
raw_prediction=self.raw_prediction,
|
156 |
+
)
|
157 |
+
|
158 |
+
@abstractmethod
|
159 |
+
def update_gradient_hessian(self, X, y, sample_weight):
|
160 |
+
"""Update gradient and Hessian."""
|
161 |
+
|
162 |
+
@abstractmethod
|
163 |
+
def inner_solve(self, X, y, sample_weight):
|
164 |
+
"""Compute Newton step.
|
165 |
+
|
166 |
+
Sets:
|
167 |
+
- self.coef_newton
|
168 |
+
- self.gradient_times_newton
|
169 |
+
"""
|
170 |
+
|
171 |
+
def fallback_lbfgs_solve(self, X, y, sample_weight):
|
172 |
+
"""Fallback solver in case of emergency.
|
173 |
+
|
174 |
+
If a solver detects convergence problems, it may fall back to this methods in
|
175 |
+
the hope to exit with success instead of raising an error.
|
176 |
+
|
177 |
+
Sets:
|
178 |
+
- self.coef
|
179 |
+
- self.converged
|
180 |
+
"""
|
181 |
+
opt_res = scipy.optimize.minimize(
|
182 |
+
self.linear_loss.loss_gradient,
|
183 |
+
self.coef,
|
184 |
+
method="L-BFGS-B",
|
185 |
+
jac=True,
|
186 |
+
options={
|
187 |
+
"maxiter": self.max_iter,
|
188 |
+
"maxls": 50, # default is 20
|
189 |
+
"iprint": self.verbose - 1,
|
190 |
+
"gtol": self.tol,
|
191 |
+
"ftol": 64 * np.finfo(np.float64).eps,
|
192 |
+
},
|
193 |
+
args=(X, y, sample_weight, self.l2_reg_strength, self.n_threads),
|
194 |
+
)
|
195 |
+
self.n_iter_ = _check_optimize_result("lbfgs", opt_res)
|
196 |
+
self.coef = opt_res.x
|
197 |
+
self.converged = opt_res.status == 0
|
198 |
+
|
199 |
+
def line_search(self, X, y, sample_weight):
|
200 |
+
"""Backtracking line search.
|
201 |
+
|
202 |
+
Sets:
|
203 |
+
- self.coef_old
|
204 |
+
- self.coef
|
205 |
+
- self.loss_value_old
|
206 |
+
- self.loss_value
|
207 |
+
- self.gradient_old
|
208 |
+
- self.gradient
|
209 |
+
- self.raw_prediction
|
210 |
+
"""
|
211 |
+
# line search parameters
|
212 |
+
beta, sigma = 0.5, 0.00048828125 # 1/2, 1/2**11
|
213 |
+
eps = 16 * np.finfo(self.loss_value.dtype).eps
|
214 |
+
t = 1 # step size
|
215 |
+
|
216 |
+
# gradient_times_newton = self.gradient @ self.coef_newton
|
217 |
+
# was computed in inner_solve.
|
218 |
+
armijo_term = sigma * self.gradient_times_newton
|
219 |
+
_, _, raw_prediction_newton = self.linear_loss.weight_intercept_raw(
|
220 |
+
self.coef_newton, X
|
221 |
+
)
|
222 |
+
|
223 |
+
self.coef_old = self.coef
|
224 |
+
self.loss_value_old = self.loss_value
|
225 |
+
self.gradient_old = self.gradient
|
226 |
+
|
227 |
+
# np.sum(np.abs(self.gradient_old))
|
228 |
+
sum_abs_grad_old = -1
|
229 |
+
|
230 |
+
is_verbose = self.verbose >= 2
|
231 |
+
if is_verbose:
|
232 |
+
print(" Backtracking Line Search")
|
233 |
+
print(f" eps=10 * finfo.eps={eps}")
|
234 |
+
|
235 |
+
for i in range(21): # until and including t = beta**20 ~ 1e-6
|
236 |
+
self.coef = self.coef_old + t * self.coef_newton
|
237 |
+
raw = self.raw_prediction + t * raw_prediction_newton
|
238 |
+
self.loss_value, self.gradient = self.linear_loss.loss_gradient(
|
239 |
+
coef=self.coef,
|
240 |
+
X=X,
|
241 |
+
y=y,
|
242 |
+
sample_weight=sample_weight,
|
243 |
+
l2_reg_strength=self.l2_reg_strength,
|
244 |
+
n_threads=self.n_threads,
|
245 |
+
raw_prediction=raw,
|
246 |
+
)
|
247 |
+
# Note: If coef_newton is too large, loss_gradient may produce inf values,
|
248 |
+
# potentially accompanied by a RuntimeWarning.
|
249 |
+
# This case will be captured by the Armijo condition.
|
250 |
+
|
251 |
+
# 1. Check Armijo / sufficient decrease condition.
|
252 |
+
# The smaller (more negative) the better.
|
253 |
+
loss_improvement = self.loss_value - self.loss_value_old
|
254 |
+
check = loss_improvement <= t * armijo_term
|
255 |
+
if is_verbose:
|
256 |
+
print(
|
257 |
+
f" line search iteration={i+1}, step size={t}\n"
|
258 |
+
f" check loss improvement <= armijo term: {loss_improvement} "
|
259 |
+
f"<= {t * armijo_term} {check}"
|
260 |
+
)
|
261 |
+
if check:
|
262 |
+
break
|
263 |
+
# 2. Deal with relative loss differences around machine precision.
|
264 |
+
tiny_loss = np.abs(self.loss_value_old * eps)
|
265 |
+
check = np.abs(loss_improvement) <= tiny_loss
|
266 |
+
if is_verbose:
|
267 |
+
print(
|
268 |
+
" check loss |improvement| <= eps * |loss_old|:"
|
269 |
+
f" {np.abs(loss_improvement)} <= {tiny_loss} {check}"
|
270 |
+
)
|
271 |
+
if check:
|
272 |
+
if sum_abs_grad_old < 0:
|
273 |
+
sum_abs_grad_old = scipy.linalg.norm(self.gradient_old, ord=1)
|
274 |
+
# 2.1 Check sum of absolute gradients as alternative condition.
|
275 |
+
sum_abs_grad = scipy.linalg.norm(self.gradient, ord=1)
|
276 |
+
check = sum_abs_grad < sum_abs_grad_old
|
277 |
+
if is_verbose:
|
278 |
+
print(
|
279 |
+
" check sum(|gradient|) < sum(|gradient_old|): "
|
280 |
+
f"{sum_abs_grad} < {sum_abs_grad_old} {check}"
|
281 |
+
)
|
282 |
+
if check:
|
283 |
+
break
|
284 |
+
|
285 |
+
t *= beta
|
286 |
+
else:
|
287 |
+
warnings.warn(
|
288 |
+
(
|
289 |
+
f"Line search of Newton solver {self.__class__.__name__} at"
|
290 |
+
f" iteration #{self.iteration} did no converge after 21 line search"
|
291 |
+
" refinement iterations. It will now resort to lbfgs instead."
|
292 |
+
),
|
293 |
+
ConvergenceWarning,
|
294 |
+
)
|
295 |
+
if self.verbose:
|
296 |
+
print(" Line search did not converge and resorts to lbfgs instead.")
|
297 |
+
self.use_fallback_lbfgs_solve = True
|
298 |
+
return
|
299 |
+
|
300 |
+
self.raw_prediction = raw
|
301 |
+
|
302 |
+
def check_convergence(self, X, y, sample_weight):
|
303 |
+
"""Check for convergence.
|
304 |
+
|
305 |
+
Sets self.converged.
|
306 |
+
"""
|
307 |
+
if self.verbose:
|
308 |
+
print(" Check Convergence")
|
309 |
+
# Note: Checking maximum relative change of coefficient <= tol is a bad
|
310 |
+
# convergence criterion because even a large step could have brought us close
|
311 |
+
# to the true minimum.
|
312 |
+
# coef_step = self.coef - self.coef_old
|
313 |
+
# check = np.max(np.abs(coef_step) / np.maximum(1, np.abs(self.coef_old)))
|
314 |
+
|
315 |
+
# 1. Criterion: maximum |gradient| <= tol
|
316 |
+
# The gradient was already updated in line_search()
|
317 |
+
check = np.max(np.abs(self.gradient))
|
318 |
+
if self.verbose:
|
319 |
+
print(f" 1. max |gradient| {check} <= {self.tol}")
|
320 |
+
if check > self.tol:
|
321 |
+
return
|
322 |
+
|
323 |
+
# 2. Criterion: For Newton decrement d, check 1/2 * d^2 <= tol
|
324 |
+
# d = sqrt(grad @ hessian^-1 @ grad)
|
325 |
+
# = sqrt(coef_newton @ hessian @ coef_newton)
|
326 |
+
# See Boyd, Vanderberghe (2009) "Convex Optimization" Chapter 9.5.1.
|
327 |
+
d2 = self.coef_newton @ self.hessian @ self.coef_newton
|
328 |
+
if self.verbose:
|
329 |
+
print(f" 2. Newton decrement {0.5 * d2} <= {self.tol}")
|
330 |
+
if 0.5 * d2 > self.tol:
|
331 |
+
return
|
332 |
+
|
333 |
+
if self.verbose:
|
334 |
+
loss_value = self.linear_loss.loss(
|
335 |
+
coef=self.coef,
|
336 |
+
X=X,
|
337 |
+
y=y,
|
338 |
+
sample_weight=sample_weight,
|
339 |
+
l2_reg_strength=self.l2_reg_strength,
|
340 |
+
n_threads=self.n_threads,
|
341 |
+
)
|
342 |
+
print(f" Solver did converge at loss = {loss_value}.")
|
343 |
+
self.converged = True
|
344 |
+
|
345 |
+
def finalize(self, X, y, sample_weight):
|
346 |
+
"""Finalize the solvers results.
|
347 |
+
|
348 |
+
Some solvers may need this, others not.
|
349 |
+
"""
|
350 |
+
pass
|
351 |
+
|
352 |
+
def solve(self, X, y, sample_weight):
|
353 |
+
"""Solve the optimization problem.
|
354 |
+
|
355 |
+
This is the main routine.
|
356 |
+
|
357 |
+
Order of calls:
|
358 |
+
self.setup()
|
359 |
+
while iteration:
|
360 |
+
self.update_gradient_hessian()
|
361 |
+
self.inner_solve()
|
362 |
+
self.line_search()
|
363 |
+
self.check_convergence()
|
364 |
+
self.finalize()
|
365 |
+
|
366 |
+
Returns
|
367 |
+
-------
|
368 |
+
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
|
369 |
+
Solution of the optimization problem.
|
370 |
+
"""
|
371 |
+
# setup usually:
|
372 |
+
# - initializes self.coef if needed
|
373 |
+
# - initializes and calculates self.raw_predictions, self.loss_value
|
374 |
+
self.setup(X=X, y=y, sample_weight=sample_weight)
|
375 |
+
|
376 |
+
self.iteration = 1
|
377 |
+
self.converged = False
|
378 |
+
self.use_fallback_lbfgs_solve = False
|
379 |
+
|
380 |
+
while self.iteration <= self.max_iter and not self.converged:
|
381 |
+
if self.verbose:
|
382 |
+
print(f"Newton iter={self.iteration}")
|
383 |
+
|
384 |
+
self.use_fallback_lbfgs_solve = False # Fallback solver.
|
385 |
+
|
386 |
+
# 1. Update Hessian and gradient
|
387 |
+
self.update_gradient_hessian(X=X, y=y, sample_weight=sample_weight)
|
388 |
+
|
389 |
+
# TODO:
|
390 |
+
# if iteration == 1:
|
391 |
+
# We might stop early, e.g. we already are close to the optimum,
|
392 |
+
# usually detected by zero gradients at this stage.
|
393 |
+
|
394 |
+
# 2. Inner solver
|
395 |
+
# Calculate Newton step/direction
|
396 |
+
# This usually sets self.coef_newton and self.gradient_times_newton.
|
397 |
+
self.inner_solve(X=X, y=y, sample_weight=sample_weight)
|
398 |
+
if self.use_fallback_lbfgs_solve:
|
399 |
+
break
|
400 |
+
|
401 |
+
# 3. Backtracking line search
|
402 |
+
# This usually sets self.coef_old, self.coef, self.loss_value_old
|
403 |
+
# self.loss_value, self.gradient_old, self.gradient,
|
404 |
+
# self.raw_prediction.
|
405 |
+
self.line_search(X=X, y=y, sample_weight=sample_weight)
|
406 |
+
if self.use_fallback_lbfgs_solve:
|
407 |
+
break
|
408 |
+
|
409 |
+
# 4. Check convergence
|
410 |
+
# Sets self.converged.
|
411 |
+
self.check_convergence(X=X, y=y, sample_weight=sample_weight)
|
412 |
+
|
413 |
+
# 5. Next iteration
|
414 |
+
self.iteration += 1
|
415 |
+
|
416 |
+
if not self.converged:
|
417 |
+
if self.use_fallback_lbfgs_solve:
|
418 |
+
# Note: The fallback solver circumvents check_convergence and relies on
|
419 |
+
# the convergence checks of lbfgs instead. Enough warnings have been
|
420 |
+
# raised on the way.
|
421 |
+
self.fallback_lbfgs_solve(X=X, y=y, sample_weight=sample_weight)
|
422 |
+
else:
|
423 |
+
warnings.warn(
|
424 |
+
(
|
425 |
+
f"Newton solver did not converge after {self.iteration - 1} "
|
426 |
+
"iterations."
|
427 |
+
),
|
428 |
+
ConvergenceWarning,
|
429 |
+
)
|
430 |
+
|
431 |
+
self.iteration -= 1
|
432 |
+
self.finalize(X=X, y=y, sample_weight=sample_weight)
|
433 |
+
return self.coef
|
434 |
+
|
435 |
+
|
436 |
+
class NewtonCholeskySolver(NewtonSolver):
|
437 |
+
"""Cholesky based Newton solver.
|
438 |
+
|
439 |
+
Inner solver for finding the Newton step H w_newton = -g uses Cholesky based linear
|
440 |
+
solver.
|
441 |
+
"""
|
442 |
+
|
443 |
+
def setup(self, X, y, sample_weight):
|
444 |
+
super().setup(X=X, y=y, sample_weight=sample_weight)
|
445 |
+
n_dof = X.shape[1]
|
446 |
+
if self.linear_loss.fit_intercept:
|
447 |
+
n_dof += 1
|
448 |
+
self.gradient = np.empty_like(self.coef)
|
449 |
+
self.hessian = np.empty_like(self.coef, shape=(n_dof, n_dof))
|
450 |
+
|
451 |
+
def update_gradient_hessian(self, X, y, sample_weight):
|
452 |
+
_, _, self.hessian_warning = self.linear_loss.gradient_hessian(
|
453 |
+
coef=self.coef,
|
454 |
+
X=X,
|
455 |
+
y=y,
|
456 |
+
sample_weight=sample_weight,
|
457 |
+
l2_reg_strength=self.l2_reg_strength,
|
458 |
+
n_threads=self.n_threads,
|
459 |
+
gradient_out=self.gradient,
|
460 |
+
hessian_out=self.hessian,
|
461 |
+
raw_prediction=self.raw_prediction, # this was updated in line_search
|
462 |
+
)
|
463 |
+
|
464 |
+
def inner_solve(self, X, y, sample_weight):
|
465 |
+
if self.hessian_warning:
|
466 |
+
warnings.warn(
|
467 |
+
(
|
468 |
+
f"The inner solver of {self.__class__.__name__} detected a "
|
469 |
+
"pointwise hessian with many negative values at iteration "
|
470 |
+
f"#{self.iteration}. It will now resort to lbfgs instead."
|
471 |
+
),
|
472 |
+
ConvergenceWarning,
|
473 |
+
)
|
474 |
+
if self.verbose:
|
475 |
+
print(
|
476 |
+
" The inner solver detected a pointwise Hessian with many "
|
477 |
+
"negative values and resorts to lbfgs instead."
|
478 |
+
)
|
479 |
+
self.use_fallback_lbfgs_solve = True
|
480 |
+
return
|
481 |
+
|
482 |
+
try:
|
483 |
+
with warnings.catch_warnings():
|
484 |
+
warnings.simplefilter("error", scipy.linalg.LinAlgWarning)
|
485 |
+
self.coef_newton = scipy.linalg.solve(
|
486 |
+
self.hessian, -self.gradient, check_finite=False, assume_a="sym"
|
487 |
+
)
|
488 |
+
self.gradient_times_newton = self.gradient @ self.coef_newton
|
489 |
+
if self.gradient_times_newton > 0:
|
490 |
+
if self.verbose:
|
491 |
+
print(
|
492 |
+
" The inner solver found a Newton step that is not a "
|
493 |
+
"descent direction and resorts to LBFGS steps instead."
|
494 |
+
)
|
495 |
+
self.use_fallback_lbfgs_solve = True
|
496 |
+
return
|
497 |
+
except (np.linalg.LinAlgError, scipy.linalg.LinAlgWarning) as e:
|
498 |
+
warnings.warn(
|
499 |
+
f"The inner solver of {self.__class__.__name__} stumbled upon a "
|
500 |
+
"singular or very ill-conditioned Hessian matrix at iteration "
|
501 |
+
f"#{self.iteration}. It will now resort to lbfgs instead.\n"
|
502 |
+
"Further options are to use another solver or to avoid such situation "
|
503 |
+
"in the first place. Possible remedies are removing collinear features"
|
504 |
+
" of X or increasing the penalization strengths.\n"
|
505 |
+
"The original Linear Algebra message was:\n"
|
506 |
+
+ str(e),
|
507 |
+
scipy.linalg.LinAlgWarning,
|
508 |
+
)
|
509 |
+
# Possible causes:
|
510 |
+
# 1. hess_pointwise is negative. But this is already taken care in
|
511 |
+
# LinearModelLoss.gradient_hessian.
|
512 |
+
# 2. X is singular or ill-conditioned
|
513 |
+
# This might be the most probable cause.
|
514 |
+
#
|
515 |
+
# There are many possible ways to deal with this situation. Most of them
|
516 |
+
# add, explicitly or implicitly, a matrix to the hessian to make it
|
517 |
+
# positive definite, confer to Chapter 3.4 of Nocedal & Wright 2nd ed.
|
518 |
+
# Instead, we resort to lbfgs.
|
519 |
+
if self.verbose:
|
520 |
+
print(
|
521 |
+
" The inner solver stumbled upon an singular or ill-conditioned "
|
522 |
+
"Hessian matrix and resorts to LBFGS instead."
|
523 |
+
)
|
524 |
+
self.use_fallback_lbfgs_solve = True
|
525 |
+
return
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_glm/glm.py
ADDED
@@ -0,0 +1,904 @@
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|
|
|
1 |
+
"""
|
2 |
+
Generalized Linear Models with Exponential Dispersion Family
|
3 |
+
"""
|
4 |
+
|
5 |
+
# Author: Christian Lorentzen <[email protected]>
|
6 |
+
# some parts and tricks stolen from other sklearn files.
|
7 |
+
# License: BSD 3 clause
|
8 |
+
|
9 |
+
from numbers import Integral, Real
|
10 |
+
|
11 |
+
import numpy as np
|
12 |
+
import scipy.optimize
|
13 |
+
|
14 |
+
from ..._loss.loss import (
|
15 |
+
HalfGammaLoss,
|
16 |
+
HalfPoissonLoss,
|
17 |
+
HalfSquaredError,
|
18 |
+
HalfTweedieLoss,
|
19 |
+
HalfTweedieLossIdentity,
|
20 |
+
)
|
21 |
+
from ...base import BaseEstimator, RegressorMixin, _fit_context
|
22 |
+
from ...utils import check_array
|
23 |
+
from ...utils._openmp_helpers import _openmp_effective_n_threads
|
24 |
+
from ...utils._param_validation import Hidden, Interval, StrOptions
|
25 |
+
from ...utils.optimize import _check_optimize_result
|
26 |
+
from ...utils.validation import _check_sample_weight, check_is_fitted
|
27 |
+
from .._linear_loss import LinearModelLoss
|
28 |
+
from ._newton_solver import NewtonCholeskySolver, NewtonSolver
|
29 |
+
|
30 |
+
|
31 |
+
class _GeneralizedLinearRegressor(RegressorMixin, BaseEstimator):
|
32 |
+
"""Regression via a penalized Generalized Linear Model (GLM).
|
33 |
+
|
34 |
+
GLMs based on a reproductive Exponential Dispersion Model (EDM) aim at fitting and
|
35 |
+
predicting the mean of the target y as y_pred=h(X*w) with coefficients w.
|
36 |
+
Therefore, the fit minimizes the following objective function with L2 priors as
|
37 |
+
regularizer::
|
38 |
+
|
39 |
+
1/(2*sum(s_i)) * sum(s_i * deviance(y_i, h(x_i*w)) + 1/2 * alpha * ||w||_2^2
|
40 |
+
|
41 |
+
with inverse link function h, s=sample_weight and per observation (unit) deviance
|
42 |
+
deviance(y_i, h(x_i*w)). Note that for an EDM, 1/2 * deviance is the negative
|
43 |
+
log-likelihood up to a constant (in w) term.
|
44 |
+
The parameter ``alpha`` corresponds to the lambda parameter in glmnet.
|
45 |
+
|
46 |
+
Instead of implementing the EDM family and a link function separately, we directly
|
47 |
+
use the loss functions `from sklearn._loss` which have the link functions included
|
48 |
+
in them for performance reasons. We pick the loss functions that implement
|
49 |
+
(1/2 times) EDM deviances.
|
50 |
+
|
51 |
+
Read more in the :ref:`User Guide <Generalized_linear_models>`.
|
52 |
+
|
53 |
+
.. versionadded:: 0.23
|
54 |
+
|
55 |
+
Parameters
|
56 |
+
----------
|
57 |
+
alpha : float, default=1
|
58 |
+
Constant that multiplies the penalty term and thus determines the
|
59 |
+
regularization strength. ``alpha = 0`` is equivalent to unpenalized
|
60 |
+
GLMs. In this case, the design matrix `X` must have full column rank
|
61 |
+
(no collinearities).
|
62 |
+
Values must be in the range `[0.0, inf)`.
|
63 |
+
|
64 |
+
fit_intercept : bool, default=True
|
65 |
+
Specifies if a constant (a.k.a. bias or intercept) should be
|
66 |
+
added to the linear predictor (X @ coef + intercept).
|
67 |
+
|
68 |
+
solver : {'lbfgs', 'newton-cholesky'}, default='lbfgs'
|
69 |
+
Algorithm to use in the optimization problem:
|
70 |
+
|
71 |
+
'lbfgs'
|
72 |
+
Calls scipy's L-BFGS-B optimizer.
|
73 |
+
|
74 |
+
'newton-cholesky'
|
75 |
+
Uses Newton-Raphson steps (in arbitrary precision arithmetic equivalent to
|
76 |
+
iterated reweighted least squares) with an inner Cholesky based solver.
|
77 |
+
This solver is a good choice for `n_samples` >> `n_features`, especially
|
78 |
+
with one-hot encoded categorical features with rare categories. Be aware
|
79 |
+
that the memory usage of this solver has a quadratic dependency on
|
80 |
+
`n_features` because it explicitly computes the Hessian matrix.
|
81 |
+
|
82 |
+
.. versionadded:: 1.2
|
83 |
+
|
84 |
+
max_iter : int, default=100
|
85 |
+
The maximal number of iterations for the solver.
|
86 |
+
Values must be in the range `[1, inf)`.
|
87 |
+
|
88 |
+
tol : float, default=1e-4
|
89 |
+
Stopping criterion. For the lbfgs solver,
|
90 |
+
the iteration will stop when ``max{|g_j|, j = 1, ..., d} <= tol``
|
91 |
+
where ``g_j`` is the j-th component of the gradient (derivative) of
|
92 |
+
the objective function.
|
93 |
+
Values must be in the range `(0.0, inf)`.
|
94 |
+
|
95 |
+
warm_start : bool, default=False
|
96 |
+
If set to ``True``, reuse the solution of the previous call to ``fit``
|
97 |
+
as initialization for ``coef_`` and ``intercept_``.
|
98 |
+
|
99 |
+
verbose : int, default=0
|
100 |
+
For the lbfgs solver set verbose to any positive number for verbosity.
|
101 |
+
Values must be in the range `[0, inf)`.
|
102 |
+
|
103 |
+
Attributes
|
104 |
+
----------
|
105 |
+
coef_ : array of shape (n_features,)
|
106 |
+
Estimated coefficients for the linear predictor (`X @ coef_ +
|
107 |
+
intercept_`) in the GLM.
|
108 |
+
|
109 |
+
intercept_ : float
|
110 |
+
Intercept (a.k.a. bias) added to linear predictor.
|
111 |
+
|
112 |
+
n_iter_ : int
|
113 |
+
Actual number of iterations used in the solver.
|
114 |
+
|
115 |
+
_base_loss : BaseLoss, default=HalfSquaredError()
|
116 |
+
This is set during fit via `self._get_loss()`.
|
117 |
+
A `_base_loss` contains a specific loss function as well as the link
|
118 |
+
function. The loss to be minimized specifies the distributional assumption of
|
119 |
+
the GLM, i.e. the distribution from the EDM. Here are some examples:
|
120 |
+
|
121 |
+
======================= ======== ==========================
|
122 |
+
_base_loss Link Target Domain
|
123 |
+
======================= ======== ==========================
|
124 |
+
HalfSquaredError identity y any real number
|
125 |
+
HalfPoissonLoss log 0 <= y
|
126 |
+
HalfGammaLoss log 0 < y
|
127 |
+
HalfTweedieLoss log dependent on tweedie power
|
128 |
+
HalfTweedieLossIdentity identity dependent on tweedie power
|
129 |
+
======================= ======== ==========================
|
130 |
+
|
131 |
+
The link function of the GLM, i.e. mapping from linear predictor
|
132 |
+
`X @ coeff + intercept` to prediction `y_pred`. For instance, with a log link,
|
133 |
+
we have `y_pred = exp(X @ coeff + intercept)`.
|
134 |
+
"""
|
135 |
+
|
136 |
+
# We allow for NewtonSolver classes for the "solver" parameter but do not
|
137 |
+
# make them public in the docstrings. This facilitates testing and
|
138 |
+
# benchmarking.
|
139 |
+
_parameter_constraints: dict = {
|
140 |
+
"alpha": [Interval(Real, 0.0, None, closed="left")],
|
141 |
+
"fit_intercept": ["boolean"],
|
142 |
+
"solver": [
|
143 |
+
StrOptions({"lbfgs", "newton-cholesky"}),
|
144 |
+
Hidden(type),
|
145 |
+
],
|
146 |
+
"max_iter": [Interval(Integral, 1, None, closed="left")],
|
147 |
+
"tol": [Interval(Real, 0.0, None, closed="neither")],
|
148 |
+
"warm_start": ["boolean"],
|
149 |
+
"verbose": ["verbose"],
|
150 |
+
}
|
151 |
+
|
152 |
+
def __init__(
|
153 |
+
self,
|
154 |
+
*,
|
155 |
+
alpha=1.0,
|
156 |
+
fit_intercept=True,
|
157 |
+
solver="lbfgs",
|
158 |
+
max_iter=100,
|
159 |
+
tol=1e-4,
|
160 |
+
warm_start=False,
|
161 |
+
verbose=0,
|
162 |
+
):
|
163 |
+
self.alpha = alpha
|
164 |
+
self.fit_intercept = fit_intercept
|
165 |
+
self.solver = solver
|
166 |
+
self.max_iter = max_iter
|
167 |
+
self.tol = tol
|
168 |
+
self.warm_start = warm_start
|
169 |
+
self.verbose = verbose
|
170 |
+
|
171 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
172 |
+
def fit(self, X, y, sample_weight=None):
|
173 |
+
"""Fit a Generalized Linear Model.
|
174 |
+
|
175 |
+
Parameters
|
176 |
+
----------
|
177 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
178 |
+
Training data.
|
179 |
+
|
180 |
+
y : array-like of shape (n_samples,)
|
181 |
+
Target values.
|
182 |
+
|
183 |
+
sample_weight : array-like of shape (n_samples,), default=None
|
184 |
+
Sample weights.
|
185 |
+
|
186 |
+
Returns
|
187 |
+
-------
|
188 |
+
self : object
|
189 |
+
Fitted model.
|
190 |
+
"""
|
191 |
+
X, y = self._validate_data(
|
192 |
+
X,
|
193 |
+
y,
|
194 |
+
accept_sparse=["csc", "csr"],
|
195 |
+
dtype=[np.float64, np.float32],
|
196 |
+
y_numeric=True,
|
197 |
+
multi_output=False,
|
198 |
+
)
|
199 |
+
|
200 |
+
# required by losses
|
201 |
+
if self.solver == "lbfgs":
|
202 |
+
# lbfgs will force coef and therefore raw_prediction to be float64. The
|
203 |
+
# base_loss needs y, X @ coef and sample_weight all of same dtype
|
204 |
+
# (and contiguous).
|
205 |
+
loss_dtype = np.float64
|
206 |
+
else:
|
207 |
+
loss_dtype = min(max(y.dtype, X.dtype), np.float64)
|
208 |
+
y = check_array(y, dtype=loss_dtype, order="C", ensure_2d=False)
|
209 |
+
|
210 |
+
if sample_weight is not None:
|
211 |
+
# Note that _check_sample_weight calls check_array(order="C") required by
|
212 |
+
# losses.
|
213 |
+
sample_weight = _check_sample_weight(sample_weight, X, dtype=loss_dtype)
|
214 |
+
|
215 |
+
n_samples, n_features = X.shape
|
216 |
+
self._base_loss = self._get_loss()
|
217 |
+
|
218 |
+
linear_loss = LinearModelLoss(
|
219 |
+
base_loss=self._base_loss,
|
220 |
+
fit_intercept=self.fit_intercept,
|
221 |
+
)
|
222 |
+
|
223 |
+
if not linear_loss.base_loss.in_y_true_range(y):
|
224 |
+
raise ValueError(
|
225 |
+
"Some value(s) of y are out of the valid range of the loss"
|
226 |
+
f" {self._base_loss.__class__.__name__!r}."
|
227 |
+
)
|
228 |
+
|
229 |
+
# TODO: if alpha=0 check that X is not rank deficient
|
230 |
+
|
231 |
+
# NOTE: Rescaling of sample_weight:
|
232 |
+
# We want to minimize
|
233 |
+
# obj = 1/(2 * sum(sample_weight)) * sum(sample_weight * deviance)
|
234 |
+
# + 1/2 * alpha * L2,
|
235 |
+
# with
|
236 |
+
# deviance = 2 * loss.
|
237 |
+
# The objective is invariant to multiplying sample_weight by a constant. We
|
238 |
+
# could choose this constant such that sum(sample_weight) = 1 in order to end
|
239 |
+
# up with
|
240 |
+
# obj = sum(sample_weight * loss) + 1/2 * alpha * L2.
|
241 |
+
# But LinearModelLoss.loss() already computes
|
242 |
+
# average(loss, weights=sample_weight)
|
243 |
+
# Thus, without rescaling, we have
|
244 |
+
# obj = LinearModelLoss.loss(...)
|
245 |
+
|
246 |
+
if self.warm_start and hasattr(self, "coef_"):
|
247 |
+
if self.fit_intercept:
|
248 |
+
# LinearModelLoss needs intercept at the end of coefficient array.
|
249 |
+
coef = np.concatenate((self.coef_, np.array([self.intercept_])))
|
250 |
+
else:
|
251 |
+
coef = self.coef_
|
252 |
+
coef = coef.astype(loss_dtype, copy=False)
|
253 |
+
else:
|
254 |
+
coef = linear_loss.init_zero_coef(X, dtype=loss_dtype)
|
255 |
+
if self.fit_intercept:
|
256 |
+
coef[-1] = linear_loss.base_loss.link.link(
|
257 |
+
np.average(y, weights=sample_weight)
|
258 |
+
)
|
259 |
+
|
260 |
+
l2_reg_strength = self.alpha
|
261 |
+
n_threads = _openmp_effective_n_threads()
|
262 |
+
|
263 |
+
# Algorithms for optimization:
|
264 |
+
# Note again that our losses implement 1/2 * deviance.
|
265 |
+
if self.solver == "lbfgs":
|
266 |
+
func = linear_loss.loss_gradient
|
267 |
+
|
268 |
+
opt_res = scipy.optimize.minimize(
|
269 |
+
func,
|
270 |
+
coef,
|
271 |
+
method="L-BFGS-B",
|
272 |
+
jac=True,
|
273 |
+
options={
|
274 |
+
"maxiter": self.max_iter,
|
275 |
+
"maxls": 50, # default is 20
|
276 |
+
"iprint": self.verbose - 1,
|
277 |
+
"gtol": self.tol,
|
278 |
+
# The constant 64 was found empirically to pass the test suite.
|
279 |
+
# The point is that ftol is very small, but a bit larger than
|
280 |
+
# machine precision for float64, which is the dtype used by lbfgs.
|
281 |
+
"ftol": 64 * np.finfo(float).eps,
|
282 |
+
},
|
283 |
+
args=(X, y, sample_weight, l2_reg_strength, n_threads),
|
284 |
+
)
|
285 |
+
self.n_iter_ = _check_optimize_result("lbfgs", opt_res)
|
286 |
+
coef = opt_res.x
|
287 |
+
elif self.solver == "newton-cholesky":
|
288 |
+
sol = NewtonCholeskySolver(
|
289 |
+
coef=coef,
|
290 |
+
linear_loss=linear_loss,
|
291 |
+
l2_reg_strength=l2_reg_strength,
|
292 |
+
tol=self.tol,
|
293 |
+
max_iter=self.max_iter,
|
294 |
+
n_threads=n_threads,
|
295 |
+
verbose=self.verbose,
|
296 |
+
)
|
297 |
+
coef = sol.solve(X, y, sample_weight)
|
298 |
+
self.n_iter_ = sol.iteration
|
299 |
+
elif issubclass(self.solver, NewtonSolver):
|
300 |
+
sol = self.solver(
|
301 |
+
coef=coef,
|
302 |
+
linear_loss=linear_loss,
|
303 |
+
l2_reg_strength=l2_reg_strength,
|
304 |
+
tol=self.tol,
|
305 |
+
max_iter=self.max_iter,
|
306 |
+
n_threads=n_threads,
|
307 |
+
)
|
308 |
+
coef = sol.solve(X, y, sample_weight)
|
309 |
+
self.n_iter_ = sol.iteration
|
310 |
+
else:
|
311 |
+
raise ValueError(f"Invalid solver={self.solver}.")
|
312 |
+
|
313 |
+
if self.fit_intercept:
|
314 |
+
self.intercept_ = coef[-1]
|
315 |
+
self.coef_ = coef[:-1]
|
316 |
+
else:
|
317 |
+
# set intercept to zero as the other linear models do
|
318 |
+
self.intercept_ = 0.0
|
319 |
+
self.coef_ = coef
|
320 |
+
|
321 |
+
return self
|
322 |
+
|
323 |
+
def _linear_predictor(self, X):
|
324 |
+
"""Compute the linear_predictor = `X @ coef_ + intercept_`.
|
325 |
+
|
326 |
+
Note that we often use the term raw_prediction instead of linear predictor.
|
327 |
+
|
328 |
+
Parameters
|
329 |
+
----------
|
330 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
331 |
+
Samples.
|
332 |
+
|
333 |
+
Returns
|
334 |
+
-------
|
335 |
+
y_pred : array of shape (n_samples,)
|
336 |
+
Returns predicted values of linear predictor.
|
337 |
+
"""
|
338 |
+
check_is_fitted(self)
|
339 |
+
X = self._validate_data(
|
340 |
+
X,
|
341 |
+
accept_sparse=["csr", "csc", "coo"],
|
342 |
+
dtype=[np.float64, np.float32],
|
343 |
+
ensure_2d=True,
|
344 |
+
allow_nd=False,
|
345 |
+
reset=False,
|
346 |
+
)
|
347 |
+
return X @ self.coef_ + self.intercept_
|
348 |
+
|
349 |
+
def predict(self, X):
|
350 |
+
"""Predict using GLM with feature matrix X.
|
351 |
+
|
352 |
+
Parameters
|
353 |
+
----------
|
354 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
355 |
+
Samples.
|
356 |
+
|
357 |
+
Returns
|
358 |
+
-------
|
359 |
+
y_pred : array of shape (n_samples,)
|
360 |
+
Returns predicted values.
|
361 |
+
"""
|
362 |
+
# check_array is done in _linear_predictor
|
363 |
+
raw_prediction = self._linear_predictor(X)
|
364 |
+
y_pred = self._base_loss.link.inverse(raw_prediction)
|
365 |
+
return y_pred
|
366 |
+
|
367 |
+
def score(self, X, y, sample_weight=None):
|
368 |
+
"""Compute D^2, the percentage of deviance explained.
|
369 |
+
|
370 |
+
D^2 is a generalization of the coefficient of determination R^2.
|
371 |
+
R^2 uses squared error and D^2 uses the deviance of this GLM, see the
|
372 |
+
:ref:`User Guide <regression_metrics>`.
|
373 |
+
|
374 |
+
D^2 is defined as
|
375 |
+
:math:`D^2 = 1-\\frac{D(y_{true},y_{pred})}{D_{null}}`,
|
376 |
+
:math:`D_{null}` is the null deviance, i.e. the deviance of a model
|
377 |
+
with intercept alone, which corresponds to :math:`y_{pred} = \\bar{y}`.
|
378 |
+
The mean :math:`\\bar{y}` is averaged by sample_weight.
|
379 |
+
Best possible score is 1.0 and it can be negative (because the model
|
380 |
+
can be arbitrarily worse).
|
381 |
+
|
382 |
+
Parameters
|
383 |
+
----------
|
384 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
385 |
+
Test samples.
|
386 |
+
|
387 |
+
y : array-like of shape (n_samples,)
|
388 |
+
True values of target.
|
389 |
+
|
390 |
+
sample_weight : array-like of shape (n_samples,), default=None
|
391 |
+
Sample weights.
|
392 |
+
|
393 |
+
Returns
|
394 |
+
-------
|
395 |
+
score : float
|
396 |
+
D^2 of self.predict(X) w.r.t. y.
|
397 |
+
"""
|
398 |
+
# TODO: Adapt link to User Guide in the docstring, once
|
399 |
+
# https://github.com/scikit-learn/scikit-learn/pull/22118 is merged.
|
400 |
+
#
|
401 |
+
# Note, default score defined in RegressorMixin is R^2 score.
|
402 |
+
# TODO: make D^2 a score function in module metrics (and thereby get
|
403 |
+
# input validation and so on)
|
404 |
+
raw_prediction = self._linear_predictor(X) # validates X
|
405 |
+
# required by losses
|
406 |
+
y = check_array(y, dtype=raw_prediction.dtype, order="C", ensure_2d=False)
|
407 |
+
|
408 |
+
if sample_weight is not None:
|
409 |
+
# Note that _check_sample_weight calls check_array(order="C") required by
|
410 |
+
# losses.
|
411 |
+
sample_weight = _check_sample_weight(sample_weight, X, dtype=y.dtype)
|
412 |
+
|
413 |
+
base_loss = self._base_loss
|
414 |
+
|
415 |
+
if not base_loss.in_y_true_range(y):
|
416 |
+
raise ValueError(
|
417 |
+
"Some value(s) of y are out of the valid range of the loss"
|
418 |
+
f" {base_loss.__name__}."
|
419 |
+
)
|
420 |
+
|
421 |
+
constant = np.average(
|
422 |
+
base_loss.constant_to_optimal_zero(y_true=y, sample_weight=None),
|
423 |
+
weights=sample_weight,
|
424 |
+
)
|
425 |
+
|
426 |
+
# Missing factor of 2 in deviance cancels out.
|
427 |
+
deviance = base_loss(
|
428 |
+
y_true=y,
|
429 |
+
raw_prediction=raw_prediction,
|
430 |
+
sample_weight=sample_weight,
|
431 |
+
n_threads=1,
|
432 |
+
)
|
433 |
+
y_mean = base_loss.link.link(np.average(y, weights=sample_weight))
|
434 |
+
deviance_null = base_loss(
|
435 |
+
y_true=y,
|
436 |
+
raw_prediction=np.tile(y_mean, y.shape[0]),
|
437 |
+
sample_weight=sample_weight,
|
438 |
+
n_threads=1,
|
439 |
+
)
|
440 |
+
return 1 - (deviance + constant) / (deviance_null + constant)
|
441 |
+
|
442 |
+
def _more_tags(self):
|
443 |
+
try:
|
444 |
+
# Create instance of BaseLoss if fit wasn't called yet. This is necessary as
|
445 |
+
# TweedieRegressor might set the used loss during fit different from
|
446 |
+
# self._base_loss.
|
447 |
+
base_loss = self._get_loss()
|
448 |
+
return {"requires_positive_y": not base_loss.in_y_true_range(-1.0)}
|
449 |
+
except (ValueError, AttributeError, TypeError):
|
450 |
+
# This happens when the link or power parameter of TweedieRegressor is
|
451 |
+
# invalid. We fallback on the default tags in that case.
|
452 |
+
return {}
|
453 |
+
|
454 |
+
def _get_loss(self):
|
455 |
+
"""This is only necessary because of the link and power arguments of the
|
456 |
+
TweedieRegressor.
|
457 |
+
|
458 |
+
Note that we do not need to pass sample_weight to the loss class as this is
|
459 |
+
only needed to set loss.constant_hessian on which GLMs do not rely.
|
460 |
+
"""
|
461 |
+
return HalfSquaredError()
|
462 |
+
|
463 |
+
|
464 |
+
class PoissonRegressor(_GeneralizedLinearRegressor):
|
465 |
+
"""Generalized Linear Model with a Poisson distribution.
|
466 |
+
|
467 |
+
This regressor uses the 'log' link function.
|
468 |
+
|
469 |
+
Read more in the :ref:`User Guide <Generalized_linear_models>`.
|
470 |
+
|
471 |
+
.. versionadded:: 0.23
|
472 |
+
|
473 |
+
Parameters
|
474 |
+
----------
|
475 |
+
alpha : float, default=1
|
476 |
+
Constant that multiplies the L2 penalty term and determines the
|
477 |
+
regularization strength. ``alpha = 0`` is equivalent to unpenalized
|
478 |
+
GLMs. In this case, the design matrix `X` must have full column rank
|
479 |
+
(no collinearities).
|
480 |
+
Values of `alpha` must be in the range `[0.0, inf)`.
|
481 |
+
|
482 |
+
fit_intercept : bool, default=True
|
483 |
+
Specifies if a constant (a.k.a. bias or intercept) should be
|
484 |
+
added to the linear predictor (`X @ coef + intercept`).
|
485 |
+
|
486 |
+
solver : {'lbfgs', 'newton-cholesky'}, default='lbfgs'
|
487 |
+
Algorithm to use in the optimization problem:
|
488 |
+
|
489 |
+
'lbfgs'
|
490 |
+
Calls scipy's L-BFGS-B optimizer.
|
491 |
+
|
492 |
+
'newton-cholesky'
|
493 |
+
Uses Newton-Raphson steps (in arbitrary precision arithmetic equivalent to
|
494 |
+
iterated reweighted least squares) with an inner Cholesky based solver.
|
495 |
+
This solver is a good choice for `n_samples` >> `n_features`, especially
|
496 |
+
with one-hot encoded categorical features with rare categories. Be aware
|
497 |
+
that the memory usage of this solver has a quadratic dependency on
|
498 |
+
`n_features` because it explicitly computes the Hessian matrix.
|
499 |
+
|
500 |
+
.. versionadded:: 1.2
|
501 |
+
|
502 |
+
max_iter : int, default=100
|
503 |
+
The maximal number of iterations for the solver.
|
504 |
+
Values must be in the range `[1, inf)`.
|
505 |
+
|
506 |
+
tol : float, default=1e-4
|
507 |
+
Stopping criterion. For the lbfgs solver,
|
508 |
+
the iteration will stop when ``max{|g_j|, j = 1, ..., d} <= tol``
|
509 |
+
where ``g_j`` is the j-th component of the gradient (derivative) of
|
510 |
+
the objective function.
|
511 |
+
Values must be in the range `(0.0, inf)`.
|
512 |
+
|
513 |
+
warm_start : bool, default=False
|
514 |
+
If set to ``True``, reuse the solution of the previous call to ``fit``
|
515 |
+
as initialization for ``coef_`` and ``intercept_`` .
|
516 |
+
|
517 |
+
verbose : int, default=0
|
518 |
+
For the lbfgs solver set verbose to any positive number for verbosity.
|
519 |
+
Values must be in the range `[0, inf)`.
|
520 |
+
|
521 |
+
Attributes
|
522 |
+
----------
|
523 |
+
coef_ : array of shape (n_features,)
|
524 |
+
Estimated coefficients for the linear predictor (`X @ coef_ +
|
525 |
+
intercept_`) in the GLM.
|
526 |
+
|
527 |
+
intercept_ : float
|
528 |
+
Intercept (a.k.a. bias) added to linear predictor.
|
529 |
+
|
530 |
+
n_features_in_ : int
|
531 |
+
Number of features seen during :term:`fit`.
|
532 |
+
|
533 |
+
.. versionadded:: 0.24
|
534 |
+
|
535 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
536 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
537 |
+
has feature names that are all strings.
|
538 |
+
|
539 |
+
.. versionadded:: 1.0
|
540 |
+
|
541 |
+
n_iter_ : int
|
542 |
+
Actual number of iterations used in the solver.
|
543 |
+
|
544 |
+
See Also
|
545 |
+
--------
|
546 |
+
TweedieRegressor : Generalized Linear Model with a Tweedie distribution.
|
547 |
+
|
548 |
+
Examples
|
549 |
+
--------
|
550 |
+
>>> from sklearn import linear_model
|
551 |
+
>>> clf = linear_model.PoissonRegressor()
|
552 |
+
>>> X = [[1, 2], [2, 3], [3, 4], [4, 3]]
|
553 |
+
>>> y = [12, 17, 22, 21]
|
554 |
+
>>> clf.fit(X, y)
|
555 |
+
PoissonRegressor()
|
556 |
+
>>> clf.score(X, y)
|
557 |
+
0.990...
|
558 |
+
>>> clf.coef_
|
559 |
+
array([0.121..., 0.158...])
|
560 |
+
>>> clf.intercept_
|
561 |
+
2.088...
|
562 |
+
>>> clf.predict([[1, 1], [3, 4]])
|
563 |
+
array([10.676..., 21.875...])
|
564 |
+
"""
|
565 |
+
|
566 |
+
_parameter_constraints: dict = {
|
567 |
+
**_GeneralizedLinearRegressor._parameter_constraints
|
568 |
+
}
|
569 |
+
|
570 |
+
def __init__(
|
571 |
+
self,
|
572 |
+
*,
|
573 |
+
alpha=1.0,
|
574 |
+
fit_intercept=True,
|
575 |
+
solver="lbfgs",
|
576 |
+
max_iter=100,
|
577 |
+
tol=1e-4,
|
578 |
+
warm_start=False,
|
579 |
+
verbose=0,
|
580 |
+
):
|
581 |
+
super().__init__(
|
582 |
+
alpha=alpha,
|
583 |
+
fit_intercept=fit_intercept,
|
584 |
+
solver=solver,
|
585 |
+
max_iter=max_iter,
|
586 |
+
tol=tol,
|
587 |
+
warm_start=warm_start,
|
588 |
+
verbose=verbose,
|
589 |
+
)
|
590 |
+
|
591 |
+
def _get_loss(self):
|
592 |
+
return HalfPoissonLoss()
|
593 |
+
|
594 |
+
|
595 |
+
class GammaRegressor(_GeneralizedLinearRegressor):
|
596 |
+
"""Generalized Linear Model with a Gamma distribution.
|
597 |
+
|
598 |
+
This regressor uses the 'log' link function.
|
599 |
+
|
600 |
+
Read more in the :ref:`User Guide <Generalized_linear_models>`.
|
601 |
+
|
602 |
+
.. versionadded:: 0.23
|
603 |
+
|
604 |
+
Parameters
|
605 |
+
----------
|
606 |
+
alpha : float, default=1
|
607 |
+
Constant that multiplies the L2 penalty term and determines the
|
608 |
+
regularization strength. ``alpha = 0`` is equivalent to unpenalized
|
609 |
+
GLMs. In this case, the design matrix `X` must have full column rank
|
610 |
+
(no collinearities).
|
611 |
+
Values of `alpha` must be in the range `[0.0, inf)`.
|
612 |
+
|
613 |
+
fit_intercept : bool, default=True
|
614 |
+
Specifies if a constant (a.k.a. bias or intercept) should be
|
615 |
+
added to the linear predictor `X @ coef_ + intercept_`.
|
616 |
+
|
617 |
+
solver : {'lbfgs', 'newton-cholesky'}, default='lbfgs'
|
618 |
+
Algorithm to use in the optimization problem:
|
619 |
+
|
620 |
+
'lbfgs'
|
621 |
+
Calls scipy's L-BFGS-B optimizer.
|
622 |
+
|
623 |
+
'newton-cholesky'
|
624 |
+
Uses Newton-Raphson steps (in arbitrary precision arithmetic equivalent to
|
625 |
+
iterated reweighted least squares) with an inner Cholesky based solver.
|
626 |
+
This solver is a good choice for `n_samples` >> `n_features`, especially
|
627 |
+
with one-hot encoded categorical features with rare categories. Be aware
|
628 |
+
that the memory usage of this solver has a quadratic dependency on
|
629 |
+
`n_features` because it explicitly computes the Hessian matrix.
|
630 |
+
|
631 |
+
.. versionadded:: 1.2
|
632 |
+
|
633 |
+
max_iter : int, default=100
|
634 |
+
The maximal number of iterations for the solver.
|
635 |
+
Values must be in the range `[1, inf)`.
|
636 |
+
|
637 |
+
tol : float, default=1e-4
|
638 |
+
Stopping criterion. For the lbfgs solver,
|
639 |
+
the iteration will stop when ``max{|g_j|, j = 1, ..., d} <= tol``
|
640 |
+
where ``g_j`` is the j-th component of the gradient (derivative) of
|
641 |
+
the objective function.
|
642 |
+
Values must be in the range `(0.0, inf)`.
|
643 |
+
|
644 |
+
warm_start : bool, default=False
|
645 |
+
If set to ``True``, reuse the solution of the previous call to ``fit``
|
646 |
+
as initialization for `coef_` and `intercept_`.
|
647 |
+
|
648 |
+
verbose : int, default=0
|
649 |
+
For the lbfgs solver set verbose to any positive number for verbosity.
|
650 |
+
Values must be in the range `[0, inf)`.
|
651 |
+
|
652 |
+
Attributes
|
653 |
+
----------
|
654 |
+
coef_ : array of shape (n_features,)
|
655 |
+
Estimated coefficients for the linear predictor (`X @ coef_ +
|
656 |
+
intercept_`) in the GLM.
|
657 |
+
|
658 |
+
intercept_ : float
|
659 |
+
Intercept (a.k.a. bias) added to linear predictor.
|
660 |
+
|
661 |
+
n_features_in_ : int
|
662 |
+
Number of features seen during :term:`fit`.
|
663 |
+
|
664 |
+
.. versionadded:: 0.24
|
665 |
+
|
666 |
+
n_iter_ : int
|
667 |
+
Actual number of iterations used in the solver.
|
668 |
+
|
669 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
670 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
671 |
+
has feature names that are all strings.
|
672 |
+
|
673 |
+
.. versionadded:: 1.0
|
674 |
+
|
675 |
+
See Also
|
676 |
+
--------
|
677 |
+
PoissonRegressor : Generalized Linear Model with a Poisson distribution.
|
678 |
+
TweedieRegressor : Generalized Linear Model with a Tweedie distribution.
|
679 |
+
|
680 |
+
Examples
|
681 |
+
--------
|
682 |
+
>>> from sklearn import linear_model
|
683 |
+
>>> clf = linear_model.GammaRegressor()
|
684 |
+
>>> X = [[1, 2], [2, 3], [3, 4], [4, 3]]
|
685 |
+
>>> y = [19, 26, 33, 30]
|
686 |
+
>>> clf.fit(X, y)
|
687 |
+
GammaRegressor()
|
688 |
+
>>> clf.score(X, y)
|
689 |
+
0.773...
|
690 |
+
>>> clf.coef_
|
691 |
+
array([0.072..., 0.066...])
|
692 |
+
>>> clf.intercept_
|
693 |
+
2.896...
|
694 |
+
>>> clf.predict([[1, 0], [2, 8]])
|
695 |
+
array([19.483..., 35.795...])
|
696 |
+
"""
|
697 |
+
|
698 |
+
_parameter_constraints: dict = {
|
699 |
+
**_GeneralizedLinearRegressor._parameter_constraints
|
700 |
+
}
|
701 |
+
|
702 |
+
def __init__(
|
703 |
+
self,
|
704 |
+
*,
|
705 |
+
alpha=1.0,
|
706 |
+
fit_intercept=True,
|
707 |
+
solver="lbfgs",
|
708 |
+
max_iter=100,
|
709 |
+
tol=1e-4,
|
710 |
+
warm_start=False,
|
711 |
+
verbose=0,
|
712 |
+
):
|
713 |
+
super().__init__(
|
714 |
+
alpha=alpha,
|
715 |
+
fit_intercept=fit_intercept,
|
716 |
+
solver=solver,
|
717 |
+
max_iter=max_iter,
|
718 |
+
tol=tol,
|
719 |
+
warm_start=warm_start,
|
720 |
+
verbose=verbose,
|
721 |
+
)
|
722 |
+
|
723 |
+
def _get_loss(self):
|
724 |
+
return HalfGammaLoss()
|
725 |
+
|
726 |
+
|
727 |
+
class TweedieRegressor(_GeneralizedLinearRegressor):
|
728 |
+
"""Generalized Linear Model with a Tweedie distribution.
|
729 |
+
|
730 |
+
This estimator can be used to model different GLMs depending on the
|
731 |
+
``power`` parameter, which determines the underlying distribution.
|
732 |
+
|
733 |
+
Read more in the :ref:`User Guide <Generalized_linear_models>`.
|
734 |
+
|
735 |
+
.. versionadded:: 0.23
|
736 |
+
|
737 |
+
Parameters
|
738 |
+
----------
|
739 |
+
power : float, default=0
|
740 |
+
The power determines the underlying target distribution according
|
741 |
+
to the following table:
|
742 |
+
|
743 |
+
+-------+------------------------+
|
744 |
+
| Power | Distribution |
|
745 |
+
+=======+========================+
|
746 |
+
| 0 | Normal |
|
747 |
+
+-------+------------------------+
|
748 |
+
| 1 | Poisson |
|
749 |
+
+-------+------------------------+
|
750 |
+
| (1,2) | Compound Poisson Gamma |
|
751 |
+
+-------+------------------------+
|
752 |
+
| 2 | Gamma |
|
753 |
+
+-------+------------------------+
|
754 |
+
| 3 | Inverse Gaussian |
|
755 |
+
+-------+------------------------+
|
756 |
+
|
757 |
+
For ``0 < power < 1``, no distribution exists.
|
758 |
+
|
759 |
+
alpha : float, default=1
|
760 |
+
Constant that multiplies the L2 penalty term and determines the
|
761 |
+
regularization strength. ``alpha = 0`` is equivalent to unpenalized
|
762 |
+
GLMs. In this case, the design matrix `X` must have full column rank
|
763 |
+
(no collinearities).
|
764 |
+
Values of `alpha` must be in the range `[0.0, inf)`.
|
765 |
+
|
766 |
+
fit_intercept : bool, default=True
|
767 |
+
Specifies if a constant (a.k.a. bias or intercept) should be
|
768 |
+
added to the linear predictor (`X @ coef + intercept`).
|
769 |
+
|
770 |
+
link : {'auto', 'identity', 'log'}, default='auto'
|
771 |
+
The link function of the GLM, i.e. mapping from linear predictor
|
772 |
+
`X @ coeff + intercept` to prediction `y_pred`. Option 'auto' sets
|
773 |
+
the link depending on the chosen `power` parameter as follows:
|
774 |
+
|
775 |
+
- 'identity' for ``power <= 0``, e.g. for the Normal distribution
|
776 |
+
- 'log' for ``power > 0``, e.g. for Poisson, Gamma and Inverse Gaussian
|
777 |
+
distributions
|
778 |
+
|
779 |
+
solver : {'lbfgs', 'newton-cholesky'}, default='lbfgs'
|
780 |
+
Algorithm to use in the optimization problem:
|
781 |
+
|
782 |
+
'lbfgs'
|
783 |
+
Calls scipy's L-BFGS-B optimizer.
|
784 |
+
|
785 |
+
'newton-cholesky'
|
786 |
+
Uses Newton-Raphson steps (in arbitrary precision arithmetic equivalent to
|
787 |
+
iterated reweighted least squares) with an inner Cholesky based solver.
|
788 |
+
This solver is a good choice for `n_samples` >> `n_features`, especially
|
789 |
+
with one-hot encoded categorical features with rare categories. Be aware
|
790 |
+
that the memory usage of this solver has a quadratic dependency on
|
791 |
+
`n_features` because it explicitly computes the Hessian matrix.
|
792 |
+
|
793 |
+
.. versionadded:: 1.2
|
794 |
+
|
795 |
+
max_iter : int, default=100
|
796 |
+
The maximal number of iterations for the solver.
|
797 |
+
Values must be in the range `[1, inf)`.
|
798 |
+
|
799 |
+
tol : float, default=1e-4
|
800 |
+
Stopping criterion. For the lbfgs solver,
|
801 |
+
the iteration will stop when ``max{|g_j|, j = 1, ..., d} <= tol``
|
802 |
+
where ``g_j`` is the j-th component of the gradient (derivative) of
|
803 |
+
the objective function.
|
804 |
+
Values must be in the range `(0.0, inf)`.
|
805 |
+
|
806 |
+
warm_start : bool, default=False
|
807 |
+
If set to ``True``, reuse the solution of the previous call to ``fit``
|
808 |
+
as initialization for ``coef_`` and ``intercept_`` .
|
809 |
+
|
810 |
+
verbose : int, default=0
|
811 |
+
For the lbfgs solver set verbose to any positive number for verbosity.
|
812 |
+
Values must be in the range `[0, inf)`.
|
813 |
+
|
814 |
+
Attributes
|
815 |
+
----------
|
816 |
+
coef_ : array of shape (n_features,)
|
817 |
+
Estimated coefficients for the linear predictor (`X @ coef_ +
|
818 |
+
intercept_`) in the GLM.
|
819 |
+
|
820 |
+
intercept_ : float
|
821 |
+
Intercept (a.k.a. bias) added to linear predictor.
|
822 |
+
|
823 |
+
n_iter_ : int
|
824 |
+
Actual number of iterations used in the solver.
|
825 |
+
|
826 |
+
n_features_in_ : int
|
827 |
+
Number of features seen during :term:`fit`.
|
828 |
+
|
829 |
+
.. versionadded:: 0.24
|
830 |
+
|
831 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
832 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
833 |
+
has feature names that are all strings.
|
834 |
+
|
835 |
+
.. versionadded:: 1.0
|
836 |
+
|
837 |
+
See Also
|
838 |
+
--------
|
839 |
+
PoissonRegressor : Generalized Linear Model with a Poisson distribution.
|
840 |
+
GammaRegressor : Generalized Linear Model with a Gamma distribution.
|
841 |
+
|
842 |
+
Examples
|
843 |
+
--------
|
844 |
+
>>> from sklearn import linear_model
|
845 |
+
>>> clf = linear_model.TweedieRegressor()
|
846 |
+
>>> X = [[1, 2], [2, 3], [3, 4], [4, 3]]
|
847 |
+
>>> y = [2, 3.5, 5, 5.5]
|
848 |
+
>>> clf.fit(X, y)
|
849 |
+
TweedieRegressor()
|
850 |
+
>>> clf.score(X, y)
|
851 |
+
0.839...
|
852 |
+
>>> clf.coef_
|
853 |
+
array([0.599..., 0.299...])
|
854 |
+
>>> clf.intercept_
|
855 |
+
1.600...
|
856 |
+
>>> clf.predict([[1, 1], [3, 4]])
|
857 |
+
array([2.500..., 4.599...])
|
858 |
+
"""
|
859 |
+
|
860 |
+
_parameter_constraints: dict = {
|
861 |
+
**_GeneralizedLinearRegressor._parameter_constraints,
|
862 |
+
"power": [Interval(Real, None, None, closed="neither")],
|
863 |
+
"link": [StrOptions({"auto", "identity", "log"})],
|
864 |
+
}
|
865 |
+
|
866 |
+
def __init__(
|
867 |
+
self,
|
868 |
+
*,
|
869 |
+
power=0.0,
|
870 |
+
alpha=1.0,
|
871 |
+
fit_intercept=True,
|
872 |
+
link="auto",
|
873 |
+
solver="lbfgs",
|
874 |
+
max_iter=100,
|
875 |
+
tol=1e-4,
|
876 |
+
warm_start=False,
|
877 |
+
verbose=0,
|
878 |
+
):
|
879 |
+
super().__init__(
|
880 |
+
alpha=alpha,
|
881 |
+
fit_intercept=fit_intercept,
|
882 |
+
solver=solver,
|
883 |
+
max_iter=max_iter,
|
884 |
+
tol=tol,
|
885 |
+
warm_start=warm_start,
|
886 |
+
verbose=verbose,
|
887 |
+
)
|
888 |
+
self.link = link
|
889 |
+
self.power = power
|
890 |
+
|
891 |
+
def _get_loss(self):
|
892 |
+
if self.link == "auto":
|
893 |
+
if self.power <= 0:
|
894 |
+
# identity link
|
895 |
+
return HalfTweedieLossIdentity(power=self.power)
|
896 |
+
else:
|
897 |
+
# log link
|
898 |
+
return HalfTweedieLoss(power=self.power)
|
899 |
+
|
900 |
+
if self.link == "log":
|
901 |
+
return HalfTweedieLoss(power=self.power)
|
902 |
+
|
903 |
+
if self.link == "identity":
|
904 |
+
return HalfTweedieLossIdentity(power=self.power)
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_glm/tests/__init__.py
ADDED
@@ -0,0 +1 @@
|
|
|
|
|
1 |
+
# License: BSD 3 clause
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_glm/tests/__pycache__/__init__.cpython-310.pyc
ADDED
Binary file (196 Bytes). View file
|
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_glm/tests/__pycache__/test_glm.cpython-310.pyc
ADDED
Binary file (23.8 kB). View file
|
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_glm/tests/test_glm.py
ADDED
@@ -0,0 +1,1112 @@
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|
1 |
+
# Authors: Christian Lorentzen <[email protected]>
|
2 |
+
#
|
3 |
+
# License: BSD 3 clause
|
4 |
+
|
5 |
+
import itertools
|
6 |
+
import warnings
|
7 |
+
from functools import partial
|
8 |
+
|
9 |
+
import numpy as np
|
10 |
+
import pytest
|
11 |
+
import scipy
|
12 |
+
from numpy.testing import assert_allclose
|
13 |
+
from scipy import linalg
|
14 |
+
from scipy.optimize import minimize, root
|
15 |
+
|
16 |
+
from sklearn._loss import HalfBinomialLoss, HalfPoissonLoss, HalfTweedieLoss
|
17 |
+
from sklearn._loss.link import IdentityLink, LogLink
|
18 |
+
from sklearn.base import clone
|
19 |
+
from sklearn.datasets import make_low_rank_matrix, make_regression
|
20 |
+
from sklearn.exceptions import ConvergenceWarning
|
21 |
+
from sklearn.linear_model import (
|
22 |
+
GammaRegressor,
|
23 |
+
PoissonRegressor,
|
24 |
+
Ridge,
|
25 |
+
TweedieRegressor,
|
26 |
+
)
|
27 |
+
from sklearn.linear_model._glm import _GeneralizedLinearRegressor
|
28 |
+
from sklearn.linear_model._glm._newton_solver import NewtonCholeskySolver
|
29 |
+
from sklearn.linear_model._linear_loss import LinearModelLoss
|
30 |
+
from sklearn.metrics import d2_tweedie_score, mean_poisson_deviance
|
31 |
+
from sklearn.model_selection import train_test_split
|
32 |
+
|
33 |
+
SOLVERS = ["lbfgs", "newton-cholesky"]
|
34 |
+
|
35 |
+
|
36 |
+
class BinomialRegressor(_GeneralizedLinearRegressor):
|
37 |
+
def _get_loss(self):
|
38 |
+
return HalfBinomialLoss()
|
39 |
+
|
40 |
+
|
41 |
+
def _special_minimize(fun, grad, x, tol_NM, tol):
|
42 |
+
# Find good starting point by Nelder-Mead
|
43 |
+
res_NM = minimize(
|
44 |
+
fun, x, method="Nelder-Mead", options={"xatol": tol_NM, "fatol": tol_NM}
|
45 |
+
)
|
46 |
+
# Now refine via root finding on the gradient of the function, which is
|
47 |
+
# more precise than minimizing the function itself.
|
48 |
+
res = root(
|
49 |
+
grad,
|
50 |
+
res_NM.x,
|
51 |
+
method="lm",
|
52 |
+
options={"ftol": tol, "xtol": tol, "gtol": tol},
|
53 |
+
)
|
54 |
+
return res.x
|
55 |
+
|
56 |
+
|
57 |
+
@pytest.fixture(scope="module")
|
58 |
+
def regression_data():
|
59 |
+
X, y = make_regression(
|
60 |
+
n_samples=107, n_features=10, n_informative=80, noise=0.5, random_state=2
|
61 |
+
)
|
62 |
+
return X, y
|
63 |
+
|
64 |
+
|
65 |
+
@pytest.fixture(
|
66 |
+
params=itertools.product(
|
67 |
+
["long", "wide"],
|
68 |
+
[
|
69 |
+
BinomialRegressor(),
|
70 |
+
PoissonRegressor(),
|
71 |
+
GammaRegressor(),
|
72 |
+
# TweedieRegressor(power=3.0), # too difficult
|
73 |
+
# TweedieRegressor(power=0, link="log"), # too difficult
|
74 |
+
TweedieRegressor(power=1.5),
|
75 |
+
],
|
76 |
+
),
|
77 |
+
ids=lambda param: f"{param[0]}-{param[1]}",
|
78 |
+
)
|
79 |
+
def glm_dataset(global_random_seed, request):
|
80 |
+
"""Dataset with GLM solutions, well conditioned X.
|
81 |
+
|
82 |
+
This is inspired by ols_ridge_dataset in test_ridge.py.
|
83 |
+
|
84 |
+
The construction is based on the SVD decomposition of X = U S V'.
|
85 |
+
|
86 |
+
Parameters
|
87 |
+
----------
|
88 |
+
type : {"long", "wide"}
|
89 |
+
If "long", then n_samples > n_features.
|
90 |
+
If "wide", then n_features > n_samples.
|
91 |
+
model : a GLM model
|
92 |
+
|
93 |
+
For "wide", we return the minimum norm solution:
|
94 |
+
|
95 |
+
min ||w||_2 subject to w = argmin deviance(X, y, w)
|
96 |
+
|
97 |
+
Note that the deviance is always minimized if y = inverse_link(X w) is possible to
|
98 |
+
achieve, which it is in the wide data case. Therefore, we can construct the
|
99 |
+
solution with minimum norm like (wide) OLS:
|
100 |
+
|
101 |
+
min ||w||_2 subject to link(y) = raw_prediction = X w
|
102 |
+
|
103 |
+
Returns
|
104 |
+
-------
|
105 |
+
model : GLM model
|
106 |
+
X : ndarray
|
107 |
+
Last column of 1, i.e. intercept.
|
108 |
+
y : ndarray
|
109 |
+
coef_unpenalized : ndarray
|
110 |
+
Minimum norm solutions, i.e. min sum(loss(w)) (with minimum ||w||_2 in
|
111 |
+
case of ambiguity)
|
112 |
+
Last coefficient is intercept.
|
113 |
+
coef_penalized : ndarray
|
114 |
+
GLM solution with alpha=l2_reg_strength=1, i.e.
|
115 |
+
min 1/n * sum(loss) + ||w[:-1]||_2^2.
|
116 |
+
Last coefficient is intercept.
|
117 |
+
l2_reg_strength : float
|
118 |
+
Always equal 1.
|
119 |
+
"""
|
120 |
+
data_type, model = request.param
|
121 |
+
# Make larger dim more than double as big as the smaller one.
|
122 |
+
# This helps when constructing singular matrices like (X, X).
|
123 |
+
if data_type == "long":
|
124 |
+
n_samples, n_features = 12, 4
|
125 |
+
else:
|
126 |
+
n_samples, n_features = 4, 12
|
127 |
+
k = min(n_samples, n_features)
|
128 |
+
rng = np.random.RandomState(global_random_seed)
|
129 |
+
X = make_low_rank_matrix(
|
130 |
+
n_samples=n_samples,
|
131 |
+
n_features=n_features,
|
132 |
+
effective_rank=k,
|
133 |
+
tail_strength=0.1,
|
134 |
+
random_state=rng,
|
135 |
+
)
|
136 |
+
X[:, -1] = 1 # last columns acts as intercept
|
137 |
+
U, s, Vt = linalg.svd(X, full_matrices=False)
|
138 |
+
assert np.all(s > 1e-3) # to be sure
|
139 |
+
assert np.max(s) / np.min(s) < 100 # condition number of X
|
140 |
+
|
141 |
+
if data_type == "long":
|
142 |
+
coef_unpenalized = rng.uniform(low=1, high=3, size=n_features)
|
143 |
+
coef_unpenalized *= rng.choice([-1, 1], size=n_features)
|
144 |
+
raw_prediction = X @ coef_unpenalized
|
145 |
+
else:
|
146 |
+
raw_prediction = rng.uniform(low=-3, high=3, size=n_samples)
|
147 |
+
# minimum norm solution min ||w||_2 such that raw_prediction = X w:
|
148 |
+
# w = X'(XX')^-1 raw_prediction = V s^-1 U' raw_prediction
|
149 |
+
coef_unpenalized = Vt.T @ np.diag(1 / s) @ U.T @ raw_prediction
|
150 |
+
|
151 |
+
linear_loss = LinearModelLoss(base_loss=model._get_loss(), fit_intercept=True)
|
152 |
+
sw = np.full(shape=n_samples, fill_value=1 / n_samples)
|
153 |
+
y = linear_loss.base_loss.link.inverse(raw_prediction)
|
154 |
+
|
155 |
+
# Add penalty l2_reg_strength * ||coef||_2^2 for l2_reg_strength=1 and solve with
|
156 |
+
# optimizer. Note that the problem is well conditioned such that we get accurate
|
157 |
+
# results.
|
158 |
+
l2_reg_strength = 1
|
159 |
+
fun = partial(
|
160 |
+
linear_loss.loss,
|
161 |
+
X=X[:, :-1],
|
162 |
+
y=y,
|
163 |
+
sample_weight=sw,
|
164 |
+
l2_reg_strength=l2_reg_strength,
|
165 |
+
)
|
166 |
+
grad = partial(
|
167 |
+
linear_loss.gradient,
|
168 |
+
X=X[:, :-1],
|
169 |
+
y=y,
|
170 |
+
sample_weight=sw,
|
171 |
+
l2_reg_strength=l2_reg_strength,
|
172 |
+
)
|
173 |
+
coef_penalized_with_intercept = _special_minimize(
|
174 |
+
fun, grad, coef_unpenalized, tol_NM=1e-6, tol=1e-14
|
175 |
+
)
|
176 |
+
|
177 |
+
linear_loss = LinearModelLoss(base_loss=model._get_loss(), fit_intercept=False)
|
178 |
+
fun = partial(
|
179 |
+
linear_loss.loss,
|
180 |
+
X=X[:, :-1],
|
181 |
+
y=y,
|
182 |
+
sample_weight=sw,
|
183 |
+
l2_reg_strength=l2_reg_strength,
|
184 |
+
)
|
185 |
+
grad = partial(
|
186 |
+
linear_loss.gradient,
|
187 |
+
X=X[:, :-1],
|
188 |
+
y=y,
|
189 |
+
sample_weight=sw,
|
190 |
+
l2_reg_strength=l2_reg_strength,
|
191 |
+
)
|
192 |
+
coef_penalized_without_intercept = _special_minimize(
|
193 |
+
fun, grad, coef_unpenalized[:-1], tol_NM=1e-6, tol=1e-14
|
194 |
+
)
|
195 |
+
|
196 |
+
# To be sure
|
197 |
+
assert np.linalg.norm(coef_penalized_with_intercept) < np.linalg.norm(
|
198 |
+
coef_unpenalized
|
199 |
+
)
|
200 |
+
|
201 |
+
return (
|
202 |
+
model,
|
203 |
+
X,
|
204 |
+
y,
|
205 |
+
coef_unpenalized,
|
206 |
+
coef_penalized_with_intercept,
|
207 |
+
coef_penalized_without_intercept,
|
208 |
+
l2_reg_strength,
|
209 |
+
)
|
210 |
+
|
211 |
+
|
212 |
+
@pytest.mark.parametrize("solver", SOLVERS)
|
213 |
+
@pytest.mark.parametrize("fit_intercept", [False, True])
|
214 |
+
def test_glm_regression(solver, fit_intercept, glm_dataset):
|
215 |
+
"""Test that GLM converges for all solvers to correct solution.
|
216 |
+
|
217 |
+
We work with a simple constructed data set with known solution.
|
218 |
+
"""
|
219 |
+
model, X, y, _, coef_with_intercept, coef_without_intercept, alpha = glm_dataset
|
220 |
+
params = dict(
|
221 |
+
alpha=alpha,
|
222 |
+
fit_intercept=fit_intercept,
|
223 |
+
solver=solver,
|
224 |
+
tol=1e-12,
|
225 |
+
max_iter=1000,
|
226 |
+
)
|
227 |
+
|
228 |
+
model = clone(model).set_params(**params)
|
229 |
+
X = X[:, :-1] # remove intercept
|
230 |
+
if fit_intercept:
|
231 |
+
coef = coef_with_intercept
|
232 |
+
intercept = coef[-1]
|
233 |
+
coef = coef[:-1]
|
234 |
+
else:
|
235 |
+
coef = coef_without_intercept
|
236 |
+
intercept = 0
|
237 |
+
|
238 |
+
model.fit(X, y)
|
239 |
+
|
240 |
+
rtol = 5e-5 if solver == "lbfgs" else 1e-9
|
241 |
+
assert model.intercept_ == pytest.approx(intercept, rel=rtol)
|
242 |
+
assert_allclose(model.coef_, coef, rtol=rtol)
|
243 |
+
|
244 |
+
# Same with sample_weight.
|
245 |
+
model = (
|
246 |
+
clone(model).set_params(**params).fit(X, y, sample_weight=np.ones(X.shape[0]))
|
247 |
+
)
|
248 |
+
assert model.intercept_ == pytest.approx(intercept, rel=rtol)
|
249 |
+
assert_allclose(model.coef_, coef, rtol=rtol)
|
250 |
+
|
251 |
+
|
252 |
+
@pytest.mark.parametrize("solver", SOLVERS)
|
253 |
+
@pytest.mark.parametrize("fit_intercept", [True, False])
|
254 |
+
def test_glm_regression_hstacked_X(solver, fit_intercept, glm_dataset):
|
255 |
+
"""Test that GLM converges for all solvers to correct solution on hstacked data.
|
256 |
+
|
257 |
+
We work with a simple constructed data set with known solution.
|
258 |
+
Fit on [X] with alpha is the same as fit on [X, X]/2 with alpha/2.
|
259 |
+
For long X, [X, X] is still a long but singular matrix.
|
260 |
+
"""
|
261 |
+
model, X, y, _, coef_with_intercept, coef_without_intercept, alpha = glm_dataset
|
262 |
+
n_samples, n_features = X.shape
|
263 |
+
params = dict(
|
264 |
+
alpha=alpha / 2,
|
265 |
+
fit_intercept=fit_intercept,
|
266 |
+
solver=solver,
|
267 |
+
tol=1e-12,
|
268 |
+
max_iter=1000,
|
269 |
+
)
|
270 |
+
|
271 |
+
model = clone(model).set_params(**params)
|
272 |
+
X = X[:, :-1] # remove intercept
|
273 |
+
X = 0.5 * np.concatenate((X, X), axis=1)
|
274 |
+
assert np.linalg.matrix_rank(X) <= min(n_samples, n_features - 1)
|
275 |
+
if fit_intercept:
|
276 |
+
coef = coef_with_intercept
|
277 |
+
intercept = coef[-1]
|
278 |
+
coef = coef[:-1]
|
279 |
+
else:
|
280 |
+
coef = coef_without_intercept
|
281 |
+
intercept = 0
|
282 |
+
|
283 |
+
with warnings.catch_warnings():
|
284 |
+
# XXX: Investigate if the ConvergenceWarning that can appear in some
|
285 |
+
# cases should be considered a bug or not. In the mean time we don't
|
286 |
+
# fail when the assertions below pass irrespective of the presence of
|
287 |
+
# the warning.
|
288 |
+
warnings.simplefilter("ignore", ConvergenceWarning)
|
289 |
+
model.fit(X, y)
|
290 |
+
|
291 |
+
rtol = 2e-4 if solver == "lbfgs" else 5e-9
|
292 |
+
assert model.intercept_ == pytest.approx(intercept, rel=rtol)
|
293 |
+
assert_allclose(model.coef_, np.r_[coef, coef], rtol=rtol)
|
294 |
+
|
295 |
+
|
296 |
+
@pytest.mark.parametrize("solver", SOLVERS)
|
297 |
+
@pytest.mark.parametrize("fit_intercept", [True, False])
|
298 |
+
def test_glm_regression_vstacked_X(solver, fit_intercept, glm_dataset):
|
299 |
+
"""Test that GLM converges for all solvers to correct solution on vstacked data.
|
300 |
+
|
301 |
+
We work with a simple constructed data set with known solution.
|
302 |
+
Fit on [X] with alpha is the same as fit on [X], [y]
|
303 |
+
[X], [y] with 1 * alpha.
|
304 |
+
It is the same alpha as the average loss stays the same.
|
305 |
+
For wide X, [X', X'] is a singular matrix.
|
306 |
+
"""
|
307 |
+
model, X, y, _, coef_with_intercept, coef_without_intercept, alpha = glm_dataset
|
308 |
+
n_samples, n_features = X.shape
|
309 |
+
params = dict(
|
310 |
+
alpha=alpha,
|
311 |
+
fit_intercept=fit_intercept,
|
312 |
+
solver=solver,
|
313 |
+
tol=1e-12,
|
314 |
+
max_iter=1000,
|
315 |
+
)
|
316 |
+
|
317 |
+
model = clone(model).set_params(**params)
|
318 |
+
X = X[:, :-1] # remove intercept
|
319 |
+
X = np.concatenate((X, X), axis=0)
|
320 |
+
assert np.linalg.matrix_rank(X) <= min(n_samples, n_features)
|
321 |
+
y = np.r_[y, y]
|
322 |
+
if fit_intercept:
|
323 |
+
coef = coef_with_intercept
|
324 |
+
intercept = coef[-1]
|
325 |
+
coef = coef[:-1]
|
326 |
+
else:
|
327 |
+
coef = coef_without_intercept
|
328 |
+
intercept = 0
|
329 |
+
model.fit(X, y)
|
330 |
+
|
331 |
+
rtol = 3e-5 if solver == "lbfgs" else 5e-9
|
332 |
+
assert model.intercept_ == pytest.approx(intercept, rel=rtol)
|
333 |
+
assert_allclose(model.coef_, coef, rtol=rtol)
|
334 |
+
|
335 |
+
|
336 |
+
@pytest.mark.parametrize("solver", SOLVERS)
|
337 |
+
@pytest.mark.parametrize("fit_intercept", [True, False])
|
338 |
+
def test_glm_regression_unpenalized(solver, fit_intercept, glm_dataset):
|
339 |
+
"""Test that unpenalized GLM converges for all solvers to correct solution.
|
340 |
+
|
341 |
+
We work with a simple constructed data set with known solution.
|
342 |
+
Note: This checks the minimum norm solution for wide X, i.e.
|
343 |
+
n_samples < n_features:
|
344 |
+
min ||w||_2 subject to w = argmin deviance(X, y, w)
|
345 |
+
"""
|
346 |
+
model, X, y, coef, _, _, _ = glm_dataset
|
347 |
+
n_samples, n_features = X.shape
|
348 |
+
alpha = 0 # unpenalized
|
349 |
+
params = dict(
|
350 |
+
alpha=alpha,
|
351 |
+
fit_intercept=fit_intercept,
|
352 |
+
solver=solver,
|
353 |
+
tol=1e-12,
|
354 |
+
max_iter=1000,
|
355 |
+
)
|
356 |
+
|
357 |
+
model = clone(model).set_params(**params)
|
358 |
+
if fit_intercept:
|
359 |
+
X = X[:, :-1] # remove intercept
|
360 |
+
intercept = coef[-1]
|
361 |
+
coef = coef[:-1]
|
362 |
+
else:
|
363 |
+
intercept = 0
|
364 |
+
|
365 |
+
with warnings.catch_warnings():
|
366 |
+
if solver.startswith("newton") and n_samples < n_features:
|
367 |
+
# The newton solvers should warn and automatically fallback to LBFGS
|
368 |
+
# in this case. The model should still converge.
|
369 |
+
warnings.filterwarnings("ignore", category=scipy.linalg.LinAlgWarning)
|
370 |
+
# XXX: Investigate if the ConvergenceWarning that can appear in some
|
371 |
+
# cases should be considered a bug or not. In the mean time we don't
|
372 |
+
# fail when the assertions below pass irrespective of the presence of
|
373 |
+
# the warning.
|
374 |
+
warnings.filterwarnings("ignore", category=ConvergenceWarning)
|
375 |
+
model.fit(X, y)
|
376 |
+
|
377 |
+
# FIXME: `assert_allclose(model.coef_, coef)` should work for all cases but fails
|
378 |
+
# for the wide/fat case with n_features > n_samples. Most current GLM solvers do
|
379 |
+
# NOT return the minimum norm solution with fit_intercept=True.
|
380 |
+
if n_samples > n_features:
|
381 |
+
rtol = 5e-5 if solver == "lbfgs" else 1e-7
|
382 |
+
assert model.intercept_ == pytest.approx(intercept)
|
383 |
+
assert_allclose(model.coef_, coef, rtol=rtol)
|
384 |
+
else:
|
385 |
+
# As it is an underdetermined problem, prediction = y. The following shows that
|
386 |
+
# we get a solution, i.e. a (non-unique) minimum of the objective function ...
|
387 |
+
rtol = 5e-5
|
388 |
+
if solver == "newton-cholesky":
|
389 |
+
rtol = 5e-4
|
390 |
+
assert_allclose(model.predict(X), y, rtol=rtol)
|
391 |
+
|
392 |
+
norm_solution = np.linalg.norm(np.r_[intercept, coef])
|
393 |
+
norm_model = np.linalg.norm(np.r_[model.intercept_, model.coef_])
|
394 |
+
if solver == "newton-cholesky":
|
395 |
+
# XXX: This solver shows random behaviour. Sometimes it finds solutions
|
396 |
+
# with norm_model <= norm_solution! So we check conditionally.
|
397 |
+
if norm_model < (1 + 1e-12) * norm_solution:
|
398 |
+
assert model.intercept_ == pytest.approx(intercept)
|
399 |
+
assert_allclose(model.coef_, coef, rtol=rtol)
|
400 |
+
elif solver == "lbfgs" and fit_intercept:
|
401 |
+
# But it is not the minimum norm solution. Otherwise the norms would be
|
402 |
+
# equal.
|
403 |
+
assert norm_model > (1 + 1e-12) * norm_solution
|
404 |
+
|
405 |
+
# See https://github.com/scikit-learn/scikit-learn/issues/23670.
|
406 |
+
# Note: Even adding a tiny penalty does not give the minimal norm solution.
|
407 |
+
# XXX: We could have naively expected LBFGS to find the minimal norm
|
408 |
+
# solution by adding a very small penalty. Even that fails for a reason we
|
409 |
+
# do not properly understand at this point.
|
410 |
+
else:
|
411 |
+
# When `fit_intercept=False`, LBFGS naturally converges to the minimum norm
|
412 |
+
# solution on this problem.
|
413 |
+
# XXX: Do we have any theoretical guarantees why this should be the case?
|
414 |
+
assert model.intercept_ == pytest.approx(intercept, rel=rtol)
|
415 |
+
assert_allclose(model.coef_, coef, rtol=rtol)
|
416 |
+
|
417 |
+
|
418 |
+
@pytest.mark.parametrize("solver", SOLVERS)
|
419 |
+
@pytest.mark.parametrize("fit_intercept", [True, False])
|
420 |
+
def test_glm_regression_unpenalized_hstacked_X(solver, fit_intercept, glm_dataset):
|
421 |
+
"""Test that unpenalized GLM converges for all solvers to correct solution.
|
422 |
+
|
423 |
+
We work with a simple constructed data set with known solution.
|
424 |
+
GLM fit on [X] is the same as fit on [X, X]/2.
|
425 |
+
For long X, [X, X] is a singular matrix and we check against the minimum norm
|
426 |
+
solution:
|
427 |
+
min ||w||_2 subject to w = argmin deviance(X, y, w)
|
428 |
+
"""
|
429 |
+
model, X, y, coef, _, _, _ = glm_dataset
|
430 |
+
n_samples, n_features = X.shape
|
431 |
+
alpha = 0 # unpenalized
|
432 |
+
params = dict(
|
433 |
+
alpha=alpha,
|
434 |
+
fit_intercept=fit_intercept,
|
435 |
+
solver=solver,
|
436 |
+
tol=1e-12,
|
437 |
+
max_iter=1000,
|
438 |
+
)
|
439 |
+
|
440 |
+
model = clone(model).set_params(**params)
|
441 |
+
if fit_intercept:
|
442 |
+
intercept = coef[-1]
|
443 |
+
coef = coef[:-1]
|
444 |
+
if n_samples > n_features:
|
445 |
+
X = X[:, :-1] # remove intercept
|
446 |
+
X = 0.5 * np.concatenate((X, X), axis=1)
|
447 |
+
else:
|
448 |
+
# To know the minimum norm solution, we keep one intercept column and do
|
449 |
+
# not divide by 2. Later on, we must take special care.
|
450 |
+
X = np.c_[X[:, :-1], X[:, :-1], X[:, -1]]
|
451 |
+
else:
|
452 |
+
intercept = 0
|
453 |
+
X = 0.5 * np.concatenate((X, X), axis=1)
|
454 |
+
assert np.linalg.matrix_rank(X) <= min(n_samples, n_features)
|
455 |
+
|
456 |
+
with warnings.catch_warnings():
|
457 |
+
if solver.startswith("newton"):
|
458 |
+
# The newton solvers should warn and automatically fallback to LBFGS
|
459 |
+
# in this case. The model should still converge.
|
460 |
+
warnings.filterwarnings("ignore", category=scipy.linalg.LinAlgWarning)
|
461 |
+
# XXX: Investigate if the ConvergenceWarning that can appear in some
|
462 |
+
# cases should be considered a bug or not. In the mean time we don't
|
463 |
+
# fail when the assertions below pass irrespective of the presence of
|
464 |
+
# the warning.
|
465 |
+
warnings.filterwarnings("ignore", category=ConvergenceWarning)
|
466 |
+
model.fit(X, y)
|
467 |
+
|
468 |
+
if fit_intercept and n_samples < n_features:
|
469 |
+
# Here we take special care.
|
470 |
+
model_intercept = 2 * model.intercept_
|
471 |
+
model_coef = 2 * model.coef_[:-1] # exclude the other intercept term.
|
472 |
+
# For minimum norm solution, we would have
|
473 |
+
# assert model.intercept_ == pytest.approx(model.coef_[-1])
|
474 |
+
else:
|
475 |
+
model_intercept = model.intercept_
|
476 |
+
model_coef = model.coef_
|
477 |
+
|
478 |
+
if n_samples > n_features:
|
479 |
+
assert model_intercept == pytest.approx(intercept)
|
480 |
+
rtol = 1e-4
|
481 |
+
assert_allclose(model_coef, np.r_[coef, coef], rtol=rtol)
|
482 |
+
else:
|
483 |
+
# As it is an underdetermined problem, prediction = y. The following shows that
|
484 |
+
# we get a solution, i.e. a (non-unique) minimum of the objective function ...
|
485 |
+
rtol = 1e-6 if solver == "lbfgs" else 5e-6
|
486 |
+
assert_allclose(model.predict(X), y, rtol=rtol)
|
487 |
+
if (solver == "lbfgs" and fit_intercept) or solver == "newton-cholesky":
|
488 |
+
# Same as in test_glm_regression_unpenalized.
|
489 |
+
# But it is not the minimum norm solution. Otherwise the norms would be
|
490 |
+
# equal.
|
491 |
+
norm_solution = np.linalg.norm(
|
492 |
+
0.5 * np.r_[intercept, intercept, coef, coef]
|
493 |
+
)
|
494 |
+
norm_model = np.linalg.norm(np.r_[model.intercept_, model.coef_])
|
495 |
+
assert norm_model > (1 + 1e-12) * norm_solution
|
496 |
+
# For minimum norm solution, we would have
|
497 |
+
# assert model.intercept_ == pytest.approx(model.coef_[-1])
|
498 |
+
else:
|
499 |
+
assert model_intercept == pytest.approx(intercept, rel=5e-6)
|
500 |
+
assert_allclose(model_coef, np.r_[coef, coef], rtol=1e-4)
|
501 |
+
|
502 |
+
|
503 |
+
@pytest.mark.parametrize("solver", SOLVERS)
|
504 |
+
@pytest.mark.parametrize("fit_intercept", [True, False])
|
505 |
+
def test_glm_regression_unpenalized_vstacked_X(solver, fit_intercept, glm_dataset):
|
506 |
+
"""Test that unpenalized GLM converges for all solvers to correct solution.
|
507 |
+
|
508 |
+
We work with a simple constructed data set with known solution.
|
509 |
+
GLM fit on [X] is the same as fit on [X], [y]
|
510 |
+
[X], [y].
|
511 |
+
For wide X, [X', X'] is a singular matrix and we check against the minimum norm
|
512 |
+
solution:
|
513 |
+
min ||w||_2 subject to w = argmin deviance(X, y, w)
|
514 |
+
"""
|
515 |
+
model, X, y, coef, _, _, _ = glm_dataset
|
516 |
+
n_samples, n_features = X.shape
|
517 |
+
alpha = 0 # unpenalized
|
518 |
+
params = dict(
|
519 |
+
alpha=alpha,
|
520 |
+
fit_intercept=fit_intercept,
|
521 |
+
solver=solver,
|
522 |
+
tol=1e-12,
|
523 |
+
max_iter=1000,
|
524 |
+
)
|
525 |
+
|
526 |
+
model = clone(model).set_params(**params)
|
527 |
+
if fit_intercept:
|
528 |
+
X = X[:, :-1] # remove intercept
|
529 |
+
intercept = coef[-1]
|
530 |
+
coef = coef[:-1]
|
531 |
+
else:
|
532 |
+
intercept = 0
|
533 |
+
X = np.concatenate((X, X), axis=0)
|
534 |
+
assert np.linalg.matrix_rank(X) <= min(n_samples, n_features)
|
535 |
+
y = np.r_[y, y]
|
536 |
+
|
537 |
+
with warnings.catch_warnings():
|
538 |
+
if solver.startswith("newton") and n_samples < n_features:
|
539 |
+
# The newton solvers should warn and automatically fallback to LBFGS
|
540 |
+
# in this case. The model should still converge.
|
541 |
+
warnings.filterwarnings("ignore", category=scipy.linalg.LinAlgWarning)
|
542 |
+
# XXX: Investigate if the ConvergenceWarning that can appear in some
|
543 |
+
# cases should be considered a bug or not. In the mean time we don't
|
544 |
+
# fail when the assertions below pass irrespective of the presence of
|
545 |
+
# the warning.
|
546 |
+
warnings.filterwarnings("ignore", category=ConvergenceWarning)
|
547 |
+
model.fit(X, y)
|
548 |
+
|
549 |
+
if n_samples > n_features:
|
550 |
+
rtol = 5e-5 if solver == "lbfgs" else 1e-6
|
551 |
+
assert model.intercept_ == pytest.approx(intercept)
|
552 |
+
assert_allclose(model.coef_, coef, rtol=rtol)
|
553 |
+
else:
|
554 |
+
# As it is an underdetermined problem, prediction = y. The following shows that
|
555 |
+
# we get a solution, i.e. a (non-unique) minimum of the objective function ...
|
556 |
+
rtol = 1e-6 if solver == "lbfgs" else 5e-6
|
557 |
+
assert_allclose(model.predict(X), y, rtol=rtol)
|
558 |
+
|
559 |
+
norm_solution = np.linalg.norm(np.r_[intercept, coef])
|
560 |
+
norm_model = np.linalg.norm(np.r_[model.intercept_, model.coef_])
|
561 |
+
if solver == "newton-cholesky":
|
562 |
+
# XXX: This solver shows random behaviour. Sometimes it finds solutions
|
563 |
+
# with norm_model <= norm_solution! So we check conditionally.
|
564 |
+
if not (norm_model > (1 + 1e-12) * norm_solution):
|
565 |
+
assert model.intercept_ == pytest.approx(intercept)
|
566 |
+
assert_allclose(model.coef_, coef, rtol=1e-4)
|
567 |
+
elif solver == "lbfgs" and fit_intercept:
|
568 |
+
# Same as in test_glm_regression_unpenalized.
|
569 |
+
# But it is not the minimum norm solution. Otherwise the norms would be
|
570 |
+
# equal.
|
571 |
+
assert norm_model > (1 + 1e-12) * norm_solution
|
572 |
+
else:
|
573 |
+
rtol = 1e-5 if solver == "newton-cholesky" else 1e-4
|
574 |
+
assert model.intercept_ == pytest.approx(intercept, rel=rtol)
|
575 |
+
assert_allclose(model.coef_, coef, rtol=rtol)
|
576 |
+
|
577 |
+
|
578 |
+
def test_sample_weights_validation():
|
579 |
+
"""Test the raised errors in the validation of sample_weight."""
|
580 |
+
# scalar value but not positive
|
581 |
+
X = [[1]]
|
582 |
+
y = [1]
|
583 |
+
weights = 0
|
584 |
+
glm = _GeneralizedLinearRegressor()
|
585 |
+
|
586 |
+
# Positive weights are accepted
|
587 |
+
glm.fit(X, y, sample_weight=1)
|
588 |
+
|
589 |
+
# 2d array
|
590 |
+
weights = [[0]]
|
591 |
+
with pytest.raises(ValueError, match="must be 1D array or scalar"):
|
592 |
+
glm.fit(X, y, weights)
|
593 |
+
|
594 |
+
# 1d but wrong length
|
595 |
+
weights = [1, 0]
|
596 |
+
msg = r"sample_weight.shape == \(2,\), expected \(1,\)!"
|
597 |
+
with pytest.raises(ValueError, match=msg):
|
598 |
+
glm.fit(X, y, weights)
|
599 |
+
|
600 |
+
|
601 |
+
@pytest.mark.parametrize(
|
602 |
+
"glm",
|
603 |
+
[
|
604 |
+
TweedieRegressor(power=3),
|
605 |
+
PoissonRegressor(),
|
606 |
+
GammaRegressor(),
|
607 |
+
TweedieRegressor(power=1.5),
|
608 |
+
],
|
609 |
+
)
|
610 |
+
def test_glm_wrong_y_range(glm):
|
611 |
+
y = np.array([-1, 2])
|
612 |
+
X = np.array([[1], [1]])
|
613 |
+
msg = r"Some value\(s\) of y are out of the valid range of the loss"
|
614 |
+
with pytest.raises(ValueError, match=msg):
|
615 |
+
glm.fit(X, y)
|
616 |
+
|
617 |
+
|
618 |
+
@pytest.mark.parametrize("fit_intercept", [False, True])
|
619 |
+
def test_glm_identity_regression(fit_intercept):
|
620 |
+
"""Test GLM regression with identity link on a simple dataset."""
|
621 |
+
coef = [1.0, 2.0]
|
622 |
+
X = np.array([[1, 1, 1, 1, 1], [0, 1, 2, 3, 4]]).T
|
623 |
+
y = np.dot(X, coef)
|
624 |
+
glm = _GeneralizedLinearRegressor(
|
625 |
+
alpha=0,
|
626 |
+
fit_intercept=fit_intercept,
|
627 |
+
tol=1e-12,
|
628 |
+
)
|
629 |
+
if fit_intercept:
|
630 |
+
glm.fit(X[:, 1:], y)
|
631 |
+
assert_allclose(glm.coef_, coef[1:], rtol=1e-10)
|
632 |
+
assert_allclose(glm.intercept_, coef[0], rtol=1e-10)
|
633 |
+
else:
|
634 |
+
glm.fit(X, y)
|
635 |
+
assert_allclose(glm.coef_, coef, rtol=1e-12)
|
636 |
+
|
637 |
+
|
638 |
+
@pytest.mark.parametrize("fit_intercept", [False, True])
|
639 |
+
@pytest.mark.parametrize("alpha", [0.0, 1.0])
|
640 |
+
@pytest.mark.parametrize(
|
641 |
+
"GLMEstimator", [_GeneralizedLinearRegressor, PoissonRegressor, GammaRegressor]
|
642 |
+
)
|
643 |
+
def test_glm_sample_weight_consistency(fit_intercept, alpha, GLMEstimator):
|
644 |
+
"""Test that the impact of sample_weight is consistent"""
|
645 |
+
rng = np.random.RandomState(0)
|
646 |
+
n_samples, n_features = 10, 5
|
647 |
+
|
648 |
+
X = rng.rand(n_samples, n_features)
|
649 |
+
y = rng.rand(n_samples)
|
650 |
+
glm_params = dict(alpha=alpha, fit_intercept=fit_intercept)
|
651 |
+
|
652 |
+
glm = GLMEstimator(**glm_params).fit(X, y)
|
653 |
+
coef = glm.coef_.copy()
|
654 |
+
|
655 |
+
# sample_weight=np.ones(..) should be equivalent to sample_weight=None
|
656 |
+
sample_weight = np.ones(y.shape)
|
657 |
+
glm.fit(X, y, sample_weight=sample_weight)
|
658 |
+
assert_allclose(glm.coef_, coef, rtol=1e-12)
|
659 |
+
|
660 |
+
# sample_weight are normalized to 1 so, scaling them has no effect
|
661 |
+
sample_weight = 2 * np.ones(y.shape)
|
662 |
+
glm.fit(X, y, sample_weight=sample_weight)
|
663 |
+
assert_allclose(glm.coef_, coef, rtol=1e-12)
|
664 |
+
|
665 |
+
# setting one element of sample_weight to 0 is equivalent to removing
|
666 |
+
# the corresponding sample
|
667 |
+
sample_weight = np.ones(y.shape)
|
668 |
+
sample_weight[-1] = 0
|
669 |
+
glm.fit(X, y, sample_weight=sample_weight)
|
670 |
+
coef1 = glm.coef_.copy()
|
671 |
+
glm.fit(X[:-1], y[:-1])
|
672 |
+
assert_allclose(glm.coef_, coef1, rtol=1e-12)
|
673 |
+
|
674 |
+
# check that multiplying sample_weight by 2 is equivalent
|
675 |
+
# to repeating corresponding samples twice
|
676 |
+
X2 = np.concatenate([X, X[: n_samples // 2]], axis=0)
|
677 |
+
y2 = np.concatenate([y, y[: n_samples // 2]])
|
678 |
+
sample_weight_1 = np.ones(len(y))
|
679 |
+
sample_weight_1[: n_samples // 2] = 2
|
680 |
+
|
681 |
+
glm1 = GLMEstimator(**glm_params).fit(X, y, sample_weight=sample_weight_1)
|
682 |
+
|
683 |
+
glm2 = GLMEstimator(**glm_params).fit(X2, y2, sample_weight=None)
|
684 |
+
assert_allclose(glm1.coef_, glm2.coef_)
|
685 |
+
|
686 |
+
|
687 |
+
@pytest.mark.parametrize("solver", SOLVERS)
|
688 |
+
@pytest.mark.parametrize("fit_intercept", [True, False])
|
689 |
+
@pytest.mark.parametrize(
|
690 |
+
"estimator",
|
691 |
+
[
|
692 |
+
PoissonRegressor(),
|
693 |
+
GammaRegressor(),
|
694 |
+
TweedieRegressor(power=3.0),
|
695 |
+
TweedieRegressor(power=0, link="log"),
|
696 |
+
TweedieRegressor(power=1.5),
|
697 |
+
TweedieRegressor(power=4.5),
|
698 |
+
],
|
699 |
+
)
|
700 |
+
def test_glm_log_regression(solver, fit_intercept, estimator):
|
701 |
+
"""Test GLM regression with log link on a simple dataset."""
|
702 |
+
coef = [0.2, -0.1]
|
703 |
+
X = np.array([[0, 1, 2, 3, 4], [1, 1, 1, 1, 1]]).T
|
704 |
+
y = np.exp(np.dot(X, coef))
|
705 |
+
glm = clone(estimator).set_params(
|
706 |
+
alpha=0,
|
707 |
+
fit_intercept=fit_intercept,
|
708 |
+
solver=solver,
|
709 |
+
tol=1e-8,
|
710 |
+
)
|
711 |
+
if fit_intercept:
|
712 |
+
res = glm.fit(X[:, :-1], y)
|
713 |
+
assert_allclose(res.coef_, coef[:-1], rtol=1e-6)
|
714 |
+
assert_allclose(res.intercept_, coef[-1], rtol=1e-6)
|
715 |
+
else:
|
716 |
+
res = glm.fit(X, y)
|
717 |
+
assert_allclose(res.coef_, coef, rtol=2e-6)
|
718 |
+
|
719 |
+
|
720 |
+
@pytest.mark.parametrize("solver", SOLVERS)
|
721 |
+
@pytest.mark.parametrize("fit_intercept", [True, False])
|
722 |
+
def test_warm_start(solver, fit_intercept, global_random_seed):
|
723 |
+
n_samples, n_features = 100, 10
|
724 |
+
X, y = make_regression(
|
725 |
+
n_samples=n_samples,
|
726 |
+
n_features=n_features,
|
727 |
+
n_informative=n_features - 2,
|
728 |
+
bias=fit_intercept * 1.0,
|
729 |
+
noise=1.0,
|
730 |
+
random_state=global_random_seed,
|
731 |
+
)
|
732 |
+
y = np.abs(y) # Poisson requires non-negative targets.
|
733 |
+
alpha = 1
|
734 |
+
params = {
|
735 |
+
"solver": solver,
|
736 |
+
"fit_intercept": fit_intercept,
|
737 |
+
"tol": 1e-10,
|
738 |
+
}
|
739 |
+
|
740 |
+
glm1 = PoissonRegressor(warm_start=False, max_iter=1000, alpha=alpha, **params)
|
741 |
+
glm1.fit(X, y)
|
742 |
+
|
743 |
+
glm2 = PoissonRegressor(warm_start=True, max_iter=1, alpha=alpha, **params)
|
744 |
+
# As we intentionally set max_iter=1 such that the solver should raise a
|
745 |
+
# ConvergenceWarning.
|
746 |
+
with pytest.warns(ConvergenceWarning):
|
747 |
+
glm2.fit(X, y)
|
748 |
+
|
749 |
+
linear_loss = LinearModelLoss(
|
750 |
+
base_loss=glm1._get_loss(),
|
751 |
+
fit_intercept=fit_intercept,
|
752 |
+
)
|
753 |
+
sw = np.full_like(y, fill_value=1 / n_samples)
|
754 |
+
|
755 |
+
objective_glm1 = linear_loss.loss(
|
756 |
+
coef=np.r_[glm1.coef_, glm1.intercept_] if fit_intercept else glm1.coef_,
|
757 |
+
X=X,
|
758 |
+
y=y,
|
759 |
+
sample_weight=sw,
|
760 |
+
l2_reg_strength=alpha,
|
761 |
+
)
|
762 |
+
objective_glm2 = linear_loss.loss(
|
763 |
+
coef=np.r_[glm2.coef_, glm2.intercept_] if fit_intercept else glm2.coef_,
|
764 |
+
X=X,
|
765 |
+
y=y,
|
766 |
+
sample_weight=sw,
|
767 |
+
l2_reg_strength=alpha,
|
768 |
+
)
|
769 |
+
assert objective_glm1 < objective_glm2
|
770 |
+
|
771 |
+
glm2.set_params(max_iter=1000)
|
772 |
+
glm2.fit(X, y)
|
773 |
+
# The two models are not exactly identical since the lbfgs solver
|
774 |
+
# computes the approximate hessian from previous iterations, which
|
775 |
+
# will not be strictly identical in the case of a warm start.
|
776 |
+
rtol = 2e-4 if solver == "lbfgs" else 1e-9
|
777 |
+
assert_allclose(glm1.coef_, glm2.coef_, rtol=rtol)
|
778 |
+
assert_allclose(glm1.score(X, y), glm2.score(X, y), rtol=1e-5)
|
779 |
+
|
780 |
+
|
781 |
+
@pytest.mark.parametrize("n_samples, n_features", [(100, 10), (10, 100)])
|
782 |
+
@pytest.mark.parametrize("fit_intercept", [True, False])
|
783 |
+
@pytest.mark.parametrize("sample_weight", [None, True])
|
784 |
+
def test_normal_ridge_comparison(
|
785 |
+
n_samples, n_features, fit_intercept, sample_weight, request
|
786 |
+
):
|
787 |
+
"""Compare with Ridge regression for Normal distributions."""
|
788 |
+
test_size = 10
|
789 |
+
X, y = make_regression(
|
790 |
+
n_samples=n_samples + test_size,
|
791 |
+
n_features=n_features,
|
792 |
+
n_informative=n_features - 2,
|
793 |
+
noise=0.5,
|
794 |
+
random_state=42,
|
795 |
+
)
|
796 |
+
|
797 |
+
if n_samples > n_features:
|
798 |
+
ridge_params = {"solver": "svd"}
|
799 |
+
else:
|
800 |
+
ridge_params = {"solver": "saga", "max_iter": 1000000, "tol": 1e-7}
|
801 |
+
|
802 |
+
(
|
803 |
+
X_train,
|
804 |
+
X_test,
|
805 |
+
y_train,
|
806 |
+
y_test,
|
807 |
+
) = train_test_split(X, y, test_size=test_size, random_state=0)
|
808 |
+
|
809 |
+
alpha = 1.0
|
810 |
+
if sample_weight is None:
|
811 |
+
sw_train = None
|
812 |
+
alpha_ridge = alpha * n_samples
|
813 |
+
else:
|
814 |
+
sw_train = np.random.RandomState(0).rand(len(y_train))
|
815 |
+
alpha_ridge = alpha * sw_train.sum()
|
816 |
+
|
817 |
+
# GLM has 1/(2*n) * Loss + 1/2*L2, Ridge has Loss + L2
|
818 |
+
ridge = Ridge(
|
819 |
+
alpha=alpha_ridge,
|
820 |
+
random_state=42,
|
821 |
+
fit_intercept=fit_intercept,
|
822 |
+
**ridge_params,
|
823 |
+
)
|
824 |
+
ridge.fit(X_train, y_train, sample_weight=sw_train)
|
825 |
+
|
826 |
+
glm = _GeneralizedLinearRegressor(
|
827 |
+
alpha=alpha,
|
828 |
+
fit_intercept=fit_intercept,
|
829 |
+
max_iter=300,
|
830 |
+
tol=1e-5,
|
831 |
+
)
|
832 |
+
glm.fit(X_train, y_train, sample_weight=sw_train)
|
833 |
+
assert glm.coef_.shape == (X.shape[1],)
|
834 |
+
assert_allclose(glm.coef_, ridge.coef_, atol=5e-5)
|
835 |
+
assert_allclose(glm.intercept_, ridge.intercept_, rtol=1e-5)
|
836 |
+
assert_allclose(glm.predict(X_train), ridge.predict(X_train), rtol=2e-4)
|
837 |
+
assert_allclose(glm.predict(X_test), ridge.predict(X_test), rtol=2e-4)
|
838 |
+
|
839 |
+
|
840 |
+
@pytest.mark.parametrize("solver", ["lbfgs", "newton-cholesky"])
|
841 |
+
def test_poisson_glmnet(solver):
|
842 |
+
"""Compare Poisson regression with L2 regularization and LogLink to glmnet"""
|
843 |
+
# library("glmnet")
|
844 |
+
# options(digits=10)
|
845 |
+
# df <- data.frame(a=c(-2,-1,1,2), b=c(0,0,1,1), y=c(0,1,1,2))
|
846 |
+
# x <- data.matrix(df[,c("a", "b")])
|
847 |
+
# y <- df$y
|
848 |
+
# fit <- glmnet(x=x, y=y, alpha=0, intercept=T, family="poisson",
|
849 |
+
# standardize=F, thresh=1e-10, nlambda=10000)
|
850 |
+
# coef(fit, s=1)
|
851 |
+
# (Intercept) -0.12889386979
|
852 |
+
# a 0.29019207995
|
853 |
+
# b 0.03741173122
|
854 |
+
X = np.array([[-2, -1, 1, 2], [0, 0, 1, 1]]).T
|
855 |
+
y = np.array([0, 1, 1, 2])
|
856 |
+
glm = PoissonRegressor(
|
857 |
+
alpha=1,
|
858 |
+
fit_intercept=True,
|
859 |
+
tol=1e-7,
|
860 |
+
max_iter=300,
|
861 |
+
solver=solver,
|
862 |
+
)
|
863 |
+
glm.fit(X, y)
|
864 |
+
assert_allclose(glm.intercept_, -0.12889386979, rtol=1e-5)
|
865 |
+
assert_allclose(glm.coef_, [0.29019207995, 0.03741173122], rtol=1e-5)
|
866 |
+
|
867 |
+
|
868 |
+
def test_convergence_warning(regression_data):
|
869 |
+
X, y = regression_data
|
870 |
+
|
871 |
+
est = _GeneralizedLinearRegressor(max_iter=1, tol=1e-20)
|
872 |
+
with pytest.warns(ConvergenceWarning):
|
873 |
+
est.fit(X, y)
|
874 |
+
|
875 |
+
|
876 |
+
@pytest.mark.parametrize(
|
877 |
+
"name, link_class", [("identity", IdentityLink), ("log", LogLink)]
|
878 |
+
)
|
879 |
+
def test_tweedie_link_argument(name, link_class):
|
880 |
+
"""Test GLM link argument set as string."""
|
881 |
+
y = np.array([0.1, 0.5]) # in range of all distributions
|
882 |
+
X = np.array([[1], [2]])
|
883 |
+
glm = TweedieRegressor(power=1, link=name).fit(X, y)
|
884 |
+
assert isinstance(glm._base_loss.link, link_class)
|
885 |
+
|
886 |
+
|
887 |
+
@pytest.mark.parametrize(
|
888 |
+
"power, expected_link_class",
|
889 |
+
[
|
890 |
+
(0, IdentityLink), # normal
|
891 |
+
(1, LogLink), # poisson
|
892 |
+
(2, LogLink), # gamma
|
893 |
+
(3, LogLink), # inverse-gaussian
|
894 |
+
],
|
895 |
+
)
|
896 |
+
def test_tweedie_link_auto(power, expected_link_class):
|
897 |
+
"""Test that link='auto' delivers the expected link function"""
|
898 |
+
y = np.array([0.1, 0.5]) # in range of all distributions
|
899 |
+
X = np.array([[1], [2]])
|
900 |
+
glm = TweedieRegressor(link="auto", power=power).fit(X, y)
|
901 |
+
assert isinstance(glm._base_loss.link, expected_link_class)
|
902 |
+
|
903 |
+
|
904 |
+
@pytest.mark.parametrize("power", [0, 1, 1.5, 2, 3])
|
905 |
+
@pytest.mark.parametrize("link", ["log", "identity"])
|
906 |
+
def test_tweedie_score(regression_data, power, link):
|
907 |
+
"""Test that GLM score equals d2_tweedie_score for Tweedie losses."""
|
908 |
+
X, y = regression_data
|
909 |
+
# make y positive
|
910 |
+
y = np.abs(y) + 1.0
|
911 |
+
glm = TweedieRegressor(power=power, link=link).fit(X, y)
|
912 |
+
assert glm.score(X, y) == pytest.approx(
|
913 |
+
d2_tweedie_score(y, glm.predict(X), power=power)
|
914 |
+
)
|
915 |
+
|
916 |
+
|
917 |
+
@pytest.mark.parametrize(
|
918 |
+
"estimator, value",
|
919 |
+
[
|
920 |
+
(PoissonRegressor(), True),
|
921 |
+
(GammaRegressor(), True),
|
922 |
+
(TweedieRegressor(power=1.5), True),
|
923 |
+
(TweedieRegressor(power=0), False),
|
924 |
+
],
|
925 |
+
)
|
926 |
+
def test_tags(estimator, value):
|
927 |
+
assert estimator._get_tags()["requires_positive_y"] is value
|
928 |
+
|
929 |
+
|
930 |
+
def test_linalg_warning_with_newton_solver(global_random_seed):
|
931 |
+
newton_solver = "newton-cholesky"
|
932 |
+
rng = np.random.RandomState(global_random_seed)
|
933 |
+
# Use at least 20 samples to reduce the likelihood of getting a degenerate
|
934 |
+
# dataset for any global_random_seed.
|
935 |
+
X_orig = rng.normal(size=(20, 3))
|
936 |
+
y = rng.poisson(
|
937 |
+
np.exp(X_orig @ np.ones(X_orig.shape[1])), size=X_orig.shape[0]
|
938 |
+
).astype(np.float64)
|
939 |
+
|
940 |
+
# Collinear variation of the same input features.
|
941 |
+
X_collinear = np.hstack([X_orig] * 10)
|
942 |
+
|
943 |
+
# Let's consider the deviance of a constant baseline on this problem.
|
944 |
+
baseline_pred = np.full_like(y, y.mean())
|
945 |
+
constant_model_deviance = mean_poisson_deviance(y, baseline_pred)
|
946 |
+
assert constant_model_deviance > 1.0
|
947 |
+
|
948 |
+
# No warning raised on well-conditioned design, even without regularization.
|
949 |
+
tol = 1e-10
|
950 |
+
with warnings.catch_warnings():
|
951 |
+
warnings.simplefilter("error")
|
952 |
+
reg = PoissonRegressor(solver=newton_solver, alpha=0.0, tol=tol).fit(X_orig, y)
|
953 |
+
original_newton_deviance = mean_poisson_deviance(y, reg.predict(X_orig))
|
954 |
+
|
955 |
+
# On this dataset, we should have enough data points to not make it
|
956 |
+
# possible to get a near zero deviance (for the any of the admissible
|
957 |
+
# random seeds). This will make it easier to interpret meaning of rtol in
|
958 |
+
# the subsequent assertions:
|
959 |
+
assert original_newton_deviance > 0.2
|
960 |
+
|
961 |
+
# We check that the model could successfully fit information in X_orig to
|
962 |
+
# improve upon the constant baseline by a large margin (when evaluated on
|
963 |
+
# the traing set).
|
964 |
+
assert constant_model_deviance - original_newton_deviance > 0.1
|
965 |
+
|
966 |
+
# LBFGS is robust to a collinear design because its approximation of the
|
967 |
+
# Hessian is Symmeric Positive Definite by construction. Let's record its
|
968 |
+
# solution
|
969 |
+
with warnings.catch_warnings():
|
970 |
+
warnings.simplefilter("error")
|
971 |
+
reg = PoissonRegressor(solver="lbfgs", alpha=0.0, tol=tol).fit(X_collinear, y)
|
972 |
+
collinear_lbfgs_deviance = mean_poisson_deviance(y, reg.predict(X_collinear))
|
973 |
+
|
974 |
+
# The LBFGS solution on the collinear is expected to reach a comparable
|
975 |
+
# solution to the Newton solution on the original data.
|
976 |
+
rtol = 1e-6
|
977 |
+
assert collinear_lbfgs_deviance == pytest.approx(original_newton_deviance, rel=rtol)
|
978 |
+
|
979 |
+
# Fitting a Newton solver on the collinear version of the training data
|
980 |
+
# without regularization should raise an informative warning and fallback
|
981 |
+
# to the LBFGS solver.
|
982 |
+
msg = (
|
983 |
+
"The inner solver of .*Newton.*Solver stumbled upon a singular or very "
|
984 |
+
"ill-conditioned Hessian matrix"
|
985 |
+
)
|
986 |
+
with pytest.warns(scipy.linalg.LinAlgWarning, match=msg):
|
987 |
+
reg = PoissonRegressor(solver=newton_solver, alpha=0.0, tol=tol).fit(
|
988 |
+
X_collinear, y
|
989 |
+
)
|
990 |
+
# As a result we should still automatically converge to a good solution.
|
991 |
+
collinear_newton_deviance = mean_poisson_deviance(y, reg.predict(X_collinear))
|
992 |
+
assert collinear_newton_deviance == pytest.approx(
|
993 |
+
original_newton_deviance, rel=rtol
|
994 |
+
)
|
995 |
+
|
996 |
+
# Increasing the regularization slightly should make the problem go away:
|
997 |
+
with warnings.catch_warnings():
|
998 |
+
warnings.simplefilter("error", scipy.linalg.LinAlgWarning)
|
999 |
+
reg = PoissonRegressor(solver=newton_solver, alpha=1e-10).fit(X_collinear, y)
|
1000 |
+
|
1001 |
+
# The slightly penalized model on the collinear data should be close enough
|
1002 |
+
# to the unpenalized model on the original data.
|
1003 |
+
penalized_collinear_newton_deviance = mean_poisson_deviance(
|
1004 |
+
y, reg.predict(X_collinear)
|
1005 |
+
)
|
1006 |
+
assert penalized_collinear_newton_deviance == pytest.approx(
|
1007 |
+
original_newton_deviance, rel=rtol
|
1008 |
+
)
|
1009 |
+
|
1010 |
+
|
1011 |
+
@pytest.mark.parametrize("verbose", [0, 1, 2])
|
1012 |
+
def test_newton_solver_verbosity(capsys, verbose):
|
1013 |
+
"""Test the std output of verbose newton solvers."""
|
1014 |
+
y = np.array([1, 2], dtype=float)
|
1015 |
+
X = np.array([[1.0, 0], [0, 1]], dtype=float)
|
1016 |
+
linear_loss = LinearModelLoss(base_loss=HalfPoissonLoss(), fit_intercept=False)
|
1017 |
+
sol = NewtonCholeskySolver(
|
1018 |
+
coef=linear_loss.init_zero_coef(X),
|
1019 |
+
linear_loss=linear_loss,
|
1020 |
+
l2_reg_strength=0,
|
1021 |
+
verbose=verbose,
|
1022 |
+
)
|
1023 |
+
sol.solve(X, y, None) # returns array([0., 0.69314758])
|
1024 |
+
captured = capsys.readouterr()
|
1025 |
+
|
1026 |
+
if verbose == 0:
|
1027 |
+
assert captured.out == ""
|
1028 |
+
else:
|
1029 |
+
msg = [
|
1030 |
+
"Newton iter=1",
|
1031 |
+
"Check Convergence",
|
1032 |
+
"1. max |gradient|",
|
1033 |
+
"2. Newton decrement",
|
1034 |
+
"Solver did converge at loss = ",
|
1035 |
+
]
|
1036 |
+
for m in msg:
|
1037 |
+
assert m in captured.out
|
1038 |
+
|
1039 |
+
if verbose >= 2:
|
1040 |
+
msg = ["Backtracking Line Search", "line search iteration="]
|
1041 |
+
for m in msg:
|
1042 |
+
assert m in captured.out
|
1043 |
+
|
1044 |
+
# Set the Newton solver to a state with a completely wrong Newton step.
|
1045 |
+
sol = NewtonCholeskySolver(
|
1046 |
+
coef=linear_loss.init_zero_coef(X),
|
1047 |
+
linear_loss=linear_loss,
|
1048 |
+
l2_reg_strength=0,
|
1049 |
+
verbose=verbose,
|
1050 |
+
)
|
1051 |
+
sol.setup(X=X, y=y, sample_weight=None)
|
1052 |
+
sol.iteration = 1
|
1053 |
+
sol.update_gradient_hessian(X=X, y=y, sample_weight=None)
|
1054 |
+
sol.coef_newton = np.array([1.0, 0])
|
1055 |
+
sol.gradient_times_newton = sol.gradient @ sol.coef_newton
|
1056 |
+
with warnings.catch_warnings():
|
1057 |
+
warnings.simplefilter("ignore", ConvergenceWarning)
|
1058 |
+
sol.line_search(X=X, y=y, sample_weight=None)
|
1059 |
+
captured = capsys.readouterr()
|
1060 |
+
if verbose >= 1:
|
1061 |
+
assert (
|
1062 |
+
"Line search did not converge and resorts to lbfgs instead." in captured.out
|
1063 |
+
)
|
1064 |
+
|
1065 |
+
# Set the Newton solver to a state with bad Newton step such that the loss
|
1066 |
+
# improvement in line search is tiny.
|
1067 |
+
sol = NewtonCholeskySolver(
|
1068 |
+
coef=np.array([1e-12, 0.69314758]),
|
1069 |
+
linear_loss=linear_loss,
|
1070 |
+
l2_reg_strength=0,
|
1071 |
+
verbose=verbose,
|
1072 |
+
)
|
1073 |
+
sol.setup(X=X, y=y, sample_weight=None)
|
1074 |
+
sol.iteration = 1
|
1075 |
+
sol.update_gradient_hessian(X=X, y=y, sample_weight=None)
|
1076 |
+
sol.coef_newton = np.array([1e-6, 0])
|
1077 |
+
sol.gradient_times_newton = sol.gradient @ sol.coef_newton
|
1078 |
+
with warnings.catch_warnings():
|
1079 |
+
warnings.simplefilter("ignore", ConvergenceWarning)
|
1080 |
+
sol.line_search(X=X, y=y, sample_weight=None)
|
1081 |
+
captured = capsys.readouterr()
|
1082 |
+
if verbose >= 2:
|
1083 |
+
msg = [
|
1084 |
+
"line search iteration=",
|
1085 |
+
"check loss improvement <= armijo term:",
|
1086 |
+
"check loss |improvement| <= eps * |loss_old|:",
|
1087 |
+
"check sum(|gradient|) < sum(|gradient_old|):",
|
1088 |
+
]
|
1089 |
+
for m in msg:
|
1090 |
+
assert m in captured.out
|
1091 |
+
|
1092 |
+
# Test for a case with negative hessian. We badly initialize coef for a Tweedie
|
1093 |
+
# loss with non-canonical link, e.g. Inverse Gaussian deviance with a log link.
|
1094 |
+
linear_loss = LinearModelLoss(
|
1095 |
+
base_loss=HalfTweedieLoss(power=3), fit_intercept=False
|
1096 |
+
)
|
1097 |
+
sol = NewtonCholeskySolver(
|
1098 |
+
coef=linear_loss.init_zero_coef(X) + 1,
|
1099 |
+
linear_loss=linear_loss,
|
1100 |
+
l2_reg_strength=0,
|
1101 |
+
verbose=verbose,
|
1102 |
+
)
|
1103 |
+
with warnings.catch_warnings():
|
1104 |
+
warnings.simplefilter("ignore", ConvergenceWarning)
|
1105 |
+
sol.solve(X, y, None)
|
1106 |
+
captured = capsys.readouterr()
|
1107 |
+
if verbose >= 1:
|
1108 |
+
assert (
|
1109 |
+
"The inner solver detected a pointwise Hessian with many negative values"
|
1110 |
+
" and resorts to lbfgs instead."
|
1111 |
+
in captured.out
|
1112 |
+
)
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_least_angle.py
ADDED
@@ -0,0 +1,2306 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
1 |
+
"""
|
2 |
+
Least Angle Regression algorithm. See the documentation on the
|
3 |
+
Generalized Linear Model for a complete discussion.
|
4 |
+
"""
|
5 |
+
# Author: Fabian Pedregosa <[email protected]>
|
6 |
+
# Alexandre Gramfort <[email protected]>
|
7 |
+
# Gael Varoquaux
|
8 |
+
#
|
9 |
+
# License: BSD 3 clause
|
10 |
+
|
11 |
+
import sys
|
12 |
+
import warnings
|
13 |
+
from math import log
|
14 |
+
from numbers import Integral, Real
|
15 |
+
|
16 |
+
import numpy as np
|
17 |
+
from scipy import interpolate, linalg
|
18 |
+
from scipy.linalg.lapack import get_lapack_funcs
|
19 |
+
|
20 |
+
from ..base import MultiOutputMixin, RegressorMixin, _fit_context
|
21 |
+
from ..exceptions import ConvergenceWarning
|
22 |
+
from ..model_selection import check_cv
|
23 |
+
|
24 |
+
# mypy error: Module 'sklearn.utils' has no attribute 'arrayfuncs'
|
25 |
+
from ..utils import ( # type: ignore
|
26 |
+
Bunch,
|
27 |
+
arrayfuncs,
|
28 |
+
as_float_array,
|
29 |
+
check_random_state,
|
30 |
+
)
|
31 |
+
from ..utils._metadata_requests import (
|
32 |
+
MetadataRouter,
|
33 |
+
MethodMapping,
|
34 |
+
_raise_for_params,
|
35 |
+
_routing_enabled,
|
36 |
+
process_routing,
|
37 |
+
)
|
38 |
+
from ..utils._param_validation import Hidden, Interval, StrOptions, validate_params
|
39 |
+
from ..utils.parallel import Parallel, delayed
|
40 |
+
from ._base import LinearModel, LinearRegression, _preprocess_data
|
41 |
+
|
42 |
+
SOLVE_TRIANGULAR_ARGS = {"check_finite": False}
|
43 |
+
|
44 |
+
|
45 |
+
@validate_params(
|
46 |
+
{
|
47 |
+
"X": [np.ndarray, None],
|
48 |
+
"y": [np.ndarray, None],
|
49 |
+
"Xy": [np.ndarray, None],
|
50 |
+
"Gram": [StrOptions({"auto"}), "boolean", np.ndarray, None],
|
51 |
+
"max_iter": [Interval(Integral, 0, None, closed="left")],
|
52 |
+
"alpha_min": [Interval(Real, 0, None, closed="left")],
|
53 |
+
"method": [StrOptions({"lar", "lasso"})],
|
54 |
+
"copy_X": ["boolean"],
|
55 |
+
"eps": [Interval(Real, 0, None, closed="neither"), None],
|
56 |
+
"copy_Gram": ["boolean"],
|
57 |
+
"verbose": ["verbose"],
|
58 |
+
"return_path": ["boolean"],
|
59 |
+
"return_n_iter": ["boolean"],
|
60 |
+
"positive": ["boolean"],
|
61 |
+
},
|
62 |
+
prefer_skip_nested_validation=True,
|
63 |
+
)
|
64 |
+
def lars_path(
|
65 |
+
X,
|
66 |
+
y,
|
67 |
+
Xy=None,
|
68 |
+
*,
|
69 |
+
Gram=None,
|
70 |
+
max_iter=500,
|
71 |
+
alpha_min=0,
|
72 |
+
method="lar",
|
73 |
+
copy_X=True,
|
74 |
+
eps=np.finfo(float).eps,
|
75 |
+
copy_Gram=True,
|
76 |
+
verbose=0,
|
77 |
+
return_path=True,
|
78 |
+
return_n_iter=False,
|
79 |
+
positive=False,
|
80 |
+
):
|
81 |
+
"""Compute Least Angle Regression or Lasso path using the LARS algorithm [1].
|
82 |
+
|
83 |
+
The optimization objective for the case method='lasso' is::
|
84 |
+
|
85 |
+
(1 / (2 * n_samples)) * ||y - Xw||^2_2 + alpha * ||w||_1
|
86 |
+
|
87 |
+
in the case of method='lar', the objective function is only known in
|
88 |
+
the form of an implicit equation (see discussion in [1]).
|
89 |
+
|
90 |
+
Read more in the :ref:`User Guide <least_angle_regression>`.
|
91 |
+
|
92 |
+
Parameters
|
93 |
+
----------
|
94 |
+
X : None or ndarray of shape (n_samples, n_features)
|
95 |
+
Input data. Note that if X is `None` then the Gram matrix must be
|
96 |
+
specified, i.e., cannot be `None` or `False`.
|
97 |
+
|
98 |
+
y : None or ndarray of shape (n_samples,)
|
99 |
+
Input targets.
|
100 |
+
|
101 |
+
Xy : array-like of shape (n_features,) or (n_features, n_targets), \
|
102 |
+
default=None
|
103 |
+
`Xy = X.T @ y` that can be precomputed. It is useful
|
104 |
+
only when the Gram matrix is precomputed.
|
105 |
+
|
106 |
+
Gram : None, 'auto', bool, ndarray of shape (n_features, n_features), \
|
107 |
+
default=None
|
108 |
+
Precomputed Gram matrix `X.T @ X`, if `'auto'`, the Gram
|
109 |
+
matrix is precomputed from the given X, if there are more samples
|
110 |
+
than features.
|
111 |
+
|
112 |
+
max_iter : int, default=500
|
113 |
+
Maximum number of iterations to perform, set to infinity for no limit.
|
114 |
+
|
115 |
+
alpha_min : float, default=0
|
116 |
+
Minimum correlation along the path. It corresponds to the
|
117 |
+
regularization parameter `alpha` in the Lasso.
|
118 |
+
|
119 |
+
method : {'lar', 'lasso'}, default='lar'
|
120 |
+
Specifies the returned model. Select `'lar'` for Least Angle
|
121 |
+
Regression, `'lasso'` for the Lasso.
|
122 |
+
|
123 |
+
copy_X : bool, default=True
|
124 |
+
If `False`, `X` is overwritten.
|
125 |
+
|
126 |
+
eps : float, default=np.finfo(float).eps
|
127 |
+
The machine-precision regularization in the computation of the
|
128 |
+
Cholesky diagonal factors. Increase this for very ill-conditioned
|
129 |
+
systems. Unlike the `tol` parameter in some iterative
|
130 |
+
optimization-based algorithms, this parameter does not control
|
131 |
+
the tolerance of the optimization.
|
132 |
+
|
133 |
+
copy_Gram : bool, default=True
|
134 |
+
If `False`, `Gram` is overwritten.
|
135 |
+
|
136 |
+
verbose : int, default=0
|
137 |
+
Controls output verbosity.
|
138 |
+
|
139 |
+
return_path : bool, default=True
|
140 |
+
If `True`, returns the entire path, else returns only the
|
141 |
+
last point of the path.
|
142 |
+
|
143 |
+
return_n_iter : bool, default=False
|
144 |
+
Whether to return the number of iterations.
|
145 |
+
|
146 |
+
positive : bool, default=False
|
147 |
+
Restrict coefficients to be >= 0.
|
148 |
+
This option is only allowed with method 'lasso'. Note that the model
|
149 |
+
coefficients will not converge to the ordinary-least-squares solution
|
150 |
+
for small values of alpha. Only coefficients up to the smallest alpha
|
151 |
+
value (`alphas_[alphas_ > 0.].min()` when fit_path=True) reached by
|
152 |
+
the stepwise Lars-Lasso algorithm are typically in congruence with the
|
153 |
+
solution of the coordinate descent `lasso_path` function.
|
154 |
+
|
155 |
+
Returns
|
156 |
+
-------
|
157 |
+
alphas : ndarray of shape (n_alphas + 1,)
|
158 |
+
Maximum of covariances (in absolute value) at each iteration.
|
159 |
+
`n_alphas` is either `max_iter`, `n_features`, or the
|
160 |
+
number of nodes in the path with `alpha >= alpha_min`, whichever
|
161 |
+
is smaller.
|
162 |
+
|
163 |
+
active : ndarray of shape (n_alphas,)
|
164 |
+
Indices of active variables at the end of the path.
|
165 |
+
|
166 |
+
coefs : ndarray of shape (n_features, n_alphas + 1)
|
167 |
+
Coefficients along the path.
|
168 |
+
|
169 |
+
n_iter : int
|
170 |
+
Number of iterations run. Returned only if `return_n_iter` is set
|
171 |
+
to True.
|
172 |
+
|
173 |
+
See Also
|
174 |
+
--------
|
175 |
+
lars_path_gram : Compute LARS path in the sufficient stats mode.
|
176 |
+
lasso_path : Compute Lasso path with coordinate descent.
|
177 |
+
LassoLars : Lasso model fit with Least Angle Regression a.k.a. Lars.
|
178 |
+
Lars : Least Angle Regression model a.k.a. LAR.
|
179 |
+
LassoLarsCV : Cross-validated Lasso, using the LARS algorithm.
|
180 |
+
LarsCV : Cross-validated Least Angle Regression model.
|
181 |
+
sklearn.decomposition.sparse_encode : Sparse coding.
|
182 |
+
|
183 |
+
References
|
184 |
+
----------
|
185 |
+
.. [1] "Least Angle Regression", Efron et al.
|
186 |
+
http://statweb.stanford.edu/~tibs/ftp/lars.pdf
|
187 |
+
|
188 |
+
.. [2] `Wikipedia entry on the Least-angle regression
|
189 |
+
<https://en.wikipedia.org/wiki/Least-angle_regression>`_
|
190 |
+
|
191 |
+
.. [3] `Wikipedia entry on the Lasso
|
192 |
+
<https://en.wikipedia.org/wiki/Lasso_(statistics)>`_
|
193 |
+
"""
|
194 |
+
if X is None and Gram is not None:
|
195 |
+
raise ValueError(
|
196 |
+
"X cannot be None if Gram is not None"
|
197 |
+
"Use lars_path_gram to avoid passing X and y."
|
198 |
+
)
|
199 |
+
return _lars_path_solver(
|
200 |
+
X=X,
|
201 |
+
y=y,
|
202 |
+
Xy=Xy,
|
203 |
+
Gram=Gram,
|
204 |
+
n_samples=None,
|
205 |
+
max_iter=max_iter,
|
206 |
+
alpha_min=alpha_min,
|
207 |
+
method=method,
|
208 |
+
copy_X=copy_X,
|
209 |
+
eps=eps,
|
210 |
+
copy_Gram=copy_Gram,
|
211 |
+
verbose=verbose,
|
212 |
+
return_path=return_path,
|
213 |
+
return_n_iter=return_n_iter,
|
214 |
+
positive=positive,
|
215 |
+
)
|
216 |
+
|
217 |
+
|
218 |
+
@validate_params(
|
219 |
+
{
|
220 |
+
"Xy": [np.ndarray],
|
221 |
+
"Gram": [np.ndarray],
|
222 |
+
"n_samples": [Interval(Integral, 0, None, closed="left")],
|
223 |
+
"max_iter": [Interval(Integral, 0, None, closed="left")],
|
224 |
+
"alpha_min": [Interval(Real, 0, None, closed="left")],
|
225 |
+
"method": [StrOptions({"lar", "lasso"})],
|
226 |
+
"copy_X": ["boolean"],
|
227 |
+
"eps": [Interval(Real, 0, None, closed="neither"), None],
|
228 |
+
"copy_Gram": ["boolean"],
|
229 |
+
"verbose": ["verbose"],
|
230 |
+
"return_path": ["boolean"],
|
231 |
+
"return_n_iter": ["boolean"],
|
232 |
+
"positive": ["boolean"],
|
233 |
+
},
|
234 |
+
prefer_skip_nested_validation=True,
|
235 |
+
)
|
236 |
+
def lars_path_gram(
|
237 |
+
Xy,
|
238 |
+
Gram,
|
239 |
+
*,
|
240 |
+
n_samples,
|
241 |
+
max_iter=500,
|
242 |
+
alpha_min=0,
|
243 |
+
method="lar",
|
244 |
+
copy_X=True,
|
245 |
+
eps=np.finfo(float).eps,
|
246 |
+
copy_Gram=True,
|
247 |
+
verbose=0,
|
248 |
+
return_path=True,
|
249 |
+
return_n_iter=False,
|
250 |
+
positive=False,
|
251 |
+
):
|
252 |
+
"""The lars_path in the sufficient stats mode [1].
|
253 |
+
|
254 |
+
The optimization objective for the case method='lasso' is::
|
255 |
+
|
256 |
+
(1 / (2 * n_samples)) * ||y - Xw||^2_2 + alpha * ||w||_1
|
257 |
+
|
258 |
+
in the case of method='lars', the objective function is only known in
|
259 |
+
the form of an implicit equation (see discussion in [1])
|
260 |
+
|
261 |
+
Read more in the :ref:`User Guide <least_angle_regression>`.
|
262 |
+
|
263 |
+
Parameters
|
264 |
+
----------
|
265 |
+
Xy : ndarray of shape (n_features,) or (n_features, n_targets)
|
266 |
+
`Xy = X.T @ y`.
|
267 |
+
|
268 |
+
Gram : ndarray of shape (n_features, n_features)
|
269 |
+
`Gram = X.T @ X`.
|
270 |
+
|
271 |
+
n_samples : int
|
272 |
+
Equivalent size of sample.
|
273 |
+
|
274 |
+
max_iter : int, default=500
|
275 |
+
Maximum number of iterations to perform, set to infinity for no limit.
|
276 |
+
|
277 |
+
alpha_min : float, default=0
|
278 |
+
Minimum correlation along the path. It corresponds to the
|
279 |
+
regularization parameter alpha parameter in the Lasso.
|
280 |
+
|
281 |
+
method : {'lar', 'lasso'}, default='lar'
|
282 |
+
Specifies the returned model. Select `'lar'` for Least Angle
|
283 |
+
Regression, ``'lasso'`` for the Lasso.
|
284 |
+
|
285 |
+
copy_X : bool, default=True
|
286 |
+
If `False`, `X` is overwritten.
|
287 |
+
|
288 |
+
eps : float, default=np.finfo(float).eps
|
289 |
+
The machine-precision regularization in the computation of the
|
290 |
+
Cholesky diagonal factors. Increase this for very ill-conditioned
|
291 |
+
systems. Unlike the `tol` parameter in some iterative
|
292 |
+
optimization-based algorithms, this parameter does not control
|
293 |
+
the tolerance of the optimization.
|
294 |
+
|
295 |
+
copy_Gram : bool, default=True
|
296 |
+
If `False`, `Gram` is overwritten.
|
297 |
+
|
298 |
+
verbose : int, default=0
|
299 |
+
Controls output verbosity.
|
300 |
+
|
301 |
+
return_path : bool, default=True
|
302 |
+
If `return_path==True` returns the entire path, else returns only the
|
303 |
+
last point of the path.
|
304 |
+
|
305 |
+
return_n_iter : bool, default=False
|
306 |
+
Whether to return the number of iterations.
|
307 |
+
|
308 |
+
positive : bool, default=False
|
309 |
+
Restrict coefficients to be >= 0.
|
310 |
+
This option is only allowed with method 'lasso'. Note that the model
|
311 |
+
coefficients will not converge to the ordinary-least-squares solution
|
312 |
+
for small values of alpha. Only coefficients up to the smallest alpha
|
313 |
+
value (`alphas_[alphas_ > 0.].min()` when `fit_path=True`) reached by
|
314 |
+
the stepwise Lars-Lasso algorithm are typically in congruence with the
|
315 |
+
solution of the coordinate descent lasso_path function.
|
316 |
+
|
317 |
+
Returns
|
318 |
+
-------
|
319 |
+
alphas : ndarray of shape (n_alphas + 1,)
|
320 |
+
Maximum of covariances (in absolute value) at each iteration.
|
321 |
+
`n_alphas` is either `max_iter`, `n_features` or the
|
322 |
+
number of nodes in the path with `alpha >= alpha_min`, whichever
|
323 |
+
is smaller.
|
324 |
+
|
325 |
+
active : ndarray of shape (n_alphas,)
|
326 |
+
Indices of active variables at the end of the path.
|
327 |
+
|
328 |
+
coefs : ndarray of shape (n_features, n_alphas + 1)
|
329 |
+
Coefficients along the path.
|
330 |
+
|
331 |
+
n_iter : int
|
332 |
+
Number of iterations run. Returned only if `return_n_iter` is set
|
333 |
+
to True.
|
334 |
+
|
335 |
+
See Also
|
336 |
+
--------
|
337 |
+
lars_path_gram : Compute LARS path.
|
338 |
+
lasso_path : Compute Lasso path with coordinate descent.
|
339 |
+
LassoLars : Lasso model fit with Least Angle Regression a.k.a. Lars.
|
340 |
+
Lars : Least Angle Regression model a.k.a. LAR.
|
341 |
+
LassoLarsCV : Cross-validated Lasso, using the LARS algorithm.
|
342 |
+
LarsCV : Cross-validated Least Angle Regression model.
|
343 |
+
sklearn.decomposition.sparse_encode : Sparse coding.
|
344 |
+
|
345 |
+
References
|
346 |
+
----------
|
347 |
+
.. [1] "Least Angle Regression", Efron et al.
|
348 |
+
http://statweb.stanford.edu/~tibs/ftp/lars.pdf
|
349 |
+
|
350 |
+
.. [2] `Wikipedia entry on the Least-angle regression
|
351 |
+
<https://en.wikipedia.org/wiki/Least-angle_regression>`_
|
352 |
+
|
353 |
+
.. [3] `Wikipedia entry on the Lasso
|
354 |
+
<https://en.wikipedia.org/wiki/Lasso_(statistics)>`_
|
355 |
+
"""
|
356 |
+
return _lars_path_solver(
|
357 |
+
X=None,
|
358 |
+
y=None,
|
359 |
+
Xy=Xy,
|
360 |
+
Gram=Gram,
|
361 |
+
n_samples=n_samples,
|
362 |
+
max_iter=max_iter,
|
363 |
+
alpha_min=alpha_min,
|
364 |
+
method=method,
|
365 |
+
copy_X=copy_X,
|
366 |
+
eps=eps,
|
367 |
+
copy_Gram=copy_Gram,
|
368 |
+
verbose=verbose,
|
369 |
+
return_path=return_path,
|
370 |
+
return_n_iter=return_n_iter,
|
371 |
+
positive=positive,
|
372 |
+
)
|
373 |
+
|
374 |
+
|
375 |
+
def _lars_path_solver(
|
376 |
+
X,
|
377 |
+
y,
|
378 |
+
Xy=None,
|
379 |
+
Gram=None,
|
380 |
+
n_samples=None,
|
381 |
+
max_iter=500,
|
382 |
+
alpha_min=0,
|
383 |
+
method="lar",
|
384 |
+
copy_X=True,
|
385 |
+
eps=np.finfo(float).eps,
|
386 |
+
copy_Gram=True,
|
387 |
+
verbose=0,
|
388 |
+
return_path=True,
|
389 |
+
return_n_iter=False,
|
390 |
+
positive=False,
|
391 |
+
):
|
392 |
+
"""Compute Least Angle Regression or Lasso path using LARS algorithm [1]
|
393 |
+
|
394 |
+
The optimization objective for the case method='lasso' is::
|
395 |
+
|
396 |
+
(1 / (2 * n_samples)) * ||y - Xw||^2_2 + alpha * ||w||_1
|
397 |
+
|
398 |
+
in the case of method='lars', the objective function is only known in
|
399 |
+
the form of an implicit equation (see discussion in [1])
|
400 |
+
|
401 |
+
Read more in the :ref:`User Guide <least_angle_regression>`.
|
402 |
+
|
403 |
+
Parameters
|
404 |
+
----------
|
405 |
+
X : None or ndarray of shape (n_samples, n_features)
|
406 |
+
Input data. Note that if X is None then Gram must be specified,
|
407 |
+
i.e., cannot be None or False.
|
408 |
+
|
409 |
+
y : None or ndarray of shape (n_samples,)
|
410 |
+
Input targets.
|
411 |
+
|
412 |
+
Xy : array-like of shape (n_features,) or (n_features, n_targets), \
|
413 |
+
default=None
|
414 |
+
`Xy = np.dot(X.T, y)` that can be precomputed. It is useful
|
415 |
+
only when the Gram matrix is precomputed.
|
416 |
+
|
417 |
+
Gram : None, 'auto' or array-like of shape (n_features, n_features), \
|
418 |
+
default=None
|
419 |
+
Precomputed Gram matrix `(X' * X)`, if ``'auto'``, the Gram
|
420 |
+
matrix is precomputed from the given X, if there are more samples
|
421 |
+
than features.
|
422 |
+
|
423 |
+
n_samples : int or float, default=None
|
424 |
+
Equivalent size of sample. If `None`, it will be `n_samples`.
|
425 |
+
|
426 |
+
max_iter : int, default=500
|
427 |
+
Maximum number of iterations to perform, set to infinity for no limit.
|
428 |
+
|
429 |
+
alpha_min : float, default=0
|
430 |
+
Minimum correlation along the path. It corresponds to the
|
431 |
+
regularization parameter alpha parameter in the Lasso.
|
432 |
+
|
433 |
+
method : {'lar', 'lasso'}, default='lar'
|
434 |
+
Specifies the returned model. Select ``'lar'`` for Least Angle
|
435 |
+
Regression, ``'lasso'`` for the Lasso.
|
436 |
+
|
437 |
+
copy_X : bool, default=True
|
438 |
+
If ``False``, ``X`` is overwritten.
|
439 |
+
|
440 |
+
eps : float, default=np.finfo(float).eps
|
441 |
+
The machine-precision regularization in the computation of the
|
442 |
+
Cholesky diagonal factors. Increase this for very ill-conditioned
|
443 |
+
systems. Unlike the ``tol`` parameter in some iterative
|
444 |
+
optimization-based algorithms, this parameter does not control
|
445 |
+
the tolerance of the optimization.
|
446 |
+
|
447 |
+
copy_Gram : bool, default=True
|
448 |
+
If ``False``, ``Gram`` is overwritten.
|
449 |
+
|
450 |
+
verbose : int, default=0
|
451 |
+
Controls output verbosity.
|
452 |
+
|
453 |
+
return_path : bool, default=True
|
454 |
+
If ``return_path==True`` returns the entire path, else returns only the
|
455 |
+
last point of the path.
|
456 |
+
|
457 |
+
return_n_iter : bool, default=False
|
458 |
+
Whether to return the number of iterations.
|
459 |
+
|
460 |
+
positive : bool, default=False
|
461 |
+
Restrict coefficients to be >= 0.
|
462 |
+
This option is only allowed with method 'lasso'. Note that the model
|
463 |
+
coefficients will not converge to the ordinary-least-squares solution
|
464 |
+
for small values of alpha. Only coefficients up to the smallest alpha
|
465 |
+
value (``alphas_[alphas_ > 0.].min()`` when fit_path=True) reached by
|
466 |
+
the stepwise Lars-Lasso algorithm are typically in congruence with the
|
467 |
+
solution of the coordinate descent lasso_path function.
|
468 |
+
|
469 |
+
Returns
|
470 |
+
-------
|
471 |
+
alphas : array-like of shape (n_alphas + 1,)
|
472 |
+
Maximum of covariances (in absolute value) at each iteration.
|
473 |
+
``n_alphas`` is either ``max_iter``, ``n_features`` or the
|
474 |
+
number of nodes in the path with ``alpha >= alpha_min``, whichever
|
475 |
+
is smaller.
|
476 |
+
|
477 |
+
active : array-like of shape (n_alphas,)
|
478 |
+
Indices of active variables at the end of the path.
|
479 |
+
|
480 |
+
coefs : array-like of shape (n_features, n_alphas + 1)
|
481 |
+
Coefficients along the path
|
482 |
+
|
483 |
+
n_iter : int
|
484 |
+
Number of iterations run. Returned only if return_n_iter is set
|
485 |
+
to True.
|
486 |
+
|
487 |
+
See Also
|
488 |
+
--------
|
489 |
+
lasso_path
|
490 |
+
LassoLars
|
491 |
+
Lars
|
492 |
+
LassoLarsCV
|
493 |
+
LarsCV
|
494 |
+
sklearn.decomposition.sparse_encode
|
495 |
+
|
496 |
+
References
|
497 |
+
----------
|
498 |
+
.. [1] "Least Angle Regression", Efron et al.
|
499 |
+
http://statweb.stanford.edu/~tibs/ftp/lars.pdf
|
500 |
+
|
501 |
+
.. [2] `Wikipedia entry on the Least-angle regression
|
502 |
+
<https://en.wikipedia.org/wiki/Least-angle_regression>`_
|
503 |
+
|
504 |
+
.. [3] `Wikipedia entry on the Lasso
|
505 |
+
<https://en.wikipedia.org/wiki/Lasso_(statistics)>`_
|
506 |
+
|
507 |
+
"""
|
508 |
+
if method == "lar" and positive:
|
509 |
+
raise ValueError("Positive constraint not supported for 'lar' coding method.")
|
510 |
+
|
511 |
+
n_samples = n_samples if n_samples is not None else y.size
|
512 |
+
|
513 |
+
if Xy is None:
|
514 |
+
Cov = np.dot(X.T, y)
|
515 |
+
else:
|
516 |
+
Cov = Xy.copy()
|
517 |
+
|
518 |
+
if Gram is None or Gram is False:
|
519 |
+
Gram = None
|
520 |
+
if X is None:
|
521 |
+
raise ValueError("X and Gram cannot both be unspecified.")
|
522 |
+
elif isinstance(Gram, str) and Gram == "auto" or Gram is True:
|
523 |
+
if Gram is True or X.shape[0] > X.shape[1]:
|
524 |
+
Gram = np.dot(X.T, X)
|
525 |
+
else:
|
526 |
+
Gram = None
|
527 |
+
elif copy_Gram:
|
528 |
+
Gram = Gram.copy()
|
529 |
+
|
530 |
+
if Gram is None:
|
531 |
+
n_features = X.shape[1]
|
532 |
+
else:
|
533 |
+
n_features = Cov.shape[0]
|
534 |
+
if Gram.shape != (n_features, n_features):
|
535 |
+
raise ValueError("The shapes of the inputs Gram and Xy do not match.")
|
536 |
+
|
537 |
+
if copy_X and X is not None and Gram is None:
|
538 |
+
# force copy. setting the array to be fortran-ordered
|
539 |
+
# speeds up the calculation of the (partial) Gram matrix
|
540 |
+
# and allows to easily swap columns
|
541 |
+
X = X.copy("F")
|
542 |
+
|
543 |
+
max_features = min(max_iter, n_features)
|
544 |
+
|
545 |
+
dtypes = set(a.dtype for a in (X, y, Xy, Gram) if a is not None)
|
546 |
+
if len(dtypes) == 1:
|
547 |
+
# use the precision level of input data if it is consistent
|
548 |
+
return_dtype = next(iter(dtypes))
|
549 |
+
else:
|
550 |
+
# fallback to double precision otherwise
|
551 |
+
return_dtype = np.float64
|
552 |
+
|
553 |
+
if return_path:
|
554 |
+
coefs = np.zeros((max_features + 1, n_features), dtype=return_dtype)
|
555 |
+
alphas = np.zeros(max_features + 1, dtype=return_dtype)
|
556 |
+
else:
|
557 |
+
coef, prev_coef = (
|
558 |
+
np.zeros(n_features, dtype=return_dtype),
|
559 |
+
np.zeros(n_features, dtype=return_dtype),
|
560 |
+
)
|
561 |
+
alpha, prev_alpha = (
|
562 |
+
np.array([0.0], dtype=return_dtype),
|
563 |
+
np.array([0.0], dtype=return_dtype),
|
564 |
+
)
|
565 |
+
# above better ideas?
|
566 |
+
|
567 |
+
n_iter, n_active = 0, 0
|
568 |
+
active, indices = list(), np.arange(n_features)
|
569 |
+
# holds the sign of covariance
|
570 |
+
sign_active = np.empty(max_features, dtype=np.int8)
|
571 |
+
drop = False
|
572 |
+
|
573 |
+
# will hold the cholesky factorization. Only lower part is
|
574 |
+
# referenced.
|
575 |
+
if Gram is None:
|
576 |
+
L = np.empty((max_features, max_features), dtype=X.dtype)
|
577 |
+
swap, nrm2 = linalg.get_blas_funcs(("swap", "nrm2"), (X,))
|
578 |
+
else:
|
579 |
+
L = np.empty((max_features, max_features), dtype=Gram.dtype)
|
580 |
+
swap, nrm2 = linalg.get_blas_funcs(("swap", "nrm2"), (Cov,))
|
581 |
+
(solve_cholesky,) = get_lapack_funcs(("potrs",), (L,))
|
582 |
+
|
583 |
+
if verbose:
|
584 |
+
if verbose > 1:
|
585 |
+
print("Step\t\tAdded\t\tDropped\t\tActive set size\t\tC")
|
586 |
+
else:
|
587 |
+
sys.stdout.write(".")
|
588 |
+
sys.stdout.flush()
|
589 |
+
|
590 |
+
tiny32 = np.finfo(np.float32).tiny # to avoid division by 0 warning
|
591 |
+
cov_precision = np.finfo(Cov.dtype).precision
|
592 |
+
equality_tolerance = np.finfo(np.float32).eps
|
593 |
+
|
594 |
+
if Gram is not None:
|
595 |
+
Gram_copy = Gram.copy()
|
596 |
+
Cov_copy = Cov.copy()
|
597 |
+
|
598 |
+
while True:
|
599 |
+
if Cov.size:
|
600 |
+
if positive:
|
601 |
+
C_idx = np.argmax(Cov)
|
602 |
+
else:
|
603 |
+
C_idx = np.argmax(np.abs(Cov))
|
604 |
+
|
605 |
+
C_ = Cov[C_idx]
|
606 |
+
|
607 |
+
if positive:
|
608 |
+
C = C_
|
609 |
+
else:
|
610 |
+
C = np.fabs(C_)
|
611 |
+
else:
|
612 |
+
C = 0.0
|
613 |
+
|
614 |
+
if return_path:
|
615 |
+
alpha = alphas[n_iter, np.newaxis]
|
616 |
+
coef = coefs[n_iter]
|
617 |
+
prev_alpha = alphas[n_iter - 1, np.newaxis]
|
618 |
+
prev_coef = coefs[n_iter - 1]
|
619 |
+
|
620 |
+
alpha[0] = C / n_samples
|
621 |
+
if alpha[0] <= alpha_min + equality_tolerance: # early stopping
|
622 |
+
if abs(alpha[0] - alpha_min) > equality_tolerance:
|
623 |
+
# interpolation factor 0 <= ss < 1
|
624 |
+
if n_iter > 0:
|
625 |
+
# In the first iteration, all alphas are zero, the formula
|
626 |
+
# below would make ss a NaN
|
627 |
+
ss = (prev_alpha[0] - alpha_min) / (prev_alpha[0] - alpha[0])
|
628 |
+
coef[:] = prev_coef + ss * (coef - prev_coef)
|
629 |
+
alpha[0] = alpha_min
|
630 |
+
if return_path:
|
631 |
+
coefs[n_iter] = coef
|
632 |
+
break
|
633 |
+
|
634 |
+
if n_iter >= max_iter or n_active >= n_features:
|
635 |
+
break
|
636 |
+
if not drop:
|
637 |
+
##########################################################
|
638 |
+
# Append x_j to the Cholesky factorization of (Xa * Xa') #
|
639 |
+
# #
|
640 |
+
# ( L 0 ) #
|
641 |
+
# L -> ( ) , where L * w = Xa' x_j #
|
642 |
+
# ( w z ) and z = ||x_j|| #
|
643 |
+
# #
|
644 |
+
##########################################################
|
645 |
+
|
646 |
+
if positive:
|
647 |
+
sign_active[n_active] = np.ones_like(C_)
|
648 |
+
else:
|
649 |
+
sign_active[n_active] = np.sign(C_)
|
650 |
+
m, n = n_active, C_idx + n_active
|
651 |
+
|
652 |
+
Cov[C_idx], Cov[0] = swap(Cov[C_idx], Cov[0])
|
653 |
+
indices[n], indices[m] = indices[m], indices[n]
|
654 |
+
Cov_not_shortened = Cov
|
655 |
+
Cov = Cov[1:] # remove Cov[0]
|
656 |
+
|
657 |
+
if Gram is None:
|
658 |
+
X.T[n], X.T[m] = swap(X.T[n], X.T[m])
|
659 |
+
c = nrm2(X.T[n_active]) ** 2
|
660 |
+
L[n_active, :n_active] = np.dot(X.T[n_active], X.T[:n_active].T)
|
661 |
+
else:
|
662 |
+
# swap does only work inplace if matrix is fortran
|
663 |
+
# contiguous ...
|
664 |
+
Gram[m], Gram[n] = swap(Gram[m], Gram[n])
|
665 |
+
Gram[:, m], Gram[:, n] = swap(Gram[:, m], Gram[:, n])
|
666 |
+
c = Gram[n_active, n_active]
|
667 |
+
L[n_active, :n_active] = Gram[n_active, :n_active]
|
668 |
+
|
669 |
+
# Update the cholesky decomposition for the Gram matrix
|
670 |
+
if n_active:
|
671 |
+
linalg.solve_triangular(
|
672 |
+
L[:n_active, :n_active],
|
673 |
+
L[n_active, :n_active],
|
674 |
+
trans=0,
|
675 |
+
lower=1,
|
676 |
+
overwrite_b=True,
|
677 |
+
**SOLVE_TRIANGULAR_ARGS,
|
678 |
+
)
|
679 |
+
|
680 |
+
v = np.dot(L[n_active, :n_active], L[n_active, :n_active])
|
681 |
+
diag = max(np.sqrt(np.abs(c - v)), eps)
|
682 |
+
L[n_active, n_active] = diag
|
683 |
+
|
684 |
+
if diag < 1e-7:
|
685 |
+
# The system is becoming too ill-conditioned.
|
686 |
+
# We have degenerate vectors in our active set.
|
687 |
+
# We'll 'drop for good' the last regressor added.
|
688 |
+
warnings.warn(
|
689 |
+
"Regressors in active set degenerate. "
|
690 |
+
"Dropping a regressor, after %i iterations, "
|
691 |
+
"i.e. alpha=%.3e, "
|
692 |
+
"with an active set of %i regressors, and "
|
693 |
+
"the smallest cholesky pivot element being %.3e."
|
694 |
+
" Reduce max_iter or increase eps parameters."
|
695 |
+
% (n_iter, alpha.item(), n_active, diag),
|
696 |
+
ConvergenceWarning,
|
697 |
+
)
|
698 |
+
|
699 |
+
# XXX: need to figure a 'drop for good' way
|
700 |
+
Cov = Cov_not_shortened
|
701 |
+
Cov[0] = 0
|
702 |
+
Cov[C_idx], Cov[0] = swap(Cov[C_idx], Cov[0])
|
703 |
+
continue
|
704 |
+
|
705 |
+
active.append(indices[n_active])
|
706 |
+
n_active += 1
|
707 |
+
|
708 |
+
if verbose > 1:
|
709 |
+
print(
|
710 |
+
"%s\t\t%s\t\t%s\t\t%s\t\t%s" % (n_iter, active[-1], "", n_active, C)
|
711 |
+
)
|
712 |
+
|
713 |
+
if method == "lasso" and n_iter > 0 and prev_alpha[0] < alpha[0]:
|
714 |
+
# alpha is increasing. This is because the updates of Cov are
|
715 |
+
# bringing in too much numerical error that is greater than
|
716 |
+
# than the remaining correlation with the
|
717 |
+
# regressors. Time to bail out
|
718 |
+
warnings.warn(
|
719 |
+
"Early stopping the lars path, as the residues "
|
720 |
+
"are small and the current value of alpha is no "
|
721 |
+
"longer well controlled. %i iterations, alpha=%.3e, "
|
722 |
+
"previous alpha=%.3e, with an active set of %i "
|
723 |
+
"regressors." % (n_iter, alpha.item(), prev_alpha.item(), n_active),
|
724 |
+
ConvergenceWarning,
|
725 |
+
)
|
726 |
+
break
|
727 |
+
|
728 |
+
# least squares solution
|
729 |
+
least_squares, _ = solve_cholesky(
|
730 |
+
L[:n_active, :n_active], sign_active[:n_active], lower=True
|
731 |
+
)
|
732 |
+
|
733 |
+
if least_squares.size == 1 and least_squares == 0:
|
734 |
+
# This happens because sign_active[:n_active] = 0
|
735 |
+
least_squares[...] = 1
|
736 |
+
AA = 1.0
|
737 |
+
else:
|
738 |
+
# is this really needed ?
|
739 |
+
AA = 1.0 / np.sqrt(np.sum(least_squares * sign_active[:n_active]))
|
740 |
+
|
741 |
+
if not np.isfinite(AA):
|
742 |
+
# L is too ill-conditioned
|
743 |
+
i = 0
|
744 |
+
L_ = L[:n_active, :n_active].copy()
|
745 |
+
while not np.isfinite(AA):
|
746 |
+
L_.flat[:: n_active + 1] += (2**i) * eps
|
747 |
+
least_squares, _ = solve_cholesky(
|
748 |
+
L_, sign_active[:n_active], lower=True
|
749 |
+
)
|
750 |
+
tmp = max(np.sum(least_squares * sign_active[:n_active]), eps)
|
751 |
+
AA = 1.0 / np.sqrt(tmp)
|
752 |
+
i += 1
|
753 |
+
least_squares *= AA
|
754 |
+
|
755 |
+
if Gram is None:
|
756 |
+
# equiangular direction of variables in the active set
|
757 |
+
eq_dir = np.dot(X.T[:n_active].T, least_squares)
|
758 |
+
# correlation between each unactive variables and
|
759 |
+
# eqiangular vector
|
760 |
+
corr_eq_dir = np.dot(X.T[n_active:], eq_dir)
|
761 |
+
else:
|
762 |
+
# if huge number of features, this takes 50% of time, I
|
763 |
+
# think could be avoided if we just update it using an
|
764 |
+
# orthogonal (QR) decomposition of X
|
765 |
+
corr_eq_dir = np.dot(Gram[:n_active, n_active:].T, least_squares)
|
766 |
+
|
767 |
+
# Explicit rounding can be necessary to avoid `np.argmax(Cov)` yielding
|
768 |
+
# unstable results because of rounding errors.
|
769 |
+
np.around(corr_eq_dir, decimals=cov_precision, out=corr_eq_dir)
|
770 |
+
|
771 |
+
g1 = arrayfuncs.min_pos((C - Cov) / (AA - corr_eq_dir + tiny32))
|
772 |
+
if positive:
|
773 |
+
gamma_ = min(g1, C / AA)
|
774 |
+
else:
|
775 |
+
g2 = arrayfuncs.min_pos((C + Cov) / (AA + corr_eq_dir + tiny32))
|
776 |
+
gamma_ = min(g1, g2, C / AA)
|
777 |
+
|
778 |
+
# TODO: better names for these variables: z
|
779 |
+
drop = False
|
780 |
+
z = -coef[active] / (least_squares + tiny32)
|
781 |
+
z_pos = arrayfuncs.min_pos(z)
|
782 |
+
if z_pos < gamma_:
|
783 |
+
# some coefficients have changed sign
|
784 |
+
idx = np.where(z == z_pos)[0][::-1]
|
785 |
+
|
786 |
+
# update the sign, important for LAR
|
787 |
+
sign_active[idx] = -sign_active[idx]
|
788 |
+
|
789 |
+
if method == "lasso":
|
790 |
+
gamma_ = z_pos
|
791 |
+
drop = True
|
792 |
+
|
793 |
+
n_iter += 1
|
794 |
+
|
795 |
+
if return_path:
|
796 |
+
if n_iter >= coefs.shape[0]:
|
797 |
+
del coef, alpha, prev_alpha, prev_coef
|
798 |
+
# resize the coefs and alphas array
|
799 |
+
add_features = 2 * max(1, (max_features - n_active))
|
800 |
+
coefs = np.resize(coefs, (n_iter + add_features, n_features))
|
801 |
+
coefs[-add_features:] = 0
|
802 |
+
alphas = np.resize(alphas, n_iter + add_features)
|
803 |
+
alphas[-add_features:] = 0
|
804 |
+
coef = coefs[n_iter]
|
805 |
+
prev_coef = coefs[n_iter - 1]
|
806 |
+
else:
|
807 |
+
# mimic the effect of incrementing n_iter on the array references
|
808 |
+
prev_coef = coef
|
809 |
+
prev_alpha[0] = alpha[0]
|
810 |
+
coef = np.zeros_like(coef)
|
811 |
+
|
812 |
+
coef[active] = prev_coef[active] + gamma_ * least_squares
|
813 |
+
|
814 |
+
# update correlations
|
815 |
+
Cov -= gamma_ * corr_eq_dir
|
816 |
+
|
817 |
+
# See if any coefficient has changed sign
|
818 |
+
if drop and method == "lasso":
|
819 |
+
# handle the case when idx is not length of 1
|
820 |
+
for ii in idx:
|
821 |
+
arrayfuncs.cholesky_delete(L[:n_active, :n_active], ii)
|
822 |
+
|
823 |
+
n_active -= 1
|
824 |
+
# handle the case when idx is not length of 1
|
825 |
+
drop_idx = [active.pop(ii) for ii in idx]
|
826 |
+
|
827 |
+
if Gram is None:
|
828 |
+
# propagate dropped variable
|
829 |
+
for ii in idx:
|
830 |
+
for i in range(ii, n_active):
|
831 |
+
X.T[i], X.T[i + 1] = swap(X.T[i], X.T[i + 1])
|
832 |
+
# yeah this is stupid
|
833 |
+
indices[i], indices[i + 1] = indices[i + 1], indices[i]
|
834 |
+
|
835 |
+
# TODO: this could be updated
|
836 |
+
residual = y - np.dot(X[:, :n_active], coef[active])
|
837 |
+
temp = np.dot(X.T[n_active], residual)
|
838 |
+
|
839 |
+
Cov = np.r_[temp, Cov]
|
840 |
+
else:
|
841 |
+
for ii in idx:
|
842 |
+
for i in range(ii, n_active):
|
843 |
+
indices[i], indices[i + 1] = indices[i + 1], indices[i]
|
844 |
+
Gram[i], Gram[i + 1] = swap(Gram[i], Gram[i + 1])
|
845 |
+
Gram[:, i], Gram[:, i + 1] = swap(Gram[:, i], Gram[:, i + 1])
|
846 |
+
|
847 |
+
# Cov_n = Cov_j + x_j * X + increment(betas) TODO:
|
848 |
+
# will this still work with multiple drops ?
|
849 |
+
|
850 |
+
# recompute covariance. Probably could be done better
|
851 |
+
# wrong as Xy is not swapped with the rest of variables
|
852 |
+
|
853 |
+
# TODO: this could be updated
|
854 |
+
temp = Cov_copy[drop_idx] - np.dot(Gram_copy[drop_idx], coef)
|
855 |
+
Cov = np.r_[temp, Cov]
|
856 |
+
|
857 |
+
sign_active = np.delete(sign_active, idx)
|
858 |
+
sign_active = np.append(sign_active, 0.0) # just to maintain size
|
859 |
+
if verbose > 1:
|
860 |
+
print(
|
861 |
+
"%s\t\t%s\t\t%s\t\t%s\t\t%s"
|
862 |
+
% (n_iter, "", drop_idx, n_active, abs(temp))
|
863 |
+
)
|
864 |
+
|
865 |
+
if return_path:
|
866 |
+
# resize coefs in case of early stop
|
867 |
+
alphas = alphas[: n_iter + 1]
|
868 |
+
coefs = coefs[: n_iter + 1]
|
869 |
+
|
870 |
+
if return_n_iter:
|
871 |
+
return alphas, active, coefs.T, n_iter
|
872 |
+
else:
|
873 |
+
return alphas, active, coefs.T
|
874 |
+
else:
|
875 |
+
if return_n_iter:
|
876 |
+
return alpha, active, coef, n_iter
|
877 |
+
else:
|
878 |
+
return alpha, active, coef
|
879 |
+
|
880 |
+
|
881 |
+
###############################################################################
|
882 |
+
# Estimator classes
|
883 |
+
|
884 |
+
|
885 |
+
class Lars(MultiOutputMixin, RegressorMixin, LinearModel):
|
886 |
+
"""Least Angle Regression model a.k.a. LAR.
|
887 |
+
|
888 |
+
Read more in the :ref:`User Guide <least_angle_regression>`.
|
889 |
+
|
890 |
+
Parameters
|
891 |
+
----------
|
892 |
+
fit_intercept : bool, default=True
|
893 |
+
Whether to calculate the intercept for this model. If set
|
894 |
+
to false, no intercept will be used in calculations
|
895 |
+
(i.e. data is expected to be centered).
|
896 |
+
|
897 |
+
verbose : bool or int, default=False
|
898 |
+
Sets the verbosity amount.
|
899 |
+
|
900 |
+
precompute : bool, 'auto' or array-like , default='auto'
|
901 |
+
Whether to use a precomputed Gram matrix to speed up
|
902 |
+
calculations. If set to ``'auto'`` let us decide. The Gram
|
903 |
+
matrix can also be passed as argument.
|
904 |
+
|
905 |
+
n_nonzero_coefs : int, default=500
|
906 |
+
Target number of non-zero coefficients. Use ``np.inf`` for no limit.
|
907 |
+
|
908 |
+
eps : float, default=np.finfo(float).eps
|
909 |
+
The machine-precision regularization in the computation of the
|
910 |
+
Cholesky diagonal factors. Increase this for very ill-conditioned
|
911 |
+
systems. Unlike the ``tol`` parameter in some iterative
|
912 |
+
optimization-based algorithms, this parameter does not control
|
913 |
+
the tolerance of the optimization.
|
914 |
+
|
915 |
+
copy_X : bool, default=True
|
916 |
+
If ``True``, X will be copied; else, it may be overwritten.
|
917 |
+
|
918 |
+
fit_path : bool, default=True
|
919 |
+
If True the full path is stored in the ``coef_path_`` attribute.
|
920 |
+
If you compute the solution for a large problem or many targets,
|
921 |
+
setting ``fit_path`` to ``False`` will lead to a speedup, especially
|
922 |
+
with a small alpha.
|
923 |
+
|
924 |
+
jitter : float, default=None
|
925 |
+
Upper bound on a uniform noise parameter to be added to the
|
926 |
+
`y` values, to satisfy the model's assumption of
|
927 |
+
one-at-a-time computations. Might help with stability.
|
928 |
+
|
929 |
+
.. versionadded:: 0.23
|
930 |
+
|
931 |
+
random_state : int, RandomState instance or None, default=None
|
932 |
+
Determines random number generation for jittering. Pass an int
|
933 |
+
for reproducible output across multiple function calls.
|
934 |
+
See :term:`Glossary <random_state>`. Ignored if `jitter` is None.
|
935 |
+
|
936 |
+
.. versionadded:: 0.23
|
937 |
+
|
938 |
+
Attributes
|
939 |
+
----------
|
940 |
+
alphas_ : array-like of shape (n_alphas + 1,) or list of such arrays
|
941 |
+
Maximum of covariances (in absolute value) at each iteration.
|
942 |
+
``n_alphas`` is either ``max_iter``, ``n_features`` or the
|
943 |
+
number of nodes in the path with ``alpha >= alpha_min``, whichever
|
944 |
+
is smaller. If this is a list of array-like, the length of the outer
|
945 |
+
list is `n_targets`.
|
946 |
+
|
947 |
+
active_ : list of shape (n_alphas,) or list of such lists
|
948 |
+
Indices of active variables at the end of the path.
|
949 |
+
If this is a list of list, the length of the outer list is `n_targets`.
|
950 |
+
|
951 |
+
coef_path_ : array-like of shape (n_features, n_alphas + 1) or list \
|
952 |
+
of such arrays
|
953 |
+
The varying values of the coefficients along the path. It is not
|
954 |
+
present if the ``fit_path`` parameter is ``False``. If this is a list
|
955 |
+
of array-like, the length of the outer list is `n_targets`.
|
956 |
+
|
957 |
+
coef_ : array-like of shape (n_features,) or (n_targets, n_features)
|
958 |
+
Parameter vector (w in the formulation formula).
|
959 |
+
|
960 |
+
intercept_ : float or array-like of shape (n_targets,)
|
961 |
+
Independent term in decision function.
|
962 |
+
|
963 |
+
n_iter_ : array-like or int
|
964 |
+
The number of iterations taken by lars_path to find the
|
965 |
+
grid of alphas for each target.
|
966 |
+
|
967 |
+
n_features_in_ : int
|
968 |
+
Number of features seen during :term:`fit`.
|
969 |
+
|
970 |
+
.. versionadded:: 0.24
|
971 |
+
|
972 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
973 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
974 |
+
has feature names that are all strings.
|
975 |
+
|
976 |
+
.. versionadded:: 1.0
|
977 |
+
|
978 |
+
See Also
|
979 |
+
--------
|
980 |
+
lars_path: Compute Least Angle Regression or Lasso
|
981 |
+
path using LARS algorithm.
|
982 |
+
LarsCV : Cross-validated Least Angle Regression model.
|
983 |
+
sklearn.decomposition.sparse_encode : Sparse coding.
|
984 |
+
|
985 |
+
Examples
|
986 |
+
--------
|
987 |
+
>>> from sklearn import linear_model
|
988 |
+
>>> reg = linear_model.Lars(n_nonzero_coefs=1)
|
989 |
+
>>> reg.fit([[-1, 1], [0, 0], [1, 1]], [-1.1111, 0, -1.1111])
|
990 |
+
Lars(n_nonzero_coefs=1)
|
991 |
+
>>> print(reg.coef_)
|
992 |
+
[ 0. -1.11...]
|
993 |
+
"""
|
994 |
+
|
995 |
+
_parameter_constraints: dict = {
|
996 |
+
"fit_intercept": ["boolean"],
|
997 |
+
"verbose": ["verbose"],
|
998 |
+
"precompute": ["boolean", StrOptions({"auto"}), np.ndarray, Hidden(None)],
|
999 |
+
"n_nonzero_coefs": [Interval(Integral, 1, None, closed="left")],
|
1000 |
+
"eps": [Interval(Real, 0, None, closed="left")],
|
1001 |
+
"copy_X": ["boolean"],
|
1002 |
+
"fit_path": ["boolean"],
|
1003 |
+
"jitter": [Interval(Real, 0, None, closed="left"), None],
|
1004 |
+
"random_state": ["random_state"],
|
1005 |
+
}
|
1006 |
+
|
1007 |
+
method = "lar"
|
1008 |
+
positive = False
|
1009 |
+
|
1010 |
+
def __init__(
|
1011 |
+
self,
|
1012 |
+
*,
|
1013 |
+
fit_intercept=True,
|
1014 |
+
verbose=False,
|
1015 |
+
precompute="auto",
|
1016 |
+
n_nonzero_coefs=500,
|
1017 |
+
eps=np.finfo(float).eps,
|
1018 |
+
copy_X=True,
|
1019 |
+
fit_path=True,
|
1020 |
+
jitter=None,
|
1021 |
+
random_state=None,
|
1022 |
+
):
|
1023 |
+
self.fit_intercept = fit_intercept
|
1024 |
+
self.verbose = verbose
|
1025 |
+
self.precompute = precompute
|
1026 |
+
self.n_nonzero_coefs = n_nonzero_coefs
|
1027 |
+
self.eps = eps
|
1028 |
+
self.copy_X = copy_X
|
1029 |
+
self.fit_path = fit_path
|
1030 |
+
self.jitter = jitter
|
1031 |
+
self.random_state = random_state
|
1032 |
+
|
1033 |
+
@staticmethod
|
1034 |
+
def _get_gram(precompute, X, y):
|
1035 |
+
if (not hasattr(precompute, "__array__")) and (
|
1036 |
+
(precompute is True)
|
1037 |
+
or (precompute == "auto" and X.shape[0] > X.shape[1])
|
1038 |
+
or (precompute == "auto" and y.shape[1] > 1)
|
1039 |
+
):
|
1040 |
+
precompute = np.dot(X.T, X)
|
1041 |
+
|
1042 |
+
return precompute
|
1043 |
+
|
1044 |
+
def _fit(self, X, y, max_iter, alpha, fit_path, Xy=None):
|
1045 |
+
"""Auxiliary method to fit the model using X, y as training data"""
|
1046 |
+
n_features = X.shape[1]
|
1047 |
+
|
1048 |
+
X, y, X_offset, y_offset, X_scale = _preprocess_data(
|
1049 |
+
X, y, fit_intercept=self.fit_intercept, copy=self.copy_X
|
1050 |
+
)
|
1051 |
+
|
1052 |
+
if y.ndim == 1:
|
1053 |
+
y = y[:, np.newaxis]
|
1054 |
+
|
1055 |
+
n_targets = y.shape[1]
|
1056 |
+
|
1057 |
+
Gram = self._get_gram(self.precompute, X, y)
|
1058 |
+
|
1059 |
+
self.alphas_ = []
|
1060 |
+
self.n_iter_ = []
|
1061 |
+
self.coef_ = np.empty((n_targets, n_features), dtype=X.dtype)
|
1062 |
+
|
1063 |
+
if fit_path:
|
1064 |
+
self.active_ = []
|
1065 |
+
self.coef_path_ = []
|
1066 |
+
for k in range(n_targets):
|
1067 |
+
this_Xy = None if Xy is None else Xy[:, k]
|
1068 |
+
alphas, active, coef_path, n_iter_ = lars_path(
|
1069 |
+
X,
|
1070 |
+
y[:, k],
|
1071 |
+
Gram=Gram,
|
1072 |
+
Xy=this_Xy,
|
1073 |
+
copy_X=self.copy_X,
|
1074 |
+
copy_Gram=True,
|
1075 |
+
alpha_min=alpha,
|
1076 |
+
method=self.method,
|
1077 |
+
verbose=max(0, self.verbose - 1),
|
1078 |
+
max_iter=max_iter,
|
1079 |
+
eps=self.eps,
|
1080 |
+
return_path=True,
|
1081 |
+
return_n_iter=True,
|
1082 |
+
positive=self.positive,
|
1083 |
+
)
|
1084 |
+
self.alphas_.append(alphas)
|
1085 |
+
self.active_.append(active)
|
1086 |
+
self.n_iter_.append(n_iter_)
|
1087 |
+
self.coef_path_.append(coef_path)
|
1088 |
+
self.coef_[k] = coef_path[:, -1]
|
1089 |
+
|
1090 |
+
if n_targets == 1:
|
1091 |
+
self.alphas_, self.active_, self.coef_path_, self.coef_ = [
|
1092 |
+
a[0]
|
1093 |
+
for a in (self.alphas_, self.active_, self.coef_path_, self.coef_)
|
1094 |
+
]
|
1095 |
+
self.n_iter_ = self.n_iter_[0]
|
1096 |
+
else:
|
1097 |
+
for k in range(n_targets):
|
1098 |
+
this_Xy = None if Xy is None else Xy[:, k]
|
1099 |
+
alphas, _, self.coef_[k], n_iter_ = lars_path(
|
1100 |
+
X,
|
1101 |
+
y[:, k],
|
1102 |
+
Gram=Gram,
|
1103 |
+
Xy=this_Xy,
|
1104 |
+
copy_X=self.copy_X,
|
1105 |
+
copy_Gram=True,
|
1106 |
+
alpha_min=alpha,
|
1107 |
+
method=self.method,
|
1108 |
+
verbose=max(0, self.verbose - 1),
|
1109 |
+
max_iter=max_iter,
|
1110 |
+
eps=self.eps,
|
1111 |
+
return_path=False,
|
1112 |
+
return_n_iter=True,
|
1113 |
+
positive=self.positive,
|
1114 |
+
)
|
1115 |
+
self.alphas_.append(alphas)
|
1116 |
+
self.n_iter_.append(n_iter_)
|
1117 |
+
if n_targets == 1:
|
1118 |
+
self.alphas_ = self.alphas_[0]
|
1119 |
+
self.n_iter_ = self.n_iter_[0]
|
1120 |
+
|
1121 |
+
self._set_intercept(X_offset, y_offset, X_scale)
|
1122 |
+
return self
|
1123 |
+
|
1124 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
1125 |
+
def fit(self, X, y, Xy=None):
|
1126 |
+
"""Fit the model using X, y as training data.
|
1127 |
+
|
1128 |
+
Parameters
|
1129 |
+
----------
|
1130 |
+
X : array-like of shape (n_samples, n_features)
|
1131 |
+
Training data.
|
1132 |
+
|
1133 |
+
y : array-like of shape (n_samples,) or (n_samples, n_targets)
|
1134 |
+
Target values.
|
1135 |
+
|
1136 |
+
Xy : array-like of shape (n_features,) or (n_features, n_targets), \
|
1137 |
+
default=None
|
1138 |
+
Xy = np.dot(X.T, y) that can be precomputed. It is useful
|
1139 |
+
only when the Gram matrix is precomputed.
|
1140 |
+
|
1141 |
+
Returns
|
1142 |
+
-------
|
1143 |
+
self : object
|
1144 |
+
Returns an instance of self.
|
1145 |
+
"""
|
1146 |
+
X, y = self._validate_data(X, y, y_numeric=True, multi_output=True)
|
1147 |
+
|
1148 |
+
alpha = getattr(self, "alpha", 0.0)
|
1149 |
+
if hasattr(self, "n_nonzero_coefs"):
|
1150 |
+
alpha = 0.0 # n_nonzero_coefs parametrization takes priority
|
1151 |
+
max_iter = self.n_nonzero_coefs
|
1152 |
+
else:
|
1153 |
+
max_iter = self.max_iter
|
1154 |
+
|
1155 |
+
if self.jitter is not None:
|
1156 |
+
rng = check_random_state(self.random_state)
|
1157 |
+
|
1158 |
+
noise = rng.uniform(high=self.jitter, size=len(y))
|
1159 |
+
y = y + noise
|
1160 |
+
|
1161 |
+
self._fit(
|
1162 |
+
X,
|
1163 |
+
y,
|
1164 |
+
max_iter=max_iter,
|
1165 |
+
alpha=alpha,
|
1166 |
+
fit_path=self.fit_path,
|
1167 |
+
Xy=Xy,
|
1168 |
+
)
|
1169 |
+
|
1170 |
+
return self
|
1171 |
+
|
1172 |
+
|
1173 |
+
class LassoLars(Lars):
|
1174 |
+
"""Lasso model fit with Least Angle Regression a.k.a. Lars.
|
1175 |
+
|
1176 |
+
It is a Linear Model trained with an L1 prior as regularizer.
|
1177 |
+
|
1178 |
+
The optimization objective for Lasso is::
|
1179 |
+
|
1180 |
+
(1 / (2 * n_samples)) * ||y - Xw||^2_2 + alpha * ||w||_1
|
1181 |
+
|
1182 |
+
Read more in the :ref:`User Guide <least_angle_regression>`.
|
1183 |
+
|
1184 |
+
Parameters
|
1185 |
+
----------
|
1186 |
+
alpha : float, default=1.0
|
1187 |
+
Constant that multiplies the penalty term. Defaults to 1.0.
|
1188 |
+
``alpha = 0`` is equivalent to an ordinary least square, solved
|
1189 |
+
by :class:`LinearRegression`. For numerical reasons, using
|
1190 |
+
``alpha = 0`` with the LassoLars object is not advised and you
|
1191 |
+
should prefer the LinearRegression object.
|
1192 |
+
|
1193 |
+
fit_intercept : bool, default=True
|
1194 |
+
Whether to calculate the intercept for this model. If set
|
1195 |
+
to false, no intercept will be used in calculations
|
1196 |
+
(i.e. data is expected to be centered).
|
1197 |
+
|
1198 |
+
verbose : bool or int, default=False
|
1199 |
+
Sets the verbosity amount.
|
1200 |
+
|
1201 |
+
precompute : bool, 'auto' or array-like, default='auto'
|
1202 |
+
Whether to use a precomputed Gram matrix to speed up
|
1203 |
+
calculations. If set to ``'auto'`` let us decide. The Gram
|
1204 |
+
matrix can also be passed as argument.
|
1205 |
+
|
1206 |
+
max_iter : int, default=500
|
1207 |
+
Maximum number of iterations to perform.
|
1208 |
+
|
1209 |
+
eps : float, default=np.finfo(float).eps
|
1210 |
+
The machine-precision regularization in the computation of the
|
1211 |
+
Cholesky diagonal factors. Increase this for very ill-conditioned
|
1212 |
+
systems. Unlike the ``tol`` parameter in some iterative
|
1213 |
+
optimization-based algorithms, this parameter does not control
|
1214 |
+
the tolerance of the optimization.
|
1215 |
+
|
1216 |
+
copy_X : bool, default=True
|
1217 |
+
If True, X will be copied; else, it may be overwritten.
|
1218 |
+
|
1219 |
+
fit_path : bool, default=True
|
1220 |
+
If ``True`` the full path is stored in the ``coef_path_`` attribute.
|
1221 |
+
If you compute the solution for a large problem or many targets,
|
1222 |
+
setting ``fit_path`` to ``False`` will lead to a speedup, especially
|
1223 |
+
with a small alpha.
|
1224 |
+
|
1225 |
+
positive : bool, default=False
|
1226 |
+
Restrict coefficients to be >= 0. Be aware that you might want to
|
1227 |
+
remove fit_intercept which is set True by default.
|
1228 |
+
Under the positive restriction the model coefficients will not converge
|
1229 |
+
to the ordinary-least-squares solution for small values of alpha.
|
1230 |
+
Only coefficients up to the smallest alpha value (``alphas_[alphas_ >
|
1231 |
+
0.].min()`` when fit_path=True) reached by the stepwise Lars-Lasso
|
1232 |
+
algorithm are typically in congruence with the solution of the
|
1233 |
+
coordinate descent Lasso estimator.
|
1234 |
+
|
1235 |
+
jitter : float, default=None
|
1236 |
+
Upper bound on a uniform noise parameter to be added to the
|
1237 |
+
`y` values, to satisfy the model's assumption of
|
1238 |
+
one-at-a-time computations. Might help with stability.
|
1239 |
+
|
1240 |
+
.. versionadded:: 0.23
|
1241 |
+
|
1242 |
+
random_state : int, RandomState instance or None, default=None
|
1243 |
+
Determines random number generation for jittering. Pass an int
|
1244 |
+
for reproducible output across multiple function calls.
|
1245 |
+
See :term:`Glossary <random_state>`. Ignored if `jitter` is None.
|
1246 |
+
|
1247 |
+
.. versionadded:: 0.23
|
1248 |
+
|
1249 |
+
Attributes
|
1250 |
+
----------
|
1251 |
+
alphas_ : array-like of shape (n_alphas + 1,) or list of such arrays
|
1252 |
+
Maximum of covariances (in absolute value) at each iteration.
|
1253 |
+
``n_alphas`` is either ``max_iter``, ``n_features`` or the
|
1254 |
+
number of nodes in the path with ``alpha >= alpha_min``, whichever
|
1255 |
+
is smaller. If this is a list of array-like, the length of the outer
|
1256 |
+
list is `n_targets`.
|
1257 |
+
|
1258 |
+
active_ : list of length n_alphas or list of such lists
|
1259 |
+
Indices of active variables at the end of the path.
|
1260 |
+
If this is a list of list, the length of the outer list is `n_targets`.
|
1261 |
+
|
1262 |
+
coef_path_ : array-like of shape (n_features, n_alphas + 1) or list \
|
1263 |
+
of such arrays
|
1264 |
+
If a list is passed it's expected to be one of n_targets such arrays.
|
1265 |
+
The varying values of the coefficients along the path. It is not
|
1266 |
+
present if the ``fit_path`` parameter is ``False``. If this is a list
|
1267 |
+
of array-like, the length of the outer list is `n_targets`.
|
1268 |
+
|
1269 |
+
coef_ : array-like of shape (n_features,) or (n_targets, n_features)
|
1270 |
+
Parameter vector (w in the formulation formula).
|
1271 |
+
|
1272 |
+
intercept_ : float or array-like of shape (n_targets,)
|
1273 |
+
Independent term in decision function.
|
1274 |
+
|
1275 |
+
n_iter_ : array-like or int
|
1276 |
+
The number of iterations taken by lars_path to find the
|
1277 |
+
grid of alphas for each target.
|
1278 |
+
|
1279 |
+
n_features_in_ : int
|
1280 |
+
Number of features seen during :term:`fit`.
|
1281 |
+
|
1282 |
+
.. versionadded:: 0.24
|
1283 |
+
|
1284 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
1285 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
1286 |
+
has feature names that are all strings.
|
1287 |
+
|
1288 |
+
.. versionadded:: 1.0
|
1289 |
+
|
1290 |
+
See Also
|
1291 |
+
--------
|
1292 |
+
lars_path : Compute Least Angle Regression or Lasso
|
1293 |
+
path using LARS algorithm.
|
1294 |
+
lasso_path : Compute Lasso path with coordinate descent.
|
1295 |
+
Lasso : Linear Model trained with L1 prior as
|
1296 |
+
regularizer (aka the Lasso).
|
1297 |
+
LassoCV : Lasso linear model with iterative fitting
|
1298 |
+
along a regularization path.
|
1299 |
+
LassoLarsCV: Cross-validated Lasso, using the LARS algorithm.
|
1300 |
+
LassoLarsIC : Lasso model fit with Lars using BIC
|
1301 |
+
or AIC for model selection.
|
1302 |
+
sklearn.decomposition.sparse_encode : Sparse coding.
|
1303 |
+
|
1304 |
+
Examples
|
1305 |
+
--------
|
1306 |
+
>>> from sklearn import linear_model
|
1307 |
+
>>> reg = linear_model.LassoLars(alpha=0.01)
|
1308 |
+
>>> reg.fit([[-1, 1], [0, 0], [1, 1]], [-1, 0, -1])
|
1309 |
+
LassoLars(alpha=0.01)
|
1310 |
+
>>> print(reg.coef_)
|
1311 |
+
[ 0. -0.955...]
|
1312 |
+
"""
|
1313 |
+
|
1314 |
+
_parameter_constraints: dict = {
|
1315 |
+
**Lars._parameter_constraints,
|
1316 |
+
"alpha": [Interval(Real, 0, None, closed="left")],
|
1317 |
+
"max_iter": [Interval(Integral, 0, None, closed="left")],
|
1318 |
+
"positive": ["boolean"],
|
1319 |
+
}
|
1320 |
+
_parameter_constraints.pop("n_nonzero_coefs")
|
1321 |
+
|
1322 |
+
method = "lasso"
|
1323 |
+
|
1324 |
+
def __init__(
|
1325 |
+
self,
|
1326 |
+
alpha=1.0,
|
1327 |
+
*,
|
1328 |
+
fit_intercept=True,
|
1329 |
+
verbose=False,
|
1330 |
+
precompute="auto",
|
1331 |
+
max_iter=500,
|
1332 |
+
eps=np.finfo(float).eps,
|
1333 |
+
copy_X=True,
|
1334 |
+
fit_path=True,
|
1335 |
+
positive=False,
|
1336 |
+
jitter=None,
|
1337 |
+
random_state=None,
|
1338 |
+
):
|
1339 |
+
self.alpha = alpha
|
1340 |
+
self.fit_intercept = fit_intercept
|
1341 |
+
self.max_iter = max_iter
|
1342 |
+
self.verbose = verbose
|
1343 |
+
self.positive = positive
|
1344 |
+
self.precompute = precompute
|
1345 |
+
self.copy_X = copy_X
|
1346 |
+
self.eps = eps
|
1347 |
+
self.fit_path = fit_path
|
1348 |
+
self.jitter = jitter
|
1349 |
+
self.random_state = random_state
|
1350 |
+
|
1351 |
+
|
1352 |
+
###############################################################################
|
1353 |
+
# Cross-validated estimator classes
|
1354 |
+
|
1355 |
+
|
1356 |
+
def _check_copy_and_writeable(array, copy=False):
|
1357 |
+
if copy or not array.flags.writeable:
|
1358 |
+
return array.copy()
|
1359 |
+
return array
|
1360 |
+
|
1361 |
+
|
1362 |
+
def _lars_path_residues(
|
1363 |
+
X_train,
|
1364 |
+
y_train,
|
1365 |
+
X_test,
|
1366 |
+
y_test,
|
1367 |
+
Gram=None,
|
1368 |
+
copy=True,
|
1369 |
+
method="lar",
|
1370 |
+
verbose=False,
|
1371 |
+
fit_intercept=True,
|
1372 |
+
max_iter=500,
|
1373 |
+
eps=np.finfo(float).eps,
|
1374 |
+
positive=False,
|
1375 |
+
):
|
1376 |
+
"""Compute the residues on left-out data for a full LARS path
|
1377 |
+
|
1378 |
+
Parameters
|
1379 |
+
-----------
|
1380 |
+
X_train : array-like of shape (n_samples, n_features)
|
1381 |
+
The data to fit the LARS on
|
1382 |
+
|
1383 |
+
y_train : array-like of shape (n_samples,)
|
1384 |
+
The target variable to fit LARS on
|
1385 |
+
|
1386 |
+
X_test : array-like of shape (n_samples, n_features)
|
1387 |
+
The data to compute the residues on
|
1388 |
+
|
1389 |
+
y_test : array-like of shape (n_samples,)
|
1390 |
+
The target variable to compute the residues on
|
1391 |
+
|
1392 |
+
Gram : None, 'auto' or array-like of shape (n_features, n_features), \
|
1393 |
+
default=None
|
1394 |
+
Precomputed Gram matrix (X' * X), if ``'auto'``, the Gram
|
1395 |
+
matrix is precomputed from the given X, if there are more samples
|
1396 |
+
than features
|
1397 |
+
|
1398 |
+
copy : bool, default=True
|
1399 |
+
Whether X_train, X_test, y_train and y_test should be copied;
|
1400 |
+
if False, they may be overwritten.
|
1401 |
+
|
1402 |
+
method : {'lar' , 'lasso'}, default='lar'
|
1403 |
+
Specifies the returned model. Select ``'lar'`` for Least Angle
|
1404 |
+
Regression, ``'lasso'`` for the Lasso.
|
1405 |
+
|
1406 |
+
verbose : bool or int, default=False
|
1407 |
+
Sets the amount of verbosity
|
1408 |
+
|
1409 |
+
fit_intercept : bool, default=True
|
1410 |
+
whether to calculate the intercept for this model. If set
|
1411 |
+
to false, no intercept will be used in calculations
|
1412 |
+
(i.e. data is expected to be centered).
|
1413 |
+
|
1414 |
+
positive : bool, default=False
|
1415 |
+
Restrict coefficients to be >= 0. Be aware that you might want to
|
1416 |
+
remove fit_intercept which is set True by default.
|
1417 |
+
See reservations for using this option in combination with method
|
1418 |
+
'lasso' for expected small values of alpha in the doc of LassoLarsCV
|
1419 |
+
and LassoLarsIC.
|
1420 |
+
|
1421 |
+
max_iter : int, default=500
|
1422 |
+
Maximum number of iterations to perform.
|
1423 |
+
|
1424 |
+
eps : float, default=np.finfo(float).eps
|
1425 |
+
The machine-precision regularization in the computation of the
|
1426 |
+
Cholesky diagonal factors. Increase this for very ill-conditioned
|
1427 |
+
systems. Unlike the ``tol`` parameter in some iterative
|
1428 |
+
optimization-based algorithms, this parameter does not control
|
1429 |
+
the tolerance of the optimization.
|
1430 |
+
|
1431 |
+
Returns
|
1432 |
+
--------
|
1433 |
+
alphas : array-like of shape (n_alphas,)
|
1434 |
+
Maximum of covariances (in absolute value) at each iteration.
|
1435 |
+
``n_alphas`` is either ``max_iter`` or ``n_features``, whichever
|
1436 |
+
is smaller.
|
1437 |
+
|
1438 |
+
active : list
|
1439 |
+
Indices of active variables at the end of the path.
|
1440 |
+
|
1441 |
+
coefs : array-like of shape (n_features, n_alphas)
|
1442 |
+
Coefficients along the path
|
1443 |
+
|
1444 |
+
residues : array-like of shape (n_alphas, n_samples)
|
1445 |
+
Residues of the prediction on the test data
|
1446 |
+
"""
|
1447 |
+
X_train = _check_copy_and_writeable(X_train, copy)
|
1448 |
+
y_train = _check_copy_and_writeable(y_train, copy)
|
1449 |
+
X_test = _check_copy_and_writeable(X_test, copy)
|
1450 |
+
y_test = _check_copy_and_writeable(y_test, copy)
|
1451 |
+
|
1452 |
+
if fit_intercept:
|
1453 |
+
X_mean = X_train.mean(axis=0)
|
1454 |
+
X_train -= X_mean
|
1455 |
+
X_test -= X_mean
|
1456 |
+
y_mean = y_train.mean(axis=0)
|
1457 |
+
y_train = as_float_array(y_train, copy=False)
|
1458 |
+
y_train -= y_mean
|
1459 |
+
y_test = as_float_array(y_test, copy=False)
|
1460 |
+
y_test -= y_mean
|
1461 |
+
|
1462 |
+
alphas, active, coefs = lars_path(
|
1463 |
+
X_train,
|
1464 |
+
y_train,
|
1465 |
+
Gram=Gram,
|
1466 |
+
copy_X=False,
|
1467 |
+
copy_Gram=False,
|
1468 |
+
method=method,
|
1469 |
+
verbose=max(0, verbose - 1),
|
1470 |
+
max_iter=max_iter,
|
1471 |
+
eps=eps,
|
1472 |
+
positive=positive,
|
1473 |
+
)
|
1474 |
+
residues = np.dot(X_test, coefs) - y_test[:, np.newaxis]
|
1475 |
+
return alphas, active, coefs, residues.T
|
1476 |
+
|
1477 |
+
|
1478 |
+
class LarsCV(Lars):
|
1479 |
+
"""Cross-validated Least Angle Regression model.
|
1480 |
+
|
1481 |
+
See glossary entry for :term:`cross-validation estimator`.
|
1482 |
+
|
1483 |
+
Read more in the :ref:`User Guide <least_angle_regression>`.
|
1484 |
+
|
1485 |
+
Parameters
|
1486 |
+
----------
|
1487 |
+
fit_intercept : bool, default=True
|
1488 |
+
Whether to calculate the intercept for this model. If set
|
1489 |
+
to false, no intercept will be used in calculations
|
1490 |
+
(i.e. data is expected to be centered).
|
1491 |
+
|
1492 |
+
verbose : bool or int, default=False
|
1493 |
+
Sets the verbosity amount.
|
1494 |
+
|
1495 |
+
max_iter : int, default=500
|
1496 |
+
Maximum number of iterations to perform.
|
1497 |
+
|
1498 |
+
precompute : bool, 'auto' or array-like , default='auto'
|
1499 |
+
Whether to use a precomputed Gram matrix to speed up
|
1500 |
+
calculations. If set to ``'auto'`` let us decide. The Gram matrix
|
1501 |
+
cannot be passed as argument since we will use only subsets of X.
|
1502 |
+
|
1503 |
+
cv : int, cross-validation generator or an iterable, default=None
|
1504 |
+
Determines the cross-validation splitting strategy.
|
1505 |
+
Possible inputs for cv are:
|
1506 |
+
|
1507 |
+
- None, to use the default 5-fold cross-validation,
|
1508 |
+
- integer, to specify the number of folds.
|
1509 |
+
- :term:`CV splitter`,
|
1510 |
+
- An iterable yielding (train, test) splits as arrays of indices.
|
1511 |
+
|
1512 |
+
For integer/None inputs, :class:`~sklearn.model_selection.KFold` is used.
|
1513 |
+
|
1514 |
+
Refer :ref:`User Guide <cross_validation>` for the various
|
1515 |
+
cross-validation strategies that can be used here.
|
1516 |
+
|
1517 |
+
.. versionchanged:: 0.22
|
1518 |
+
``cv`` default value if None changed from 3-fold to 5-fold.
|
1519 |
+
|
1520 |
+
max_n_alphas : int, default=1000
|
1521 |
+
The maximum number of points on the path used to compute the
|
1522 |
+
residuals in the cross-validation.
|
1523 |
+
|
1524 |
+
n_jobs : int or None, default=None
|
1525 |
+
Number of CPUs to use during the cross validation.
|
1526 |
+
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
|
1527 |
+
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
|
1528 |
+
for more details.
|
1529 |
+
|
1530 |
+
eps : float, default=np.finfo(float).eps
|
1531 |
+
The machine-precision regularization in the computation of the
|
1532 |
+
Cholesky diagonal factors. Increase this for very ill-conditioned
|
1533 |
+
systems. Unlike the ``tol`` parameter in some iterative
|
1534 |
+
optimization-based algorithms, this parameter does not control
|
1535 |
+
the tolerance of the optimization.
|
1536 |
+
|
1537 |
+
copy_X : bool, default=True
|
1538 |
+
If ``True``, X will be copied; else, it may be overwritten.
|
1539 |
+
|
1540 |
+
Attributes
|
1541 |
+
----------
|
1542 |
+
active_ : list of length n_alphas or list of such lists
|
1543 |
+
Indices of active variables at the end of the path.
|
1544 |
+
If this is a list of lists, the outer list length is `n_targets`.
|
1545 |
+
|
1546 |
+
coef_ : array-like of shape (n_features,)
|
1547 |
+
parameter vector (w in the formulation formula)
|
1548 |
+
|
1549 |
+
intercept_ : float
|
1550 |
+
independent term in decision function
|
1551 |
+
|
1552 |
+
coef_path_ : array-like of shape (n_features, n_alphas)
|
1553 |
+
the varying values of the coefficients along the path
|
1554 |
+
|
1555 |
+
alpha_ : float
|
1556 |
+
the estimated regularization parameter alpha
|
1557 |
+
|
1558 |
+
alphas_ : array-like of shape (n_alphas,)
|
1559 |
+
the different values of alpha along the path
|
1560 |
+
|
1561 |
+
cv_alphas_ : array-like of shape (n_cv_alphas,)
|
1562 |
+
all the values of alpha along the path for the different folds
|
1563 |
+
|
1564 |
+
mse_path_ : array-like of shape (n_folds, n_cv_alphas)
|
1565 |
+
the mean square error on left-out for each fold along the path
|
1566 |
+
(alpha values given by ``cv_alphas``)
|
1567 |
+
|
1568 |
+
n_iter_ : array-like or int
|
1569 |
+
the number of iterations run by Lars with the optimal alpha.
|
1570 |
+
|
1571 |
+
n_features_in_ : int
|
1572 |
+
Number of features seen during :term:`fit`.
|
1573 |
+
|
1574 |
+
.. versionadded:: 0.24
|
1575 |
+
|
1576 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
1577 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
1578 |
+
has feature names that are all strings.
|
1579 |
+
|
1580 |
+
.. versionadded:: 1.0
|
1581 |
+
|
1582 |
+
See Also
|
1583 |
+
--------
|
1584 |
+
lars_path : Compute Least Angle Regression or Lasso
|
1585 |
+
path using LARS algorithm.
|
1586 |
+
lasso_path : Compute Lasso path with coordinate descent.
|
1587 |
+
Lasso : Linear Model trained with L1 prior as
|
1588 |
+
regularizer (aka the Lasso).
|
1589 |
+
LassoCV : Lasso linear model with iterative fitting
|
1590 |
+
along a regularization path.
|
1591 |
+
LassoLars : Lasso model fit with Least Angle Regression a.k.a. Lars.
|
1592 |
+
LassoLarsIC : Lasso model fit with Lars using BIC
|
1593 |
+
or AIC for model selection.
|
1594 |
+
sklearn.decomposition.sparse_encode : Sparse coding.
|
1595 |
+
|
1596 |
+
Notes
|
1597 |
+
-----
|
1598 |
+
In `fit`, once the best parameter `alpha` is found through
|
1599 |
+
cross-validation, the model is fit again using the entire training set.
|
1600 |
+
|
1601 |
+
Examples
|
1602 |
+
--------
|
1603 |
+
>>> from sklearn.linear_model import LarsCV
|
1604 |
+
>>> from sklearn.datasets import make_regression
|
1605 |
+
>>> X, y = make_regression(n_samples=200, noise=4.0, random_state=0)
|
1606 |
+
>>> reg = LarsCV(cv=5).fit(X, y)
|
1607 |
+
>>> reg.score(X, y)
|
1608 |
+
0.9996...
|
1609 |
+
>>> reg.alpha_
|
1610 |
+
0.2961...
|
1611 |
+
>>> reg.predict(X[:1,])
|
1612 |
+
array([154.3996...])
|
1613 |
+
"""
|
1614 |
+
|
1615 |
+
_parameter_constraints: dict = {
|
1616 |
+
**Lars._parameter_constraints,
|
1617 |
+
"max_iter": [Interval(Integral, 0, None, closed="left")],
|
1618 |
+
"cv": ["cv_object"],
|
1619 |
+
"max_n_alphas": [Interval(Integral, 1, None, closed="left")],
|
1620 |
+
"n_jobs": [Integral, None],
|
1621 |
+
}
|
1622 |
+
|
1623 |
+
for parameter in ["n_nonzero_coefs", "jitter", "fit_path", "random_state"]:
|
1624 |
+
_parameter_constraints.pop(parameter)
|
1625 |
+
|
1626 |
+
method = "lar"
|
1627 |
+
|
1628 |
+
def __init__(
|
1629 |
+
self,
|
1630 |
+
*,
|
1631 |
+
fit_intercept=True,
|
1632 |
+
verbose=False,
|
1633 |
+
max_iter=500,
|
1634 |
+
precompute="auto",
|
1635 |
+
cv=None,
|
1636 |
+
max_n_alphas=1000,
|
1637 |
+
n_jobs=None,
|
1638 |
+
eps=np.finfo(float).eps,
|
1639 |
+
copy_X=True,
|
1640 |
+
):
|
1641 |
+
self.max_iter = max_iter
|
1642 |
+
self.cv = cv
|
1643 |
+
self.max_n_alphas = max_n_alphas
|
1644 |
+
self.n_jobs = n_jobs
|
1645 |
+
super().__init__(
|
1646 |
+
fit_intercept=fit_intercept,
|
1647 |
+
verbose=verbose,
|
1648 |
+
precompute=precompute,
|
1649 |
+
n_nonzero_coefs=500,
|
1650 |
+
eps=eps,
|
1651 |
+
copy_X=copy_X,
|
1652 |
+
fit_path=True,
|
1653 |
+
)
|
1654 |
+
|
1655 |
+
def _more_tags(self):
|
1656 |
+
return {"multioutput": False}
|
1657 |
+
|
1658 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
1659 |
+
def fit(self, X, y, **params):
|
1660 |
+
"""Fit the model using X, y as training data.
|
1661 |
+
|
1662 |
+
Parameters
|
1663 |
+
----------
|
1664 |
+
X : array-like of shape (n_samples, n_features)
|
1665 |
+
Training data.
|
1666 |
+
|
1667 |
+
y : array-like of shape (n_samples,)
|
1668 |
+
Target values.
|
1669 |
+
|
1670 |
+
**params : dict, default=None
|
1671 |
+
Parameters to be passed to the CV splitter.
|
1672 |
+
|
1673 |
+
.. versionadded:: 1.4
|
1674 |
+
Only available if `enable_metadata_routing=True`,
|
1675 |
+
which can be set by using
|
1676 |
+
``sklearn.set_config(enable_metadata_routing=True)``.
|
1677 |
+
See :ref:`Metadata Routing User Guide <metadata_routing>` for
|
1678 |
+
more details.
|
1679 |
+
|
1680 |
+
Returns
|
1681 |
+
-------
|
1682 |
+
self : object
|
1683 |
+
Returns an instance of self.
|
1684 |
+
"""
|
1685 |
+
_raise_for_params(params, self, "fit")
|
1686 |
+
|
1687 |
+
X, y = self._validate_data(X, y, y_numeric=True)
|
1688 |
+
X = as_float_array(X, copy=self.copy_X)
|
1689 |
+
y = as_float_array(y, copy=self.copy_X)
|
1690 |
+
|
1691 |
+
# init cross-validation generator
|
1692 |
+
cv = check_cv(self.cv, classifier=False)
|
1693 |
+
|
1694 |
+
if _routing_enabled():
|
1695 |
+
routed_params = process_routing(self, "fit", **params)
|
1696 |
+
else:
|
1697 |
+
routed_params = Bunch(splitter=Bunch(split={}))
|
1698 |
+
|
1699 |
+
# As we use cross-validation, the Gram matrix is not precomputed here
|
1700 |
+
Gram = self.precompute
|
1701 |
+
if hasattr(Gram, "__array__"):
|
1702 |
+
warnings.warn(
|
1703 |
+
'Parameter "precompute" cannot be an array in '
|
1704 |
+
'%s. Automatically switch to "auto" instead.'
|
1705 |
+
% self.__class__.__name__
|
1706 |
+
)
|
1707 |
+
Gram = "auto"
|
1708 |
+
|
1709 |
+
cv_paths = Parallel(n_jobs=self.n_jobs, verbose=self.verbose)(
|
1710 |
+
delayed(_lars_path_residues)(
|
1711 |
+
X[train],
|
1712 |
+
y[train],
|
1713 |
+
X[test],
|
1714 |
+
y[test],
|
1715 |
+
Gram=Gram,
|
1716 |
+
copy=False,
|
1717 |
+
method=self.method,
|
1718 |
+
verbose=max(0, self.verbose - 1),
|
1719 |
+
fit_intercept=self.fit_intercept,
|
1720 |
+
max_iter=self.max_iter,
|
1721 |
+
eps=self.eps,
|
1722 |
+
positive=self.positive,
|
1723 |
+
)
|
1724 |
+
for train, test in cv.split(X, y, **routed_params.splitter.split)
|
1725 |
+
)
|
1726 |
+
all_alphas = np.concatenate(list(zip(*cv_paths))[0])
|
1727 |
+
# Unique also sorts
|
1728 |
+
all_alphas = np.unique(all_alphas)
|
1729 |
+
# Take at most max_n_alphas values
|
1730 |
+
stride = int(max(1, int(len(all_alphas) / float(self.max_n_alphas))))
|
1731 |
+
all_alphas = all_alphas[::stride]
|
1732 |
+
|
1733 |
+
mse_path = np.empty((len(all_alphas), len(cv_paths)))
|
1734 |
+
for index, (alphas, _, _, residues) in enumerate(cv_paths):
|
1735 |
+
alphas = alphas[::-1]
|
1736 |
+
residues = residues[::-1]
|
1737 |
+
if alphas[0] != 0:
|
1738 |
+
alphas = np.r_[0, alphas]
|
1739 |
+
residues = np.r_[residues[0, np.newaxis], residues]
|
1740 |
+
if alphas[-1] != all_alphas[-1]:
|
1741 |
+
alphas = np.r_[alphas, all_alphas[-1]]
|
1742 |
+
residues = np.r_[residues, residues[-1, np.newaxis]]
|
1743 |
+
this_residues = interpolate.interp1d(alphas, residues, axis=0)(all_alphas)
|
1744 |
+
this_residues **= 2
|
1745 |
+
mse_path[:, index] = np.mean(this_residues, axis=-1)
|
1746 |
+
|
1747 |
+
mask = np.all(np.isfinite(mse_path), axis=-1)
|
1748 |
+
all_alphas = all_alphas[mask]
|
1749 |
+
mse_path = mse_path[mask]
|
1750 |
+
# Select the alpha that minimizes left-out error
|
1751 |
+
i_best_alpha = np.argmin(mse_path.mean(axis=-1))
|
1752 |
+
best_alpha = all_alphas[i_best_alpha]
|
1753 |
+
|
1754 |
+
# Store our parameters
|
1755 |
+
self.alpha_ = best_alpha
|
1756 |
+
self.cv_alphas_ = all_alphas
|
1757 |
+
self.mse_path_ = mse_path
|
1758 |
+
|
1759 |
+
# Now compute the full model using best_alpha
|
1760 |
+
# it will call a lasso internally when self if LassoLarsCV
|
1761 |
+
# as self.method == 'lasso'
|
1762 |
+
self._fit(
|
1763 |
+
X,
|
1764 |
+
y,
|
1765 |
+
max_iter=self.max_iter,
|
1766 |
+
alpha=best_alpha,
|
1767 |
+
Xy=None,
|
1768 |
+
fit_path=True,
|
1769 |
+
)
|
1770 |
+
return self
|
1771 |
+
|
1772 |
+
def get_metadata_routing(self):
|
1773 |
+
"""Get metadata routing of this object.
|
1774 |
+
|
1775 |
+
Please check :ref:`User Guide <metadata_routing>` on how the routing
|
1776 |
+
mechanism works.
|
1777 |
+
|
1778 |
+
.. versionadded:: 1.4
|
1779 |
+
|
1780 |
+
Returns
|
1781 |
+
-------
|
1782 |
+
routing : MetadataRouter
|
1783 |
+
A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating
|
1784 |
+
routing information.
|
1785 |
+
"""
|
1786 |
+
router = MetadataRouter(owner=self.__class__.__name__).add(
|
1787 |
+
splitter=check_cv(self.cv),
|
1788 |
+
method_mapping=MethodMapping().add(callee="split", caller="fit"),
|
1789 |
+
)
|
1790 |
+
return router
|
1791 |
+
|
1792 |
+
|
1793 |
+
class LassoLarsCV(LarsCV):
|
1794 |
+
"""Cross-validated Lasso, using the LARS algorithm.
|
1795 |
+
|
1796 |
+
See glossary entry for :term:`cross-validation estimator`.
|
1797 |
+
|
1798 |
+
The optimization objective for Lasso is::
|
1799 |
+
|
1800 |
+
(1 / (2 * n_samples)) * ||y - Xw||^2_2 + alpha * ||w||_1
|
1801 |
+
|
1802 |
+
Read more in the :ref:`User Guide <least_angle_regression>`.
|
1803 |
+
|
1804 |
+
Parameters
|
1805 |
+
----------
|
1806 |
+
fit_intercept : bool, default=True
|
1807 |
+
Whether to calculate the intercept for this model. If set
|
1808 |
+
to false, no intercept will be used in calculations
|
1809 |
+
(i.e. data is expected to be centered).
|
1810 |
+
|
1811 |
+
verbose : bool or int, default=False
|
1812 |
+
Sets the verbosity amount.
|
1813 |
+
|
1814 |
+
max_iter : int, default=500
|
1815 |
+
Maximum number of iterations to perform.
|
1816 |
+
|
1817 |
+
precompute : bool or 'auto' , default='auto'
|
1818 |
+
Whether to use a precomputed Gram matrix to speed up
|
1819 |
+
calculations. If set to ``'auto'`` let us decide. The Gram matrix
|
1820 |
+
cannot be passed as argument since we will use only subsets of X.
|
1821 |
+
|
1822 |
+
cv : int, cross-validation generator or an iterable, default=None
|
1823 |
+
Determines the cross-validation splitting strategy.
|
1824 |
+
Possible inputs for cv are:
|
1825 |
+
|
1826 |
+
- None, to use the default 5-fold cross-validation,
|
1827 |
+
- integer, to specify the number of folds.
|
1828 |
+
- :term:`CV splitter`,
|
1829 |
+
- An iterable yielding (train, test) splits as arrays of indices.
|
1830 |
+
|
1831 |
+
For integer/None inputs, :class:`~sklearn.model_selection.KFold` is used.
|
1832 |
+
|
1833 |
+
Refer :ref:`User Guide <cross_validation>` for the various
|
1834 |
+
cross-validation strategies that can be used here.
|
1835 |
+
|
1836 |
+
.. versionchanged:: 0.22
|
1837 |
+
``cv`` default value if None changed from 3-fold to 5-fold.
|
1838 |
+
|
1839 |
+
max_n_alphas : int, default=1000
|
1840 |
+
The maximum number of points on the path used to compute the
|
1841 |
+
residuals in the cross-validation.
|
1842 |
+
|
1843 |
+
n_jobs : int or None, default=None
|
1844 |
+
Number of CPUs to use during the cross validation.
|
1845 |
+
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
|
1846 |
+
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
|
1847 |
+
for more details.
|
1848 |
+
|
1849 |
+
eps : float, default=np.finfo(float).eps
|
1850 |
+
The machine-precision regularization in the computation of the
|
1851 |
+
Cholesky diagonal factors. Increase this for very ill-conditioned
|
1852 |
+
systems. Unlike the ``tol`` parameter in some iterative
|
1853 |
+
optimization-based algorithms, this parameter does not control
|
1854 |
+
the tolerance of the optimization.
|
1855 |
+
|
1856 |
+
copy_X : bool, default=True
|
1857 |
+
If True, X will be copied; else, it may be overwritten.
|
1858 |
+
|
1859 |
+
positive : bool, default=False
|
1860 |
+
Restrict coefficients to be >= 0. Be aware that you might want to
|
1861 |
+
remove fit_intercept which is set True by default.
|
1862 |
+
Under the positive restriction the model coefficients do not converge
|
1863 |
+
to the ordinary-least-squares solution for small values of alpha.
|
1864 |
+
Only coefficients up to the smallest alpha value (``alphas_[alphas_ >
|
1865 |
+
0.].min()`` when fit_path=True) reached by the stepwise Lars-Lasso
|
1866 |
+
algorithm are typically in congruence with the solution of the
|
1867 |
+
coordinate descent Lasso estimator.
|
1868 |
+
As a consequence using LassoLarsCV only makes sense for problems where
|
1869 |
+
a sparse solution is expected and/or reached.
|
1870 |
+
|
1871 |
+
Attributes
|
1872 |
+
----------
|
1873 |
+
coef_ : array-like of shape (n_features,)
|
1874 |
+
parameter vector (w in the formulation formula)
|
1875 |
+
|
1876 |
+
intercept_ : float
|
1877 |
+
independent term in decision function.
|
1878 |
+
|
1879 |
+
coef_path_ : array-like of shape (n_features, n_alphas)
|
1880 |
+
the varying values of the coefficients along the path
|
1881 |
+
|
1882 |
+
alpha_ : float
|
1883 |
+
the estimated regularization parameter alpha
|
1884 |
+
|
1885 |
+
alphas_ : array-like of shape (n_alphas,)
|
1886 |
+
the different values of alpha along the path
|
1887 |
+
|
1888 |
+
cv_alphas_ : array-like of shape (n_cv_alphas,)
|
1889 |
+
all the values of alpha along the path for the different folds
|
1890 |
+
|
1891 |
+
mse_path_ : array-like of shape (n_folds, n_cv_alphas)
|
1892 |
+
the mean square error on left-out for each fold along the path
|
1893 |
+
(alpha values given by ``cv_alphas``)
|
1894 |
+
|
1895 |
+
n_iter_ : array-like or int
|
1896 |
+
the number of iterations run by Lars with the optimal alpha.
|
1897 |
+
|
1898 |
+
active_ : list of int
|
1899 |
+
Indices of active variables at the end of the path.
|
1900 |
+
|
1901 |
+
n_features_in_ : int
|
1902 |
+
Number of features seen during :term:`fit`.
|
1903 |
+
|
1904 |
+
.. versionadded:: 0.24
|
1905 |
+
|
1906 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
1907 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
1908 |
+
has feature names that are all strings.
|
1909 |
+
|
1910 |
+
.. versionadded:: 1.0
|
1911 |
+
|
1912 |
+
See Also
|
1913 |
+
--------
|
1914 |
+
lars_path : Compute Least Angle Regression or Lasso
|
1915 |
+
path using LARS algorithm.
|
1916 |
+
lasso_path : Compute Lasso path with coordinate descent.
|
1917 |
+
Lasso : Linear Model trained with L1 prior as
|
1918 |
+
regularizer (aka the Lasso).
|
1919 |
+
LassoCV : Lasso linear model with iterative fitting
|
1920 |
+
along a regularization path.
|
1921 |
+
LassoLars : Lasso model fit with Least Angle Regression a.k.a. Lars.
|
1922 |
+
LassoLarsIC : Lasso model fit with Lars using BIC
|
1923 |
+
or AIC for model selection.
|
1924 |
+
sklearn.decomposition.sparse_encode : Sparse coding.
|
1925 |
+
|
1926 |
+
Notes
|
1927 |
+
-----
|
1928 |
+
The object solves the same problem as the
|
1929 |
+
:class:`~sklearn.linear_model.LassoCV` object. However, unlike the
|
1930 |
+
:class:`~sklearn.linear_model.LassoCV`, it find the relevant alphas values
|
1931 |
+
by itself. In general, because of this property, it will be more stable.
|
1932 |
+
However, it is more fragile to heavily multicollinear datasets.
|
1933 |
+
|
1934 |
+
It is more efficient than the :class:`~sklearn.linear_model.LassoCV` if
|
1935 |
+
only a small number of features are selected compared to the total number,
|
1936 |
+
for instance if there are very few samples compared to the number of
|
1937 |
+
features.
|
1938 |
+
|
1939 |
+
In `fit`, once the best parameter `alpha` is found through
|
1940 |
+
cross-validation, the model is fit again using the entire training set.
|
1941 |
+
|
1942 |
+
Examples
|
1943 |
+
--------
|
1944 |
+
>>> from sklearn.linear_model import LassoLarsCV
|
1945 |
+
>>> from sklearn.datasets import make_regression
|
1946 |
+
>>> X, y = make_regression(noise=4.0, random_state=0)
|
1947 |
+
>>> reg = LassoLarsCV(cv=5).fit(X, y)
|
1948 |
+
>>> reg.score(X, y)
|
1949 |
+
0.9993...
|
1950 |
+
>>> reg.alpha_
|
1951 |
+
0.3972...
|
1952 |
+
>>> reg.predict(X[:1,])
|
1953 |
+
array([-78.4831...])
|
1954 |
+
"""
|
1955 |
+
|
1956 |
+
_parameter_constraints = {
|
1957 |
+
**LarsCV._parameter_constraints,
|
1958 |
+
"positive": ["boolean"],
|
1959 |
+
}
|
1960 |
+
|
1961 |
+
method = "lasso"
|
1962 |
+
|
1963 |
+
def __init__(
|
1964 |
+
self,
|
1965 |
+
*,
|
1966 |
+
fit_intercept=True,
|
1967 |
+
verbose=False,
|
1968 |
+
max_iter=500,
|
1969 |
+
precompute="auto",
|
1970 |
+
cv=None,
|
1971 |
+
max_n_alphas=1000,
|
1972 |
+
n_jobs=None,
|
1973 |
+
eps=np.finfo(float).eps,
|
1974 |
+
copy_X=True,
|
1975 |
+
positive=False,
|
1976 |
+
):
|
1977 |
+
self.fit_intercept = fit_intercept
|
1978 |
+
self.verbose = verbose
|
1979 |
+
self.max_iter = max_iter
|
1980 |
+
self.precompute = precompute
|
1981 |
+
self.cv = cv
|
1982 |
+
self.max_n_alphas = max_n_alphas
|
1983 |
+
self.n_jobs = n_jobs
|
1984 |
+
self.eps = eps
|
1985 |
+
self.copy_X = copy_X
|
1986 |
+
self.positive = positive
|
1987 |
+
# XXX : we don't use super().__init__
|
1988 |
+
# to avoid setting n_nonzero_coefs
|
1989 |
+
|
1990 |
+
|
1991 |
+
class LassoLarsIC(LassoLars):
|
1992 |
+
"""Lasso model fit with Lars using BIC or AIC for model selection.
|
1993 |
+
|
1994 |
+
The optimization objective for Lasso is::
|
1995 |
+
|
1996 |
+
(1 / (2 * n_samples)) * ||y - Xw||^2_2 + alpha * ||w||_1
|
1997 |
+
|
1998 |
+
AIC is the Akaike information criterion [2]_ and BIC is the Bayes
|
1999 |
+
Information criterion [3]_. Such criteria are useful to select the value
|
2000 |
+
of the regularization parameter by making a trade-off between the
|
2001 |
+
goodness of fit and the complexity of the model. A good model should
|
2002 |
+
explain well the data while being simple.
|
2003 |
+
|
2004 |
+
Read more in the :ref:`User Guide <lasso_lars_ic>`.
|
2005 |
+
|
2006 |
+
Parameters
|
2007 |
+
----------
|
2008 |
+
criterion : {'aic', 'bic'}, default='aic'
|
2009 |
+
The type of criterion to use.
|
2010 |
+
|
2011 |
+
fit_intercept : bool, default=True
|
2012 |
+
Whether to calculate the intercept for this model. If set
|
2013 |
+
to false, no intercept will be used in calculations
|
2014 |
+
(i.e. data is expected to be centered).
|
2015 |
+
|
2016 |
+
verbose : bool or int, default=False
|
2017 |
+
Sets the verbosity amount.
|
2018 |
+
|
2019 |
+
precompute : bool, 'auto' or array-like, default='auto'
|
2020 |
+
Whether to use a precomputed Gram matrix to speed up
|
2021 |
+
calculations. If set to ``'auto'`` let us decide. The Gram
|
2022 |
+
matrix can also be passed as argument.
|
2023 |
+
|
2024 |
+
max_iter : int, default=500
|
2025 |
+
Maximum number of iterations to perform. Can be used for
|
2026 |
+
early stopping.
|
2027 |
+
|
2028 |
+
eps : float, default=np.finfo(float).eps
|
2029 |
+
The machine-precision regularization in the computation of the
|
2030 |
+
Cholesky diagonal factors. Increase this for very ill-conditioned
|
2031 |
+
systems. Unlike the ``tol`` parameter in some iterative
|
2032 |
+
optimization-based algorithms, this parameter does not control
|
2033 |
+
the tolerance of the optimization.
|
2034 |
+
|
2035 |
+
copy_X : bool, default=True
|
2036 |
+
If True, X will be copied; else, it may be overwritten.
|
2037 |
+
|
2038 |
+
positive : bool, default=False
|
2039 |
+
Restrict coefficients to be >= 0. Be aware that you might want to
|
2040 |
+
remove fit_intercept which is set True by default.
|
2041 |
+
Under the positive restriction the model coefficients do not converge
|
2042 |
+
to the ordinary-least-squares solution for small values of alpha.
|
2043 |
+
Only coefficients up to the smallest alpha value (``alphas_[alphas_ >
|
2044 |
+
0.].min()`` when fit_path=True) reached by the stepwise Lars-Lasso
|
2045 |
+
algorithm are typically in congruence with the solution of the
|
2046 |
+
coordinate descent Lasso estimator.
|
2047 |
+
As a consequence using LassoLarsIC only makes sense for problems where
|
2048 |
+
a sparse solution is expected and/or reached.
|
2049 |
+
|
2050 |
+
noise_variance : float, default=None
|
2051 |
+
The estimated noise variance of the data. If `None`, an unbiased
|
2052 |
+
estimate is computed by an OLS model. However, it is only possible
|
2053 |
+
in the case where `n_samples > n_features + fit_intercept`.
|
2054 |
+
|
2055 |
+
.. versionadded:: 1.1
|
2056 |
+
|
2057 |
+
Attributes
|
2058 |
+
----------
|
2059 |
+
coef_ : array-like of shape (n_features,)
|
2060 |
+
parameter vector (w in the formulation formula)
|
2061 |
+
|
2062 |
+
intercept_ : float
|
2063 |
+
independent term in decision function.
|
2064 |
+
|
2065 |
+
alpha_ : float
|
2066 |
+
the alpha parameter chosen by the information criterion
|
2067 |
+
|
2068 |
+
alphas_ : array-like of shape (n_alphas + 1,) or list of such arrays
|
2069 |
+
Maximum of covariances (in absolute value) at each iteration.
|
2070 |
+
``n_alphas`` is either ``max_iter``, ``n_features`` or the
|
2071 |
+
number of nodes in the path with ``alpha >= alpha_min``, whichever
|
2072 |
+
is smaller. If a list, it will be of length `n_targets`.
|
2073 |
+
|
2074 |
+
n_iter_ : int
|
2075 |
+
number of iterations run by lars_path to find the grid of
|
2076 |
+
alphas.
|
2077 |
+
|
2078 |
+
criterion_ : array-like of shape (n_alphas,)
|
2079 |
+
The value of the information criteria ('aic', 'bic') across all
|
2080 |
+
alphas. The alpha which has the smallest information criterion is
|
2081 |
+
chosen, as specified in [1]_.
|
2082 |
+
|
2083 |
+
noise_variance_ : float
|
2084 |
+
The estimated noise variance from the data used to compute the
|
2085 |
+
criterion.
|
2086 |
+
|
2087 |
+
.. versionadded:: 1.1
|
2088 |
+
|
2089 |
+
n_features_in_ : int
|
2090 |
+
Number of features seen during :term:`fit`.
|
2091 |
+
|
2092 |
+
.. versionadded:: 0.24
|
2093 |
+
|
2094 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
2095 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
2096 |
+
has feature names that are all strings.
|
2097 |
+
|
2098 |
+
.. versionadded:: 1.0
|
2099 |
+
|
2100 |
+
See Also
|
2101 |
+
--------
|
2102 |
+
lars_path : Compute Least Angle Regression or Lasso
|
2103 |
+
path using LARS algorithm.
|
2104 |
+
lasso_path : Compute Lasso path with coordinate descent.
|
2105 |
+
Lasso : Linear Model trained with L1 prior as
|
2106 |
+
regularizer (aka the Lasso).
|
2107 |
+
LassoCV : Lasso linear model with iterative fitting
|
2108 |
+
along a regularization path.
|
2109 |
+
LassoLars : Lasso model fit with Least Angle Regression a.k.a. Lars.
|
2110 |
+
LassoLarsCV: Cross-validated Lasso, using the LARS algorithm.
|
2111 |
+
sklearn.decomposition.sparse_encode : Sparse coding.
|
2112 |
+
|
2113 |
+
Notes
|
2114 |
+
-----
|
2115 |
+
The number of degrees of freedom is computed as in [1]_.
|
2116 |
+
|
2117 |
+
To have more details regarding the mathematical formulation of the
|
2118 |
+
AIC and BIC criteria, please refer to :ref:`User Guide <lasso_lars_ic>`.
|
2119 |
+
|
2120 |
+
References
|
2121 |
+
----------
|
2122 |
+
.. [1] :arxiv:`Zou, Hui, Trevor Hastie, and Robert Tibshirani.
|
2123 |
+
"On the degrees of freedom of the lasso."
|
2124 |
+
The Annals of Statistics 35.5 (2007): 2173-2192.
|
2125 |
+
<0712.0881>`
|
2126 |
+
|
2127 |
+
.. [2] `Wikipedia entry on the Akaike information criterion
|
2128 |
+
<https://en.wikipedia.org/wiki/Akaike_information_criterion>`_
|
2129 |
+
|
2130 |
+
.. [3] `Wikipedia entry on the Bayesian information criterion
|
2131 |
+
<https://en.wikipedia.org/wiki/Bayesian_information_criterion>`_
|
2132 |
+
|
2133 |
+
Examples
|
2134 |
+
--------
|
2135 |
+
>>> from sklearn import linear_model
|
2136 |
+
>>> reg = linear_model.LassoLarsIC(criterion='bic')
|
2137 |
+
>>> X = [[-2, 2], [-1, 1], [0, 0], [1, 1], [2, 2]]
|
2138 |
+
>>> y = [-2.2222, -1.1111, 0, -1.1111, -2.2222]
|
2139 |
+
>>> reg.fit(X, y)
|
2140 |
+
LassoLarsIC(criterion='bic')
|
2141 |
+
>>> print(reg.coef_)
|
2142 |
+
[ 0. -1.11...]
|
2143 |
+
"""
|
2144 |
+
|
2145 |
+
_parameter_constraints: dict = {
|
2146 |
+
**LassoLars._parameter_constraints,
|
2147 |
+
"criterion": [StrOptions({"aic", "bic"})],
|
2148 |
+
"noise_variance": [Interval(Real, 0, None, closed="left"), None],
|
2149 |
+
}
|
2150 |
+
|
2151 |
+
for parameter in ["jitter", "fit_path", "alpha", "random_state"]:
|
2152 |
+
_parameter_constraints.pop(parameter)
|
2153 |
+
|
2154 |
+
def __init__(
|
2155 |
+
self,
|
2156 |
+
criterion="aic",
|
2157 |
+
*,
|
2158 |
+
fit_intercept=True,
|
2159 |
+
verbose=False,
|
2160 |
+
precompute="auto",
|
2161 |
+
max_iter=500,
|
2162 |
+
eps=np.finfo(float).eps,
|
2163 |
+
copy_X=True,
|
2164 |
+
positive=False,
|
2165 |
+
noise_variance=None,
|
2166 |
+
):
|
2167 |
+
self.criterion = criterion
|
2168 |
+
self.fit_intercept = fit_intercept
|
2169 |
+
self.positive = positive
|
2170 |
+
self.max_iter = max_iter
|
2171 |
+
self.verbose = verbose
|
2172 |
+
self.copy_X = copy_X
|
2173 |
+
self.precompute = precompute
|
2174 |
+
self.eps = eps
|
2175 |
+
self.fit_path = True
|
2176 |
+
self.noise_variance = noise_variance
|
2177 |
+
|
2178 |
+
def _more_tags(self):
|
2179 |
+
return {"multioutput": False}
|
2180 |
+
|
2181 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
2182 |
+
def fit(self, X, y, copy_X=None):
|
2183 |
+
"""Fit the model using X, y as training data.
|
2184 |
+
|
2185 |
+
Parameters
|
2186 |
+
----------
|
2187 |
+
X : array-like of shape (n_samples, n_features)
|
2188 |
+
Training data.
|
2189 |
+
|
2190 |
+
y : array-like of shape (n_samples,)
|
2191 |
+
Target values. Will be cast to X's dtype if necessary.
|
2192 |
+
|
2193 |
+
copy_X : bool, default=None
|
2194 |
+
If provided, this parameter will override the choice
|
2195 |
+
of copy_X made at instance creation.
|
2196 |
+
If ``True``, X will be copied; else, it may be overwritten.
|
2197 |
+
|
2198 |
+
Returns
|
2199 |
+
-------
|
2200 |
+
self : object
|
2201 |
+
Returns an instance of self.
|
2202 |
+
"""
|
2203 |
+
if copy_X is None:
|
2204 |
+
copy_X = self.copy_X
|
2205 |
+
X, y = self._validate_data(X, y, y_numeric=True)
|
2206 |
+
|
2207 |
+
X, y, Xmean, ymean, Xstd = _preprocess_data(
|
2208 |
+
X, y, fit_intercept=self.fit_intercept, copy=copy_X
|
2209 |
+
)
|
2210 |
+
|
2211 |
+
Gram = self.precompute
|
2212 |
+
|
2213 |
+
alphas_, _, coef_path_, self.n_iter_ = lars_path(
|
2214 |
+
X,
|
2215 |
+
y,
|
2216 |
+
Gram=Gram,
|
2217 |
+
copy_X=copy_X,
|
2218 |
+
copy_Gram=True,
|
2219 |
+
alpha_min=0.0,
|
2220 |
+
method="lasso",
|
2221 |
+
verbose=self.verbose,
|
2222 |
+
max_iter=self.max_iter,
|
2223 |
+
eps=self.eps,
|
2224 |
+
return_n_iter=True,
|
2225 |
+
positive=self.positive,
|
2226 |
+
)
|
2227 |
+
|
2228 |
+
n_samples = X.shape[0]
|
2229 |
+
|
2230 |
+
if self.criterion == "aic":
|
2231 |
+
criterion_factor = 2
|
2232 |
+
elif self.criterion == "bic":
|
2233 |
+
criterion_factor = log(n_samples)
|
2234 |
+
else:
|
2235 |
+
raise ValueError(
|
2236 |
+
f"criterion should be either bic or aic, got {self.criterion!r}"
|
2237 |
+
)
|
2238 |
+
|
2239 |
+
residuals = y[:, np.newaxis] - np.dot(X, coef_path_)
|
2240 |
+
residuals_sum_squares = np.sum(residuals**2, axis=0)
|
2241 |
+
degrees_of_freedom = np.zeros(coef_path_.shape[1], dtype=int)
|
2242 |
+
for k, coef in enumerate(coef_path_.T):
|
2243 |
+
mask = np.abs(coef) > np.finfo(coef.dtype).eps
|
2244 |
+
if not np.any(mask):
|
2245 |
+
continue
|
2246 |
+
# get the number of degrees of freedom equal to:
|
2247 |
+
# Xc = X[:, mask]
|
2248 |
+
# Trace(Xc * inv(Xc.T, Xc) * Xc.T) ie the number of non-zero coefs
|
2249 |
+
degrees_of_freedom[k] = np.sum(mask)
|
2250 |
+
|
2251 |
+
self.alphas_ = alphas_
|
2252 |
+
|
2253 |
+
if self.noise_variance is None:
|
2254 |
+
self.noise_variance_ = self._estimate_noise_variance(
|
2255 |
+
X, y, positive=self.positive
|
2256 |
+
)
|
2257 |
+
else:
|
2258 |
+
self.noise_variance_ = self.noise_variance
|
2259 |
+
|
2260 |
+
self.criterion_ = (
|
2261 |
+
n_samples * np.log(2 * np.pi * self.noise_variance_)
|
2262 |
+
+ residuals_sum_squares / self.noise_variance_
|
2263 |
+
+ criterion_factor * degrees_of_freedom
|
2264 |
+
)
|
2265 |
+
n_best = np.argmin(self.criterion_)
|
2266 |
+
|
2267 |
+
self.alpha_ = alphas_[n_best]
|
2268 |
+
self.coef_ = coef_path_[:, n_best]
|
2269 |
+
self._set_intercept(Xmean, ymean, Xstd)
|
2270 |
+
return self
|
2271 |
+
|
2272 |
+
def _estimate_noise_variance(self, X, y, positive):
|
2273 |
+
"""Compute an estimate of the variance with an OLS model.
|
2274 |
+
|
2275 |
+
Parameters
|
2276 |
+
----------
|
2277 |
+
X : ndarray of shape (n_samples, n_features)
|
2278 |
+
Data to be fitted by the OLS model. We expect the data to be
|
2279 |
+
centered.
|
2280 |
+
|
2281 |
+
y : ndarray of shape (n_samples,)
|
2282 |
+
Associated target.
|
2283 |
+
|
2284 |
+
positive : bool, default=False
|
2285 |
+
Restrict coefficients to be >= 0. This should be inline with
|
2286 |
+
the `positive` parameter from `LassoLarsIC`.
|
2287 |
+
|
2288 |
+
Returns
|
2289 |
+
-------
|
2290 |
+
noise_variance : float
|
2291 |
+
An estimator of the noise variance of an OLS model.
|
2292 |
+
"""
|
2293 |
+
if X.shape[0] <= X.shape[1] + self.fit_intercept:
|
2294 |
+
raise ValueError(
|
2295 |
+
f"You are using {self.__class__.__name__} in the case where the number "
|
2296 |
+
"of samples is smaller than the number of features. In this setting, "
|
2297 |
+
"getting a good estimate for the variance of the noise is not "
|
2298 |
+
"possible. Provide an estimate of the noise variance in the "
|
2299 |
+
"constructor."
|
2300 |
+
)
|
2301 |
+
# X and y are already centered and we don't need to fit with an intercept
|
2302 |
+
ols_model = LinearRegression(positive=positive, fit_intercept=False)
|
2303 |
+
y_pred = ols_model.fit(X, y).predict(X)
|
2304 |
+
return np.sum((y - y_pred) ** 2) / (
|
2305 |
+
X.shape[0] - X.shape[1] - self.fit_intercept
|
2306 |
+
)
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_linear_loss.py
ADDED
@@ -0,0 +1,671 @@
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|
1 |
+
"""
|
2 |
+
Loss functions for linear models with raw_prediction = X @ coef
|
3 |
+
"""
|
4 |
+
import numpy as np
|
5 |
+
from scipy import sparse
|
6 |
+
|
7 |
+
from ..utils.extmath import squared_norm
|
8 |
+
|
9 |
+
|
10 |
+
class LinearModelLoss:
|
11 |
+
"""General class for loss functions with raw_prediction = X @ coef + intercept.
|
12 |
+
|
13 |
+
Note that raw_prediction is also known as linear predictor.
|
14 |
+
|
15 |
+
The loss is the average of per sample losses and includes a term for L2
|
16 |
+
regularization::
|
17 |
+
|
18 |
+
loss = 1 / s_sum * sum_i s_i loss(y_i, X_i @ coef + intercept)
|
19 |
+
+ 1/2 * l2_reg_strength * ||coef||_2^2
|
20 |
+
|
21 |
+
with sample weights s_i=1 if sample_weight=None and s_sum=sum_i s_i.
|
22 |
+
|
23 |
+
Gradient and hessian, for simplicity without intercept, are::
|
24 |
+
|
25 |
+
gradient = 1 / s_sum * X.T @ loss.gradient + l2_reg_strength * coef
|
26 |
+
hessian = 1 / s_sum * X.T @ diag(loss.hessian) @ X
|
27 |
+
+ l2_reg_strength * identity
|
28 |
+
|
29 |
+
Conventions:
|
30 |
+
if fit_intercept:
|
31 |
+
n_dof = n_features + 1
|
32 |
+
else:
|
33 |
+
n_dof = n_features
|
34 |
+
|
35 |
+
if base_loss.is_multiclass:
|
36 |
+
coef.shape = (n_classes, n_dof) or ravelled (n_classes * n_dof,)
|
37 |
+
else:
|
38 |
+
coef.shape = (n_dof,)
|
39 |
+
|
40 |
+
The intercept term is at the end of the coef array:
|
41 |
+
if base_loss.is_multiclass:
|
42 |
+
if coef.shape (n_classes, n_dof):
|
43 |
+
intercept = coef[:, -1]
|
44 |
+
if coef.shape (n_classes * n_dof,)
|
45 |
+
intercept = coef[n_features::n_dof] = coef[(n_dof-1)::n_dof]
|
46 |
+
intercept.shape = (n_classes,)
|
47 |
+
else:
|
48 |
+
intercept = coef[-1]
|
49 |
+
|
50 |
+
Note: If coef has shape (n_classes * n_dof,), the 2d-array can be reconstructed as
|
51 |
+
|
52 |
+
coef.reshape((n_classes, -1), order="F")
|
53 |
+
|
54 |
+
The option order="F" makes coef[:, i] contiguous. This, in turn, makes the
|
55 |
+
coefficients without intercept, coef[:, :-1], contiguous and speeds up
|
56 |
+
matrix-vector computations.
|
57 |
+
|
58 |
+
Note: If the average loss per sample is wanted instead of the sum of the loss per
|
59 |
+
sample, one can simply use a rescaled sample_weight such that
|
60 |
+
sum(sample_weight) = 1.
|
61 |
+
|
62 |
+
Parameters
|
63 |
+
----------
|
64 |
+
base_loss : instance of class BaseLoss from sklearn._loss.
|
65 |
+
fit_intercept : bool
|
66 |
+
"""
|
67 |
+
|
68 |
+
def __init__(self, base_loss, fit_intercept):
|
69 |
+
self.base_loss = base_loss
|
70 |
+
self.fit_intercept = fit_intercept
|
71 |
+
|
72 |
+
def init_zero_coef(self, X, dtype=None):
|
73 |
+
"""Allocate coef of correct shape with zeros.
|
74 |
+
|
75 |
+
Parameters:
|
76 |
+
-----------
|
77 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
78 |
+
Training data.
|
79 |
+
dtype : data-type, default=None
|
80 |
+
Overrides the data type of coef. With dtype=None, coef will have the same
|
81 |
+
dtype as X.
|
82 |
+
|
83 |
+
Returns
|
84 |
+
-------
|
85 |
+
coef : ndarray of shape (n_dof,) or (n_classes, n_dof)
|
86 |
+
Coefficients of a linear model.
|
87 |
+
"""
|
88 |
+
n_features = X.shape[1]
|
89 |
+
n_classes = self.base_loss.n_classes
|
90 |
+
if self.fit_intercept:
|
91 |
+
n_dof = n_features + 1
|
92 |
+
else:
|
93 |
+
n_dof = n_features
|
94 |
+
if self.base_loss.is_multiclass:
|
95 |
+
coef = np.zeros_like(X, shape=(n_classes, n_dof), dtype=dtype, order="F")
|
96 |
+
else:
|
97 |
+
coef = np.zeros_like(X, shape=n_dof, dtype=dtype)
|
98 |
+
return coef
|
99 |
+
|
100 |
+
def weight_intercept(self, coef):
|
101 |
+
"""Helper function to get coefficients and intercept.
|
102 |
+
|
103 |
+
Parameters
|
104 |
+
----------
|
105 |
+
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
|
106 |
+
Coefficients of a linear model.
|
107 |
+
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
|
108 |
+
i.e. one reconstructs the 2d-array via
|
109 |
+
coef.reshape((n_classes, -1), order="F").
|
110 |
+
|
111 |
+
Returns
|
112 |
+
-------
|
113 |
+
weights : ndarray of shape (n_features,) or (n_classes, n_features)
|
114 |
+
Coefficients without intercept term.
|
115 |
+
intercept : float or ndarray of shape (n_classes,)
|
116 |
+
Intercept terms.
|
117 |
+
"""
|
118 |
+
if not self.base_loss.is_multiclass:
|
119 |
+
if self.fit_intercept:
|
120 |
+
intercept = coef[-1]
|
121 |
+
weights = coef[:-1]
|
122 |
+
else:
|
123 |
+
intercept = 0.0
|
124 |
+
weights = coef
|
125 |
+
else:
|
126 |
+
# reshape to (n_classes, n_dof)
|
127 |
+
if coef.ndim == 1:
|
128 |
+
weights = coef.reshape((self.base_loss.n_classes, -1), order="F")
|
129 |
+
else:
|
130 |
+
weights = coef
|
131 |
+
if self.fit_intercept:
|
132 |
+
intercept = weights[:, -1]
|
133 |
+
weights = weights[:, :-1]
|
134 |
+
else:
|
135 |
+
intercept = 0.0
|
136 |
+
|
137 |
+
return weights, intercept
|
138 |
+
|
139 |
+
def weight_intercept_raw(self, coef, X):
|
140 |
+
"""Helper function to get coefficients, intercept and raw_prediction.
|
141 |
+
|
142 |
+
Parameters
|
143 |
+
----------
|
144 |
+
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
|
145 |
+
Coefficients of a linear model.
|
146 |
+
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
|
147 |
+
i.e. one reconstructs the 2d-array via
|
148 |
+
coef.reshape((n_classes, -1), order="F").
|
149 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
150 |
+
Training data.
|
151 |
+
|
152 |
+
Returns
|
153 |
+
-------
|
154 |
+
weights : ndarray of shape (n_features,) or (n_classes, n_features)
|
155 |
+
Coefficients without intercept term.
|
156 |
+
intercept : float or ndarray of shape (n_classes,)
|
157 |
+
Intercept terms.
|
158 |
+
raw_prediction : ndarray of shape (n_samples,) or \
|
159 |
+
(n_samples, n_classes)
|
160 |
+
"""
|
161 |
+
weights, intercept = self.weight_intercept(coef)
|
162 |
+
|
163 |
+
if not self.base_loss.is_multiclass:
|
164 |
+
raw_prediction = X @ weights + intercept
|
165 |
+
else:
|
166 |
+
# weights has shape (n_classes, n_dof)
|
167 |
+
raw_prediction = X @ weights.T + intercept # ndarray, likely C-contiguous
|
168 |
+
|
169 |
+
return weights, intercept, raw_prediction
|
170 |
+
|
171 |
+
def l2_penalty(self, weights, l2_reg_strength):
|
172 |
+
"""Compute L2 penalty term l2_reg_strength/2 *||w||_2^2."""
|
173 |
+
norm2_w = weights @ weights if weights.ndim == 1 else squared_norm(weights)
|
174 |
+
return 0.5 * l2_reg_strength * norm2_w
|
175 |
+
|
176 |
+
def loss(
|
177 |
+
self,
|
178 |
+
coef,
|
179 |
+
X,
|
180 |
+
y,
|
181 |
+
sample_weight=None,
|
182 |
+
l2_reg_strength=0.0,
|
183 |
+
n_threads=1,
|
184 |
+
raw_prediction=None,
|
185 |
+
):
|
186 |
+
"""Compute the loss as weighted average over point-wise losses.
|
187 |
+
|
188 |
+
Parameters
|
189 |
+
----------
|
190 |
+
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
|
191 |
+
Coefficients of a linear model.
|
192 |
+
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
|
193 |
+
i.e. one reconstructs the 2d-array via
|
194 |
+
coef.reshape((n_classes, -1), order="F").
|
195 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
196 |
+
Training data.
|
197 |
+
y : contiguous array of shape (n_samples,)
|
198 |
+
Observed, true target values.
|
199 |
+
sample_weight : None or contiguous array of shape (n_samples,), default=None
|
200 |
+
Sample weights.
|
201 |
+
l2_reg_strength : float, default=0.0
|
202 |
+
L2 regularization strength
|
203 |
+
n_threads : int, default=1
|
204 |
+
Number of OpenMP threads to use.
|
205 |
+
raw_prediction : C-contiguous array of shape (n_samples,) or array of \
|
206 |
+
shape (n_samples, n_classes)
|
207 |
+
Raw prediction values (in link space). If provided, these are used. If
|
208 |
+
None, then raw_prediction = X @ coef + intercept is calculated.
|
209 |
+
|
210 |
+
Returns
|
211 |
+
-------
|
212 |
+
loss : float
|
213 |
+
Weighted average of losses per sample, plus penalty.
|
214 |
+
"""
|
215 |
+
if raw_prediction is None:
|
216 |
+
weights, intercept, raw_prediction = self.weight_intercept_raw(coef, X)
|
217 |
+
else:
|
218 |
+
weights, intercept = self.weight_intercept(coef)
|
219 |
+
|
220 |
+
loss = self.base_loss.loss(
|
221 |
+
y_true=y,
|
222 |
+
raw_prediction=raw_prediction,
|
223 |
+
sample_weight=None,
|
224 |
+
n_threads=n_threads,
|
225 |
+
)
|
226 |
+
loss = np.average(loss, weights=sample_weight)
|
227 |
+
|
228 |
+
return loss + self.l2_penalty(weights, l2_reg_strength)
|
229 |
+
|
230 |
+
def loss_gradient(
|
231 |
+
self,
|
232 |
+
coef,
|
233 |
+
X,
|
234 |
+
y,
|
235 |
+
sample_weight=None,
|
236 |
+
l2_reg_strength=0.0,
|
237 |
+
n_threads=1,
|
238 |
+
raw_prediction=None,
|
239 |
+
):
|
240 |
+
"""Computes the sum of loss and gradient w.r.t. coef.
|
241 |
+
|
242 |
+
Parameters
|
243 |
+
----------
|
244 |
+
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
|
245 |
+
Coefficients of a linear model.
|
246 |
+
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
|
247 |
+
i.e. one reconstructs the 2d-array via
|
248 |
+
coef.reshape((n_classes, -1), order="F").
|
249 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
250 |
+
Training data.
|
251 |
+
y : contiguous array of shape (n_samples,)
|
252 |
+
Observed, true target values.
|
253 |
+
sample_weight : None or contiguous array of shape (n_samples,), default=None
|
254 |
+
Sample weights.
|
255 |
+
l2_reg_strength : float, default=0.0
|
256 |
+
L2 regularization strength
|
257 |
+
n_threads : int, default=1
|
258 |
+
Number of OpenMP threads to use.
|
259 |
+
raw_prediction : C-contiguous array of shape (n_samples,) or array of \
|
260 |
+
shape (n_samples, n_classes)
|
261 |
+
Raw prediction values (in link space). If provided, these are used. If
|
262 |
+
None, then raw_prediction = X @ coef + intercept is calculated.
|
263 |
+
|
264 |
+
Returns
|
265 |
+
-------
|
266 |
+
loss : float
|
267 |
+
Weighted average of losses per sample, plus penalty.
|
268 |
+
|
269 |
+
gradient : ndarray of shape coef.shape
|
270 |
+
The gradient of the loss.
|
271 |
+
"""
|
272 |
+
(n_samples, n_features), n_classes = X.shape, self.base_loss.n_classes
|
273 |
+
n_dof = n_features + int(self.fit_intercept)
|
274 |
+
|
275 |
+
if raw_prediction is None:
|
276 |
+
weights, intercept, raw_prediction = self.weight_intercept_raw(coef, X)
|
277 |
+
else:
|
278 |
+
weights, intercept = self.weight_intercept(coef)
|
279 |
+
|
280 |
+
loss, grad_pointwise = self.base_loss.loss_gradient(
|
281 |
+
y_true=y,
|
282 |
+
raw_prediction=raw_prediction,
|
283 |
+
sample_weight=sample_weight,
|
284 |
+
n_threads=n_threads,
|
285 |
+
)
|
286 |
+
sw_sum = n_samples if sample_weight is None else np.sum(sample_weight)
|
287 |
+
loss = loss.sum() / sw_sum
|
288 |
+
loss += self.l2_penalty(weights, l2_reg_strength)
|
289 |
+
|
290 |
+
grad_pointwise /= sw_sum
|
291 |
+
|
292 |
+
if not self.base_loss.is_multiclass:
|
293 |
+
grad = np.empty_like(coef, dtype=weights.dtype)
|
294 |
+
grad[:n_features] = X.T @ grad_pointwise + l2_reg_strength * weights
|
295 |
+
if self.fit_intercept:
|
296 |
+
grad[-1] = grad_pointwise.sum()
|
297 |
+
else:
|
298 |
+
grad = np.empty((n_classes, n_dof), dtype=weights.dtype, order="F")
|
299 |
+
# grad_pointwise.shape = (n_samples, n_classes)
|
300 |
+
grad[:, :n_features] = grad_pointwise.T @ X + l2_reg_strength * weights
|
301 |
+
if self.fit_intercept:
|
302 |
+
grad[:, -1] = grad_pointwise.sum(axis=0)
|
303 |
+
if coef.ndim == 1:
|
304 |
+
grad = grad.ravel(order="F")
|
305 |
+
|
306 |
+
return loss, grad
|
307 |
+
|
308 |
+
def gradient(
|
309 |
+
self,
|
310 |
+
coef,
|
311 |
+
X,
|
312 |
+
y,
|
313 |
+
sample_weight=None,
|
314 |
+
l2_reg_strength=0.0,
|
315 |
+
n_threads=1,
|
316 |
+
raw_prediction=None,
|
317 |
+
):
|
318 |
+
"""Computes the gradient w.r.t. coef.
|
319 |
+
|
320 |
+
Parameters
|
321 |
+
----------
|
322 |
+
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
|
323 |
+
Coefficients of a linear model.
|
324 |
+
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
|
325 |
+
i.e. one reconstructs the 2d-array via
|
326 |
+
coef.reshape((n_classes, -1), order="F").
|
327 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
328 |
+
Training data.
|
329 |
+
y : contiguous array of shape (n_samples,)
|
330 |
+
Observed, true target values.
|
331 |
+
sample_weight : None or contiguous array of shape (n_samples,), default=None
|
332 |
+
Sample weights.
|
333 |
+
l2_reg_strength : float, default=0.0
|
334 |
+
L2 regularization strength
|
335 |
+
n_threads : int, default=1
|
336 |
+
Number of OpenMP threads to use.
|
337 |
+
raw_prediction : C-contiguous array of shape (n_samples,) or array of \
|
338 |
+
shape (n_samples, n_classes)
|
339 |
+
Raw prediction values (in link space). If provided, these are used. If
|
340 |
+
None, then raw_prediction = X @ coef + intercept is calculated.
|
341 |
+
|
342 |
+
Returns
|
343 |
+
-------
|
344 |
+
gradient : ndarray of shape coef.shape
|
345 |
+
The gradient of the loss.
|
346 |
+
"""
|
347 |
+
(n_samples, n_features), n_classes = X.shape, self.base_loss.n_classes
|
348 |
+
n_dof = n_features + int(self.fit_intercept)
|
349 |
+
|
350 |
+
if raw_prediction is None:
|
351 |
+
weights, intercept, raw_prediction = self.weight_intercept_raw(coef, X)
|
352 |
+
else:
|
353 |
+
weights, intercept = self.weight_intercept(coef)
|
354 |
+
|
355 |
+
grad_pointwise = self.base_loss.gradient(
|
356 |
+
y_true=y,
|
357 |
+
raw_prediction=raw_prediction,
|
358 |
+
sample_weight=sample_weight,
|
359 |
+
n_threads=n_threads,
|
360 |
+
)
|
361 |
+
sw_sum = n_samples if sample_weight is None else np.sum(sample_weight)
|
362 |
+
grad_pointwise /= sw_sum
|
363 |
+
|
364 |
+
if not self.base_loss.is_multiclass:
|
365 |
+
grad = np.empty_like(coef, dtype=weights.dtype)
|
366 |
+
grad[:n_features] = X.T @ grad_pointwise + l2_reg_strength * weights
|
367 |
+
if self.fit_intercept:
|
368 |
+
grad[-1] = grad_pointwise.sum()
|
369 |
+
return grad
|
370 |
+
else:
|
371 |
+
grad = np.empty((n_classes, n_dof), dtype=weights.dtype, order="F")
|
372 |
+
# gradient.shape = (n_samples, n_classes)
|
373 |
+
grad[:, :n_features] = grad_pointwise.T @ X + l2_reg_strength * weights
|
374 |
+
if self.fit_intercept:
|
375 |
+
grad[:, -1] = grad_pointwise.sum(axis=0)
|
376 |
+
if coef.ndim == 1:
|
377 |
+
return grad.ravel(order="F")
|
378 |
+
else:
|
379 |
+
return grad
|
380 |
+
|
381 |
+
def gradient_hessian(
|
382 |
+
self,
|
383 |
+
coef,
|
384 |
+
X,
|
385 |
+
y,
|
386 |
+
sample_weight=None,
|
387 |
+
l2_reg_strength=0.0,
|
388 |
+
n_threads=1,
|
389 |
+
gradient_out=None,
|
390 |
+
hessian_out=None,
|
391 |
+
raw_prediction=None,
|
392 |
+
):
|
393 |
+
"""Computes gradient and hessian w.r.t. coef.
|
394 |
+
|
395 |
+
Parameters
|
396 |
+
----------
|
397 |
+
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
|
398 |
+
Coefficients of a linear model.
|
399 |
+
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
|
400 |
+
i.e. one reconstructs the 2d-array via
|
401 |
+
coef.reshape((n_classes, -1), order="F").
|
402 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
403 |
+
Training data.
|
404 |
+
y : contiguous array of shape (n_samples,)
|
405 |
+
Observed, true target values.
|
406 |
+
sample_weight : None or contiguous array of shape (n_samples,), default=None
|
407 |
+
Sample weights.
|
408 |
+
l2_reg_strength : float, default=0.0
|
409 |
+
L2 regularization strength
|
410 |
+
n_threads : int, default=1
|
411 |
+
Number of OpenMP threads to use.
|
412 |
+
gradient_out : None or ndarray of shape coef.shape
|
413 |
+
A location into which the gradient is stored. If None, a new array
|
414 |
+
might be created.
|
415 |
+
hessian_out : None or ndarray
|
416 |
+
A location into which the hessian is stored. If None, a new array
|
417 |
+
might be created.
|
418 |
+
raw_prediction : C-contiguous array of shape (n_samples,) or array of \
|
419 |
+
shape (n_samples, n_classes)
|
420 |
+
Raw prediction values (in link space). If provided, these are used. If
|
421 |
+
None, then raw_prediction = X @ coef + intercept is calculated.
|
422 |
+
|
423 |
+
Returns
|
424 |
+
-------
|
425 |
+
gradient : ndarray of shape coef.shape
|
426 |
+
The gradient of the loss.
|
427 |
+
|
428 |
+
hessian : ndarray
|
429 |
+
Hessian matrix.
|
430 |
+
|
431 |
+
hessian_warning : bool
|
432 |
+
True if pointwise hessian has more than half of its elements non-positive.
|
433 |
+
"""
|
434 |
+
n_samples, n_features = X.shape
|
435 |
+
n_dof = n_features + int(self.fit_intercept)
|
436 |
+
|
437 |
+
if raw_prediction is None:
|
438 |
+
weights, intercept, raw_prediction = self.weight_intercept_raw(coef, X)
|
439 |
+
else:
|
440 |
+
weights, intercept = self.weight_intercept(coef)
|
441 |
+
|
442 |
+
grad_pointwise, hess_pointwise = self.base_loss.gradient_hessian(
|
443 |
+
y_true=y,
|
444 |
+
raw_prediction=raw_prediction,
|
445 |
+
sample_weight=sample_weight,
|
446 |
+
n_threads=n_threads,
|
447 |
+
)
|
448 |
+
sw_sum = n_samples if sample_weight is None else np.sum(sample_weight)
|
449 |
+
grad_pointwise /= sw_sum
|
450 |
+
hess_pointwise /= sw_sum
|
451 |
+
|
452 |
+
# For non-canonical link functions and far away from the optimum, the pointwise
|
453 |
+
# hessian can be negative. We take care that 75% of the hessian entries are
|
454 |
+
# positive.
|
455 |
+
hessian_warning = np.mean(hess_pointwise <= 0) > 0.25
|
456 |
+
hess_pointwise = np.abs(hess_pointwise)
|
457 |
+
|
458 |
+
if not self.base_loss.is_multiclass:
|
459 |
+
# gradient
|
460 |
+
if gradient_out is None:
|
461 |
+
grad = np.empty_like(coef, dtype=weights.dtype)
|
462 |
+
else:
|
463 |
+
grad = gradient_out
|
464 |
+
grad[:n_features] = X.T @ grad_pointwise + l2_reg_strength * weights
|
465 |
+
if self.fit_intercept:
|
466 |
+
grad[-1] = grad_pointwise.sum()
|
467 |
+
|
468 |
+
# hessian
|
469 |
+
if hessian_out is None:
|
470 |
+
hess = np.empty(shape=(n_dof, n_dof), dtype=weights.dtype)
|
471 |
+
else:
|
472 |
+
hess = hessian_out
|
473 |
+
|
474 |
+
if hessian_warning:
|
475 |
+
# Exit early without computing the hessian.
|
476 |
+
return grad, hess, hessian_warning
|
477 |
+
|
478 |
+
# TODO: This "sandwich product", X' diag(W) X, is the main computational
|
479 |
+
# bottleneck for solvers. A dedicated Cython routine might improve it
|
480 |
+
# exploiting the symmetry (as opposed to, e.g., BLAS gemm).
|
481 |
+
if sparse.issparse(X):
|
482 |
+
hess[:n_features, :n_features] = (
|
483 |
+
X.T
|
484 |
+
@ sparse.dia_matrix(
|
485 |
+
(hess_pointwise, 0), shape=(n_samples, n_samples)
|
486 |
+
)
|
487 |
+
@ X
|
488 |
+
).toarray()
|
489 |
+
else:
|
490 |
+
# np.einsum may use less memory but the following, using BLAS matrix
|
491 |
+
# multiplication (gemm), is by far faster.
|
492 |
+
WX = hess_pointwise[:, None] * X
|
493 |
+
hess[:n_features, :n_features] = np.dot(X.T, WX)
|
494 |
+
|
495 |
+
if l2_reg_strength > 0:
|
496 |
+
# The L2 penalty enters the Hessian on the diagonal only. To add those
|
497 |
+
# terms, we use a flattened view on the array.
|
498 |
+
hess.reshape(-1)[
|
499 |
+
: (n_features * n_dof) : (n_dof + 1)
|
500 |
+
] += l2_reg_strength
|
501 |
+
|
502 |
+
if self.fit_intercept:
|
503 |
+
# With intercept included as added column to X, the hessian becomes
|
504 |
+
# hess = (X, 1)' @ diag(h) @ (X, 1)
|
505 |
+
# = (X' @ diag(h) @ X, X' @ h)
|
506 |
+
# ( h @ X, sum(h))
|
507 |
+
# The left upper part has already been filled, it remains to compute
|
508 |
+
# the last row and the last column.
|
509 |
+
Xh = X.T @ hess_pointwise
|
510 |
+
hess[:-1, -1] = Xh
|
511 |
+
hess[-1, :-1] = Xh
|
512 |
+
hess[-1, -1] = hess_pointwise.sum()
|
513 |
+
else:
|
514 |
+
# Here we may safely assume HalfMultinomialLoss aka categorical
|
515 |
+
# cross-entropy.
|
516 |
+
raise NotImplementedError
|
517 |
+
|
518 |
+
return grad, hess, hessian_warning
|
519 |
+
|
520 |
+
def gradient_hessian_product(
|
521 |
+
self, coef, X, y, sample_weight=None, l2_reg_strength=0.0, n_threads=1
|
522 |
+
):
|
523 |
+
"""Computes gradient and hessp (hessian product function) w.r.t. coef.
|
524 |
+
|
525 |
+
Parameters
|
526 |
+
----------
|
527 |
+
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
|
528 |
+
Coefficients of a linear model.
|
529 |
+
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
|
530 |
+
i.e. one reconstructs the 2d-array via
|
531 |
+
coef.reshape((n_classes, -1), order="F").
|
532 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
533 |
+
Training data.
|
534 |
+
y : contiguous array of shape (n_samples,)
|
535 |
+
Observed, true target values.
|
536 |
+
sample_weight : None or contiguous array of shape (n_samples,), default=None
|
537 |
+
Sample weights.
|
538 |
+
l2_reg_strength : float, default=0.0
|
539 |
+
L2 regularization strength
|
540 |
+
n_threads : int, default=1
|
541 |
+
Number of OpenMP threads to use.
|
542 |
+
|
543 |
+
Returns
|
544 |
+
-------
|
545 |
+
gradient : ndarray of shape coef.shape
|
546 |
+
The gradient of the loss.
|
547 |
+
|
548 |
+
hessp : callable
|
549 |
+
Function that takes in a vector input of shape of gradient and
|
550 |
+
and returns matrix-vector product with hessian.
|
551 |
+
"""
|
552 |
+
(n_samples, n_features), n_classes = X.shape, self.base_loss.n_classes
|
553 |
+
n_dof = n_features + int(self.fit_intercept)
|
554 |
+
weights, intercept, raw_prediction = self.weight_intercept_raw(coef, X)
|
555 |
+
sw_sum = n_samples if sample_weight is None else np.sum(sample_weight)
|
556 |
+
|
557 |
+
if not self.base_loss.is_multiclass:
|
558 |
+
grad_pointwise, hess_pointwise = self.base_loss.gradient_hessian(
|
559 |
+
y_true=y,
|
560 |
+
raw_prediction=raw_prediction,
|
561 |
+
sample_weight=sample_weight,
|
562 |
+
n_threads=n_threads,
|
563 |
+
)
|
564 |
+
grad_pointwise /= sw_sum
|
565 |
+
hess_pointwise /= sw_sum
|
566 |
+
grad = np.empty_like(coef, dtype=weights.dtype)
|
567 |
+
grad[:n_features] = X.T @ grad_pointwise + l2_reg_strength * weights
|
568 |
+
if self.fit_intercept:
|
569 |
+
grad[-1] = grad_pointwise.sum()
|
570 |
+
|
571 |
+
# Precompute as much as possible: hX, hX_sum and hessian_sum
|
572 |
+
hessian_sum = hess_pointwise.sum()
|
573 |
+
if sparse.issparse(X):
|
574 |
+
hX = (
|
575 |
+
sparse.dia_matrix((hess_pointwise, 0), shape=(n_samples, n_samples))
|
576 |
+
@ X
|
577 |
+
)
|
578 |
+
else:
|
579 |
+
hX = hess_pointwise[:, np.newaxis] * X
|
580 |
+
|
581 |
+
if self.fit_intercept:
|
582 |
+
# Calculate the double derivative with respect to intercept.
|
583 |
+
# Note: In case hX is sparse, hX.sum is a matrix object.
|
584 |
+
hX_sum = np.squeeze(np.asarray(hX.sum(axis=0)))
|
585 |
+
# prevent squeezing to zero-dim array if n_features == 1
|
586 |
+
hX_sum = np.atleast_1d(hX_sum)
|
587 |
+
|
588 |
+
# With intercept included and l2_reg_strength = 0, hessp returns
|
589 |
+
# res = (X, 1)' @ diag(h) @ (X, 1) @ s
|
590 |
+
# = (X, 1)' @ (hX @ s[:n_features], sum(h) * s[-1])
|
591 |
+
# res[:n_features] = X' @ hX @ s[:n_features] + sum(h) * s[-1]
|
592 |
+
# res[-1] = 1' @ hX @ s[:n_features] + sum(h) * s[-1]
|
593 |
+
def hessp(s):
|
594 |
+
ret = np.empty_like(s)
|
595 |
+
if sparse.issparse(X):
|
596 |
+
ret[:n_features] = X.T @ (hX @ s[:n_features])
|
597 |
+
else:
|
598 |
+
ret[:n_features] = np.linalg.multi_dot([X.T, hX, s[:n_features]])
|
599 |
+
ret[:n_features] += l2_reg_strength * s[:n_features]
|
600 |
+
|
601 |
+
if self.fit_intercept:
|
602 |
+
ret[:n_features] += s[-1] * hX_sum
|
603 |
+
ret[-1] = hX_sum @ s[:n_features] + hessian_sum * s[-1]
|
604 |
+
return ret
|
605 |
+
|
606 |
+
else:
|
607 |
+
# Here we may safely assume HalfMultinomialLoss aka categorical
|
608 |
+
# cross-entropy.
|
609 |
+
# HalfMultinomialLoss computes only the diagonal part of the hessian, i.e.
|
610 |
+
# diagonal in the classes. Here, we want the matrix-vector product of the
|
611 |
+
# full hessian. Therefore, we call gradient_proba.
|
612 |
+
grad_pointwise, proba = self.base_loss.gradient_proba(
|
613 |
+
y_true=y,
|
614 |
+
raw_prediction=raw_prediction,
|
615 |
+
sample_weight=sample_weight,
|
616 |
+
n_threads=n_threads,
|
617 |
+
)
|
618 |
+
grad_pointwise /= sw_sum
|
619 |
+
grad = np.empty((n_classes, n_dof), dtype=weights.dtype, order="F")
|
620 |
+
grad[:, :n_features] = grad_pointwise.T @ X + l2_reg_strength * weights
|
621 |
+
if self.fit_intercept:
|
622 |
+
grad[:, -1] = grad_pointwise.sum(axis=0)
|
623 |
+
|
624 |
+
# Full hessian-vector product, i.e. not only the diagonal part of the
|
625 |
+
# hessian. Derivation with some index battle for input vector s:
|
626 |
+
# - sample index i
|
627 |
+
# - feature indices j, m
|
628 |
+
# - class indices k, l
|
629 |
+
# - 1_{k=l} is one if k=l else 0
|
630 |
+
# - p_i_k is the (predicted) probability that sample i belongs to class k
|
631 |
+
# for all i: sum_k p_i_k = 1
|
632 |
+
# - s_l_m is input vector for class l and feature m
|
633 |
+
# - X' = X transposed
|
634 |
+
#
|
635 |
+
# Note: Hessian with dropping most indices is just:
|
636 |
+
# X' @ p_k (1(k=l) - p_l) @ X
|
637 |
+
#
|
638 |
+
# result_{k j} = sum_{i, l, m} Hessian_{i, k j, m l} * s_l_m
|
639 |
+
# = sum_{i, l, m} (X')_{ji} * p_i_k * (1_{k=l} - p_i_l)
|
640 |
+
# * X_{im} s_l_m
|
641 |
+
# = sum_{i, m} (X')_{ji} * p_i_k
|
642 |
+
# * (X_{im} * s_k_m - sum_l p_i_l * X_{im} * s_l_m)
|
643 |
+
#
|
644 |
+
# See also https://github.com/scikit-learn/scikit-learn/pull/3646#discussion_r17461411 # noqa
|
645 |
+
def hessp(s):
|
646 |
+
s = s.reshape((n_classes, -1), order="F") # shape = (n_classes, n_dof)
|
647 |
+
if self.fit_intercept:
|
648 |
+
s_intercept = s[:, -1]
|
649 |
+
s = s[:, :-1] # shape = (n_classes, n_features)
|
650 |
+
else:
|
651 |
+
s_intercept = 0
|
652 |
+
tmp = X @ s.T + s_intercept # X_{im} * s_k_m
|
653 |
+
tmp += (-proba * tmp).sum(axis=1)[:, np.newaxis] # - sum_l ..
|
654 |
+
tmp *= proba # * p_i_k
|
655 |
+
if sample_weight is not None:
|
656 |
+
tmp *= sample_weight[:, np.newaxis]
|
657 |
+
# hess_prod = empty_like(grad), but we ravel grad below and this
|
658 |
+
# function is run after that.
|
659 |
+
hess_prod = np.empty((n_classes, n_dof), dtype=weights.dtype, order="F")
|
660 |
+
hess_prod[:, :n_features] = (tmp.T @ X) / sw_sum + l2_reg_strength * s
|
661 |
+
if self.fit_intercept:
|
662 |
+
hess_prod[:, -1] = tmp.sum(axis=0) / sw_sum
|
663 |
+
if coef.ndim == 1:
|
664 |
+
return hess_prod.ravel(order="F")
|
665 |
+
else:
|
666 |
+
return hess_prod
|
667 |
+
|
668 |
+
if coef.ndim == 1:
|
669 |
+
return grad.ravel(order="F"), hessp
|
670 |
+
|
671 |
+
return grad, hessp
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_perceptron.py
ADDED
@@ -0,0 +1,229 @@
|
|
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|
|
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|
|
|
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|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
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|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
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|
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|
|
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|
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|
|
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|
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|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# Author: Mathieu Blondel
|
2 |
+
# License: BSD 3 clause
|
3 |
+
from numbers import Real
|
4 |
+
|
5 |
+
from ..utils._param_validation import Interval, StrOptions
|
6 |
+
from ._stochastic_gradient import BaseSGDClassifier
|
7 |
+
|
8 |
+
|
9 |
+
class Perceptron(BaseSGDClassifier):
|
10 |
+
"""Linear perceptron classifier.
|
11 |
+
|
12 |
+
The implementation is a wrapper around :class:`~sklearn.linear_model.SGDClassifier`
|
13 |
+
by fixing the `loss` and `learning_rate` parameters as::
|
14 |
+
|
15 |
+
SGDClassifier(loss="perceptron", learning_rate="constant")
|
16 |
+
|
17 |
+
Other available parameters are described below and are forwarded to
|
18 |
+
:class:`~sklearn.linear_model.SGDClassifier`.
|
19 |
+
|
20 |
+
Read more in the :ref:`User Guide <perceptron>`.
|
21 |
+
|
22 |
+
Parameters
|
23 |
+
----------
|
24 |
+
|
25 |
+
penalty : {'l2','l1','elasticnet'}, default=None
|
26 |
+
The penalty (aka regularization term) to be used.
|
27 |
+
|
28 |
+
alpha : float, default=0.0001
|
29 |
+
Constant that multiplies the regularization term if regularization is
|
30 |
+
used.
|
31 |
+
|
32 |
+
l1_ratio : float, default=0.15
|
33 |
+
The Elastic Net mixing parameter, with `0 <= l1_ratio <= 1`.
|
34 |
+
`l1_ratio=0` corresponds to L2 penalty, `l1_ratio=1` to L1.
|
35 |
+
Only used if `penalty='elasticnet'`.
|
36 |
+
|
37 |
+
.. versionadded:: 0.24
|
38 |
+
|
39 |
+
fit_intercept : bool, default=True
|
40 |
+
Whether the intercept should be estimated or not. If False, the
|
41 |
+
data is assumed to be already centered.
|
42 |
+
|
43 |
+
max_iter : int, default=1000
|
44 |
+
The maximum number of passes over the training data (aka epochs).
|
45 |
+
It only impacts the behavior in the ``fit`` method, and not the
|
46 |
+
:meth:`partial_fit` method.
|
47 |
+
|
48 |
+
.. versionadded:: 0.19
|
49 |
+
|
50 |
+
tol : float or None, default=1e-3
|
51 |
+
The stopping criterion. If it is not None, the iterations will stop
|
52 |
+
when (loss > previous_loss - tol).
|
53 |
+
|
54 |
+
.. versionadded:: 0.19
|
55 |
+
|
56 |
+
shuffle : bool, default=True
|
57 |
+
Whether or not the training data should be shuffled after each epoch.
|
58 |
+
|
59 |
+
verbose : int, default=0
|
60 |
+
The verbosity level.
|
61 |
+
|
62 |
+
eta0 : float, default=1
|
63 |
+
Constant by which the updates are multiplied.
|
64 |
+
|
65 |
+
n_jobs : int, default=None
|
66 |
+
The number of CPUs to use to do the OVA (One Versus All, for
|
67 |
+
multi-class problems) computation.
|
68 |
+
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
|
69 |
+
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
|
70 |
+
for more details.
|
71 |
+
|
72 |
+
random_state : int, RandomState instance or None, default=0
|
73 |
+
Used to shuffle the training data, when ``shuffle`` is set to
|
74 |
+
``True``. Pass an int for reproducible output across multiple
|
75 |
+
function calls.
|
76 |
+
See :term:`Glossary <random_state>`.
|
77 |
+
|
78 |
+
early_stopping : bool, default=False
|
79 |
+
Whether to use early stopping to terminate training when validation
|
80 |
+
score is not improving. If set to True, it will automatically set aside
|
81 |
+
a stratified fraction of training data as validation and terminate
|
82 |
+
training when validation score is not improving by at least `tol` for
|
83 |
+
`n_iter_no_change` consecutive epochs.
|
84 |
+
|
85 |
+
.. versionadded:: 0.20
|
86 |
+
|
87 |
+
validation_fraction : float, default=0.1
|
88 |
+
The proportion of training data to set aside as validation set for
|
89 |
+
early stopping. Must be between 0 and 1.
|
90 |
+
Only used if early_stopping is True.
|
91 |
+
|
92 |
+
.. versionadded:: 0.20
|
93 |
+
|
94 |
+
n_iter_no_change : int, default=5
|
95 |
+
Number of iterations with no improvement to wait before early stopping.
|
96 |
+
|
97 |
+
.. versionadded:: 0.20
|
98 |
+
|
99 |
+
class_weight : dict, {class_label: weight} or "balanced", default=None
|
100 |
+
Preset for the class_weight fit parameter.
|
101 |
+
|
102 |
+
Weights associated with classes. If not given, all classes
|
103 |
+
are supposed to have weight one.
|
104 |
+
|
105 |
+
The "balanced" mode uses the values of y to automatically adjust
|
106 |
+
weights inversely proportional to class frequencies in the input data
|
107 |
+
as ``n_samples / (n_classes * np.bincount(y))``.
|
108 |
+
|
109 |
+
warm_start : bool, default=False
|
110 |
+
When set to True, reuse the solution of the previous call to fit as
|
111 |
+
initialization, otherwise, just erase the previous solution. See
|
112 |
+
:term:`the Glossary <warm_start>`.
|
113 |
+
|
114 |
+
Attributes
|
115 |
+
----------
|
116 |
+
classes_ : ndarray of shape (n_classes,)
|
117 |
+
The unique classes labels.
|
118 |
+
|
119 |
+
coef_ : ndarray of shape (1, n_features) if n_classes == 2 else \
|
120 |
+
(n_classes, n_features)
|
121 |
+
Weights assigned to the features.
|
122 |
+
|
123 |
+
intercept_ : ndarray of shape (1,) if n_classes == 2 else (n_classes,)
|
124 |
+
Constants in decision function.
|
125 |
+
|
126 |
+
loss_function_ : concrete LossFunction
|
127 |
+
The function that determines the loss, or difference between the
|
128 |
+
output of the algorithm and the target values.
|
129 |
+
|
130 |
+
n_features_in_ : int
|
131 |
+
Number of features seen during :term:`fit`.
|
132 |
+
|
133 |
+
.. versionadded:: 0.24
|
134 |
+
|
135 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
136 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
137 |
+
has feature names that are all strings.
|
138 |
+
|
139 |
+
.. versionadded:: 1.0
|
140 |
+
|
141 |
+
n_iter_ : int
|
142 |
+
The actual number of iterations to reach the stopping criterion.
|
143 |
+
For multiclass fits, it is the maximum over every binary fit.
|
144 |
+
|
145 |
+
t_ : int
|
146 |
+
Number of weight updates performed during training.
|
147 |
+
Same as ``(n_iter_ * n_samples + 1)``.
|
148 |
+
|
149 |
+
See Also
|
150 |
+
--------
|
151 |
+
sklearn.linear_model.SGDClassifier : Linear classifiers
|
152 |
+
(SVM, logistic regression, etc.) with SGD training.
|
153 |
+
|
154 |
+
Notes
|
155 |
+
-----
|
156 |
+
``Perceptron`` is a classification algorithm which shares the same
|
157 |
+
underlying implementation with ``SGDClassifier``. In fact,
|
158 |
+
``Perceptron()`` is equivalent to `SGDClassifier(loss="perceptron",
|
159 |
+
eta0=1, learning_rate="constant", penalty=None)`.
|
160 |
+
|
161 |
+
References
|
162 |
+
----------
|
163 |
+
https://en.wikipedia.org/wiki/Perceptron and references therein.
|
164 |
+
|
165 |
+
Examples
|
166 |
+
--------
|
167 |
+
>>> from sklearn.datasets import load_digits
|
168 |
+
>>> from sklearn.linear_model import Perceptron
|
169 |
+
>>> X, y = load_digits(return_X_y=True)
|
170 |
+
>>> clf = Perceptron(tol=1e-3, random_state=0)
|
171 |
+
>>> clf.fit(X, y)
|
172 |
+
Perceptron()
|
173 |
+
>>> clf.score(X, y)
|
174 |
+
0.939...
|
175 |
+
"""
|
176 |
+
|
177 |
+
_parameter_constraints: dict = {**BaseSGDClassifier._parameter_constraints}
|
178 |
+
_parameter_constraints.pop("loss")
|
179 |
+
_parameter_constraints.pop("average")
|
180 |
+
_parameter_constraints.update(
|
181 |
+
{
|
182 |
+
"penalty": [StrOptions({"l2", "l1", "elasticnet"}), None],
|
183 |
+
"alpha": [Interval(Real, 0, None, closed="left")],
|
184 |
+
"l1_ratio": [Interval(Real, 0, 1, closed="both")],
|
185 |
+
"eta0": [Interval(Real, 0, None, closed="left")],
|
186 |
+
}
|
187 |
+
)
|
188 |
+
|
189 |
+
def __init__(
|
190 |
+
self,
|
191 |
+
*,
|
192 |
+
penalty=None,
|
193 |
+
alpha=0.0001,
|
194 |
+
l1_ratio=0.15,
|
195 |
+
fit_intercept=True,
|
196 |
+
max_iter=1000,
|
197 |
+
tol=1e-3,
|
198 |
+
shuffle=True,
|
199 |
+
verbose=0,
|
200 |
+
eta0=1.0,
|
201 |
+
n_jobs=None,
|
202 |
+
random_state=0,
|
203 |
+
early_stopping=False,
|
204 |
+
validation_fraction=0.1,
|
205 |
+
n_iter_no_change=5,
|
206 |
+
class_weight=None,
|
207 |
+
warm_start=False,
|
208 |
+
):
|
209 |
+
super().__init__(
|
210 |
+
loss="perceptron",
|
211 |
+
penalty=penalty,
|
212 |
+
alpha=alpha,
|
213 |
+
l1_ratio=l1_ratio,
|
214 |
+
fit_intercept=fit_intercept,
|
215 |
+
max_iter=max_iter,
|
216 |
+
tol=tol,
|
217 |
+
shuffle=shuffle,
|
218 |
+
verbose=verbose,
|
219 |
+
random_state=random_state,
|
220 |
+
learning_rate="constant",
|
221 |
+
eta0=eta0,
|
222 |
+
early_stopping=early_stopping,
|
223 |
+
validation_fraction=validation_fraction,
|
224 |
+
n_iter_no_change=n_iter_no_change,
|
225 |
+
power_t=0.5,
|
226 |
+
warm_start=warm_start,
|
227 |
+
class_weight=class_weight,
|
228 |
+
n_jobs=n_jobs,
|
229 |
+
)
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_quantile.py
ADDED
@@ -0,0 +1,308 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# Authors: David Dale <[email protected]>
|
2 |
+
# Christian Lorentzen <[email protected]>
|
3 |
+
# License: BSD 3 clause
|
4 |
+
import warnings
|
5 |
+
from numbers import Real
|
6 |
+
|
7 |
+
import numpy as np
|
8 |
+
from scipy import sparse
|
9 |
+
from scipy.optimize import linprog
|
10 |
+
|
11 |
+
from ..base import BaseEstimator, RegressorMixin, _fit_context
|
12 |
+
from ..exceptions import ConvergenceWarning
|
13 |
+
from ..utils import _safe_indexing
|
14 |
+
from ..utils._param_validation import Interval, StrOptions
|
15 |
+
from ..utils.fixes import parse_version, sp_version
|
16 |
+
from ..utils.validation import _check_sample_weight
|
17 |
+
from ._base import LinearModel
|
18 |
+
|
19 |
+
|
20 |
+
class QuantileRegressor(LinearModel, RegressorMixin, BaseEstimator):
|
21 |
+
"""Linear regression model that predicts conditional quantiles.
|
22 |
+
|
23 |
+
The linear :class:`QuantileRegressor` optimizes the pinball loss for a
|
24 |
+
desired `quantile` and is robust to outliers.
|
25 |
+
|
26 |
+
This model uses an L1 regularization like
|
27 |
+
:class:`~sklearn.linear_model.Lasso`.
|
28 |
+
|
29 |
+
Read more in the :ref:`User Guide <quantile_regression>`.
|
30 |
+
|
31 |
+
.. versionadded:: 1.0
|
32 |
+
|
33 |
+
Parameters
|
34 |
+
----------
|
35 |
+
quantile : float, default=0.5
|
36 |
+
The quantile that the model tries to predict. It must be strictly
|
37 |
+
between 0 and 1. If 0.5 (default), the model predicts the 50%
|
38 |
+
quantile, i.e. the median.
|
39 |
+
|
40 |
+
alpha : float, default=1.0
|
41 |
+
Regularization constant that multiplies the L1 penalty term.
|
42 |
+
|
43 |
+
fit_intercept : bool, default=True
|
44 |
+
Whether or not to fit the intercept.
|
45 |
+
|
46 |
+
solver : {'highs-ds', 'highs-ipm', 'highs', 'interior-point', \
|
47 |
+
'revised simplex'}, default='highs'
|
48 |
+
Method used by :func:`scipy.optimize.linprog` to solve the linear
|
49 |
+
programming formulation.
|
50 |
+
|
51 |
+
From `scipy>=1.6.0`, it is recommended to use the highs methods because
|
52 |
+
they are the fastest ones. Solvers "highs-ds", "highs-ipm" and "highs"
|
53 |
+
support sparse input data and, in fact, always convert to sparse csc.
|
54 |
+
|
55 |
+
From `scipy>=1.11.0`, "interior-point" is not available anymore.
|
56 |
+
|
57 |
+
.. versionchanged:: 1.4
|
58 |
+
The default of `solver` changed to `"highs"` in version 1.4.
|
59 |
+
|
60 |
+
solver_options : dict, default=None
|
61 |
+
Additional parameters passed to :func:`scipy.optimize.linprog` as
|
62 |
+
options. If `None` and if `solver='interior-point'`, then
|
63 |
+
`{"lstsq": True}` is passed to :func:`scipy.optimize.linprog` for the
|
64 |
+
sake of stability.
|
65 |
+
|
66 |
+
Attributes
|
67 |
+
----------
|
68 |
+
coef_ : array of shape (n_features,)
|
69 |
+
Estimated coefficients for the features.
|
70 |
+
|
71 |
+
intercept_ : float
|
72 |
+
The intercept of the model, aka bias term.
|
73 |
+
|
74 |
+
n_features_in_ : int
|
75 |
+
Number of features seen during :term:`fit`.
|
76 |
+
|
77 |
+
.. versionadded:: 0.24
|
78 |
+
|
79 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
80 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
81 |
+
has feature names that are all strings.
|
82 |
+
|
83 |
+
.. versionadded:: 1.0
|
84 |
+
|
85 |
+
n_iter_ : int
|
86 |
+
The actual number of iterations performed by the solver.
|
87 |
+
|
88 |
+
See Also
|
89 |
+
--------
|
90 |
+
Lasso : The Lasso is a linear model that estimates sparse coefficients
|
91 |
+
with l1 regularization.
|
92 |
+
HuberRegressor : Linear regression model that is robust to outliers.
|
93 |
+
|
94 |
+
Examples
|
95 |
+
--------
|
96 |
+
>>> from sklearn.linear_model import QuantileRegressor
|
97 |
+
>>> import numpy as np
|
98 |
+
>>> n_samples, n_features = 10, 2
|
99 |
+
>>> rng = np.random.RandomState(0)
|
100 |
+
>>> y = rng.randn(n_samples)
|
101 |
+
>>> X = rng.randn(n_samples, n_features)
|
102 |
+
>>> # the two following lines are optional in practice
|
103 |
+
>>> from sklearn.utils.fixes import sp_version, parse_version
|
104 |
+
>>> solver = "highs" if sp_version >= parse_version("1.6.0") else "interior-point"
|
105 |
+
>>> reg = QuantileRegressor(quantile=0.8, solver=solver).fit(X, y)
|
106 |
+
>>> np.mean(y <= reg.predict(X))
|
107 |
+
0.8
|
108 |
+
"""
|
109 |
+
|
110 |
+
_parameter_constraints: dict = {
|
111 |
+
"quantile": [Interval(Real, 0, 1, closed="neither")],
|
112 |
+
"alpha": [Interval(Real, 0, None, closed="left")],
|
113 |
+
"fit_intercept": ["boolean"],
|
114 |
+
"solver": [
|
115 |
+
StrOptions(
|
116 |
+
{
|
117 |
+
"highs-ds",
|
118 |
+
"highs-ipm",
|
119 |
+
"highs",
|
120 |
+
"interior-point",
|
121 |
+
"revised simplex",
|
122 |
+
}
|
123 |
+
),
|
124 |
+
],
|
125 |
+
"solver_options": [dict, None],
|
126 |
+
}
|
127 |
+
|
128 |
+
def __init__(
|
129 |
+
self,
|
130 |
+
*,
|
131 |
+
quantile=0.5,
|
132 |
+
alpha=1.0,
|
133 |
+
fit_intercept=True,
|
134 |
+
solver="highs",
|
135 |
+
solver_options=None,
|
136 |
+
):
|
137 |
+
self.quantile = quantile
|
138 |
+
self.alpha = alpha
|
139 |
+
self.fit_intercept = fit_intercept
|
140 |
+
self.solver = solver
|
141 |
+
self.solver_options = solver_options
|
142 |
+
|
143 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
144 |
+
def fit(self, X, y, sample_weight=None):
|
145 |
+
"""Fit the model according to the given training data.
|
146 |
+
|
147 |
+
Parameters
|
148 |
+
----------
|
149 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
150 |
+
Training data.
|
151 |
+
|
152 |
+
y : array-like of shape (n_samples,)
|
153 |
+
Target values.
|
154 |
+
|
155 |
+
sample_weight : array-like of shape (n_samples,), default=None
|
156 |
+
Sample weights.
|
157 |
+
|
158 |
+
Returns
|
159 |
+
-------
|
160 |
+
self : object
|
161 |
+
Returns self.
|
162 |
+
"""
|
163 |
+
X, y = self._validate_data(
|
164 |
+
X,
|
165 |
+
y,
|
166 |
+
accept_sparse=["csc", "csr", "coo"],
|
167 |
+
y_numeric=True,
|
168 |
+
multi_output=False,
|
169 |
+
)
|
170 |
+
sample_weight = _check_sample_weight(sample_weight, X)
|
171 |
+
|
172 |
+
n_features = X.shape[1]
|
173 |
+
n_params = n_features
|
174 |
+
|
175 |
+
if self.fit_intercept:
|
176 |
+
n_params += 1
|
177 |
+
# Note that centering y and X with _preprocess_data does not work
|
178 |
+
# for quantile regression.
|
179 |
+
|
180 |
+
# The objective is defined as 1/n * sum(pinball loss) + alpha * L1.
|
181 |
+
# So we rescale the penalty term, which is equivalent.
|
182 |
+
alpha = np.sum(sample_weight) * self.alpha
|
183 |
+
|
184 |
+
if self.solver in (
|
185 |
+
"highs-ds",
|
186 |
+
"highs-ipm",
|
187 |
+
"highs",
|
188 |
+
) and sp_version < parse_version("1.6.0"):
|
189 |
+
raise ValueError(
|
190 |
+
f"Solver {self.solver} is only available "
|
191 |
+
f"with scipy>=1.6.0, got {sp_version}"
|
192 |
+
)
|
193 |
+
else:
|
194 |
+
solver = self.solver
|
195 |
+
|
196 |
+
if solver == "interior-point" and sp_version >= parse_version("1.11.0"):
|
197 |
+
raise ValueError(
|
198 |
+
f"Solver {solver} is not anymore available in SciPy >= 1.11.0."
|
199 |
+
)
|
200 |
+
|
201 |
+
if sparse.issparse(X) and solver not in ["highs", "highs-ds", "highs-ipm"]:
|
202 |
+
raise ValueError(
|
203 |
+
f"Solver {self.solver} does not support sparse X. "
|
204 |
+
"Use solver 'highs' for example."
|
205 |
+
)
|
206 |
+
# make default solver more stable
|
207 |
+
if self.solver_options is None and solver == "interior-point":
|
208 |
+
solver_options = {"lstsq": True}
|
209 |
+
else:
|
210 |
+
solver_options = self.solver_options
|
211 |
+
|
212 |
+
# After rescaling alpha, the minimization problem is
|
213 |
+
# min sum(pinball loss) + alpha * L1
|
214 |
+
# Use linear programming formulation of quantile regression
|
215 |
+
# min_x c x
|
216 |
+
# A_eq x = b_eq
|
217 |
+
# 0 <= x
|
218 |
+
# x = (s0, s, t0, t, u, v) = slack variables >= 0
|
219 |
+
# intercept = s0 - t0
|
220 |
+
# coef = s - t
|
221 |
+
# c = (0, alpha * 1_p, 0, alpha * 1_p, quantile * 1_n, (1-quantile) * 1_n)
|
222 |
+
# residual = y - X@coef - intercept = u - v
|
223 |
+
# A_eq = (1_n, X, -1_n, -X, diag(1_n), -diag(1_n))
|
224 |
+
# b_eq = y
|
225 |
+
# p = n_features
|
226 |
+
# n = n_samples
|
227 |
+
# 1_n = vector of length n with entries equal one
|
228 |
+
# see https://stats.stackexchange.com/questions/384909/
|
229 |
+
#
|
230 |
+
# Filtering out zero sample weights from the beginning makes life
|
231 |
+
# easier for the linprog solver.
|
232 |
+
indices = np.nonzero(sample_weight)[0]
|
233 |
+
n_indices = len(indices) # use n_mask instead of n_samples
|
234 |
+
if n_indices < len(sample_weight):
|
235 |
+
sample_weight = sample_weight[indices]
|
236 |
+
X = _safe_indexing(X, indices)
|
237 |
+
y = _safe_indexing(y, indices)
|
238 |
+
c = np.concatenate(
|
239 |
+
[
|
240 |
+
np.full(2 * n_params, fill_value=alpha),
|
241 |
+
sample_weight * self.quantile,
|
242 |
+
sample_weight * (1 - self.quantile),
|
243 |
+
]
|
244 |
+
)
|
245 |
+
if self.fit_intercept:
|
246 |
+
# do not penalize the intercept
|
247 |
+
c[0] = 0
|
248 |
+
c[n_params] = 0
|
249 |
+
|
250 |
+
if solver in ["highs", "highs-ds", "highs-ipm"]:
|
251 |
+
# Note that highs methods always use a sparse CSC memory layout internally,
|
252 |
+
# even for optimization problems parametrized using dense numpy arrays.
|
253 |
+
# Therefore, we work with CSC matrices as early as possible to limit
|
254 |
+
# unnecessary repeated memory copies.
|
255 |
+
eye = sparse.eye(n_indices, dtype=X.dtype, format="csc")
|
256 |
+
if self.fit_intercept:
|
257 |
+
ones = sparse.csc_matrix(np.ones(shape=(n_indices, 1), dtype=X.dtype))
|
258 |
+
A_eq = sparse.hstack([ones, X, -ones, -X, eye, -eye], format="csc")
|
259 |
+
else:
|
260 |
+
A_eq = sparse.hstack([X, -X, eye, -eye], format="csc")
|
261 |
+
else:
|
262 |
+
eye = np.eye(n_indices)
|
263 |
+
if self.fit_intercept:
|
264 |
+
ones = np.ones((n_indices, 1))
|
265 |
+
A_eq = np.concatenate([ones, X, -ones, -X, eye, -eye], axis=1)
|
266 |
+
else:
|
267 |
+
A_eq = np.concatenate([X, -X, eye, -eye], axis=1)
|
268 |
+
|
269 |
+
b_eq = y
|
270 |
+
|
271 |
+
result = linprog(
|
272 |
+
c=c,
|
273 |
+
A_eq=A_eq,
|
274 |
+
b_eq=b_eq,
|
275 |
+
method=solver,
|
276 |
+
options=solver_options,
|
277 |
+
)
|
278 |
+
solution = result.x
|
279 |
+
if not result.success:
|
280 |
+
failure = {
|
281 |
+
1: "Iteration limit reached.",
|
282 |
+
2: "Problem appears to be infeasible.",
|
283 |
+
3: "Problem appears to be unbounded.",
|
284 |
+
4: "Numerical difficulties encountered.",
|
285 |
+
}
|
286 |
+
warnings.warn(
|
287 |
+
"Linear programming for QuantileRegressor did not succeed.\n"
|
288 |
+
f"Status is {result.status}: "
|
289 |
+
+ failure.setdefault(result.status, "unknown reason")
|
290 |
+
+ "\n"
|
291 |
+
+ "Result message of linprog:\n"
|
292 |
+
+ result.message,
|
293 |
+
ConvergenceWarning,
|
294 |
+
)
|
295 |
+
|
296 |
+
# positive slack - negative slack
|
297 |
+
# solution is an array with (params_pos, params_neg, u, v)
|
298 |
+
params = solution[:n_params] - solution[n_params : 2 * n_params]
|
299 |
+
|
300 |
+
self.n_iter_ = result.nit
|
301 |
+
|
302 |
+
if self.fit_intercept:
|
303 |
+
self.coef_ = params[1:]
|
304 |
+
self.intercept_ = params[0]
|
305 |
+
else:
|
306 |
+
self.coef_ = params
|
307 |
+
self.intercept_ = 0.0
|
308 |
+
return self
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_ransac.py
ADDED
@@ -0,0 +1,623 @@
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|
1 |
+
# Author: Johannes Schönberger
|
2 |
+
#
|
3 |
+
# License: BSD 3 clause
|
4 |
+
|
5 |
+
import warnings
|
6 |
+
from numbers import Integral, Real
|
7 |
+
|
8 |
+
import numpy as np
|
9 |
+
|
10 |
+
from ..base import (
|
11 |
+
BaseEstimator,
|
12 |
+
MetaEstimatorMixin,
|
13 |
+
MultiOutputMixin,
|
14 |
+
RegressorMixin,
|
15 |
+
_fit_context,
|
16 |
+
clone,
|
17 |
+
)
|
18 |
+
from ..exceptions import ConvergenceWarning
|
19 |
+
from ..utils import check_consistent_length, check_random_state
|
20 |
+
from ..utils._param_validation import (
|
21 |
+
HasMethods,
|
22 |
+
Interval,
|
23 |
+
Options,
|
24 |
+
RealNotInt,
|
25 |
+
StrOptions,
|
26 |
+
)
|
27 |
+
from ..utils.metadata_routing import (
|
28 |
+
_raise_for_unsupported_routing,
|
29 |
+
_RoutingNotSupportedMixin,
|
30 |
+
)
|
31 |
+
from ..utils.random import sample_without_replacement
|
32 |
+
from ..utils.validation import _check_sample_weight, check_is_fitted, has_fit_parameter
|
33 |
+
from ._base import LinearRegression
|
34 |
+
|
35 |
+
_EPSILON = np.spacing(1)
|
36 |
+
|
37 |
+
|
38 |
+
def _dynamic_max_trials(n_inliers, n_samples, min_samples, probability):
|
39 |
+
"""Determine number trials such that at least one outlier-free subset is
|
40 |
+
sampled for the given inlier/outlier ratio.
|
41 |
+
|
42 |
+
Parameters
|
43 |
+
----------
|
44 |
+
n_inliers : int
|
45 |
+
Number of inliers in the data.
|
46 |
+
|
47 |
+
n_samples : int
|
48 |
+
Total number of samples in the data.
|
49 |
+
|
50 |
+
min_samples : int
|
51 |
+
Minimum number of samples chosen randomly from original data.
|
52 |
+
|
53 |
+
probability : float
|
54 |
+
Probability (confidence) that one outlier-free sample is generated.
|
55 |
+
|
56 |
+
Returns
|
57 |
+
-------
|
58 |
+
trials : int
|
59 |
+
Number of trials.
|
60 |
+
|
61 |
+
"""
|
62 |
+
inlier_ratio = n_inliers / float(n_samples)
|
63 |
+
nom = max(_EPSILON, 1 - probability)
|
64 |
+
denom = max(_EPSILON, 1 - inlier_ratio**min_samples)
|
65 |
+
if nom == 1:
|
66 |
+
return 0
|
67 |
+
if denom == 1:
|
68 |
+
return float("inf")
|
69 |
+
return abs(float(np.ceil(np.log(nom) / np.log(denom))))
|
70 |
+
|
71 |
+
|
72 |
+
class RANSACRegressor(
|
73 |
+
_RoutingNotSupportedMixin,
|
74 |
+
MetaEstimatorMixin,
|
75 |
+
RegressorMixin,
|
76 |
+
MultiOutputMixin,
|
77 |
+
BaseEstimator,
|
78 |
+
):
|
79 |
+
"""RANSAC (RANdom SAmple Consensus) algorithm.
|
80 |
+
|
81 |
+
RANSAC is an iterative algorithm for the robust estimation of parameters
|
82 |
+
from a subset of inliers from the complete data set.
|
83 |
+
|
84 |
+
Read more in the :ref:`User Guide <ransac_regression>`.
|
85 |
+
|
86 |
+
Parameters
|
87 |
+
----------
|
88 |
+
estimator : object, default=None
|
89 |
+
Base estimator object which implements the following methods:
|
90 |
+
|
91 |
+
* `fit(X, y)`: Fit model to given training data and target values.
|
92 |
+
* `score(X, y)`: Returns the mean accuracy on the given test data,
|
93 |
+
which is used for the stop criterion defined by `stop_score`.
|
94 |
+
Additionally, the score is used to decide which of two equally
|
95 |
+
large consensus sets is chosen as the better one.
|
96 |
+
* `predict(X)`: Returns predicted values using the linear model,
|
97 |
+
which is used to compute residual error using loss function.
|
98 |
+
|
99 |
+
If `estimator` is None, then
|
100 |
+
:class:`~sklearn.linear_model.LinearRegression` is used for
|
101 |
+
target values of dtype float.
|
102 |
+
|
103 |
+
Note that the current implementation only supports regression
|
104 |
+
estimators.
|
105 |
+
|
106 |
+
min_samples : int (>= 1) or float ([0, 1]), default=None
|
107 |
+
Minimum number of samples chosen randomly from original data. Treated
|
108 |
+
as an absolute number of samples for `min_samples >= 1`, treated as a
|
109 |
+
relative number `ceil(min_samples * X.shape[0])` for
|
110 |
+
`min_samples < 1`. This is typically chosen as the minimal number of
|
111 |
+
samples necessary to estimate the given `estimator`. By default a
|
112 |
+
:class:`~sklearn.linear_model.LinearRegression` estimator is assumed and
|
113 |
+
`min_samples` is chosen as ``X.shape[1] + 1``. This parameter is highly
|
114 |
+
dependent upon the model, so if a `estimator` other than
|
115 |
+
:class:`~sklearn.linear_model.LinearRegression` is used, the user must
|
116 |
+
provide a value.
|
117 |
+
|
118 |
+
residual_threshold : float, default=None
|
119 |
+
Maximum residual for a data sample to be classified as an inlier.
|
120 |
+
By default the threshold is chosen as the MAD (median absolute
|
121 |
+
deviation) of the target values `y`. Points whose residuals are
|
122 |
+
strictly equal to the threshold are considered as inliers.
|
123 |
+
|
124 |
+
is_data_valid : callable, default=None
|
125 |
+
This function is called with the randomly selected data before the
|
126 |
+
model is fitted to it: `is_data_valid(X, y)`. If its return value is
|
127 |
+
False the current randomly chosen sub-sample is skipped.
|
128 |
+
|
129 |
+
is_model_valid : callable, default=None
|
130 |
+
This function is called with the estimated model and the randomly
|
131 |
+
selected data: `is_model_valid(model, X, y)`. If its return value is
|
132 |
+
False the current randomly chosen sub-sample is skipped.
|
133 |
+
Rejecting samples with this function is computationally costlier than
|
134 |
+
with `is_data_valid`. `is_model_valid` should therefore only be used if
|
135 |
+
the estimated model is needed for making the rejection decision.
|
136 |
+
|
137 |
+
max_trials : int, default=100
|
138 |
+
Maximum number of iterations for random sample selection.
|
139 |
+
|
140 |
+
max_skips : int, default=np.inf
|
141 |
+
Maximum number of iterations that can be skipped due to finding zero
|
142 |
+
inliers or invalid data defined by ``is_data_valid`` or invalid models
|
143 |
+
defined by ``is_model_valid``.
|
144 |
+
|
145 |
+
.. versionadded:: 0.19
|
146 |
+
|
147 |
+
stop_n_inliers : int, default=np.inf
|
148 |
+
Stop iteration if at least this number of inliers are found.
|
149 |
+
|
150 |
+
stop_score : float, default=np.inf
|
151 |
+
Stop iteration if score is greater equal than this threshold.
|
152 |
+
|
153 |
+
stop_probability : float in range [0, 1], default=0.99
|
154 |
+
RANSAC iteration stops if at least one outlier-free set of the training
|
155 |
+
data is sampled in RANSAC. This requires to generate at least N
|
156 |
+
samples (iterations)::
|
157 |
+
|
158 |
+
N >= log(1 - probability) / log(1 - e**m)
|
159 |
+
|
160 |
+
where the probability (confidence) is typically set to high value such
|
161 |
+
as 0.99 (the default) and e is the current fraction of inliers w.r.t.
|
162 |
+
the total number of samples.
|
163 |
+
|
164 |
+
loss : str, callable, default='absolute_error'
|
165 |
+
String inputs, 'absolute_error' and 'squared_error' are supported which
|
166 |
+
find the absolute error and squared error per sample respectively.
|
167 |
+
|
168 |
+
If ``loss`` is a callable, then it should be a function that takes
|
169 |
+
two arrays as inputs, the true and predicted value and returns a 1-D
|
170 |
+
array with the i-th value of the array corresponding to the loss
|
171 |
+
on ``X[i]``.
|
172 |
+
|
173 |
+
If the loss on a sample is greater than the ``residual_threshold``,
|
174 |
+
then this sample is classified as an outlier.
|
175 |
+
|
176 |
+
.. versionadded:: 0.18
|
177 |
+
|
178 |
+
random_state : int, RandomState instance, default=None
|
179 |
+
The generator used to initialize the centers.
|
180 |
+
Pass an int for reproducible output across multiple function calls.
|
181 |
+
See :term:`Glossary <random_state>`.
|
182 |
+
|
183 |
+
Attributes
|
184 |
+
----------
|
185 |
+
estimator_ : object
|
186 |
+
Best fitted model (copy of the `estimator` object).
|
187 |
+
|
188 |
+
n_trials_ : int
|
189 |
+
Number of random selection trials until one of the stop criteria is
|
190 |
+
met. It is always ``<= max_trials``.
|
191 |
+
|
192 |
+
inlier_mask_ : bool array of shape [n_samples]
|
193 |
+
Boolean mask of inliers classified as ``True``.
|
194 |
+
|
195 |
+
n_skips_no_inliers_ : int
|
196 |
+
Number of iterations skipped due to finding zero inliers.
|
197 |
+
|
198 |
+
.. versionadded:: 0.19
|
199 |
+
|
200 |
+
n_skips_invalid_data_ : int
|
201 |
+
Number of iterations skipped due to invalid data defined by
|
202 |
+
``is_data_valid``.
|
203 |
+
|
204 |
+
.. versionadded:: 0.19
|
205 |
+
|
206 |
+
n_skips_invalid_model_ : int
|
207 |
+
Number of iterations skipped due to an invalid model defined by
|
208 |
+
``is_model_valid``.
|
209 |
+
|
210 |
+
.. versionadded:: 0.19
|
211 |
+
|
212 |
+
n_features_in_ : int
|
213 |
+
Number of features seen during :term:`fit`.
|
214 |
+
|
215 |
+
.. versionadded:: 0.24
|
216 |
+
|
217 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
218 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
219 |
+
has feature names that are all strings.
|
220 |
+
|
221 |
+
.. versionadded:: 1.0
|
222 |
+
|
223 |
+
See Also
|
224 |
+
--------
|
225 |
+
HuberRegressor : Linear regression model that is robust to outliers.
|
226 |
+
TheilSenRegressor : Theil-Sen Estimator robust multivariate regression model.
|
227 |
+
SGDRegressor : Fitted by minimizing a regularized empirical loss with SGD.
|
228 |
+
|
229 |
+
References
|
230 |
+
----------
|
231 |
+
.. [1] https://en.wikipedia.org/wiki/RANSAC
|
232 |
+
.. [2] https://www.sri.com/wp-content/uploads/2021/12/ransac-publication.pdf
|
233 |
+
.. [3] http://www.bmva.org/bmvc/2009/Papers/Paper355/Paper355.pdf
|
234 |
+
|
235 |
+
Examples
|
236 |
+
--------
|
237 |
+
>>> from sklearn.linear_model import RANSACRegressor
|
238 |
+
>>> from sklearn.datasets import make_regression
|
239 |
+
>>> X, y = make_regression(
|
240 |
+
... n_samples=200, n_features=2, noise=4.0, random_state=0)
|
241 |
+
>>> reg = RANSACRegressor(random_state=0).fit(X, y)
|
242 |
+
>>> reg.score(X, y)
|
243 |
+
0.9885...
|
244 |
+
>>> reg.predict(X[:1,])
|
245 |
+
array([-31.9417...])
|
246 |
+
""" # noqa: E501
|
247 |
+
|
248 |
+
_parameter_constraints: dict = {
|
249 |
+
"estimator": [HasMethods(["fit", "score", "predict"]), None],
|
250 |
+
"min_samples": [
|
251 |
+
Interval(Integral, 1, None, closed="left"),
|
252 |
+
Interval(RealNotInt, 0, 1, closed="both"),
|
253 |
+
None,
|
254 |
+
],
|
255 |
+
"residual_threshold": [Interval(Real, 0, None, closed="left"), None],
|
256 |
+
"is_data_valid": [callable, None],
|
257 |
+
"is_model_valid": [callable, None],
|
258 |
+
"max_trials": [
|
259 |
+
Interval(Integral, 0, None, closed="left"),
|
260 |
+
Options(Real, {np.inf}),
|
261 |
+
],
|
262 |
+
"max_skips": [
|
263 |
+
Interval(Integral, 0, None, closed="left"),
|
264 |
+
Options(Real, {np.inf}),
|
265 |
+
],
|
266 |
+
"stop_n_inliers": [
|
267 |
+
Interval(Integral, 0, None, closed="left"),
|
268 |
+
Options(Real, {np.inf}),
|
269 |
+
],
|
270 |
+
"stop_score": [Interval(Real, None, None, closed="both")],
|
271 |
+
"stop_probability": [Interval(Real, 0, 1, closed="both")],
|
272 |
+
"loss": [StrOptions({"absolute_error", "squared_error"}), callable],
|
273 |
+
"random_state": ["random_state"],
|
274 |
+
}
|
275 |
+
|
276 |
+
def __init__(
|
277 |
+
self,
|
278 |
+
estimator=None,
|
279 |
+
*,
|
280 |
+
min_samples=None,
|
281 |
+
residual_threshold=None,
|
282 |
+
is_data_valid=None,
|
283 |
+
is_model_valid=None,
|
284 |
+
max_trials=100,
|
285 |
+
max_skips=np.inf,
|
286 |
+
stop_n_inliers=np.inf,
|
287 |
+
stop_score=np.inf,
|
288 |
+
stop_probability=0.99,
|
289 |
+
loss="absolute_error",
|
290 |
+
random_state=None,
|
291 |
+
):
|
292 |
+
self.estimator = estimator
|
293 |
+
self.min_samples = min_samples
|
294 |
+
self.residual_threshold = residual_threshold
|
295 |
+
self.is_data_valid = is_data_valid
|
296 |
+
self.is_model_valid = is_model_valid
|
297 |
+
self.max_trials = max_trials
|
298 |
+
self.max_skips = max_skips
|
299 |
+
self.stop_n_inliers = stop_n_inliers
|
300 |
+
self.stop_score = stop_score
|
301 |
+
self.stop_probability = stop_probability
|
302 |
+
self.random_state = random_state
|
303 |
+
self.loss = loss
|
304 |
+
|
305 |
+
@_fit_context(
|
306 |
+
# RansacRegressor.estimator is not validated yet
|
307 |
+
prefer_skip_nested_validation=False
|
308 |
+
)
|
309 |
+
def fit(self, X, y, sample_weight=None):
|
310 |
+
"""Fit estimator using RANSAC algorithm.
|
311 |
+
|
312 |
+
Parameters
|
313 |
+
----------
|
314 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
315 |
+
Training data.
|
316 |
+
|
317 |
+
y : array-like of shape (n_samples,) or (n_samples, n_targets)
|
318 |
+
Target values.
|
319 |
+
|
320 |
+
sample_weight : array-like of shape (n_samples,), default=None
|
321 |
+
Individual weights for each sample
|
322 |
+
raises error if sample_weight is passed and estimator
|
323 |
+
fit method does not support it.
|
324 |
+
|
325 |
+
.. versionadded:: 0.18
|
326 |
+
|
327 |
+
Returns
|
328 |
+
-------
|
329 |
+
self : object
|
330 |
+
Fitted `RANSACRegressor` estimator.
|
331 |
+
|
332 |
+
Raises
|
333 |
+
------
|
334 |
+
ValueError
|
335 |
+
If no valid consensus set could be found. This occurs if
|
336 |
+
`is_data_valid` and `is_model_valid` return False for all
|
337 |
+
`max_trials` randomly chosen sub-samples.
|
338 |
+
"""
|
339 |
+
_raise_for_unsupported_routing(self, "fit", sample_weight=sample_weight)
|
340 |
+
# Need to validate separately here. We can't pass multi_output=True
|
341 |
+
# because that would allow y to be csr. Delay expensive finiteness
|
342 |
+
# check to the estimator's own input validation.
|
343 |
+
check_X_params = dict(accept_sparse="csr", force_all_finite=False)
|
344 |
+
check_y_params = dict(ensure_2d=False)
|
345 |
+
X, y = self._validate_data(
|
346 |
+
X, y, validate_separately=(check_X_params, check_y_params)
|
347 |
+
)
|
348 |
+
check_consistent_length(X, y)
|
349 |
+
|
350 |
+
if self.estimator is not None:
|
351 |
+
estimator = clone(self.estimator)
|
352 |
+
else:
|
353 |
+
estimator = LinearRegression()
|
354 |
+
|
355 |
+
if self.min_samples is None:
|
356 |
+
if not isinstance(estimator, LinearRegression):
|
357 |
+
raise ValueError(
|
358 |
+
"`min_samples` needs to be explicitly set when estimator "
|
359 |
+
"is not a LinearRegression."
|
360 |
+
)
|
361 |
+
min_samples = X.shape[1] + 1
|
362 |
+
elif 0 < self.min_samples < 1:
|
363 |
+
min_samples = np.ceil(self.min_samples * X.shape[0])
|
364 |
+
elif self.min_samples >= 1:
|
365 |
+
min_samples = self.min_samples
|
366 |
+
if min_samples > X.shape[0]:
|
367 |
+
raise ValueError(
|
368 |
+
"`min_samples` may not be larger than number "
|
369 |
+
"of samples: n_samples = %d." % (X.shape[0])
|
370 |
+
)
|
371 |
+
|
372 |
+
if self.residual_threshold is None:
|
373 |
+
# MAD (median absolute deviation)
|
374 |
+
residual_threshold = np.median(np.abs(y - np.median(y)))
|
375 |
+
else:
|
376 |
+
residual_threshold = self.residual_threshold
|
377 |
+
|
378 |
+
if self.loss == "absolute_error":
|
379 |
+
if y.ndim == 1:
|
380 |
+
loss_function = lambda y_true, y_pred: np.abs(y_true - y_pred)
|
381 |
+
else:
|
382 |
+
loss_function = lambda y_true, y_pred: np.sum(
|
383 |
+
np.abs(y_true - y_pred), axis=1
|
384 |
+
)
|
385 |
+
elif self.loss == "squared_error":
|
386 |
+
if y.ndim == 1:
|
387 |
+
loss_function = lambda y_true, y_pred: (y_true - y_pred) ** 2
|
388 |
+
else:
|
389 |
+
loss_function = lambda y_true, y_pred: np.sum(
|
390 |
+
(y_true - y_pred) ** 2, axis=1
|
391 |
+
)
|
392 |
+
|
393 |
+
elif callable(self.loss):
|
394 |
+
loss_function = self.loss
|
395 |
+
|
396 |
+
random_state = check_random_state(self.random_state)
|
397 |
+
|
398 |
+
try: # Not all estimator accept a random_state
|
399 |
+
estimator.set_params(random_state=random_state)
|
400 |
+
except ValueError:
|
401 |
+
pass
|
402 |
+
|
403 |
+
estimator_fit_has_sample_weight = has_fit_parameter(estimator, "sample_weight")
|
404 |
+
estimator_name = type(estimator).__name__
|
405 |
+
if sample_weight is not None and not estimator_fit_has_sample_weight:
|
406 |
+
raise ValueError(
|
407 |
+
"%s does not support sample_weight. Samples"
|
408 |
+
" weights are only used for the calibration"
|
409 |
+
" itself." % estimator_name
|
410 |
+
)
|
411 |
+
if sample_weight is not None:
|
412 |
+
sample_weight = _check_sample_weight(sample_weight, X)
|
413 |
+
|
414 |
+
n_inliers_best = 1
|
415 |
+
score_best = -np.inf
|
416 |
+
inlier_mask_best = None
|
417 |
+
X_inlier_best = None
|
418 |
+
y_inlier_best = None
|
419 |
+
inlier_best_idxs_subset = None
|
420 |
+
self.n_skips_no_inliers_ = 0
|
421 |
+
self.n_skips_invalid_data_ = 0
|
422 |
+
self.n_skips_invalid_model_ = 0
|
423 |
+
|
424 |
+
# number of data samples
|
425 |
+
n_samples = X.shape[0]
|
426 |
+
sample_idxs = np.arange(n_samples)
|
427 |
+
|
428 |
+
self.n_trials_ = 0
|
429 |
+
max_trials = self.max_trials
|
430 |
+
while self.n_trials_ < max_trials:
|
431 |
+
self.n_trials_ += 1
|
432 |
+
|
433 |
+
if (
|
434 |
+
self.n_skips_no_inliers_
|
435 |
+
+ self.n_skips_invalid_data_
|
436 |
+
+ self.n_skips_invalid_model_
|
437 |
+
) > self.max_skips:
|
438 |
+
break
|
439 |
+
|
440 |
+
# choose random sample set
|
441 |
+
subset_idxs = sample_without_replacement(
|
442 |
+
n_samples, min_samples, random_state=random_state
|
443 |
+
)
|
444 |
+
X_subset = X[subset_idxs]
|
445 |
+
y_subset = y[subset_idxs]
|
446 |
+
|
447 |
+
# check if random sample set is valid
|
448 |
+
if self.is_data_valid is not None and not self.is_data_valid(
|
449 |
+
X_subset, y_subset
|
450 |
+
):
|
451 |
+
self.n_skips_invalid_data_ += 1
|
452 |
+
continue
|
453 |
+
|
454 |
+
# fit model for current random sample set
|
455 |
+
if sample_weight is None:
|
456 |
+
estimator.fit(X_subset, y_subset)
|
457 |
+
else:
|
458 |
+
estimator.fit(
|
459 |
+
X_subset, y_subset, sample_weight=sample_weight[subset_idxs]
|
460 |
+
)
|
461 |
+
|
462 |
+
# check if estimated model is valid
|
463 |
+
if self.is_model_valid is not None and not self.is_model_valid(
|
464 |
+
estimator, X_subset, y_subset
|
465 |
+
):
|
466 |
+
self.n_skips_invalid_model_ += 1
|
467 |
+
continue
|
468 |
+
|
469 |
+
# residuals of all data for current random sample model
|
470 |
+
y_pred = estimator.predict(X)
|
471 |
+
residuals_subset = loss_function(y, y_pred)
|
472 |
+
|
473 |
+
# classify data into inliers and outliers
|
474 |
+
inlier_mask_subset = residuals_subset <= residual_threshold
|
475 |
+
n_inliers_subset = np.sum(inlier_mask_subset)
|
476 |
+
|
477 |
+
# less inliers -> skip current random sample
|
478 |
+
if n_inliers_subset < n_inliers_best:
|
479 |
+
self.n_skips_no_inliers_ += 1
|
480 |
+
continue
|
481 |
+
|
482 |
+
# extract inlier data set
|
483 |
+
inlier_idxs_subset = sample_idxs[inlier_mask_subset]
|
484 |
+
X_inlier_subset = X[inlier_idxs_subset]
|
485 |
+
y_inlier_subset = y[inlier_idxs_subset]
|
486 |
+
|
487 |
+
# score of inlier data set
|
488 |
+
score_subset = estimator.score(X_inlier_subset, y_inlier_subset)
|
489 |
+
|
490 |
+
# same number of inliers but worse score -> skip current random
|
491 |
+
# sample
|
492 |
+
if n_inliers_subset == n_inliers_best and score_subset < score_best:
|
493 |
+
continue
|
494 |
+
|
495 |
+
# save current random sample as best sample
|
496 |
+
n_inliers_best = n_inliers_subset
|
497 |
+
score_best = score_subset
|
498 |
+
inlier_mask_best = inlier_mask_subset
|
499 |
+
X_inlier_best = X_inlier_subset
|
500 |
+
y_inlier_best = y_inlier_subset
|
501 |
+
inlier_best_idxs_subset = inlier_idxs_subset
|
502 |
+
|
503 |
+
max_trials = min(
|
504 |
+
max_trials,
|
505 |
+
_dynamic_max_trials(
|
506 |
+
n_inliers_best, n_samples, min_samples, self.stop_probability
|
507 |
+
),
|
508 |
+
)
|
509 |
+
|
510 |
+
# break if sufficient number of inliers or score is reached
|
511 |
+
if n_inliers_best >= self.stop_n_inliers or score_best >= self.stop_score:
|
512 |
+
break
|
513 |
+
|
514 |
+
# if none of the iterations met the required criteria
|
515 |
+
if inlier_mask_best is None:
|
516 |
+
if (
|
517 |
+
self.n_skips_no_inliers_
|
518 |
+
+ self.n_skips_invalid_data_
|
519 |
+
+ self.n_skips_invalid_model_
|
520 |
+
) > self.max_skips:
|
521 |
+
raise ValueError(
|
522 |
+
"RANSAC skipped more iterations than `max_skips` without"
|
523 |
+
" finding a valid consensus set. Iterations were skipped"
|
524 |
+
" because each randomly chosen sub-sample failed the"
|
525 |
+
" passing criteria. See estimator attributes for"
|
526 |
+
" diagnostics (n_skips*)."
|
527 |
+
)
|
528 |
+
else:
|
529 |
+
raise ValueError(
|
530 |
+
"RANSAC could not find a valid consensus set. All"
|
531 |
+
" `max_trials` iterations were skipped because each"
|
532 |
+
" randomly chosen sub-sample failed the passing criteria."
|
533 |
+
" See estimator attributes for diagnostics (n_skips*)."
|
534 |
+
)
|
535 |
+
else:
|
536 |
+
if (
|
537 |
+
self.n_skips_no_inliers_
|
538 |
+
+ self.n_skips_invalid_data_
|
539 |
+
+ self.n_skips_invalid_model_
|
540 |
+
) > self.max_skips:
|
541 |
+
warnings.warn(
|
542 |
+
(
|
543 |
+
"RANSAC found a valid consensus set but exited"
|
544 |
+
" early due to skipping more iterations than"
|
545 |
+
" `max_skips`. See estimator attributes for"
|
546 |
+
" diagnostics (n_skips*)."
|
547 |
+
),
|
548 |
+
ConvergenceWarning,
|
549 |
+
)
|
550 |
+
|
551 |
+
# estimate final model using all inliers
|
552 |
+
if sample_weight is None:
|
553 |
+
estimator.fit(X_inlier_best, y_inlier_best)
|
554 |
+
else:
|
555 |
+
estimator.fit(
|
556 |
+
X_inlier_best,
|
557 |
+
y_inlier_best,
|
558 |
+
sample_weight=sample_weight[inlier_best_idxs_subset],
|
559 |
+
)
|
560 |
+
|
561 |
+
self.estimator_ = estimator
|
562 |
+
self.inlier_mask_ = inlier_mask_best
|
563 |
+
return self
|
564 |
+
|
565 |
+
def predict(self, X):
|
566 |
+
"""Predict using the estimated model.
|
567 |
+
|
568 |
+
This is a wrapper for `estimator_.predict(X)`.
|
569 |
+
|
570 |
+
Parameters
|
571 |
+
----------
|
572 |
+
X : {array-like or sparse matrix} of shape (n_samples, n_features)
|
573 |
+
Input data.
|
574 |
+
|
575 |
+
Returns
|
576 |
+
-------
|
577 |
+
y : array, shape = [n_samples] or [n_samples, n_targets]
|
578 |
+
Returns predicted values.
|
579 |
+
"""
|
580 |
+
check_is_fitted(self)
|
581 |
+
X = self._validate_data(
|
582 |
+
X,
|
583 |
+
force_all_finite=False,
|
584 |
+
accept_sparse=True,
|
585 |
+
reset=False,
|
586 |
+
)
|
587 |
+
return self.estimator_.predict(X)
|
588 |
+
|
589 |
+
def score(self, X, y):
|
590 |
+
"""Return the score of the prediction.
|
591 |
+
|
592 |
+
This is a wrapper for `estimator_.score(X, y)`.
|
593 |
+
|
594 |
+
Parameters
|
595 |
+
----------
|
596 |
+
X : (array-like or sparse matrix} of shape (n_samples, n_features)
|
597 |
+
Training data.
|
598 |
+
|
599 |
+
y : array-like of shape (n_samples,) or (n_samples, n_targets)
|
600 |
+
Target values.
|
601 |
+
|
602 |
+
Returns
|
603 |
+
-------
|
604 |
+
z : float
|
605 |
+
Score of the prediction.
|
606 |
+
"""
|
607 |
+
check_is_fitted(self)
|
608 |
+
X = self._validate_data(
|
609 |
+
X,
|
610 |
+
force_all_finite=False,
|
611 |
+
accept_sparse=True,
|
612 |
+
reset=False,
|
613 |
+
)
|
614 |
+
return self.estimator_.score(X, y)
|
615 |
+
|
616 |
+
def _more_tags(self):
|
617 |
+
return {
|
618 |
+
"_xfail_checks": {
|
619 |
+
"check_sample_weights_invariance": (
|
620 |
+
"zero sample_weight is not equivalent to removing samples"
|
621 |
+
),
|
622 |
+
}
|
623 |
+
}
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_ridge.py
ADDED
@@ -0,0 +1,2612 @@
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|
1 |
+
"""
|
2 |
+
Ridge regression
|
3 |
+
"""
|
4 |
+
|
5 |
+
# Author: Mathieu Blondel <[email protected]>
|
6 |
+
# Reuben Fletcher-Costin <[email protected]>
|
7 |
+
# Fabian Pedregosa <[email protected]>
|
8 |
+
# Michael Eickenberg <[email protected]>
|
9 |
+
# License: BSD 3 clause
|
10 |
+
|
11 |
+
|
12 |
+
import numbers
|
13 |
+
import warnings
|
14 |
+
from abc import ABCMeta, abstractmethod
|
15 |
+
from functools import partial
|
16 |
+
from numbers import Integral, Real
|
17 |
+
|
18 |
+
import numpy as np
|
19 |
+
from scipy import linalg, optimize, sparse
|
20 |
+
from scipy.sparse import linalg as sp_linalg
|
21 |
+
|
22 |
+
from ..base import MultiOutputMixin, RegressorMixin, _fit_context, is_classifier
|
23 |
+
from ..exceptions import ConvergenceWarning
|
24 |
+
from ..metrics import check_scoring, get_scorer_names
|
25 |
+
from ..model_selection import GridSearchCV
|
26 |
+
from ..preprocessing import LabelBinarizer
|
27 |
+
from ..utils import (
|
28 |
+
check_array,
|
29 |
+
check_consistent_length,
|
30 |
+
check_scalar,
|
31 |
+
column_or_1d,
|
32 |
+
compute_sample_weight,
|
33 |
+
)
|
34 |
+
from ..utils._param_validation import Interval, StrOptions, validate_params
|
35 |
+
from ..utils.extmath import row_norms, safe_sparse_dot
|
36 |
+
from ..utils.fixes import _sparse_linalg_cg
|
37 |
+
from ..utils.metadata_routing import (
|
38 |
+
_raise_for_unsupported_routing,
|
39 |
+
_RoutingNotSupportedMixin,
|
40 |
+
)
|
41 |
+
from ..utils.sparsefuncs import mean_variance_axis
|
42 |
+
from ..utils.validation import _check_sample_weight, check_is_fitted
|
43 |
+
from ._base import LinearClassifierMixin, LinearModel, _preprocess_data, _rescale_data
|
44 |
+
from ._sag import sag_solver
|
45 |
+
|
46 |
+
|
47 |
+
def _get_rescaled_operator(X, X_offset, sample_weight_sqrt):
|
48 |
+
"""Create LinearOperator for matrix products with implicit centering.
|
49 |
+
|
50 |
+
Matrix product `LinearOperator @ coef` returns `(X - X_offset) @ coef`.
|
51 |
+
"""
|
52 |
+
|
53 |
+
def matvec(b):
|
54 |
+
return X.dot(b) - sample_weight_sqrt * b.dot(X_offset)
|
55 |
+
|
56 |
+
def rmatvec(b):
|
57 |
+
return X.T.dot(b) - X_offset * b.dot(sample_weight_sqrt)
|
58 |
+
|
59 |
+
X1 = sparse.linalg.LinearOperator(shape=X.shape, matvec=matvec, rmatvec=rmatvec)
|
60 |
+
return X1
|
61 |
+
|
62 |
+
|
63 |
+
def _solve_sparse_cg(
|
64 |
+
X,
|
65 |
+
y,
|
66 |
+
alpha,
|
67 |
+
max_iter=None,
|
68 |
+
tol=1e-4,
|
69 |
+
verbose=0,
|
70 |
+
X_offset=None,
|
71 |
+
X_scale=None,
|
72 |
+
sample_weight_sqrt=None,
|
73 |
+
):
|
74 |
+
if sample_weight_sqrt is None:
|
75 |
+
sample_weight_sqrt = np.ones(X.shape[0], dtype=X.dtype)
|
76 |
+
|
77 |
+
n_samples, n_features = X.shape
|
78 |
+
|
79 |
+
if X_offset is None or X_scale is None:
|
80 |
+
X1 = sp_linalg.aslinearoperator(X)
|
81 |
+
else:
|
82 |
+
X_offset_scale = X_offset / X_scale
|
83 |
+
X1 = _get_rescaled_operator(X, X_offset_scale, sample_weight_sqrt)
|
84 |
+
|
85 |
+
coefs = np.empty((y.shape[1], n_features), dtype=X.dtype)
|
86 |
+
|
87 |
+
if n_features > n_samples:
|
88 |
+
|
89 |
+
def create_mv(curr_alpha):
|
90 |
+
def _mv(x):
|
91 |
+
return X1.matvec(X1.rmatvec(x)) + curr_alpha * x
|
92 |
+
|
93 |
+
return _mv
|
94 |
+
|
95 |
+
else:
|
96 |
+
|
97 |
+
def create_mv(curr_alpha):
|
98 |
+
def _mv(x):
|
99 |
+
return X1.rmatvec(X1.matvec(x)) + curr_alpha * x
|
100 |
+
|
101 |
+
return _mv
|
102 |
+
|
103 |
+
for i in range(y.shape[1]):
|
104 |
+
y_column = y[:, i]
|
105 |
+
|
106 |
+
mv = create_mv(alpha[i])
|
107 |
+
if n_features > n_samples:
|
108 |
+
# kernel ridge
|
109 |
+
# w = X.T * inv(X X^t + alpha*Id) y
|
110 |
+
C = sp_linalg.LinearOperator(
|
111 |
+
(n_samples, n_samples), matvec=mv, dtype=X.dtype
|
112 |
+
)
|
113 |
+
coef, info = _sparse_linalg_cg(C, y_column, rtol=tol)
|
114 |
+
coefs[i] = X1.rmatvec(coef)
|
115 |
+
else:
|
116 |
+
# linear ridge
|
117 |
+
# w = inv(X^t X + alpha*Id) * X.T y
|
118 |
+
y_column = X1.rmatvec(y_column)
|
119 |
+
C = sp_linalg.LinearOperator(
|
120 |
+
(n_features, n_features), matvec=mv, dtype=X.dtype
|
121 |
+
)
|
122 |
+
coefs[i], info = _sparse_linalg_cg(C, y_column, maxiter=max_iter, rtol=tol)
|
123 |
+
|
124 |
+
if info < 0:
|
125 |
+
raise ValueError("Failed with error code %d" % info)
|
126 |
+
|
127 |
+
if max_iter is None and info > 0 and verbose:
|
128 |
+
warnings.warn(
|
129 |
+
"sparse_cg did not converge after %d iterations." % info,
|
130 |
+
ConvergenceWarning,
|
131 |
+
)
|
132 |
+
|
133 |
+
return coefs
|
134 |
+
|
135 |
+
|
136 |
+
def _solve_lsqr(
|
137 |
+
X,
|
138 |
+
y,
|
139 |
+
*,
|
140 |
+
alpha,
|
141 |
+
fit_intercept=True,
|
142 |
+
max_iter=None,
|
143 |
+
tol=1e-4,
|
144 |
+
X_offset=None,
|
145 |
+
X_scale=None,
|
146 |
+
sample_weight_sqrt=None,
|
147 |
+
):
|
148 |
+
"""Solve Ridge regression via LSQR.
|
149 |
+
|
150 |
+
We expect that y is always mean centered.
|
151 |
+
If X is dense, we expect it to be mean centered such that we can solve
|
152 |
+
||y - Xw||_2^2 + alpha * ||w||_2^2
|
153 |
+
|
154 |
+
If X is sparse, we expect X_offset to be given such that we can solve
|
155 |
+
||y - (X - X_offset)w||_2^2 + alpha * ||w||_2^2
|
156 |
+
|
157 |
+
With sample weights S=diag(sample_weight), this becomes
|
158 |
+
||sqrt(S) (y - (X - X_offset) w)||_2^2 + alpha * ||w||_2^2
|
159 |
+
and we expect y and X to already be rescaled, i.e. sqrt(S) @ y, sqrt(S) @ X. In
|
160 |
+
this case, X_offset is the sample_weight weighted mean of X before scaling by
|
161 |
+
sqrt(S). The objective then reads
|
162 |
+
||y - (X - sqrt(S) X_offset) w)||_2^2 + alpha * ||w||_2^2
|
163 |
+
"""
|
164 |
+
if sample_weight_sqrt is None:
|
165 |
+
sample_weight_sqrt = np.ones(X.shape[0], dtype=X.dtype)
|
166 |
+
|
167 |
+
if sparse.issparse(X) and fit_intercept:
|
168 |
+
X_offset_scale = X_offset / X_scale
|
169 |
+
X1 = _get_rescaled_operator(X, X_offset_scale, sample_weight_sqrt)
|
170 |
+
else:
|
171 |
+
# No need to touch anything
|
172 |
+
X1 = X
|
173 |
+
|
174 |
+
n_samples, n_features = X.shape
|
175 |
+
coefs = np.empty((y.shape[1], n_features), dtype=X.dtype)
|
176 |
+
n_iter = np.empty(y.shape[1], dtype=np.int32)
|
177 |
+
|
178 |
+
# According to the lsqr documentation, alpha = damp^2.
|
179 |
+
sqrt_alpha = np.sqrt(alpha)
|
180 |
+
|
181 |
+
for i in range(y.shape[1]):
|
182 |
+
y_column = y[:, i]
|
183 |
+
info = sp_linalg.lsqr(
|
184 |
+
X1, y_column, damp=sqrt_alpha[i], atol=tol, btol=tol, iter_lim=max_iter
|
185 |
+
)
|
186 |
+
coefs[i] = info[0]
|
187 |
+
n_iter[i] = info[2]
|
188 |
+
|
189 |
+
return coefs, n_iter
|
190 |
+
|
191 |
+
|
192 |
+
def _solve_cholesky(X, y, alpha):
|
193 |
+
# w = inv(X^t X + alpha*Id) * X.T y
|
194 |
+
n_features = X.shape[1]
|
195 |
+
n_targets = y.shape[1]
|
196 |
+
|
197 |
+
A = safe_sparse_dot(X.T, X, dense_output=True)
|
198 |
+
Xy = safe_sparse_dot(X.T, y, dense_output=True)
|
199 |
+
|
200 |
+
one_alpha = np.array_equal(alpha, len(alpha) * [alpha[0]])
|
201 |
+
|
202 |
+
if one_alpha:
|
203 |
+
A.flat[:: n_features + 1] += alpha[0]
|
204 |
+
return linalg.solve(A, Xy, assume_a="pos", overwrite_a=True).T
|
205 |
+
else:
|
206 |
+
coefs = np.empty([n_targets, n_features], dtype=X.dtype)
|
207 |
+
for coef, target, current_alpha in zip(coefs, Xy.T, alpha):
|
208 |
+
A.flat[:: n_features + 1] += current_alpha
|
209 |
+
coef[:] = linalg.solve(A, target, assume_a="pos", overwrite_a=False).ravel()
|
210 |
+
A.flat[:: n_features + 1] -= current_alpha
|
211 |
+
return coefs
|
212 |
+
|
213 |
+
|
214 |
+
def _solve_cholesky_kernel(K, y, alpha, sample_weight=None, copy=False):
|
215 |
+
# dual_coef = inv(X X^t + alpha*Id) y
|
216 |
+
n_samples = K.shape[0]
|
217 |
+
n_targets = y.shape[1]
|
218 |
+
|
219 |
+
if copy:
|
220 |
+
K = K.copy()
|
221 |
+
|
222 |
+
alpha = np.atleast_1d(alpha)
|
223 |
+
one_alpha = (alpha == alpha[0]).all()
|
224 |
+
has_sw = isinstance(sample_weight, np.ndarray) or sample_weight not in [1.0, None]
|
225 |
+
|
226 |
+
if has_sw:
|
227 |
+
# Unlike other solvers, we need to support sample_weight directly
|
228 |
+
# because K might be a pre-computed kernel.
|
229 |
+
sw = np.sqrt(np.atleast_1d(sample_weight))
|
230 |
+
y = y * sw[:, np.newaxis]
|
231 |
+
K *= np.outer(sw, sw)
|
232 |
+
|
233 |
+
if one_alpha:
|
234 |
+
# Only one penalty, we can solve multi-target problems in one time.
|
235 |
+
K.flat[:: n_samples + 1] += alpha[0]
|
236 |
+
|
237 |
+
try:
|
238 |
+
# Note: we must use overwrite_a=False in order to be able to
|
239 |
+
# use the fall-back solution below in case a LinAlgError
|
240 |
+
# is raised
|
241 |
+
dual_coef = linalg.solve(K, y, assume_a="pos", overwrite_a=False)
|
242 |
+
except np.linalg.LinAlgError:
|
243 |
+
warnings.warn(
|
244 |
+
"Singular matrix in solving dual problem. Using "
|
245 |
+
"least-squares solution instead."
|
246 |
+
)
|
247 |
+
dual_coef = linalg.lstsq(K, y)[0]
|
248 |
+
|
249 |
+
# K is expensive to compute and store in memory so change it back in
|
250 |
+
# case it was user-given.
|
251 |
+
K.flat[:: n_samples + 1] -= alpha[0]
|
252 |
+
|
253 |
+
if has_sw:
|
254 |
+
dual_coef *= sw[:, np.newaxis]
|
255 |
+
|
256 |
+
return dual_coef
|
257 |
+
else:
|
258 |
+
# One penalty per target. We need to solve each target separately.
|
259 |
+
dual_coefs = np.empty([n_targets, n_samples], K.dtype)
|
260 |
+
|
261 |
+
for dual_coef, target, current_alpha in zip(dual_coefs, y.T, alpha):
|
262 |
+
K.flat[:: n_samples + 1] += current_alpha
|
263 |
+
|
264 |
+
dual_coef[:] = linalg.solve(
|
265 |
+
K, target, assume_a="pos", overwrite_a=False
|
266 |
+
).ravel()
|
267 |
+
|
268 |
+
K.flat[:: n_samples + 1] -= current_alpha
|
269 |
+
|
270 |
+
if has_sw:
|
271 |
+
dual_coefs *= sw[np.newaxis, :]
|
272 |
+
|
273 |
+
return dual_coefs.T
|
274 |
+
|
275 |
+
|
276 |
+
def _solve_svd(X, y, alpha):
|
277 |
+
U, s, Vt = linalg.svd(X, full_matrices=False)
|
278 |
+
idx = s > 1e-15 # same default value as scipy.linalg.pinv
|
279 |
+
s_nnz = s[idx][:, np.newaxis]
|
280 |
+
UTy = np.dot(U.T, y)
|
281 |
+
d = np.zeros((s.size, alpha.size), dtype=X.dtype)
|
282 |
+
d[idx] = s_nnz / (s_nnz**2 + alpha)
|
283 |
+
d_UT_y = d * UTy
|
284 |
+
return np.dot(Vt.T, d_UT_y).T
|
285 |
+
|
286 |
+
|
287 |
+
def _solve_lbfgs(
|
288 |
+
X,
|
289 |
+
y,
|
290 |
+
alpha,
|
291 |
+
positive=True,
|
292 |
+
max_iter=None,
|
293 |
+
tol=1e-4,
|
294 |
+
X_offset=None,
|
295 |
+
X_scale=None,
|
296 |
+
sample_weight_sqrt=None,
|
297 |
+
):
|
298 |
+
"""Solve ridge regression with LBFGS.
|
299 |
+
|
300 |
+
The main purpose is fitting with forcing coefficients to be positive.
|
301 |
+
For unconstrained ridge regression, there are faster dedicated solver methods.
|
302 |
+
Note that with positive bounds on the coefficients, LBFGS seems faster
|
303 |
+
than scipy.optimize.lsq_linear.
|
304 |
+
"""
|
305 |
+
n_samples, n_features = X.shape
|
306 |
+
|
307 |
+
options = {}
|
308 |
+
if max_iter is not None:
|
309 |
+
options["maxiter"] = max_iter
|
310 |
+
config = {
|
311 |
+
"method": "L-BFGS-B",
|
312 |
+
"tol": tol,
|
313 |
+
"jac": True,
|
314 |
+
"options": options,
|
315 |
+
}
|
316 |
+
if positive:
|
317 |
+
config["bounds"] = [(0, np.inf)] * n_features
|
318 |
+
|
319 |
+
if X_offset is not None and X_scale is not None:
|
320 |
+
X_offset_scale = X_offset / X_scale
|
321 |
+
else:
|
322 |
+
X_offset_scale = None
|
323 |
+
|
324 |
+
if sample_weight_sqrt is None:
|
325 |
+
sample_weight_sqrt = np.ones(X.shape[0], dtype=X.dtype)
|
326 |
+
|
327 |
+
coefs = np.empty((y.shape[1], n_features), dtype=X.dtype)
|
328 |
+
|
329 |
+
for i in range(y.shape[1]):
|
330 |
+
x0 = np.zeros((n_features,))
|
331 |
+
y_column = y[:, i]
|
332 |
+
|
333 |
+
def func(w):
|
334 |
+
residual = X.dot(w) - y_column
|
335 |
+
if X_offset_scale is not None:
|
336 |
+
residual -= sample_weight_sqrt * w.dot(X_offset_scale)
|
337 |
+
f = 0.5 * residual.dot(residual) + 0.5 * alpha[i] * w.dot(w)
|
338 |
+
grad = X.T @ residual + alpha[i] * w
|
339 |
+
if X_offset_scale is not None:
|
340 |
+
grad -= X_offset_scale * residual.dot(sample_weight_sqrt)
|
341 |
+
|
342 |
+
return f, grad
|
343 |
+
|
344 |
+
result = optimize.minimize(func, x0, **config)
|
345 |
+
if not result["success"]:
|
346 |
+
warnings.warn(
|
347 |
+
(
|
348 |
+
"The lbfgs solver did not converge. Try increasing max_iter "
|
349 |
+
f"or tol. Currently: max_iter={max_iter} and tol={tol}"
|
350 |
+
),
|
351 |
+
ConvergenceWarning,
|
352 |
+
)
|
353 |
+
coefs[i] = result["x"]
|
354 |
+
|
355 |
+
return coefs
|
356 |
+
|
357 |
+
|
358 |
+
def _get_valid_accept_sparse(is_X_sparse, solver):
|
359 |
+
if is_X_sparse and solver in ["auto", "sag", "saga"]:
|
360 |
+
return "csr"
|
361 |
+
else:
|
362 |
+
return ["csr", "csc", "coo"]
|
363 |
+
|
364 |
+
|
365 |
+
@validate_params(
|
366 |
+
{
|
367 |
+
"X": ["array-like", "sparse matrix", sp_linalg.LinearOperator],
|
368 |
+
"y": ["array-like"],
|
369 |
+
"alpha": [Interval(Real, 0, None, closed="left"), "array-like"],
|
370 |
+
"sample_weight": [
|
371 |
+
Interval(Real, None, None, closed="neither"),
|
372 |
+
"array-like",
|
373 |
+
None,
|
374 |
+
],
|
375 |
+
"solver": [
|
376 |
+
StrOptions(
|
377 |
+
{"auto", "svd", "cholesky", "lsqr", "sparse_cg", "sag", "saga", "lbfgs"}
|
378 |
+
)
|
379 |
+
],
|
380 |
+
"max_iter": [Interval(Integral, 0, None, closed="left"), None],
|
381 |
+
"tol": [Interval(Real, 0, None, closed="left")],
|
382 |
+
"verbose": ["verbose"],
|
383 |
+
"positive": ["boolean"],
|
384 |
+
"random_state": ["random_state"],
|
385 |
+
"return_n_iter": ["boolean"],
|
386 |
+
"return_intercept": ["boolean"],
|
387 |
+
"check_input": ["boolean"],
|
388 |
+
},
|
389 |
+
prefer_skip_nested_validation=True,
|
390 |
+
)
|
391 |
+
def ridge_regression(
|
392 |
+
X,
|
393 |
+
y,
|
394 |
+
alpha,
|
395 |
+
*,
|
396 |
+
sample_weight=None,
|
397 |
+
solver="auto",
|
398 |
+
max_iter=None,
|
399 |
+
tol=1e-4,
|
400 |
+
verbose=0,
|
401 |
+
positive=False,
|
402 |
+
random_state=None,
|
403 |
+
return_n_iter=False,
|
404 |
+
return_intercept=False,
|
405 |
+
check_input=True,
|
406 |
+
):
|
407 |
+
"""Solve the ridge equation by the method of normal equations.
|
408 |
+
|
409 |
+
Read more in the :ref:`User Guide <ridge_regression>`.
|
410 |
+
|
411 |
+
Parameters
|
412 |
+
----------
|
413 |
+
X : {array-like, sparse matrix, LinearOperator} of shape \
|
414 |
+
(n_samples, n_features)
|
415 |
+
Training data.
|
416 |
+
|
417 |
+
y : array-like of shape (n_samples,) or (n_samples, n_targets)
|
418 |
+
Target values.
|
419 |
+
|
420 |
+
alpha : float or array-like of shape (n_targets,)
|
421 |
+
Constant that multiplies the L2 term, controlling regularization
|
422 |
+
strength. `alpha` must be a non-negative float i.e. in `[0, inf)`.
|
423 |
+
|
424 |
+
When `alpha = 0`, the objective is equivalent to ordinary least
|
425 |
+
squares, solved by the :class:`LinearRegression` object. For numerical
|
426 |
+
reasons, using `alpha = 0` with the `Ridge` object is not advised.
|
427 |
+
Instead, you should use the :class:`LinearRegression` object.
|
428 |
+
|
429 |
+
If an array is passed, penalties are assumed to be specific to the
|
430 |
+
targets. Hence they must correspond in number.
|
431 |
+
|
432 |
+
sample_weight : float or array-like of shape (n_samples,), default=None
|
433 |
+
Individual weights for each sample. If given a float, every sample
|
434 |
+
will have the same weight. If sample_weight is not None and
|
435 |
+
solver='auto', the solver will be set to 'cholesky'.
|
436 |
+
|
437 |
+
.. versionadded:: 0.17
|
438 |
+
|
439 |
+
solver : {'auto', 'svd', 'cholesky', 'lsqr', 'sparse_cg', \
|
440 |
+
'sag', 'saga', 'lbfgs'}, default='auto'
|
441 |
+
Solver to use in the computational routines:
|
442 |
+
|
443 |
+
- 'auto' chooses the solver automatically based on the type of data.
|
444 |
+
|
445 |
+
- 'svd' uses a Singular Value Decomposition of X to compute the Ridge
|
446 |
+
coefficients. It is the most stable solver, in particular more stable
|
447 |
+
for singular matrices than 'cholesky' at the cost of being slower.
|
448 |
+
|
449 |
+
- 'cholesky' uses the standard scipy.linalg.solve function to
|
450 |
+
obtain a closed-form solution via a Cholesky decomposition of
|
451 |
+
dot(X.T, X)
|
452 |
+
|
453 |
+
- 'sparse_cg' uses the conjugate gradient solver as found in
|
454 |
+
scipy.sparse.linalg.cg. As an iterative algorithm, this solver is
|
455 |
+
more appropriate than 'cholesky' for large-scale data
|
456 |
+
(possibility to set `tol` and `max_iter`).
|
457 |
+
|
458 |
+
- 'lsqr' uses the dedicated regularized least-squares routine
|
459 |
+
scipy.sparse.linalg.lsqr. It is the fastest and uses an iterative
|
460 |
+
procedure.
|
461 |
+
|
462 |
+
- 'sag' uses a Stochastic Average Gradient descent, and 'saga' uses
|
463 |
+
its improved, unbiased version named SAGA. Both methods also use an
|
464 |
+
iterative procedure, and are often faster than other solvers when
|
465 |
+
both n_samples and n_features are large. Note that 'sag' and
|
466 |
+
'saga' fast convergence is only guaranteed on features with
|
467 |
+
approximately the same scale. You can preprocess the data with a
|
468 |
+
scaler from sklearn.preprocessing.
|
469 |
+
|
470 |
+
- 'lbfgs' uses L-BFGS-B algorithm implemented in
|
471 |
+
`scipy.optimize.minimize`. It can be used only when `positive`
|
472 |
+
is True.
|
473 |
+
|
474 |
+
All solvers except 'svd' support both dense and sparse data. However, only
|
475 |
+
'lsqr', 'sag', 'sparse_cg', and 'lbfgs' support sparse input when
|
476 |
+
`fit_intercept` is True.
|
477 |
+
|
478 |
+
.. versionadded:: 0.17
|
479 |
+
Stochastic Average Gradient descent solver.
|
480 |
+
.. versionadded:: 0.19
|
481 |
+
SAGA solver.
|
482 |
+
|
483 |
+
max_iter : int, default=None
|
484 |
+
Maximum number of iterations for conjugate gradient solver.
|
485 |
+
For the 'sparse_cg' and 'lsqr' solvers, the default value is determined
|
486 |
+
by scipy.sparse.linalg. For 'sag' and saga solver, the default value is
|
487 |
+
1000. For 'lbfgs' solver, the default value is 15000.
|
488 |
+
|
489 |
+
tol : float, default=1e-4
|
490 |
+
Precision of the solution. Note that `tol` has no effect for solvers 'svd' and
|
491 |
+
'cholesky'.
|
492 |
+
|
493 |
+
.. versionchanged:: 1.2
|
494 |
+
Default value changed from 1e-3 to 1e-4 for consistency with other linear
|
495 |
+
models.
|
496 |
+
|
497 |
+
verbose : int, default=0
|
498 |
+
Verbosity level. Setting verbose > 0 will display additional
|
499 |
+
information depending on the solver used.
|
500 |
+
|
501 |
+
positive : bool, default=False
|
502 |
+
When set to ``True``, forces the coefficients to be positive.
|
503 |
+
Only 'lbfgs' solver is supported in this case.
|
504 |
+
|
505 |
+
random_state : int, RandomState instance, default=None
|
506 |
+
Used when ``solver`` == 'sag' or 'saga' to shuffle the data.
|
507 |
+
See :term:`Glossary <random_state>` for details.
|
508 |
+
|
509 |
+
return_n_iter : bool, default=False
|
510 |
+
If True, the method also returns `n_iter`, the actual number of
|
511 |
+
iteration performed by the solver.
|
512 |
+
|
513 |
+
.. versionadded:: 0.17
|
514 |
+
|
515 |
+
return_intercept : bool, default=False
|
516 |
+
If True and if X is sparse, the method also returns the intercept,
|
517 |
+
and the solver is automatically changed to 'sag'. This is only a
|
518 |
+
temporary fix for fitting the intercept with sparse data. For dense
|
519 |
+
data, use sklearn.linear_model._preprocess_data before your regression.
|
520 |
+
|
521 |
+
.. versionadded:: 0.17
|
522 |
+
|
523 |
+
check_input : bool, default=True
|
524 |
+
If False, the input arrays X and y will not be checked.
|
525 |
+
|
526 |
+
.. versionadded:: 0.21
|
527 |
+
|
528 |
+
Returns
|
529 |
+
-------
|
530 |
+
coef : ndarray of shape (n_features,) or (n_targets, n_features)
|
531 |
+
Weight vector(s).
|
532 |
+
|
533 |
+
n_iter : int, optional
|
534 |
+
The actual number of iteration performed by the solver.
|
535 |
+
Only returned if `return_n_iter` is True.
|
536 |
+
|
537 |
+
intercept : float or ndarray of shape (n_targets,)
|
538 |
+
The intercept of the model. Only returned if `return_intercept`
|
539 |
+
is True and if X is a scipy sparse array.
|
540 |
+
|
541 |
+
Notes
|
542 |
+
-----
|
543 |
+
This function won't compute the intercept.
|
544 |
+
|
545 |
+
Regularization improves the conditioning of the problem and
|
546 |
+
reduces the variance of the estimates. Larger values specify stronger
|
547 |
+
regularization. Alpha corresponds to ``1 / (2C)`` in other linear
|
548 |
+
models such as :class:`~sklearn.linear_model.LogisticRegression` or
|
549 |
+
:class:`~sklearn.svm.LinearSVC`. If an array is passed, penalties are
|
550 |
+
assumed to be specific to the targets. Hence they must correspond in
|
551 |
+
number.
|
552 |
+
|
553 |
+
Examples
|
554 |
+
--------
|
555 |
+
>>> import numpy as np
|
556 |
+
>>> from sklearn.datasets import make_regression
|
557 |
+
>>> from sklearn.linear_model import ridge_regression
|
558 |
+
>>> rng = np.random.RandomState(0)
|
559 |
+
>>> X = rng.randn(100, 4)
|
560 |
+
>>> y = 2.0 * X[:, 0] - 1.0 * X[:, 1] + 0.1 * rng.standard_normal(100)
|
561 |
+
>>> coef, intercept = ridge_regression(X, y, alpha=1.0, return_intercept=True)
|
562 |
+
>>> list(coef)
|
563 |
+
[1.9..., -1.0..., -0.0..., -0.0...]
|
564 |
+
>>> intercept
|
565 |
+
-0.0...
|
566 |
+
"""
|
567 |
+
return _ridge_regression(
|
568 |
+
X,
|
569 |
+
y,
|
570 |
+
alpha,
|
571 |
+
sample_weight=sample_weight,
|
572 |
+
solver=solver,
|
573 |
+
max_iter=max_iter,
|
574 |
+
tol=tol,
|
575 |
+
verbose=verbose,
|
576 |
+
positive=positive,
|
577 |
+
random_state=random_state,
|
578 |
+
return_n_iter=return_n_iter,
|
579 |
+
return_intercept=return_intercept,
|
580 |
+
X_scale=None,
|
581 |
+
X_offset=None,
|
582 |
+
check_input=check_input,
|
583 |
+
)
|
584 |
+
|
585 |
+
|
586 |
+
def _ridge_regression(
|
587 |
+
X,
|
588 |
+
y,
|
589 |
+
alpha,
|
590 |
+
sample_weight=None,
|
591 |
+
solver="auto",
|
592 |
+
max_iter=None,
|
593 |
+
tol=1e-4,
|
594 |
+
verbose=0,
|
595 |
+
positive=False,
|
596 |
+
random_state=None,
|
597 |
+
return_n_iter=False,
|
598 |
+
return_intercept=False,
|
599 |
+
X_scale=None,
|
600 |
+
X_offset=None,
|
601 |
+
check_input=True,
|
602 |
+
fit_intercept=False,
|
603 |
+
):
|
604 |
+
has_sw = sample_weight is not None
|
605 |
+
|
606 |
+
if solver == "auto":
|
607 |
+
if positive:
|
608 |
+
solver = "lbfgs"
|
609 |
+
elif return_intercept:
|
610 |
+
# sag supports fitting intercept directly
|
611 |
+
solver = "sag"
|
612 |
+
elif not sparse.issparse(X):
|
613 |
+
solver = "cholesky"
|
614 |
+
else:
|
615 |
+
solver = "sparse_cg"
|
616 |
+
|
617 |
+
if solver not in ("sparse_cg", "cholesky", "svd", "lsqr", "sag", "saga", "lbfgs"):
|
618 |
+
raise ValueError(
|
619 |
+
"Known solvers are 'sparse_cg', 'cholesky', 'svd'"
|
620 |
+
" 'lsqr', 'sag', 'saga' or 'lbfgs'. Got %s." % solver
|
621 |
+
)
|
622 |
+
|
623 |
+
if positive and solver != "lbfgs":
|
624 |
+
raise ValueError(
|
625 |
+
"When positive=True, only 'lbfgs' solver can be used. "
|
626 |
+
f"Please change solver {solver} to 'lbfgs' "
|
627 |
+
"or set positive=False."
|
628 |
+
)
|
629 |
+
|
630 |
+
if solver == "lbfgs" and not positive:
|
631 |
+
raise ValueError(
|
632 |
+
"'lbfgs' solver can be used only when positive=True. "
|
633 |
+
"Please use another solver."
|
634 |
+
)
|
635 |
+
|
636 |
+
if return_intercept and solver != "sag":
|
637 |
+
raise ValueError(
|
638 |
+
"In Ridge, only 'sag' solver can directly fit the "
|
639 |
+
"intercept. Please change solver to 'sag' or set "
|
640 |
+
"return_intercept=False."
|
641 |
+
)
|
642 |
+
|
643 |
+
if check_input:
|
644 |
+
_dtype = [np.float64, np.float32]
|
645 |
+
_accept_sparse = _get_valid_accept_sparse(sparse.issparse(X), solver)
|
646 |
+
X = check_array(X, accept_sparse=_accept_sparse, dtype=_dtype, order="C")
|
647 |
+
y = check_array(y, dtype=X.dtype, ensure_2d=False, order=None)
|
648 |
+
check_consistent_length(X, y)
|
649 |
+
|
650 |
+
n_samples, n_features = X.shape
|
651 |
+
|
652 |
+
if y.ndim > 2:
|
653 |
+
raise ValueError("Target y has the wrong shape %s" % str(y.shape))
|
654 |
+
|
655 |
+
ravel = False
|
656 |
+
if y.ndim == 1:
|
657 |
+
y = y.reshape(-1, 1)
|
658 |
+
ravel = True
|
659 |
+
|
660 |
+
n_samples_, n_targets = y.shape
|
661 |
+
|
662 |
+
if n_samples != n_samples_:
|
663 |
+
raise ValueError(
|
664 |
+
"Number of samples in X and y does not correspond: %d != %d"
|
665 |
+
% (n_samples, n_samples_)
|
666 |
+
)
|
667 |
+
|
668 |
+
if has_sw:
|
669 |
+
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
|
670 |
+
|
671 |
+
if solver not in ["sag", "saga"]:
|
672 |
+
# SAG supports sample_weight directly. For other solvers,
|
673 |
+
# we implement sample_weight via a simple rescaling.
|
674 |
+
X, y, sample_weight_sqrt = _rescale_data(X, y, sample_weight)
|
675 |
+
|
676 |
+
# Some callers of this method might pass alpha as single
|
677 |
+
# element array which already has been validated.
|
678 |
+
if alpha is not None and not isinstance(alpha, np.ndarray):
|
679 |
+
alpha = check_scalar(
|
680 |
+
alpha,
|
681 |
+
"alpha",
|
682 |
+
target_type=numbers.Real,
|
683 |
+
min_val=0.0,
|
684 |
+
include_boundaries="left",
|
685 |
+
)
|
686 |
+
|
687 |
+
# There should be either 1 or n_targets penalties
|
688 |
+
alpha = np.asarray(alpha, dtype=X.dtype).ravel()
|
689 |
+
if alpha.size not in [1, n_targets]:
|
690 |
+
raise ValueError(
|
691 |
+
"Number of targets and number of penalties do not correspond: %d != %d"
|
692 |
+
% (alpha.size, n_targets)
|
693 |
+
)
|
694 |
+
|
695 |
+
if alpha.size == 1 and n_targets > 1:
|
696 |
+
alpha = np.repeat(alpha, n_targets)
|
697 |
+
|
698 |
+
n_iter = None
|
699 |
+
if solver == "sparse_cg":
|
700 |
+
coef = _solve_sparse_cg(
|
701 |
+
X,
|
702 |
+
y,
|
703 |
+
alpha,
|
704 |
+
max_iter=max_iter,
|
705 |
+
tol=tol,
|
706 |
+
verbose=verbose,
|
707 |
+
X_offset=X_offset,
|
708 |
+
X_scale=X_scale,
|
709 |
+
sample_weight_sqrt=sample_weight_sqrt if has_sw else None,
|
710 |
+
)
|
711 |
+
|
712 |
+
elif solver == "lsqr":
|
713 |
+
coef, n_iter = _solve_lsqr(
|
714 |
+
X,
|
715 |
+
y,
|
716 |
+
alpha=alpha,
|
717 |
+
fit_intercept=fit_intercept,
|
718 |
+
max_iter=max_iter,
|
719 |
+
tol=tol,
|
720 |
+
X_offset=X_offset,
|
721 |
+
X_scale=X_scale,
|
722 |
+
sample_weight_sqrt=sample_weight_sqrt if has_sw else None,
|
723 |
+
)
|
724 |
+
|
725 |
+
elif solver == "cholesky":
|
726 |
+
if n_features > n_samples:
|
727 |
+
K = safe_sparse_dot(X, X.T, dense_output=True)
|
728 |
+
try:
|
729 |
+
dual_coef = _solve_cholesky_kernel(K, y, alpha)
|
730 |
+
|
731 |
+
coef = safe_sparse_dot(X.T, dual_coef, dense_output=True).T
|
732 |
+
except linalg.LinAlgError:
|
733 |
+
# use SVD solver if matrix is singular
|
734 |
+
solver = "svd"
|
735 |
+
else:
|
736 |
+
try:
|
737 |
+
coef = _solve_cholesky(X, y, alpha)
|
738 |
+
except linalg.LinAlgError:
|
739 |
+
# use SVD solver if matrix is singular
|
740 |
+
solver = "svd"
|
741 |
+
|
742 |
+
elif solver in ["sag", "saga"]:
|
743 |
+
# precompute max_squared_sum for all targets
|
744 |
+
max_squared_sum = row_norms(X, squared=True).max()
|
745 |
+
|
746 |
+
coef = np.empty((y.shape[1], n_features), dtype=X.dtype)
|
747 |
+
n_iter = np.empty(y.shape[1], dtype=np.int32)
|
748 |
+
intercept = np.zeros((y.shape[1],), dtype=X.dtype)
|
749 |
+
for i, (alpha_i, target) in enumerate(zip(alpha, y.T)):
|
750 |
+
init = {
|
751 |
+
"coef": np.zeros((n_features + int(return_intercept), 1), dtype=X.dtype)
|
752 |
+
}
|
753 |
+
coef_, n_iter_, _ = sag_solver(
|
754 |
+
X,
|
755 |
+
target.ravel(),
|
756 |
+
sample_weight,
|
757 |
+
"squared",
|
758 |
+
alpha_i,
|
759 |
+
0,
|
760 |
+
max_iter,
|
761 |
+
tol,
|
762 |
+
verbose,
|
763 |
+
random_state,
|
764 |
+
False,
|
765 |
+
max_squared_sum,
|
766 |
+
init,
|
767 |
+
is_saga=solver == "saga",
|
768 |
+
)
|
769 |
+
if return_intercept:
|
770 |
+
coef[i] = coef_[:-1]
|
771 |
+
intercept[i] = coef_[-1]
|
772 |
+
else:
|
773 |
+
coef[i] = coef_
|
774 |
+
n_iter[i] = n_iter_
|
775 |
+
|
776 |
+
if intercept.shape[0] == 1:
|
777 |
+
intercept = intercept[0]
|
778 |
+
coef = np.asarray(coef)
|
779 |
+
|
780 |
+
elif solver == "lbfgs":
|
781 |
+
coef = _solve_lbfgs(
|
782 |
+
X,
|
783 |
+
y,
|
784 |
+
alpha,
|
785 |
+
positive=positive,
|
786 |
+
tol=tol,
|
787 |
+
max_iter=max_iter,
|
788 |
+
X_offset=X_offset,
|
789 |
+
X_scale=X_scale,
|
790 |
+
sample_weight_sqrt=sample_weight_sqrt if has_sw else None,
|
791 |
+
)
|
792 |
+
|
793 |
+
if solver == "svd":
|
794 |
+
if sparse.issparse(X):
|
795 |
+
raise TypeError("SVD solver does not support sparse inputs currently")
|
796 |
+
coef = _solve_svd(X, y, alpha)
|
797 |
+
|
798 |
+
if ravel:
|
799 |
+
# When y was passed as a 1d-array, we flatten the coefficients.
|
800 |
+
coef = coef.ravel()
|
801 |
+
|
802 |
+
if return_n_iter and return_intercept:
|
803 |
+
return coef, n_iter, intercept
|
804 |
+
elif return_intercept:
|
805 |
+
return coef, intercept
|
806 |
+
elif return_n_iter:
|
807 |
+
return coef, n_iter
|
808 |
+
else:
|
809 |
+
return coef
|
810 |
+
|
811 |
+
|
812 |
+
class _BaseRidge(LinearModel, metaclass=ABCMeta):
|
813 |
+
_parameter_constraints: dict = {
|
814 |
+
"alpha": [Interval(Real, 0, None, closed="left"), np.ndarray],
|
815 |
+
"fit_intercept": ["boolean"],
|
816 |
+
"copy_X": ["boolean"],
|
817 |
+
"max_iter": [Interval(Integral, 1, None, closed="left"), None],
|
818 |
+
"tol": [Interval(Real, 0, None, closed="left")],
|
819 |
+
"solver": [
|
820 |
+
StrOptions(
|
821 |
+
{"auto", "svd", "cholesky", "lsqr", "sparse_cg", "sag", "saga", "lbfgs"}
|
822 |
+
)
|
823 |
+
],
|
824 |
+
"positive": ["boolean"],
|
825 |
+
"random_state": ["random_state"],
|
826 |
+
}
|
827 |
+
|
828 |
+
@abstractmethod
|
829 |
+
def __init__(
|
830 |
+
self,
|
831 |
+
alpha=1.0,
|
832 |
+
*,
|
833 |
+
fit_intercept=True,
|
834 |
+
copy_X=True,
|
835 |
+
max_iter=None,
|
836 |
+
tol=1e-4,
|
837 |
+
solver="auto",
|
838 |
+
positive=False,
|
839 |
+
random_state=None,
|
840 |
+
):
|
841 |
+
self.alpha = alpha
|
842 |
+
self.fit_intercept = fit_intercept
|
843 |
+
self.copy_X = copy_X
|
844 |
+
self.max_iter = max_iter
|
845 |
+
self.tol = tol
|
846 |
+
self.solver = solver
|
847 |
+
self.positive = positive
|
848 |
+
self.random_state = random_state
|
849 |
+
|
850 |
+
def fit(self, X, y, sample_weight=None):
|
851 |
+
if self.solver == "lbfgs" and not self.positive:
|
852 |
+
raise ValueError(
|
853 |
+
"'lbfgs' solver can be used only when positive=True. "
|
854 |
+
"Please use another solver."
|
855 |
+
)
|
856 |
+
|
857 |
+
if self.positive:
|
858 |
+
if self.solver not in ["auto", "lbfgs"]:
|
859 |
+
raise ValueError(
|
860 |
+
f"solver='{self.solver}' does not support positive fitting. Please"
|
861 |
+
" set the solver to 'auto' or 'lbfgs', or set `positive=False`"
|
862 |
+
)
|
863 |
+
else:
|
864 |
+
solver = self.solver
|
865 |
+
elif sparse.issparse(X) and self.fit_intercept:
|
866 |
+
if self.solver not in ["auto", "lbfgs", "lsqr", "sag", "sparse_cg"]:
|
867 |
+
raise ValueError(
|
868 |
+
"solver='{}' does not support fitting the intercept "
|
869 |
+
"on sparse data. Please set the solver to 'auto' or "
|
870 |
+
"'lsqr', 'sparse_cg', 'sag', 'lbfgs' "
|
871 |
+
"or set `fit_intercept=False`".format(self.solver)
|
872 |
+
)
|
873 |
+
if self.solver in ["lsqr", "lbfgs"]:
|
874 |
+
solver = self.solver
|
875 |
+
elif self.solver == "sag" and self.max_iter is None and self.tol > 1e-4:
|
876 |
+
warnings.warn(
|
877 |
+
'"sag" solver requires many iterations to fit '
|
878 |
+
"an intercept with sparse inputs. Either set the "
|
879 |
+
'solver to "auto" or "sparse_cg", or set a low '
|
880 |
+
'"tol" and a high "max_iter" (especially if inputs are '
|
881 |
+
"not standardized)."
|
882 |
+
)
|
883 |
+
solver = "sag"
|
884 |
+
else:
|
885 |
+
solver = "sparse_cg"
|
886 |
+
else:
|
887 |
+
solver = self.solver
|
888 |
+
|
889 |
+
if sample_weight is not None:
|
890 |
+
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
|
891 |
+
|
892 |
+
# when X is sparse we only remove offset from y
|
893 |
+
X, y, X_offset, y_offset, X_scale = _preprocess_data(
|
894 |
+
X,
|
895 |
+
y,
|
896 |
+
fit_intercept=self.fit_intercept,
|
897 |
+
copy=self.copy_X,
|
898 |
+
sample_weight=sample_weight,
|
899 |
+
)
|
900 |
+
|
901 |
+
if solver == "sag" and sparse.issparse(X) and self.fit_intercept:
|
902 |
+
self.coef_, self.n_iter_, self.intercept_ = _ridge_regression(
|
903 |
+
X,
|
904 |
+
y,
|
905 |
+
alpha=self.alpha,
|
906 |
+
sample_weight=sample_weight,
|
907 |
+
max_iter=self.max_iter,
|
908 |
+
tol=self.tol,
|
909 |
+
solver="sag",
|
910 |
+
positive=self.positive,
|
911 |
+
random_state=self.random_state,
|
912 |
+
return_n_iter=True,
|
913 |
+
return_intercept=True,
|
914 |
+
check_input=False,
|
915 |
+
)
|
916 |
+
# add the offset which was subtracted by _preprocess_data
|
917 |
+
self.intercept_ += y_offset
|
918 |
+
|
919 |
+
else:
|
920 |
+
if sparse.issparse(X) and self.fit_intercept:
|
921 |
+
# required to fit intercept with sparse_cg and lbfgs solver
|
922 |
+
params = {"X_offset": X_offset, "X_scale": X_scale}
|
923 |
+
else:
|
924 |
+
# for dense matrices or when intercept is set to 0
|
925 |
+
params = {}
|
926 |
+
|
927 |
+
self.coef_, self.n_iter_ = _ridge_regression(
|
928 |
+
X,
|
929 |
+
y,
|
930 |
+
alpha=self.alpha,
|
931 |
+
sample_weight=sample_weight,
|
932 |
+
max_iter=self.max_iter,
|
933 |
+
tol=self.tol,
|
934 |
+
solver=solver,
|
935 |
+
positive=self.positive,
|
936 |
+
random_state=self.random_state,
|
937 |
+
return_n_iter=True,
|
938 |
+
return_intercept=False,
|
939 |
+
check_input=False,
|
940 |
+
fit_intercept=self.fit_intercept,
|
941 |
+
**params,
|
942 |
+
)
|
943 |
+
self._set_intercept(X_offset, y_offset, X_scale)
|
944 |
+
|
945 |
+
return self
|
946 |
+
|
947 |
+
|
948 |
+
class Ridge(MultiOutputMixin, RegressorMixin, _BaseRidge):
|
949 |
+
"""Linear least squares with l2 regularization.
|
950 |
+
|
951 |
+
Minimizes the objective function::
|
952 |
+
|
953 |
+
||y - Xw||^2_2 + alpha * ||w||^2_2
|
954 |
+
|
955 |
+
This model solves a regression model where the loss function is
|
956 |
+
the linear least squares function and regularization is given by
|
957 |
+
the l2-norm. Also known as Ridge Regression or Tikhonov regularization.
|
958 |
+
This estimator has built-in support for multi-variate regression
|
959 |
+
(i.e., when y is a 2d-array of shape (n_samples, n_targets)).
|
960 |
+
|
961 |
+
Read more in the :ref:`User Guide <ridge_regression>`.
|
962 |
+
|
963 |
+
Parameters
|
964 |
+
----------
|
965 |
+
alpha : {float, ndarray of shape (n_targets,)}, default=1.0
|
966 |
+
Constant that multiplies the L2 term, controlling regularization
|
967 |
+
strength. `alpha` must be a non-negative float i.e. in `[0, inf)`.
|
968 |
+
|
969 |
+
When `alpha = 0`, the objective is equivalent to ordinary least
|
970 |
+
squares, solved by the :class:`LinearRegression` object. For numerical
|
971 |
+
reasons, using `alpha = 0` with the `Ridge` object is not advised.
|
972 |
+
Instead, you should use the :class:`LinearRegression` object.
|
973 |
+
|
974 |
+
If an array is passed, penalties are assumed to be specific to the
|
975 |
+
targets. Hence they must correspond in number.
|
976 |
+
|
977 |
+
fit_intercept : bool, default=True
|
978 |
+
Whether to fit the intercept for this model. If set
|
979 |
+
to false, no intercept will be used in calculations
|
980 |
+
(i.e. ``X`` and ``y`` are expected to be centered).
|
981 |
+
|
982 |
+
copy_X : bool, default=True
|
983 |
+
If True, X will be copied; else, it may be overwritten.
|
984 |
+
|
985 |
+
max_iter : int, default=None
|
986 |
+
Maximum number of iterations for conjugate gradient solver.
|
987 |
+
For 'sparse_cg' and 'lsqr' solvers, the default value is determined
|
988 |
+
by scipy.sparse.linalg. For 'sag' solver, the default value is 1000.
|
989 |
+
For 'lbfgs' solver, the default value is 15000.
|
990 |
+
|
991 |
+
tol : float, default=1e-4
|
992 |
+
The precision of the solution (`coef_`) is determined by `tol` which
|
993 |
+
specifies a different convergence criterion for each solver:
|
994 |
+
|
995 |
+
- 'svd': `tol` has no impact.
|
996 |
+
|
997 |
+
- 'cholesky': `tol` has no impact.
|
998 |
+
|
999 |
+
- 'sparse_cg': norm of residuals smaller than `tol`.
|
1000 |
+
|
1001 |
+
- 'lsqr': `tol` is set as atol and btol of scipy.sparse.linalg.lsqr,
|
1002 |
+
which control the norm of the residual vector in terms of the norms of
|
1003 |
+
matrix and coefficients.
|
1004 |
+
|
1005 |
+
- 'sag' and 'saga': relative change of coef smaller than `tol`.
|
1006 |
+
|
1007 |
+
- 'lbfgs': maximum of the absolute (projected) gradient=max|residuals|
|
1008 |
+
smaller than `tol`.
|
1009 |
+
|
1010 |
+
.. versionchanged:: 1.2
|
1011 |
+
Default value changed from 1e-3 to 1e-4 for consistency with other linear
|
1012 |
+
models.
|
1013 |
+
|
1014 |
+
solver : {'auto', 'svd', 'cholesky', 'lsqr', 'sparse_cg', \
|
1015 |
+
'sag', 'saga', 'lbfgs'}, default='auto'
|
1016 |
+
Solver to use in the computational routines:
|
1017 |
+
|
1018 |
+
- 'auto' chooses the solver automatically based on the type of data.
|
1019 |
+
|
1020 |
+
- 'svd' uses a Singular Value Decomposition of X to compute the Ridge
|
1021 |
+
coefficients. It is the most stable solver, in particular more stable
|
1022 |
+
for singular matrices than 'cholesky' at the cost of being slower.
|
1023 |
+
|
1024 |
+
- 'cholesky' uses the standard scipy.linalg.solve function to
|
1025 |
+
obtain a closed-form solution.
|
1026 |
+
|
1027 |
+
- 'sparse_cg' uses the conjugate gradient solver as found in
|
1028 |
+
scipy.sparse.linalg.cg. As an iterative algorithm, this solver is
|
1029 |
+
more appropriate than 'cholesky' for large-scale data
|
1030 |
+
(possibility to set `tol` and `max_iter`).
|
1031 |
+
|
1032 |
+
- 'lsqr' uses the dedicated regularized least-squares routine
|
1033 |
+
scipy.sparse.linalg.lsqr. It is the fastest and uses an iterative
|
1034 |
+
procedure.
|
1035 |
+
|
1036 |
+
- 'sag' uses a Stochastic Average Gradient descent, and 'saga' uses
|
1037 |
+
its improved, unbiased version named SAGA. Both methods also use an
|
1038 |
+
iterative procedure, and are often faster than other solvers when
|
1039 |
+
both n_samples and n_features are large. Note that 'sag' and
|
1040 |
+
'saga' fast convergence is only guaranteed on features with
|
1041 |
+
approximately the same scale. You can preprocess the data with a
|
1042 |
+
scaler from sklearn.preprocessing.
|
1043 |
+
|
1044 |
+
- 'lbfgs' uses L-BFGS-B algorithm implemented in
|
1045 |
+
`scipy.optimize.minimize`. It can be used only when `positive`
|
1046 |
+
is True.
|
1047 |
+
|
1048 |
+
All solvers except 'svd' support both dense and sparse data. However, only
|
1049 |
+
'lsqr', 'sag', 'sparse_cg', and 'lbfgs' support sparse input when
|
1050 |
+
`fit_intercept` is True.
|
1051 |
+
|
1052 |
+
.. versionadded:: 0.17
|
1053 |
+
Stochastic Average Gradient descent solver.
|
1054 |
+
.. versionadded:: 0.19
|
1055 |
+
SAGA solver.
|
1056 |
+
|
1057 |
+
positive : bool, default=False
|
1058 |
+
When set to ``True``, forces the coefficients to be positive.
|
1059 |
+
Only 'lbfgs' solver is supported in this case.
|
1060 |
+
|
1061 |
+
random_state : int, RandomState instance, default=None
|
1062 |
+
Used when ``solver`` == 'sag' or 'saga' to shuffle the data.
|
1063 |
+
See :term:`Glossary <random_state>` for details.
|
1064 |
+
|
1065 |
+
.. versionadded:: 0.17
|
1066 |
+
`random_state` to support Stochastic Average Gradient.
|
1067 |
+
|
1068 |
+
Attributes
|
1069 |
+
----------
|
1070 |
+
coef_ : ndarray of shape (n_features,) or (n_targets, n_features)
|
1071 |
+
Weight vector(s).
|
1072 |
+
|
1073 |
+
intercept_ : float or ndarray of shape (n_targets,)
|
1074 |
+
Independent term in decision function. Set to 0.0 if
|
1075 |
+
``fit_intercept = False``.
|
1076 |
+
|
1077 |
+
n_iter_ : None or ndarray of shape (n_targets,)
|
1078 |
+
Actual number of iterations for each target. Available only for
|
1079 |
+
sag and lsqr solvers. Other solvers will return None.
|
1080 |
+
|
1081 |
+
.. versionadded:: 0.17
|
1082 |
+
|
1083 |
+
n_features_in_ : int
|
1084 |
+
Number of features seen during :term:`fit`.
|
1085 |
+
|
1086 |
+
.. versionadded:: 0.24
|
1087 |
+
|
1088 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
1089 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
1090 |
+
has feature names that are all strings.
|
1091 |
+
|
1092 |
+
.. versionadded:: 1.0
|
1093 |
+
|
1094 |
+
See Also
|
1095 |
+
--------
|
1096 |
+
RidgeClassifier : Ridge classifier.
|
1097 |
+
RidgeCV : Ridge regression with built-in cross validation.
|
1098 |
+
:class:`~sklearn.kernel_ridge.KernelRidge` : Kernel ridge regression
|
1099 |
+
combines ridge regression with the kernel trick.
|
1100 |
+
|
1101 |
+
Notes
|
1102 |
+
-----
|
1103 |
+
Regularization improves the conditioning of the problem and
|
1104 |
+
reduces the variance of the estimates. Larger values specify stronger
|
1105 |
+
regularization. Alpha corresponds to ``1 / (2C)`` in other linear
|
1106 |
+
models such as :class:`~sklearn.linear_model.LogisticRegression` or
|
1107 |
+
:class:`~sklearn.svm.LinearSVC`.
|
1108 |
+
|
1109 |
+
Examples
|
1110 |
+
--------
|
1111 |
+
>>> from sklearn.linear_model import Ridge
|
1112 |
+
>>> import numpy as np
|
1113 |
+
>>> n_samples, n_features = 10, 5
|
1114 |
+
>>> rng = np.random.RandomState(0)
|
1115 |
+
>>> y = rng.randn(n_samples)
|
1116 |
+
>>> X = rng.randn(n_samples, n_features)
|
1117 |
+
>>> clf = Ridge(alpha=1.0)
|
1118 |
+
>>> clf.fit(X, y)
|
1119 |
+
Ridge()
|
1120 |
+
"""
|
1121 |
+
|
1122 |
+
def __init__(
|
1123 |
+
self,
|
1124 |
+
alpha=1.0,
|
1125 |
+
*,
|
1126 |
+
fit_intercept=True,
|
1127 |
+
copy_X=True,
|
1128 |
+
max_iter=None,
|
1129 |
+
tol=1e-4,
|
1130 |
+
solver="auto",
|
1131 |
+
positive=False,
|
1132 |
+
random_state=None,
|
1133 |
+
):
|
1134 |
+
super().__init__(
|
1135 |
+
alpha=alpha,
|
1136 |
+
fit_intercept=fit_intercept,
|
1137 |
+
copy_X=copy_X,
|
1138 |
+
max_iter=max_iter,
|
1139 |
+
tol=tol,
|
1140 |
+
solver=solver,
|
1141 |
+
positive=positive,
|
1142 |
+
random_state=random_state,
|
1143 |
+
)
|
1144 |
+
|
1145 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
1146 |
+
def fit(self, X, y, sample_weight=None):
|
1147 |
+
"""Fit Ridge regression model.
|
1148 |
+
|
1149 |
+
Parameters
|
1150 |
+
----------
|
1151 |
+
X : {ndarray, sparse matrix} of shape (n_samples, n_features)
|
1152 |
+
Training data.
|
1153 |
+
|
1154 |
+
y : ndarray of shape (n_samples,) or (n_samples, n_targets)
|
1155 |
+
Target values.
|
1156 |
+
|
1157 |
+
sample_weight : float or ndarray of shape (n_samples,), default=None
|
1158 |
+
Individual weights for each sample. If given a float, every sample
|
1159 |
+
will have the same weight.
|
1160 |
+
|
1161 |
+
Returns
|
1162 |
+
-------
|
1163 |
+
self : object
|
1164 |
+
Fitted estimator.
|
1165 |
+
"""
|
1166 |
+
_accept_sparse = _get_valid_accept_sparse(sparse.issparse(X), self.solver)
|
1167 |
+
X, y = self._validate_data(
|
1168 |
+
X,
|
1169 |
+
y,
|
1170 |
+
accept_sparse=_accept_sparse,
|
1171 |
+
dtype=[np.float64, np.float32],
|
1172 |
+
multi_output=True,
|
1173 |
+
y_numeric=True,
|
1174 |
+
)
|
1175 |
+
return super().fit(X, y, sample_weight=sample_weight)
|
1176 |
+
|
1177 |
+
|
1178 |
+
class _RidgeClassifierMixin(LinearClassifierMixin):
|
1179 |
+
def _prepare_data(self, X, y, sample_weight, solver):
|
1180 |
+
"""Validate `X` and `y` and binarize `y`.
|
1181 |
+
|
1182 |
+
Parameters
|
1183 |
+
----------
|
1184 |
+
X : {ndarray, sparse matrix} of shape (n_samples, n_features)
|
1185 |
+
Training data.
|
1186 |
+
|
1187 |
+
y : ndarray of shape (n_samples,)
|
1188 |
+
Target values.
|
1189 |
+
|
1190 |
+
sample_weight : float or ndarray of shape (n_samples,), default=None
|
1191 |
+
Individual weights for each sample. If given a float, every sample
|
1192 |
+
will have the same weight.
|
1193 |
+
|
1194 |
+
solver : str
|
1195 |
+
The solver used in `Ridge` to know which sparse format to support.
|
1196 |
+
|
1197 |
+
Returns
|
1198 |
+
-------
|
1199 |
+
X : {ndarray, sparse matrix} of shape (n_samples, n_features)
|
1200 |
+
Validated training data.
|
1201 |
+
|
1202 |
+
y : ndarray of shape (n_samples,)
|
1203 |
+
Validated target values.
|
1204 |
+
|
1205 |
+
sample_weight : ndarray of shape (n_samples,)
|
1206 |
+
Validated sample weights.
|
1207 |
+
|
1208 |
+
Y : ndarray of shape (n_samples, n_classes)
|
1209 |
+
The binarized version of `y`.
|
1210 |
+
"""
|
1211 |
+
accept_sparse = _get_valid_accept_sparse(sparse.issparse(X), solver)
|
1212 |
+
X, y = self._validate_data(
|
1213 |
+
X,
|
1214 |
+
y,
|
1215 |
+
accept_sparse=accept_sparse,
|
1216 |
+
multi_output=True,
|
1217 |
+
y_numeric=False,
|
1218 |
+
)
|
1219 |
+
|
1220 |
+
self._label_binarizer = LabelBinarizer(pos_label=1, neg_label=-1)
|
1221 |
+
Y = self._label_binarizer.fit_transform(y)
|
1222 |
+
if not self._label_binarizer.y_type_.startswith("multilabel"):
|
1223 |
+
y = column_or_1d(y, warn=True)
|
1224 |
+
|
1225 |
+
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
|
1226 |
+
if self.class_weight:
|
1227 |
+
sample_weight = sample_weight * compute_sample_weight(self.class_weight, y)
|
1228 |
+
return X, y, sample_weight, Y
|
1229 |
+
|
1230 |
+
def predict(self, X):
|
1231 |
+
"""Predict class labels for samples in `X`.
|
1232 |
+
|
1233 |
+
Parameters
|
1234 |
+
----------
|
1235 |
+
X : {array-like, spare matrix} of shape (n_samples, n_features)
|
1236 |
+
The data matrix for which we want to predict the targets.
|
1237 |
+
|
1238 |
+
Returns
|
1239 |
+
-------
|
1240 |
+
y_pred : ndarray of shape (n_samples,) or (n_samples, n_outputs)
|
1241 |
+
Vector or matrix containing the predictions. In binary and
|
1242 |
+
multiclass problems, this is a vector containing `n_samples`. In
|
1243 |
+
a multilabel problem, it returns a matrix of shape
|
1244 |
+
`(n_samples, n_outputs)`.
|
1245 |
+
"""
|
1246 |
+
check_is_fitted(self, attributes=["_label_binarizer"])
|
1247 |
+
if self._label_binarizer.y_type_.startswith("multilabel"):
|
1248 |
+
# Threshold such that the negative label is -1 and positive label
|
1249 |
+
# is 1 to use the inverse transform of the label binarizer fitted
|
1250 |
+
# during fit.
|
1251 |
+
scores = 2 * (self.decision_function(X) > 0) - 1
|
1252 |
+
return self._label_binarizer.inverse_transform(scores)
|
1253 |
+
return super().predict(X)
|
1254 |
+
|
1255 |
+
@property
|
1256 |
+
def classes_(self):
|
1257 |
+
"""Classes labels."""
|
1258 |
+
return self._label_binarizer.classes_
|
1259 |
+
|
1260 |
+
def _more_tags(self):
|
1261 |
+
return {"multilabel": True}
|
1262 |
+
|
1263 |
+
|
1264 |
+
class RidgeClassifier(_RidgeClassifierMixin, _BaseRidge):
|
1265 |
+
"""Classifier using Ridge regression.
|
1266 |
+
|
1267 |
+
This classifier first converts the target values into ``{-1, 1}`` and
|
1268 |
+
then treats the problem as a regression task (multi-output regression in
|
1269 |
+
the multiclass case).
|
1270 |
+
|
1271 |
+
Read more in the :ref:`User Guide <ridge_regression>`.
|
1272 |
+
|
1273 |
+
Parameters
|
1274 |
+
----------
|
1275 |
+
alpha : float, default=1.0
|
1276 |
+
Regularization strength; must be a positive float. Regularization
|
1277 |
+
improves the conditioning of the problem and reduces the variance of
|
1278 |
+
the estimates. Larger values specify stronger regularization.
|
1279 |
+
Alpha corresponds to ``1 / (2C)`` in other linear models such as
|
1280 |
+
:class:`~sklearn.linear_model.LogisticRegression` or
|
1281 |
+
:class:`~sklearn.svm.LinearSVC`.
|
1282 |
+
|
1283 |
+
fit_intercept : bool, default=True
|
1284 |
+
Whether to calculate the intercept for this model. If set to false, no
|
1285 |
+
intercept will be used in calculations (e.g. data is expected to be
|
1286 |
+
already centered).
|
1287 |
+
|
1288 |
+
copy_X : bool, default=True
|
1289 |
+
If True, X will be copied; else, it may be overwritten.
|
1290 |
+
|
1291 |
+
max_iter : int, default=None
|
1292 |
+
Maximum number of iterations for conjugate gradient solver.
|
1293 |
+
The default value is determined by scipy.sparse.linalg.
|
1294 |
+
|
1295 |
+
tol : float, default=1e-4
|
1296 |
+
The precision of the solution (`coef_`) is determined by `tol` which
|
1297 |
+
specifies a different convergence criterion for each solver:
|
1298 |
+
|
1299 |
+
- 'svd': `tol` has no impact.
|
1300 |
+
|
1301 |
+
- 'cholesky': `tol` has no impact.
|
1302 |
+
|
1303 |
+
- 'sparse_cg': norm of residuals smaller than `tol`.
|
1304 |
+
|
1305 |
+
- 'lsqr': `tol` is set as atol and btol of scipy.sparse.linalg.lsqr,
|
1306 |
+
which control the norm of the residual vector in terms of the norms of
|
1307 |
+
matrix and coefficients.
|
1308 |
+
|
1309 |
+
- 'sag' and 'saga': relative change of coef smaller than `tol`.
|
1310 |
+
|
1311 |
+
- 'lbfgs': maximum of the absolute (projected) gradient=max|residuals|
|
1312 |
+
smaller than `tol`.
|
1313 |
+
|
1314 |
+
.. versionchanged:: 1.2
|
1315 |
+
Default value changed from 1e-3 to 1e-4 for consistency with other linear
|
1316 |
+
models.
|
1317 |
+
|
1318 |
+
class_weight : dict or 'balanced', default=None
|
1319 |
+
Weights associated with classes in the form ``{class_label: weight}``.
|
1320 |
+
If not given, all classes are supposed to have weight one.
|
1321 |
+
|
1322 |
+
The "balanced" mode uses the values of y to automatically adjust
|
1323 |
+
weights inversely proportional to class frequencies in the input data
|
1324 |
+
as ``n_samples / (n_classes * np.bincount(y))``.
|
1325 |
+
|
1326 |
+
solver : {'auto', 'svd', 'cholesky', 'lsqr', 'sparse_cg', \
|
1327 |
+
'sag', 'saga', 'lbfgs'}, default='auto'
|
1328 |
+
Solver to use in the computational routines:
|
1329 |
+
|
1330 |
+
- 'auto' chooses the solver automatically based on the type of data.
|
1331 |
+
|
1332 |
+
- 'svd' uses a Singular Value Decomposition of X to compute the Ridge
|
1333 |
+
coefficients. It is the most stable solver, in particular more stable
|
1334 |
+
for singular matrices than 'cholesky' at the cost of being slower.
|
1335 |
+
|
1336 |
+
- 'cholesky' uses the standard scipy.linalg.solve function to
|
1337 |
+
obtain a closed-form solution.
|
1338 |
+
|
1339 |
+
- 'sparse_cg' uses the conjugate gradient solver as found in
|
1340 |
+
scipy.sparse.linalg.cg. As an iterative algorithm, this solver is
|
1341 |
+
more appropriate than 'cholesky' for large-scale data
|
1342 |
+
(possibility to set `tol` and `max_iter`).
|
1343 |
+
|
1344 |
+
- 'lsqr' uses the dedicated regularized least-squares routine
|
1345 |
+
scipy.sparse.linalg.lsqr. It is the fastest and uses an iterative
|
1346 |
+
procedure.
|
1347 |
+
|
1348 |
+
- 'sag' uses a Stochastic Average Gradient descent, and 'saga' uses
|
1349 |
+
its unbiased and more flexible version named SAGA. Both methods
|
1350 |
+
use an iterative procedure, and are often faster than other solvers
|
1351 |
+
when both n_samples and n_features are large. Note that 'sag' and
|
1352 |
+
'saga' fast convergence is only guaranteed on features with
|
1353 |
+
approximately the same scale. You can preprocess the data with a
|
1354 |
+
scaler from sklearn.preprocessing.
|
1355 |
+
|
1356 |
+
.. versionadded:: 0.17
|
1357 |
+
Stochastic Average Gradient descent solver.
|
1358 |
+
.. versionadded:: 0.19
|
1359 |
+
SAGA solver.
|
1360 |
+
|
1361 |
+
- 'lbfgs' uses L-BFGS-B algorithm implemented in
|
1362 |
+
`scipy.optimize.minimize`. It can be used only when `positive`
|
1363 |
+
is True.
|
1364 |
+
|
1365 |
+
positive : bool, default=False
|
1366 |
+
When set to ``True``, forces the coefficients to be positive.
|
1367 |
+
Only 'lbfgs' solver is supported in this case.
|
1368 |
+
|
1369 |
+
random_state : int, RandomState instance, default=None
|
1370 |
+
Used when ``solver`` == 'sag' or 'saga' to shuffle the data.
|
1371 |
+
See :term:`Glossary <random_state>` for details.
|
1372 |
+
|
1373 |
+
Attributes
|
1374 |
+
----------
|
1375 |
+
coef_ : ndarray of shape (1, n_features) or (n_classes, n_features)
|
1376 |
+
Coefficient of the features in the decision function.
|
1377 |
+
|
1378 |
+
``coef_`` is of shape (1, n_features) when the given problem is binary.
|
1379 |
+
|
1380 |
+
intercept_ : float or ndarray of shape (n_targets,)
|
1381 |
+
Independent term in decision function. Set to 0.0 if
|
1382 |
+
``fit_intercept = False``.
|
1383 |
+
|
1384 |
+
n_iter_ : None or ndarray of shape (n_targets,)
|
1385 |
+
Actual number of iterations for each target. Available only for
|
1386 |
+
sag and lsqr solvers. Other solvers will return None.
|
1387 |
+
|
1388 |
+
classes_ : ndarray of shape (n_classes,)
|
1389 |
+
The classes labels.
|
1390 |
+
|
1391 |
+
n_features_in_ : int
|
1392 |
+
Number of features seen during :term:`fit`.
|
1393 |
+
|
1394 |
+
.. versionadded:: 0.24
|
1395 |
+
|
1396 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
1397 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
1398 |
+
has feature names that are all strings.
|
1399 |
+
|
1400 |
+
.. versionadded:: 1.0
|
1401 |
+
|
1402 |
+
See Also
|
1403 |
+
--------
|
1404 |
+
Ridge : Ridge regression.
|
1405 |
+
RidgeClassifierCV : Ridge classifier with built-in cross validation.
|
1406 |
+
|
1407 |
+
Notes
|
1408 |
+
-----
|
1409 |
+
For multi-class classification, n_class classifiers are trained in
|
1410 |
+
a one-versus-all approach. Concretely, this is implemented by taking
|
1411 |
+
advantage of the multi-variate response support in Ridge.
|
1412 |
+
|
1413 |
+
Examples
|
1414 |
+
--------
|
1415 |
+
>>> from sklearn.datasets import load_breast_cancer
|
1416 |
+
>>> from sklearn.linear_model import RidgeClassifier
|
1417 |
+
>>> X, y = load_breast_cancer(return_X_y=True)
|
1418 |
+
>>> clf = RidgeClassifier().fit(X, y)
|
1419 |
+
>>> clf.score(X, y)
|
1420 |
+
0.9595...
|
1421 |
+
"""
|
1422 |
+
|
1423 |
+
_parameter_constraints: dict = {
|
1424 |
+
**_BaseRidge._parameter_constraints,
|
1425 |
+
"class_weight": [dict, StrOptions({"balanced"}), None],
|
1426 |
+
}
|
1427 |
+
|
1428 |
+
def __init__(
|
1429 |
+
self,
|
1430 |
+
alpha=1.0,
|
1431 |
+
*,
|
1432 |
+
fit_intercept=True,
|
1433 |
+
copy_X=True,
|
1434 |
+
max_iter=None,
|
1435 |
+
tol=1e-4,
|
1436 |
+
class_weight=None,
|
1437 |
+
solver="auto",
|
1438 |
+
positive=False,
|
1439 |
+
random_state=None,
|
1440 |
+
):
|
1441 |
+
super().__init__(
|
1442 |
+
alpha=alpha,
|
1443 |
+
fit_intercept=fit_intercept,
|
1444 |
+
copy_X=copy_X,
|
1445 |
+
max_iter=max_iter,
|
1446 |
+
tol=tol,
|
1447 |
+
solver=solver,
|
1448 |
+
positive=positive,
|
1449 |
+
random_state=random_state,
|
1450 |
+
)
|
1451 |
+
self.class_weight = class_weight
|
1452 |
+
|
1453 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
1454 |
+
def fit(self, X, y, sample_weight=None):
|
1455 |
+
"""Fit Ridge classifier model.
|
1456 |
+
|
1457 |
+
Parameters
|
1458 |
+
----------
|
1459 |
+
X : {ndarray, sparse matrix} of shape (n_samples, n_features)
|
1460 |
+
Training data.
|
1461 |
+
|
1462 |
+
y : ndarray of shape (n_samples,)
|
1463 |
+
Target values.
|
1464 |
+
|
1465 |
+
sample_weight : float or ndarray of shape (n_samples,), default=None
|
1466 |
+
Individual weights for each sample. If given a float, every sample
|
1467 |
+
will have the same weight.
|
1468 |
+
|
1469 |
+
.. versionadded:: 0.17
|
1470 |
+
*sample_weight* support to RidgeClassifier.
|
1471 |
+
|
1472 |
+
Returns
|
1473 |
+
-------
|
1474 |
+
self : object
|
1475 |
+
Instance of the estimator.
|
1476 |
+
"""
|
1477 |
+
X, y, sample_weight, Y = self._prepare_data(X, y, sample_weight, self.solver)
|
1478 |
+
|
1479 |
+
super().fit(X, Y, sample_weight=sample_weight)
|
1480 |
+
return self
|
1481 |
+
|
1482 |
+
|
1483 |
+
def _check_gcv_mode(X, gcv_mode):
|
1484 |
+
if gcv_mode in ["eigen", "svd"]:
|
1485 |
+
return gcv_mode
|
1486 |
+
# if X has more rows than columns, use decomposition of X^T.X,
|
1487 |
+
# otherwise X.X^T
|
1488 |
+
if X.shape[0] > X.shape[1]:
|
1489 |
+
return "svd"
|
1490 |
+
return "eigen"
|
1491 |
+
|
1492 |
+
|
1493 |
+
def _find_smallest_angle(query, vectors):
|
1494 |
+
"""Find the column of vectors that is most aligned with the query.
|
1495 |
+
|
1496 |
+
Both query and the columns of vectors must have their l2 norm equal to 1.
|
1497 |
+
|
1498 |
+
Parameters
|
1499 |
+
----------
|
1500 |
+
query : ndarray of shape (n_samples,)
|
1501 |
+
Normalized query vector.
|
1502 |
+
|
1503 |
+
vectors : ndarray of shape (n_samples, n_features)
|
1504 |
+
Vectors to which we compare query, as columns. Must be normalized.
|
1505 |
+
"""
|
1506 |
+
abs_cosine = np.abs(query.dot(vectors))
|
1507 |
+
index = np.argmax(abs_cosine)
|
1508 |
+
return index
|
1509 |
+
|
1510 |
+
|
1511 |
+
class _X_CenterStackOp(sparse.linalg.LinearOperator):
|
1512 |
+
"""Behaves as centered and scaled X with an added intercept column.
|
1513 |
+
|
1514 |
+
This operator behaves as
|
1515 |
+
np.hstack([X - sqrt_sw[:, None] * X_mean, sqrt_sw[:, None]])
|
1516 |
+
"""
|
1517 |
+
|
1518 |
+
def __init__(self, X, X_mean, sqrt_sw):
|
1519 |
+
n_samples, n_features = X.shape
|
1520 |
+
super().__init__(X.dtype, (n_samples, n_features + 1))
|
1521 |
+
self.X = X
|
1522 |
+
self.X_mean = X_mean
|
1523 |
+
self.sqrt_sw = sqrt_sw
|
1524 |
+
|
1525 |
+
def _matvec(self, v):
|
1526 |
+
v = v.ravel()
|
1527 |
+
return (
|
1528 |
+
safe_sparse_dot(self.X, v[:-1], dense_output=True)
|
1529 |
+
- self.sqrt_sw * self.X_mean.dot(v[:-1])
|
1530 |
+
+ v[-1] * self.sqrt_sw
|
1531 |
+
)
|
1532 |
+
|
1533 |
+
def _matmat(self, v):
|
1534 |
+
return (
|
1535 |
+
safe_sparse_dot(self.X, v[:-1], dense_output=True)
|
1536 |
+
- self.sqrt_sw[:, None] * self.X_mean.dot(v[:-1])
|
1537 |
+
+ v[-1] * self.sqrt_sw[:, None]
|
1538 |
+
)
|
1539 |
+
|
1540 |
+
def _transpose(self):
|
1541 |
+
return _XT_CenterStackOp(self.X, self.X_mean, self.sqrt_sw)
|
1542 |
+
|
1543 |
+
|
1544 |
+
class _XT_CenterStackOp(sparse.linalg.LinearOperator):
|
1545 |
+
"""Behaves as transposed centered and scaled X with an intercept column.
|
1546 |
+
|
1547 |
+
This operator behaves as
|
1548 |
+
np.hstack([X - sqrt_sw[:, None] * X_mean, sqrt_sw[:, None]]).T
|
1549 |
+
"""
|
1550 |
+
|
1551 |
+
def __init__(self, X, X_mean, sqrt_sw):
|
1552 |
+
n_samples, n_features = X.shape
|
1553 |
+
super().__init__(X.dtype, (n_features + 1, n_samples))
|
1554 |
+
self.X = X
|
1555 |
+
self.X_mean = X_mean
|
1556 |
+
self.sqrt_sw = sqrt_sw
|
1557 |
+
|
1558 |
+
def _matvec(self, v):
|
1559 |
+
v = v.ravel()
|
1560 |
+
n_features = self.shape[0]
|
1561 |
+
res = np.empty(n_features, dtype=self.X.dtype)
|
1562 |
+
res[:-1] = safe_sparse_dot(self.X.T, v, dense_output=True) - (
|
1563 |
+
self.X_mean * self.sqrt_sw.dot(v)
|
1564 |
+
)
|
1565 |
+
res[-1] = np.dot(v, self.sqrt_sw)
|
1566 |
+
return res
|
1567 |
+
|
1568 |
+
def _matmat(self, v):
|
1569 |
+
n_features = self.shape[0]
|
1570 |
+
res = np.empty((n_features, v.shape[1]), dtype=self.X.dtype)
|
1571 |
+
res[:-1] = safe_sparse_dot(self.X.T, v, dense_output=True) - self.X_mean[
|
1572 |
+
:, None
|
1573 |
+
] * self.sqrt_sw.dot(v)
|
1574 |
+
res[-1] = np.dot(self.sqrt_sw, v)
|
1575 |
+
return res
|
1576 |
+
|
1577 |
+
|
1578 |
+
class _IdentityRegressor:
|
1579 |
+
"""Fake regressor which will directly output the prediction."""
|
1580 |
+
|
1581 |
+
def decision_function(self, y_predict):
|
1582 |
+
return y_predict
|
1583 |
+
|
1584 |
+
def predict(self, y_predict):
|
1585 |
+
return y_predict
|
1586 |
+
|
1587 |
+
|
1588 |
+
class _IdentityClassifier(LinearClassifierMixin):
|
1589 |
+
"""Fake classifier which will directly output the prediction.
|
1590 |
+
|
1591 |
+
We inherit from LinearClassifierMixin to get the proper shape for the
|
1592 |
+
output `y`.
|
1593 |
+
"""
|
1594 |
+
|
1595 |
+
def __init__(self, classes):
|
1596 |
+
self.classes_ = classes
|
1597 |
+
|
1598 |
+
def decision_function(self, y_predict):
|
1599 |
+
return y_predict
|
1600 |
+
|
1601 |
+
|
1602 |
+
class _RidgeGCV(LinearModel):
|
1603 |
+
"""Ridge regression with built-in Leave-one-out Cross-Validation.
|
1604 |
+
|
1605 |
+
This class is not intended to be used directly. Use RidgeCV instead.
|
1606 |
+
|
1607 |
+
Notes
|
1608 |
+
-----
|
1609 |
+
|
1610 |
+
We want to solve (K + alpha*Id)c = y,
|
1611 |
+
where K = X X^T is the kernel matrix.
|
1612 |
+
|
1613 |
+
Let G = (K + alpha*Id).
|
1614 |
+
|
1615 |
+
Dual solution: c = G^-1y
|
1616 |
+
Primal solution: w = X^T c
|
1617 |
+
|
1618 |
+
Compute eigendecomposition K = Q V Q^T.
|
1619 |
+
Then G^-1 = Q (V + alpha*Id)^-1 Q^T,
|
1620 |
+
where (V + alpha*Id) is diagonal.
|
1621 |
+
It is thus inexpensive to inverse for many alphas.
|
1622 |
+
|
1623 |
+
Let loov be the vector of prediction values for each example
|
1624 |
+
when the model was fitted with all examples but this example.
|
1625 |
+
|
1626 |
+
loov = (KG^-1Y - diag(KG^-1)Y) / diag(I-KG^-1)
|
1627 |
+
|
1628 |
+
Let looe be the vector of prediction errors for each example
|
1629 |
+
when the model was fitted with all examples but this example.
|
1630 |
+
|
1631 |
+
looe = y - loov = c / diag(G^-1)
|
1632 |
+
|
1633 |
+
The best score (negative mean squared error or user-provided scoring) is
|
1634 |
+
stored in the `best_score_` attribute, and the selected hyperparameter in
|
1635 |
+
`alpha_`.
|
1636 |
+
|
1637 |
+
References
|
1638 |
+
----------
|
1639 |
+
http://cbcl.mit.edu/publications/ps/MIT-CSAIL-TR-2007-025.pdf
|
1640 |
+
https://www.mit.edu/~9.520/spring07/Classes/rlsslides.pdf
|
1641 |
+
"""
|
1642 |
+
|
1643 |
+
def __init__(
|
1644 |
+
self,
|
1645 |
+
alphas=(0.1, 1.0, 10.0),
|
1646 |
+
*,
|
1647 |
+
fit_intercept=True,
|
1648 |
+
scoring=None,
|
1649 |
+
copy_X=True,
|
1650 |
+
gcv_mode=None,
|
1651 |
+
store_cv_values=False,
|
1652 |
+
is_clf=False,
|
1653 |
+
alpha_per_target=False,
|
1654 |
+
):
|
1655 |
+
self.alphas = alphas
|
1656 |
+
self.fit_intercept = fit_intercept
|
1657 |
+
self.scoring = scoring
|
1658 |
+
self.copy_X = copy_X
|
1659 |
+
self.gcv_mode = gcv_mode
|
1660 |
+
self.store_cv_values = store_cv_values
|
1661 |
+
self.is_clf = is_clf
|
1662 |
+
self.alpha_per_target = alpha_per_target
|
1663 |
+
|
1664 |
+
@staticmethod
|
1665 |
+
def _decomp_diag(v_prime, Q):
|
1666 |
+
# compute diagonal of the matrix: dot(Q, dot(diag(v_prime), Q^T))
|
1667 |
+
return (v_prime * Q**2).sum(axis=-1)
|
1668 |
+
|
1669 |
+
@staticmethod
|
1670 |
+
def _diag_dot(D, B):
|
1671 |
+
# compute dot(diag(D), B)
|
1672 |
+
if len(B.shape) > 1:
|
1673 |
+
# handle case where B is > 1-d
|
1674 |
+
D = D[(slice(None),) + (np.newaxis,) * (len(B.shape) - 1)]
|
1675 |
+
return D * B
|
1676 |
+
|
1677 |
+
def _compute_gram(self, X, sqrt_sw):
|
1678 |
+
"""Computes the Gram matrix XX^T with possible centering.
|
1679 |
+
|
1680 |
+
Parameters
|
1681 |
+
----------
|
1682 |
+
X : {ndarray, sparse matrix} of shape (n_samples, n_features)
|
1683 |
+
The preprocessed design matrix.
|
1684 |
+
|
1685 |
+
sqrt_sw : ndarray of shape (n_samples,)
|
1686 |
+
square roots of sample weights
|
1687 |
+
|
1688 |
+
Returns
|
1689 |
+
-------
|
1690 |
+
gram : ndarray of shape (n_samples, n_samples)
|
1691 |
+
The Gram matrix.
|
1692 |
+
X_mean : ndarray of shape (n_feature,)
|
1693 |
+
The weighted mean of ``X`` for each feature.
|
1694 |
+
|
1695 |
+
Notes
|
1696 |
+
-----
|
1697 |
+
When X is dense the centering has been done in preprocessing
|
1698 |
+
so the mean is 0 and we just compute XX^T.
|
1699 |
+
|
1700 |
+
When X is sparse it has not been centered in preprocessing, but it has
|
1701 |
+
been scaled by sqrt(sample weights).
|
1702 |
+
|
1703 |
+
When self.fit_intercept is False no centering is done.
|
1704 |
+
|
1705 |
+
The centered X is never actually computed because centering would break
|
1706 |
+
the sparsity of X.
|
1707 |
+
"""
|
1708 |
+
center = self.fit_intercept and sparse.issparse(X)
|
1709 |
+
if not center:
|
1710 |
+
# in this case centering has been done in preprocessing
|
1711 |
+
# or we are not fitting an intercept.
|
1712 |
+
X_mean = np.zeros(X.shape[1], dtype=X.dtype)
|
1713 |
+
return safe_sparse_dot(X, X.T, dense_output=True), X_mean
|
1714 |
+
# X is sparse
|
1715 |
+
n_samples = X.shape[0]
|
1716 |
+
sample_weight_matrix = sparse.dia_matrix(
|
1717 |
+
(sqrt_sw, 0), shape=(n_samples, n_samples)
|
1718 |
+
)
|
1719 |
+
X_weighted = sample_weight_matrix.dot(X)
|
1720 |
+
X_mean, _ = mean_variance_axis(X_weighted, axis=0)
|
1721 |
+
X_mean *= n_samples / sqrt_sw.dot(sqrt_sw)
|
1722 |
+
X_mX = sqrt_sw[:, None] * safe_sparse_dot(X_mean, X.T, dense_output=True)
|
1723 |
+
X_mX_m = np.outer(sqrt_sw, sqrt_sw) * np.dot(X_mean, X_mean)
|
1724 |
+
return (
|
1725 |
+
safe_sparse_dot(X, X.T, dense_output=True) + X_mX_m - X_mX - X_mX.T,
|
1726 |
+
X_mean,
|
1727 |
+
)
|
1728 |
+
|
1729 |
+
def _compute_covariance(self, X, sqrt_sw):
|
1730 |
+
"""Computes covariance matrix X^TX with possible centering.
|
1731 |
+
|
1732 |
+
Parameters
|
1733 |
+
----------
|
1734 |
+
X : sparse matrix of shape (n_samples, n_features)
|
1735 |
+
The preprocessed design matrix.
|
1736 |
+
|
1737 |
+
sqrt_sw : ndarray of shape (n_samples,)
|
1738 |
+
square roots of sample weights
|
1739 |
+
|
1740 |
+
Returns
|
1741 |
+
-------
|
1742 |
+
covariance : ndarray of shape (n_features, n_features)
|
1743 |
+
The covariance matrix.
|
1744 |
+
X_mean : ndarray of shape (n_feature,)
|
1745 |
+
The weighted mean of ``X`` for each feature.
|
1746 |
+
|
1747 |
+
Notes
|
1748 |
+
-----
|
1749 |
+
Since X is sparse it has not been centered in preprocessing, but it has
|
1750 |
+
been scaled by sqrt(sample weights).
|
1751 |
+
|
1752 |
+
When self.fit_intercept is False no centering is done.
|
1753 |
+
|
1754 |
+
The centered X is never actually computed because centering would break
|
1755 |
+
the sparsity of X.
|
1756 |
+
"""
|
1757 |
+
if not self.fit_intercept:
|
1758 |
+
# in this case centering has been done in preprocessing
|
1759 |
+
# or we are not fitting an intercept.
|
1760 |
+
X_mean = np.zeros(X.shape[1], dtype=X.dtype)
|
1761 |
+
return safe_sparse_dot(X.T, X, dense_output=True), X_mean
|
1762 |
+
# this function only gets called for sparse X
|
1763 |
+
n_samples = X.shape[0]
|
1764 |
+
sample_weight_matrix = sparse.dia_matrix(
|
1765 |
+
(sqrt_sw, 0), shape=(n_samples, n_samples)
|
1766 |
+
)
|
1767 |
+
X_weighted = sample_weight_matrix.dot(X)
|
1768 |
+
X_mean, _ = mean_variance_axis(X_weighted, axis=0)
|
1769 |
+
X_mean = X_mean * n_samples / sqrt_sw.dot(sqrt_sw)
|
1770 |
+
weight_sum = sqrt_sw.dot(sqrt_sw)
|
1771 |
+
return (
|
1772 |
+
safe_sparse_dot(X.T, X, dense_output=True)
|
1773 |
+
- weight_sum * np.outer(X_mean, X_mean),
|
1774 |
+
X_mean,
|
1775 |
+
)
|
1776 |
+
|
1777 |
+
def _sparse_multidot_diag(self, X, A, X_mean, sqrt_sw):
|
1778 |
+
"""Compute the diagonal of (X - X_mean).dot(A).dot((X - X_mean).T)
|
1779 |
+
without explicitly centering X nor computing X.dot(A)
|
1780 |
+
when X is sparse.
|
1781 |
+
|
1782 |
+
Parameters
|
1783 |
+
----------
|
1784 |
+
X : sparse matrix of shape (n_samples, n_features)
|
1785 |
+
|
1786 |
+
A : ndarray of shape (n_features, n_features)
|
1787 |
+
|
1788 |
+
X_mean : ndarray of shape (n_features,)
|
1789 |
+
|
1790 |
+
sqrt_sw : ndarray of shape (n_features,)
|
1791 |
+
square roots of sample weights
|
1792 |
+
|
1793 |
+
Returns
|
1794 |
+
-------
|
1795 |
+
diag : np.ndarray, shape (n_samples,)
|
1796 |
+
The computed diagonal.
|
1797 |
+
"""
|
1798 |
+
intercept_col = scale = sqrt_sw
|
1799 |
+
batch_size = X.shape[1]
|
1800 |
+
diag = np.empty(X.shape[0], dtype=X.dtype)
|
1801 |
+
for start in range(0, X.shape[0], batch_size):
|
1802 |
+
batch = slice(start, min(X.shape[0], start + batch_size), 1)
|
1803 |
+
X_batch = np.empty(
|
1804 |
+
(X[batch].shape[0], X.shape[1] + self.fit_intercept), dtype=X.dtype
|
1805 |
+
)
|
1806 |
+
if self.fit_intercept:
|
1807 |
+
X_batch[:, :-1] = X[batch].toarray() - X_mean * scale[batch][:, None]
|
1808 |
+
X_batch[:, -1] = intercept_col[batch]
|
1809 |
+
else:
|
1810 |
+
X_batch = X[batch].toarray()
|
1811 |
+
diag[batch] = (X_batch.dot(A) * X_batch).sum(axis=1)
|
1812 |
+
return diag
|
1813 |
+
|
1814 |
+
def _eigen_decompose_gram(self, X, y, sqrt_sw):
|
1815 |
+
"""Eigendecomposition of X.X^T, used when n_samples <= n_features."""
|
1816 |
+
# if X is dense it has already been centered in preprocessing
|
1817 |
+
K, X_mean = self._compute_gram(X, sqrt_sw)
|
1818 |
+
if self.fit_intercept:
|
1819 |
+
# to emulate centering X with sample weights,
|
1820 |
+
# ie removing the weighted average, we add a column
|
1821 |
+
# containing the square roots of the sample weights.
|
1822 |
+
# by centering, it is orthogonal to the other columns
|
1823 |
+
K += np.outer(sqrt_sw, sqrt_sw)
|
1824 |
+
eigvals, Q = linalg.eigh(K)
|
1825 |
+
QT_y = np.dot(Q.T, y)
|
1826 |
+
return X_mean, eigvals, Q, QT_y
|
1827 |
+
|
1828 |
+
def _solve_eigen_gram(self, alpha, y, sqrt_sw, X_mean, eigvals, Q, QT_y):
|
1829 |
+
"""Compute dual coefficients and diagonal of G^-1.
|
1830 |
+
|
1831 |
+
Used when we have a decomposition of X.X^T (n_samples <= n_features).
|
1832 |
+
"""
|
1833 |
+
w = 1.0 / (eigvals + alpha)
|
1834 |
+
if self.fit_intercept:
|
1835 |
+
# the vector containing the square roots of the sample weights (1
|
1836 |
+
# when no sample weights) is the eigenvector of XX^T which
|
1837 |
+
# corresponds to the intercept; we cancel the regularization on
|
1838 |
+
# this dimension. the corresponding eigenvalue is
|
1839 |
+
# sum(sample_weight).
|
1840 |
+
normalized_sw = sqrt_sw / np.linalg.norm(sqrt_sw)
|
1841 |
+
intercept_dim = _find_smallest_angle(normalized_sw, Q)
|
1842 |
+
w[intercept_dim] = 0 # cancel regularization for the intercept
|
1843 |
+
|
1844 |
+
c = np.dot(Q, self._diag_dot(w, QT_y))
|
1845 |
+
G_inverse_diag = self._decomp_diag(w, Q)
|
1846 |
+
# handle case where y is 2-d
|
1847 |
+
if len(y.shape) != 1:
|
1848 |
+
G_inverse_diag = G_inverse_diag[:, np.newaxis]
|
1849 |
+
return G_inverse_diag, c
|
1850 |
+
|
1851 |
+
def _eigen_decompose_covariance(self, X, y, sqrt_sw):
|
1852 |
+
"""Eigendecomposition of X^T.X, used when n_samples > n_features
|
1853 |
+
and X is sparse.
|
1854 |
+
"""
|
1855 |
+
n_samples, n_features = X.shape
|
1856 |
+
cov = np.empty((n_features + 1, n_features + 1), dtype=X.dtype)
|
1857 |
+
cov[:-1, :-1], X_mean = self._compute_covariance(X, sqrt_sw)
|
1858 |
+
if not self.fit_intercept:
|
1859 |
+
cov = cov[:-1, :-1]
|
1860 |
+
# to emulate centering X with sample weights,
|
1861 |
+
# ie removing the weighted average, we add a column
|
1862 |
+
# containing the square roots of the sample weights.
|
1863 |
+
# by centering, it is orthogonal to the other columns
|
1864 |
+
# when all samples have the same weight we add a column of 1
|
1865 |
+
else:
|
1866 |
+
cov[-1] = 0
|
1867 |
+
cov[:, -1] = 0
|
1868 |
+
cov[-1, -1] = sqrt_sw.dot(sqrt_sw)
|
1869 |
+
nullspace_dim = max(0, n_features - n_samples)
|
1870 |
+
eigvals, V = linalg.eigh(cov)
|
1871 |
+
# remove eigenvalues and vectors in the null space of X^T.X
|
1872 |
+
eigvals = eigvals[nullspace_dim:]
|
1873 |
+
V = V[:, nullspace_dim:]
|
1874 |
+
return X_mean, eigvals, V, X
|
1875 |
+
|
1876 |
+
def _solve_eigen_covariance_no_intercept(
|
1877 |
+
self, alpha, y, sqrt_sw, X_mean, eigvals, V, X
|
1878 |
+
):
|
1879 |
+
"""Compute dual coefficients and diagonal of G^-1.
|
1880 |
+
|
1881 |
+
Used when we have a decomposition of X^T.X
|
1882 |
+
(n_samples > n_features and X is sparse), and not fitting an intercept.
|
1883 |
+
"""
|
1884 |
+
w = 1 / (eigvals + alpha)
|
1885 |
+
A = (V * w).dot(V.T)
|
1886 |
+
AXy = A.dot(safe_sparse_dot(X.T, y, dense_output=True))
|
1887 |
+
y_hat = safe_sparse_dot(X, AXy, dense_output=True)
|
1888 |
+
hat_diag = self._sparse_multidot_diag(X, A, X_mean, sqrt_sw)
|
1889 |
+
if len(y.shape) != 1:
|
1890 |
+
# handle case where y is 2-d
|
1891 |
+
hat_diag = hat_diag[:, np.newaxis]
|
1892 |
+
return (1 - hat_diag) / alpha, (y - y_hat) / alpha
|
1893 |
+
|
1894 |
+
def _solve_eigen_covariance_intercept(
|
1895 |
+
self, alpha, y, sqrt_sw, X_mean, eigvals, V, X
|
1896 |
+
):
|
1897 |
+
"""Compute dual coefficients and diagonal of G^-1.
|
1898 |
+
|
1899 |
+
Used when we have a decomposition of X^T.X
|
1900 |
+
(n_samples > n_features and X is sparse),
|
1901 |
+
and we are fitting an intercept.
|
1902 |
+
"""
|
1903 |
+
# the vector [0, 0, ..., 0, 1]
|
1904 |
+
# is the eigenvector of X^TX which
|
1905 |
+
# corresponds to the intercept; we cancel the regularization on
|
1906 |
+
# this dimension. the corresponding eigenvalue is
|
1907 |
+
# sum(sample_weight), e.g. n when uniform sample weights.
|
1908 |
+
intercept_sv = np.zeros(V.shape[0])
|
1909 |
+
intercept_sv[-1] = 1
|
1910 |
+
intercept_dim = _find_smallest_angle(intercept_sv, V)
|
1911 |
+
w = 1 / (eigvals + alpha)
|
1912 |
+
w[intercept_dim] = 1 / eigvals[intercept_dim]
|
1913 |
+
A = (V * w).dot(V.T)
|
1914 |
+
# add a column to X containing the square roots of sample weights
|
1915 |
+
X_op = _X_CenterStackOp(X, X_mean, sqrt_sw)
|
1916 |
+
AXy = A.dot(X_op.T.dot(y))
|
1917 |
+
y_hat = X_op.dot(AXy)
|
1918 |
+
hat_diag = self._sparse_multidot_diag(X, A, X_mean, sqrt_sw)
|
1919 |
+
# return (1 - hat_diag), (y - y_hat)
|
1920 |
+
if len(y.shape) != 1:
|
1921 |
+
# handle case where y is 2-d
|
1922 |
+
hat_diag = hat_diag[:, np.newaxis]
|
1923 |
+
return (1 - hat_diag) / alpha, (y - y_hat) / alpha
|
1924 |
+
|
1925 |
+
def _solve_eigen_covariance(self, alpha, y, sqrt_sw, X_mean, eigvals, V, X):
|
1926 |
+
"""Compute dual coefficients and diagonal of G^-1.
|
1927 |
+
|
1928 |
+
Used when we have a decomposition of X^T.X
|
1929 |
+
(n_samples > n_features and X is sparse).
|
1930 |
+
"""
|
1931 |
+
if self.fit_intercept:
|
1932 |
+
return self._solve_eigen_covariance_intercept(
|
1933 |
+
alpha, y, sqrt_sw, X_mean, eigvals, V, X
|
1934 |
+
)
|
1935 |
+
return self._solve_eigen_covariance_no_intercept(
|
1936 |
+
alpha, y, sqrt_sw, X_mean, eigvals, V, X
|
1937 |
+
)
|
1938 |
+
|
1939 |
+
def _svd_decompose_design_matrix(self, X, y, sqrt_sw):
|
1940 |
+
# X already centered
|
1941 |
+
X_mean = np.zeros(X.shape[1], dtype=X.dtype)
|
1942 |
+
if self.fit_intercept:
|
1943 |
+
# to emulate fit_intercept=True situation, add a column
|
1944 |
+
# containing the square roots of the sample weights
|
1945 |
+
# by centering, the other columns are orthogonal to that one
|
1946 |
+
intercept_column = sqrt_sw[:, None]
|
1947 |
+
X = np.hstack((X, intercept_column))
|
1948 |
+
U, singvals, _ = linalg.svd(X, full_matrices=0)
|
1949 |
+
singvals_sq = singvals**2
|
1950 |
+
UT_y = np.dot(U.T, y)
|
1951 |
+
return X_mean, singvals_sq, U, UT_y
|
1952 |
+
|
1953 |
+
def _solve_svd_design_matrix(self, alpha, y, sqrt_sw, X_mean, singvals_sq, U, UT_y):
|
1954 |
+
"""Compute dual coefficients and diagonal of G^-1.
|
1955 |
+
|
1956 |
+
Used when we have an SVD decomposition of X
|
1957 |
+
(n_samples > n_features and X is dense).
|
1958 |
+
"""
|
1959 |
+
w = ((singvals_sq + alpha) ** -1) - (alpha**-1)
|
1960 |
+
if self.fit_intercept:
|
1961 |
+
# detect intercept column
|
1962 |
+
normalized_sw = sqrt_sw / np.linalg.norm(sqrt_sw)
|
1963 |
+
intercept_dim = _find_smallest_angle(normalized_sw, U)
|
1964 |
+
# cancel the regularization for the intercept
|
1965 |
+
w[intercept_dim] = -(alpha**-1)
|
1966 |
+
c = np.dot(U, self._diag_dot(w, UT_y)) + (alpha**-1) * y
|
1967 |
+
G_inverse_diag = self._decomp_diag(w, U) + (alpha**-1)
|
1968 |
+
if len(y.shape) != 1:
|
1969 |
+
# handle case where y is 2-d
|
1970 |
+
G_inverse_diag = G_inverse_diag[:, np.newaxis]
|
1971 |
+
return G_inverse_diag, c
|
1972 |
+
|
1973 |
+
def fit(self, X, y, sample_weight=None):
|
1974 |
+
"""Fit Ridge regression model with gcv.
|
1975 |
+
|
1976 |
+
Parameters
|
1977 |
+
----------
|
1978 |
+
X : {ndarray, sparse matrix} of shape (n_samples, n_features)
|
1979 |
+
Training data. Will be cast to float64 if necessary.
|
1980 |
+
|
1981 |
+
y : ndarray of shape (n_samples,) or (n_samples, n_targets)
|
1982 |
+
Target values. Will be cast to float64 if necessary.
|
1983 |
+
|
1984 |
+
sample_weight : float or ndarray of shape (n_samples,), default=None
|
1985 |
+
Individual weights for each sample. If given a float, every sample
|
1986 |
+
will have the same weight. Note that the scale of `sample_weight`
|
1987 |
+
has an impact on the loss; i.e. multiplying all weights by `k`
|
1988 |
+
is equivalent to setting `alpha / k`.
|
1989 |
+
|
1990 |
+
Returns
|
1991 |
+
-------
|
1992 |
+
self : object
|
1993 |
+
"""
|
1994 |
+
X, y = self._validate_data(
|
1995 |
+
X,
|
1996 |
+
y,
|
1997 |
+
accept_sparse=["csr", "csc", "coo"],
|
1998 |
+
dtype=[np.float64],
|
1999 |
+
multi_output=True,
|
2000 |
+
y_numeric=True,
|
2001 |
+
)
|
2002 |
+
|
2003 |
+
# alpha_per_target cannot be used in classifier mode. All subclasses
|
2004 |
+
# of _RidgeGCV that are classifiers keep alpha_per_target at its
|
2005 |
+
# default value: False, so the condition below should never happen.
|
2006 |
+
assert not (self.is_clf and self.alpha_per_target)
|
2007 |
+
|
2008 |
+
if sample_weight is not None:
|
2009 |
+
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
|
2010 |
+
|
2011 |
+
self.alphas = np.asarray(self.alphas)
|
2012 |
+
|
2013 |
+
X, y, X_offset, y_offset, X_scale = _preprocess_data(
|
2014 |
+
X,
|
2015 |
+
y,
|
2016 |
+
fit_intercept=self.fit_intercept,
|
2017 |
+
copy=self.copy_X,
|
2018 |
+
sample_weight=sample_weight,
|
2019 |
+
)
|
2020 |
+
|
2021 |
+
gcv_mode = _check_gcv_mode(X, self.gcv_mode)
|
2022 |
+
|
2023 |
+
if gcv_mode == "eigen":
|
2024 |
+
decompose = self._eigen_decompose_gram
|
2025 |
+
solve = self._solve_eigen_gram
|
2026 |
+
elif gcv_mode == "svd":
|
2027 |
+
if sparse.issparse(X):
|
2028 |
+
decompose = self._eigen_decompose_covariance
|
2029 |
+
solve = self._solve_eigen_covariance
|
2030 |
+
else:
|
2031 |
+
decompose = self._svd_decompose_design_matrix
|
2032 |
+
solve = self._solve_svd_design_matrix
|
2033 |
+
|
2034 |
+
n_samples = X.shape[0]
|
2035 |
+
|
2036 |
+
if sample_weight is not None:
|
2037 |
+
X, y, sqrt_sw = _rescale_data(X, y, sample_weight)
|
2038 |
+
else:
|
2039 |
+
sqrt_sw = np.ones(n_samples, dtype=X.dtype)
|
2040 |
+
|
2041 |
+
X_mean, *decomposition = decompose(X, y, sqrt_sw)
|
2042 |
+
|
2043 |
+
scorer = check_scoring(self, scoring=self.scoring, allow_none=True)
|
2044 |
+
error = scorer is None
|
2045 |
+
|
2046 |
+
n_y = 1 if len(y.shape) == 1 else y.shape[1]
|
2047 |
+
n_alphas = 1 if np.ndim(self.alphas) == 0 else len(self.alphas)
|
2048 |
+
|
2049 |
+
if self.store_cv_values:
|
2050 |
+
self.cv_values_ = np.empty((n_samples * n_y, n_alphas), dtype=X.dtype)
|
2051 |
+
|
2052 |
+
best_coef, best_score, best_alpha = None, None, None
|
2053 |
+
|
2054 |
+
for i, alpha in enumerate(np.atleast_1d(self.alphas)):
|
2055 |
+
G_inverse_diag, c = solve(float(alpha), y, sqrt_sw, X_mean, *decomposition)
|
2056 |
+
if error:
|
2057 |
+
squared_errors = (c / G_inverse_diag) ** 2
|
2058 |
+
if self.alpha_per_target:
|
2059 |
+
alpha_score = -squared_errors.mean(axis=0)
|
2060 |
+
else:
|
2061 |
+
alpha_score = -squared_errors.mean()
|
2062 |
+
if self.store_cv_values:
|
2063 |
+
self.cv_values_[:, i] = squared_errors.ravel()
|
2064 |
+
else:
|
2065 |
+
predictions = y - (c / G_inverse_diag)
|
2066 |
+
if self.store_cv_values:
|
2067 |
+
self.cv_values_[:, i] = predictions.ravel()
|
2068 |
+
|
2069 |
+
if self.is_clf:
|
2070 |
+
identity_estimator = _IdentityClassifier(classes=np.arange(n_y))
|
2071 |
+
alpha_score = scorer(
|
2072 |
+
identity_estimator, predictions, y.argmax(axis=1)
|
2073 |
+
)
|
2074 |
+
else:
|
2075 |
+
identity_estimator = _IdentityRegressor()
|
2076 |
+
if self.alpha_per_target:
|
2077 |
+
alpha_score = np.array(
|
2078 |
+
[
|
2079 |
+
scorer(identity_estimator, predictions[:, j], y[:, j])
|
2080 |
+
for j in range(n_y)
|
2081 |
+
]
|
2082 |
+
)
|
2083 |
+
else:
|
2084 |
+
alpha_score = scorer(
|
2085 |
+
identity_estimator, predictions.ravel(), y.ravel()
|
2086 |
+
)
|
2087 |
+
|
2088 |
+
# Keep track of the best model
|
2089 |
+
if best_score is None:
|
2090 |
+
# initialize
|
2091 |
+
if self.alpha_per_target and n_y > 1:
|
2092 |
+
best_coef = c
|
2093 |
+
best_score = np.atleast_1d(alpha_score)
|
2094 |
+
best_alpha = np.full(n_y, alpha)
|
2095 |
+
else:
|
2096 |
+
best_coef = c
|
2097 |
+
best_score = alpha_score
|
2098 |
+
best_alpha = alpha
|
2099 |
+
else:
|
2100 |
+
# update
|
2101 |
+
if self.alpha_per_target and n_y > 1:
|
2102 |
+
to_update = alpha_score > best_score
|
2103 |
+
best_coef[:, to_update] = c[:, to_update]
|
2104 |
+
best_score[to_update] = alpha_score[to_update]
|
2105 |
+
best_alpha[to_update] = alpha
|
2106 |
+
elif alpha_score > best_score:
|
2107 |
+
best_coef, best_score, best_alpha = c, alpha_score, alpha
|
2108 |
+
|
2109 |
+
self.alpha_ = best_alpha
|
2110 |
+
self.best_score_ = best_score
|
2111 |
+
self.dual_coef_ = best_coef
|
2112 |
+
self.coef_ = safe_sparse_dot(self.dual_coef_.T, X)
|
2113 |
+
|
2114 |
+
if sparse.issparse(X):
|
2115 |
+
X_offset = X_mean * X_scale
|
2116 |
+
else:
|
2117 |
+
X_offset += X_mean * X_scale
|
2118 |
+
self._set_intercept(X_offset, y_offset, X_scale)
|
2119 |
+
|
2120 |
+
if self.store_cv_values:
|
2121 |
+
if len(y.shape) == 1:
|
2122 |
+
cv_values_shape = n_samples, n_alphas
|
2123 |
+
else:
|
2124 |
+
cv_values_shape = n_samples, n_y, n_alphas
|
2125 |
+
self.cv_values_ = self.cv_values_.reshape(cv_values_shape)
|
2126 |
+
|
2127 |
+
return self
|
2128 |
+
|
2129 |
+
|
2130 |
+
class _BaseRidgeCV(LinearModel):
|
2131 |
+
_parameter_constraints: dict = {
|
2132 |
+
"alphas": ["array-like", Interval(Real, 0, None, closed="neither")],
|
2133 |
+
"fit_intercept": ["boolean"],
|
2134 |
+
"scoring": [StrOptions(set(get_scorer_names())), callable, None],
|
2135 |
+
"cv": ["cv_object"],
|
2136 |
+
"gcv_mode": [StrOptions({"auto", "svd", "eigen"}), None],
|
2137 |
+
"store_cv_values": ["boolean"],
|
2138 |
+
"alpha_per_target": ["boolean"],
|
2139 |
+
}
|
2140 |
+
|
2141 |
+
def __init__(
|
2142 |
+
self,
|
2143 |
+
alphas=(0.1, 1.0, 10.0),
|
2144 |
+
*,
|
2145 |
+
fit_intercept=True,
|
2146 |
+
scoring=None,
|
2147 |
+
cv=None,
|
2148 |
+
gcv_mode=None,
|
2149 |
+
store_cv_values=False,
|
2150 |
+
alpha_per_target=False,
|
2151 |
+
):
|
2152 |
+
self.alphas = alphas
|
2153 |
+
self.fit_intercept = fit_intercept
|
2154 |
+
self.scoring = scoring
|
2155 |
+
self.cv = cv
|
2156 |
+
self.gcv_mode = gcv_mode
|
2157 |
+
self.store_cv_values = store_cv_values
|
2158 |
+
self.alpha_per_target = alpha_per_target
|
2159 |
+
|
2160 |
+
def fit(self, X, y, sample_weight=None):
|
2161 |
+
"""Fit Ridge regression model with cv.
|
2162 |
+
|
2163 |
+
Parameters
|
2164 |
+
----------
|
2165 |
+
X : ndarray of shape (n_samples, n_features)
|
2166 |
+
Training data. If using GCV, will be cast to float64
|
2167 |
+
if necessary.
|
2168 |
+
|
2169 |
+
y : ndarray of shape (n_samples,) or (n_samples, n_targets)
|
2170 |
+
Target values. Will be cast to X's dtype if necessary.
|
2171 |
+
|
2172 |
+
sample_weight : float or ndarray of shape (n_samples,), default=None
|
2173 |
+
Individual weights for each sample. If given a float, every sample
|
2174 |
+
will have the same weight.
|
2175 |
+
|
2176 |
+
Returns
|
2177 |
+
-------
|
2178 |
+
self : object
|
2179 |
+
Fitted estimator.
|
2180 |
+
|
2181 |
+
Notes
|
2182 |
+
-----
|
2183 |
+
When sample_weight is provided, the selected hyperparameter may depend
|
2184 |
+
on whether we use leave-one-out cross-validation (cv=None or cv='auto')
|
2185 |
+
or another form of cross-validation, because only leave-one-out
|
2186 |
+
cross-validation takes the sample weights into account when computing
|
2187 |
+
the validation score.
|
2188 |
+
"""
|
2189 |
+
cv = self.cv
|
2190 |
+
|
2191 |
+
check_scalar_alpha = partial(
|
2192 |
+
check_scalar,
|
2193 |
+
target_type=numbers.Real,
|
2194 |
+
min_val=0.0,
|
2195 |
+
include_boundaries="neither",
|
2196 |
+
)
|
2197 |
+
|
2198 |
+
if isinstance(self.alphas, (np.ndarray, list, tuple)):
|
2199 |
+
n_alphas = 1 if np.ndim(self.alphas) == 0 else len(self.alphas)
|
2200 |
+
if n_alphas != 1:
|
2201 |
+
for index, alpha in enumerate(self.alphas):
|
2202 |
+
alpha = check_scalar_alpha(alpha, f"alphas[{index}]")
|
2203 |
+
else:
|
2204 |
+
self.alphas[0] = check_scalar_alpha(self.alphas[0], "alphas")
|
2205 |
+
alphas = np.asarray(self.alphas)
|
2206 |
+
|
2207 |
+
if cv is None:
|
2208 |
+
estimator = _RidgeGCV(
|
2209 |
+
alphas,
|
2210 |
+
fit_intercept=self.fit_intercept,
|
2211 |
+
scoring=self.scoring,
|
2212 |
+
gcv_mode=self.gcv_mode,
|
2213 |
+
store_cv_values=self.store_cv_values,
|
2214 |
+
is_clf=is_classifier(self),
|
2215 |
+
alpha_per_target=self.alpha_per_target,
|
2216 |
+
)
|
2217 |
+
estimator.fit(X, y, sample_weight=sample_weight)
|
2218 |
+
self.alpha_ = estimator.alpha_
|
2219 |
+
self.best_score_ = estimator.best_score_
|
2220 |
+
if self.store_cv_values:
|
2221 |
+
self.cv_values_ = estimator.cv_values_
|
2222 |
+
else:
|
2223 |
+
if self.store_cv_values:
|
2224 |
+
raise ValueError("cv!=None and store_cv_values=True are incompatible")
|
2225 |
+
if self.alpha_per_target:
|
2226 |
+
raise ValueError("cv!=None and alpha_per_target=True are incompatible")
|
2227 |
+
|
2228 |
+
parameters = {"alpha": alphas}
|
2229 |
+
solver = "sparse_cg" if sparse.issparse(X) else "auto"
|
2230 |
+
model = RidgeClassifier if is_classifier(self) else Ridge
|
2231 |
+
gs = GridSearchCV(
|
2232 |
+
model(
|
2233 |
+
fit_intercept=self.fit_intercept,
|
2234 |
+
solver=solver,
|
2235 |
+
),
|
2236 |
+
parameters,
|
2237 |
+
cv=cv,
|
2238 |
+
scoring=self.scoring,
|
2239 |
+
)
|
2240 |
+
gs.fit(X, y, sample_weight=sample_weight)
|
2241 |
+
estimator = gs.best_estimator_
|
2242 |
+
self.alpha_ = gs.best_estimator_.alpha
|
2243 |
+
self.best_score_ = gs.best_score_
|
2244 |
+
|
2245 |
+
self.coef_ = estimator.coef_
|
2246 |
+
self.intercept_ = estimator.intercept_
|
2247 |
+
self.n_features_in_ = estimator.n_features_in_
|
2248 |
+
if hasattr(estimator, "feature_names_in_"):
|
2249 |
+
self.feature_names_in_ = estimator.feature_names_in_
|
2250 |
+
|
2251 |
+
return self
|
2252 |
+
|
2253 |
+
|
2254 |
+
class RidgeCV(
|
2255 |
+
_RoutingNotSupportedMixin, MultiOutputMixin, RegressorMixin, _BaseRidgeCV
|
2256 |
+
):
|
2257 |
+
"""Ridge regression with built-in cross-validation.
|
2258 |
+
|
2259 |
+
See glossary entry for :term:`cross-validation estimator`.
|
2260 |
+
|
2261 |
+
By default, it performs efficient Leave-One-Out Cross-Validation.
|
2262 |
+
|
2263 |
+
Read more in the :ref:`User Guide <ridge_regression>`.
|
2264 |
+
|
2265 |
+
Parameters
|
2266 |
+
----------
|
2267 |
+
alphas : array-like of shape (n_alphas,), default=(0.1, 1.0, 10.0)
|
2268 |
+
Array of alpha values to try.
|
2269 |
+
Regularization strength; must be a positive float. Regularization
|
2270 |
+
improves the conditioning of the problem and reduces the variance of
|
2271 |
+
the estimates. Larger values specify stronger regularization.
|
2272 |
+
Alpha corresponds to ``1 / (2C)`` in other linear models such as
|
2273 |
+
:class:`~sklearn.linear_model.LogisticRegression` or
|
2274 |
+
:class:`~sklearn.svm.LinearSVC`.
|
2275 |
+
If using Leave-One-Out cross-validation, alphas must be positive.
|
2276 |
+
|
2277 |
+
fit_intercept : bool, default=True
|
2278 |
+
Whether to calculate the intercept for this model. If set
|
2279 |
+
to false, no intercept will be used in calculations
|
2280 |
+
(i.e. data is expected to be centered).
|
2281 |
+
|
2282 |
+
scoring : str, callable, default=None
|
2283 |
+
A string (see model evaluation documentation) or
|
2284 |
+
a scorer callable object / function with signature
|
2285 |
+
``scorer(estimator, X, y)``.
|
2286 |
+
If None, the negative mean squared error if cv is 'auto' or None
|
2287 |
+
(i.e. when using leave-one-out cross-validation), and r2 score
|
2288 |
+
otherwise.
|
2289 |
+
|
2290 |
+
cv : int, cross-validation generator or an iterable, default=None
|
2291 |
+
Determines the cross-validation splitting strategy.
|
2292 |
+
Possible inputs for cv are:
|
2293 |
+
|
2294 |
+
- None, to use the efficient Leave-One-Out cross-validation
|
2295 |
+
- integer, to specify the number of folds.
|
2296 |
+
- :term:`CV splitter`,
|
2297 |
+
- An iterable yielding (train, test) splits as arrays of indices.
|
2298 |
+
|
2299 |
+
For integer/None inputs, if ``y`` is binary or multiclass,
|
2300 |
+
:class:`~sklearn.model_selection.StratifiedKFold` is used, else,
|
2301 |
+
:class:`~sklearn.model_selection.KFold` is used.
|
2302 |
+
|
2303 |
+
Refer :ref:`User Guide <cross_validation>` for the various
|
2304 |
+
cross-validation strategies that can be used here.
|
2305 |
+
|
2306 |
+
gcv_mode : {'auto', 'svd', 'eigen'}, default='auto'
|
2307 |
+
Flag indicating which strategy to use when performing
|
2308 |
+
Leave-One-Out Cross-Validation. Options are::
|
2309 |
+
|
2310 |
+
'auto' : use 'svd' if n_samples > n_features, otherwise use 'eigen'
|
2311 |
+
'svd' : force use of singular value decomposition of X when X is
|
2312 |
+
dense, eigenvalue decomposition of X^T.X when X is sparse.
|
2313 |
+
'eigen' : force computation via eigendecomposition of X.X^T
|
2314 |
+
|
2315 |
+
The 'auto' mode is the default and is intended to pick the cheaper
|
2316 |
+
option of the two depending on the shape of the training data.
|
2317 |
+
|
2318 |
+
store_cv_values : bool, default=False
|
2319 |
+
Flag indicating if the cross-validation values corresponding to
|
2320 |
+
each alpha should be stored in the ``cv_values_`` attribute (see
|
2321 |
+
below). This flag is only compatible with ``cv=None`` (i.e. using
|
2322 |
+
Leave-One-Out Cross-Validation).
|
2323 |
+
|
2324 |
+
alpha_per_target : bool, default=False
|
2325 |
+
Flag indicating whether to optimize the alpha value (picked from the
|
2326 |
+
`alphas` parameter list) for each target separately (for multi-output
|
2327 |
+
settings: multiple prediction targets). When set to `True`, after
|
2328 |
+
fitting, the `alpha_` attribute will contain a value for each target.
|
2329 |
+
When set to `False`, a single alpha is used for all targets.
|
2330 |
+
|
2331 |
+
.. versionadded:: 0.24
|
2332 |
+
|
2333 |
+
Attributes
|
2334 |
+
----------
|
2335 |
+
cv_values_ : ndarray of shape (n_samples, n_alphas) or \
|
2336 |
+
shape (n_samples, n_targets, n_alphas), optional
|
2337 |
+
Cross-validation values for each alpha (only available if
|
2338 |
+
``store_cv_values=True`` and ``cv=None``). After ``fit()`` has been
|
2339 |
+
called, this attribute will contain the mean squared errors if
|
2340 |
+
`scoring is None` otherwise it will contain standardized per point
|
2341 |
+
prediction values.
|
2342 |
+
|
2343 |
+
coef_ : ndarray of shape (n_features) or (n_targets, n_features)
|
2344 |
+
Weight vector(s).
|
2345 |
+
|
2346 |
+
intercept_ : float or ndarray of shape (n_targets,)
|
2347 |
+
Independent term in decision function. Set to 0.0 if
|
2348 |
+
``fit_intercept = False``.
|
2349 |
+
|
2350 |
+
alpha_ : float or ndarray of shape (n_targets,)
|
2351 |
+
Estimated regularization parameter, or, if ``alpha_per_target=True``,
|
2352 |
+
the estimated regularization parameter for each target.
|
2353 |
+
|
2354 |
+
best_score_ : float or ndarray of shape (n_targets,)
|
2355 |
+
Score of base estimator with best alpha, or, if
|
2356 |
+
``alpha_per_target=True``, a score for each target.
|
2357 |
+
|
2358 |
+
.. versionadded:: 0.23
|
2359 |
+
|
2360 |
+
n_features_in_ : int
|
2361 |
+
Number of features seen during :term:`fit`.
|
2362 |
+
|
2363 |
+
.. versionadded:: 0.24
|
2364 |
+
|
2365 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
2366 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
2367 |
+
has feature names that are all strings.
|
2368 |
+
|
2369 |
+
.. versionadded:: 1.0
|
2370 |
+
|
2371 |
+
See Also
|
2372 |
+
--------
|
2373 |
+
Ridge : Ridge regression.
|
2374 |
+
RidgeClassifier : Classifier based on ridge regression on {-1, 1} labels.
|
2375 |
+
RidgeClassifierCV : Ridge classifier with built-in cross validation.
|
2376 |
+
|
2377 |
+
Examples
|
2378 |
+
--------
|
2379 |
+
>>> from sklearn.datasets import load_diabetes
|
2380 |
+
>>> from sklearn.linear_model import RidgeCV
|
2381 |
+
>>> X, y = load_diabetes(return_X_y=True)
|
2382 |
+
>>> clf = RidgeCV(alphas=[1e-3, 1e-2, 1e-1, 1]).fit(X, y)
|
2383 |
+
>>> clf.score(X, y)
|
2384 |
+
0.5166...
|
2385 |
+
"""
|
2386 |
+
|
2387 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
2388 |
+
def fit(self, X, y, sample_weight=None):
|
2389 |
+
"""Fit Ridge regression model with cv.
|
2390 |
+
|
2391 |
+
Parameters
|
2392 |
+
----------
|
2393 |
+
X : ndarray of shape (n_samples, n_features)
|
2394 |
+
Training data. If using GCV, will be cast to float64
|
2395 |
+
if necessary.
|
2396 |
+
|
2397 |
+
y : ndarray of shape (n_samples,) or (n_samples, n_targets)
|
2398 |
+
Target values. Will be cast to X's dtype if necessary.
|
2399 |
+
|
2400 |
+
sample_weight : float or ndarray of shape (n_samples,), default=None
|
2401 |
+
Individual weights for each sample. If given a float, every sample
|
2402 |
+
will have the same weight.
|
2403 |
+
|
2404 |
+
Returns
|
2405 |
+
-------
|
2406 |
+
self : object
|
2407 |
+
Fitted estimator.
|
2408 |
+
|
2409 |
+
Notes
|
2410 |
+
-----
|
2411 |
+
When sample_weight is provided, the selected hyperparameter may depend
|
2412 |
+
on whether we use leave-one-out cross-validation (cv=None or cv='auto')
|
2413 |
+
or another form of cross-validation, because only leave-one-out
|
2414 |
+
cross-validation takes the sample weights into account when computing
|
2415 |
+
the validation score.
|
2416 |
+
"""
|
2417 |
+
_raise_for_unsupported_routing(self, "fit", sample_weight=sample_weight)
|
2418 |
+
super().fit(X, y, sample_weight=sample_weight)
|
2419 |
+
return self
|
2420 |
+
|
2421 |
+
|
2422 |
+
class RidgeClassifierCV(_RoutingNotSupportedMixin, _RidgeClassifierMixin, _BaseRidgeCV):
|
2423 |
+
"""Ridge classifier with built-in cross-validation.
|
2424 |
+
|
2425 |
+
See glossary entry for :term:`cross-validation estimator`.
|
2426 |
+
|
2427 |
+
By default, it performs Leave-One-Out Cross-Validation. Currently,
|
2428 |
+
only the n_features > n_samples case is handled efficiently.
|
2429 |
+
|
2430 |
+
Read more in the :ref:`User Guide <ridge_regression>`.
|
2431 |
+
|
2432 |
+
Parameters
|
2433 |
+
----------
|
2434 |
+
alphas : array-like of shape (n_alphas,), default=(0.1, 1.0, 10.0)
|
2435 |
+
Array of alpha values to try.
|
2436 |
+
Regularization strength; must be a positive float. Regularization
|
2437 |
+
improves the conditioning of the problem and reduces the variance of
|
2438 |
+
the estimates. Larger values specify stronger regularization.
|
2439 |
+
Alpha corresponds to ``1 / (2C)`` in other linear models such as
|
2440 |
+
:class:`~sklearn.linear_model.LogisticRegression` or
|
2441 |
+
:class:`~sklearn.svm.LinearSVC`.
|
2442 |
+
|
2443 |
+
fit_intercept : bool, default=True
|
2444 |
+
Whether to calculate the intercept for this model. If set
|
2445 |
+
to false, no intercept will be used in calculations
|
2446 |
+
(i.e. data is expected to be centered).
|
2447 |
+
|
2448 |
+
scoring : str, callable, default=None
|
2449 |
+
A string (see model evaluation documentation) or
|
2450 |
+
a scorer callable object / function with signature
|
2451 |
+
``scorer(estimator, X, y)``.
|
2452 |
+
|
2453 |
+
cv : int, cross-validation generator or an iterable, default=None
|
2454 |
+
Determines the cross-validation splitting strategy.
|
2455 |
+
Possible inputs for cv are:
|
2456 |
+
|
2457 |
+
- None, to use the efficient Leave-One-Out cross-validation
|
2458 |
+
- integer, to specify the number of folds.
|
2459 |
+
- :term:`CV splitter`,
|
2460 |
+
- An iterable yielding (train, test) splits as arrays of indices.
|
2461 |
+
|
2462 |
+
Refer :ref:`User Guide <cross_validation>` for the various
|
2463 |
+
cross-validation strategies that can be used here.
|
2464 |
+
|
2465 |
+
class_weight : dict or 'balanced', default=None
|
2466 |
+
Weights associated with classes in the form ``{class_label: weight}``.
|
2467 |
+
If not given, all classes are supposed to have weight one.
|
2468 |
+
|
2469 |
+
The "balanced" mode uses the values of y to automatically adjust
|
2470 |
+
weights inversely proportional to class frequencies in the input data
|
2471 |
+
as ``n_samples / (n_classes * np.bincount(y))``.
|
2472 |
+
|
2473 |
+
store_cv_values : bool, default=False
|
2474 |
+
Flag indicating if the cross-validation values corresponding to
|
2475 |
+
each alpha should be stored in the ``cv_values_`` attribute (see
|
2476 |
+
below). This flag is only compatible with ``cv=None`` (i.e. using
|
2477 |
+
Leave-One-Out Cross-Validation).
|
2478 |
+
|
2479 |
+
Attributes
|
2480 |
+
----------
|
2481 |
+
cv_values_ : ndarray of shape (n_samples, n_targets, n_alphas), optional
|
2482 |
+
Cross-validation values for each alpha (only if ``store_cv_values=True`` and
|
2483 |
+
``cv=None``). After ``fit()`` has been called, this attribute will
|
2484 |
+
contain the mean squared errors if `scoring is None` otherwise it
|
2485 |
+
will contain standardized per point prediction values.
|
2486 |
+
|
2487 |
+
coef_ : ndarray of shape (1, n_features) or (n_targets, n_features)
|
2488 |
+
Coefficient of the features in the decision function.
|
2489 |
+
|
2490 |
+
``coef_`` is of shape (1, n_features) when the given problem is binary.
|
2491 |
+
|
2492 |
+
intercept_ : float or ndarray of shape (n_targets,)
|
2493 |
+
Independent term in decision function. Set to 0.0 if
|
2494 |
+
``fit_intercept = False``.
|
2495 |
+
|
2496 |
+
alpha_ : float
|
2497 |
+
Estimated regularization parameter.
|
2498 |
+
|
2499 |
+
best_score_ : float
|
2500 |
+
Score of base estimator with best alpha.
|
2501 |
+
|
2502 |
+
.. versionadded:: 0.23
|
2503 |
+
|
2504 |
+
classes_ : ndarray of shape (n_classes,)
|
2505 |
+
The classes labels.
|
2506 |
+
|
2507 |
+
n_features_in_ : int
|
2508 |
+
Number of features seen during :term:`fit`.
|
2509 |
+
|
2510 |
+
.. versionadded:: 0.24
|
2511 |
+
|
2512 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
2513 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
2514 |
+
has feature names that are all strings.
|
2515 |
+
|
2516 |
+
.. versionadded:: 1.0
|
2517 |
+
|
2518 |
+
See Also
|
2519 |
+
--------
|
2520 |
+
Ridge : Ridge regression.
|
2521 |
+
RidgeClassifier : Ridge classifier.
|
2522 |
+
RidgeCV : Ridge regression with built-in cross validation.
|
2523 |
+
|
2524 |
+
Notes
|
2525 |
+
-----
|
2526 |
+
For multi-class classification, n_class classifiers are trained in
|
2527 |
+
a one-versus-all approach. Concretely, this is implemented by taking
|
2528 |
+
advantage of the multi-variate response support in Ridge.
|
2529 |
+
|
2530 |
+
Examples
|
2531 |
+
--------
|
2532 |
+
>>> from sklearn.datasets import load_breast_cancer
|
2533 |
+
>>> from sklearn.linear_model import RidgeClassifierCV
|
2534 |
+
>>> X, y = load_breast_cancer(return_X_y=True)
|
2535 |
+
>>> clf = RidgeClassifierCV(alphas=[1e-3, 1e-2, 1e-1, 1]).fit(X, y)
|
2536 |
+
>>> clf.score(X, y)
|
2537 |
+
0.9630...
|
2538 |
+
"""
|
2539 |
+
|
2540 |
+
_parameter_constraints: dict = {
|
2541 |
+
**_BaseRidgeCV._parameter_constraints,
|
2542 |
+
"class_weight": [dict, StrOptions({"balanced"}), None],
|
2543 |
+
}
|
2544 |
+
for param in ("gcv_mode", "alpha_per_target"):
|
2545 |
+
_parameter_constraints.pop(param)
|
2546 |
+
|
2547 |
+
def __init__(
|
2548 |
+
self,
|
2549 |
+
alphas=(0.1, 1.0, 10.0),
|
2550 |
+
*,
|
2551 |
+
fit_intercept=True,
|
2552 |
+
scoring=None,
|
2553 |
+
cv=None,
|
2554 |
+
class_weight=None,
|
2555 |
+
store_cv_values=False,
|
2556 |
+
):
|
2557 |
+
super().__init__(
|
2558 |
+
alphas=alphas,
|
2559 |
+
fit_intercept=fit_intercept,
|
2560 |
+
scoring=scoring,
|
2561 |
+
cv=cv,
|
2562 |
+
store_cv_values=store_cv_values,
|
2563 |
+
)
|
2564 |
+
self.class_weight = class_weight
|
2565 |
+
|
2566 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
2567 |
+
def fit(self, X, y, sample_weight=None):
|
2568 |
+
"""Fit Ridge classifier with cv.
|
2569 |
+
|
2570 |
+
Parameters
|
2571 |
+
----------
|
2572 |
+
X : ndarray of shape (n_samples, n_features)
|
2573 |
+
Training vectors, where `n_samples` is the number of samples
|
2574 |
+
and `n_features` is the number of features. When using GCV,
|
2575 |
+
will be cast to float64 if necessary.
|
2576 |
+
|
2577 |
+
y : ndarray of shape (n_samples,)
|
2578 |
+
Target values. Will be cast to X's dtype if necessary.
|
2579 |
+
|
2580 |
+
sample_weight : float or ndarray of shape (n_samples,), default=None
|
2581 |
+
Individual weights for each sample. If given a float, every sample
|
2582 |
+
will have the same weight.
|
2583 |
+
|
2584 |
+
Returns
|
2585 |
+
-------
|
2586 |
+
self : object
|
2587 |
+
Fitted estimator.
|
2588 |
+
"""
|
2589 |
+
_raise_for_unsupported_routing(self, "fit", sample_weight=sample_weight)
|
2590 |
+
# `RidgeClassifier` does not accept "sag" or "saga" solver and thus support
|
2591 |
+
# csr, csc, and coo sparse matrices. By using solver="eigen" we force to accept
|
2592 |
+
# all sparse format.
|
2593 |
+
X, y, sample_weight, Y = self._prepare_data(X, y, sample_weight, solver="eigen")
|
2594 |
+
|
2595 |
+
# If cv is None, gcv mode will be used and we used the binarized Y
|
2596 |
+
# since y will not be binarized in _RidgeGCV estimator.
|
2597 |
+
# If cv is not None, a GridSearchCV with some RidgeClassifier
|
2598 |
+
# estimators are used where y will be binarized. Thus, we pass y
|
2599 |
+
# instead of the binarized Y.
|
2600 |
+
target = Y if self.cv is None else y
|
2601 |
+
super().fit(X, target, sample_weight=sample_weight)
|
2602 |
+
return self
|
2603 |
+
|
2604 |
+
def _more_tags(self):
|
2605 |
+
return {
|
2606 |
+
"multilabel": True,
|
2607 |
+
"_xfail_checks": {
|
2608 |
+
"check_sample_weights_invariance": (
|
2609 |
+
"zero sample_weight is not equivalent to removing samples"
|
2610 |
+
),
|
2611 |
+
},
|
2612 |
+
}
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_sgd_fast.cpython-310-x86_64-linux-gnu.so
ADDED
Binary file (385 kB). View file
|
|
env-llmeval/lib/python3.10/site-packages/sklearn/linear_model/_stochastic_gradient.py
ADDED
@@ -0,0 +1,2605 @@
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|
1 |
+
# Authors: Peter Prettenhofer <[email protected]> (main author)
|
2 |
+
# Mathieu Blondel (partial_fit support)
|
3 |
+
#
|
4 |
+
# License: BSD 3 clause
|
5 |
+
"""Classification, regression and One-Class SVM using Stochastic Gradient
|
6 |
+
Descent (SGD).
|
7 |
+
"""
|
8 |
+
|
9 |
+
import warnings
|
10 |
+
from abc import ABCMeta, abstractmethod
|
11 |
+
from numbers import Integral, Real
|
12 |
+
|
13 |
+
import numpy as np
|
14 |
+
|
15 |
+
from ..base import (
|
16 |
+
BaseEstimator,
|
17 |
+
OutlierMixin,
|
18 |
+
RegressorMixin,
|
19 |
+
_fit_context,
|
20 |
+
clone,
|
21 |
+
is_classifier,
|
22 |
+
)
|
23 |
+
from ..exceptions import ConvergenceWarning
|
24 |
+
from ..model_selection import ShuffleSplit, StratifiedShuffleSplit
|
25 |
+
from ..utils import check_random_state, compute_class_weight, deprecated
|
26 |
+
from ..utils._param_validation import Hidden, Interval, StrOptions
|
27 |
+
from ..utils.extmath import safe_sparse_dot
|
28 |
+
from ..utils.metaestimators import available_if
|
29 |
+
from ..utils.multiclass import _check_partial_fit_first_call
|
30 |
+
from ..utils.parallel import Parallel, delayed
|
31 |
+
from ..utils.validation import _check_sample_weight, check_is_fitted
|
32 |
+
from ._base import LinearClassifierMixin, SparseCoefMixin, make_dataset
|
33 |
+
from ._sgd_fast import (
|
34 |
+
EpsilonInsensitive,
|
35 |
+
Hinge,
|
36 |
+
Huber,
|
37 |
+
Log,
|
38 |
+
ModifiedHuber,
|
39 |
+
SquaredEpsilonInsensitive,
|
40 |
+
SquaredHinge,
|
41 |
+
SquaredLoss,
|
42 |
+
_plain_sgd32,
|
43 |
+
_plain_sgd64,
|
44 |
+
)
|
45 |
+
|
46 |
+
LEARNING_RATE_TYPES = {
|
47 |
+
"constant": 1,
|
48 |
+
"optimal": 2,
|
49 |
+
"invscaling": 3,
|
50 |
+
"adaptive": 4,
|
51 |
+
"pa1": 5,
|
52 |
+
"pa2": 6,
|
53 |
+
}
|
54 |
+
|
55 |
+
PENALTY_TYPES = {"none": 0, "l2": 2, "l1": 1, "elasticnet": 3}
|
56 |
+
|
57 |
+
DEFAULT_EPSILON = 0.1
|
58 |
+
# Default value of ``epsilon`` parameter.
|
59 |
+
|
60 |
+
MAX_INT = np.iinfo(np.int32).max
|
61 |
+
|
62 |
+
|
63 |
+
class _ValidationScoreCallback:
|
64 |
+
"""Callback for early stopping based on validation score"""
|
65 |
+
|
66 |
+
def __init__(self, estimator, X_val, y_val, sample_weight_val, classes=None):
|
67 |
+
self.estimator = clone(estimator)
|
68 |
+
self.estimator.t_ = 1 # to pass check_is_fitted
|
69 |
+
if classes is not None:
|
70 |
+
self.estimator.classes_ = classes
|
71 |
+
self.X_val = X_val
|
72 |
+
self.y_val = y_val
|
73 |
+
self.sample_weight_val = sample_weight_val
|
74 |
+
|
75 |
+
def __call__(self, coef, intercept):
|
76 |
+
est = self.estimator
|
77 |
+
est.coef_ = coef.reshape(1, -1)
|
78 |
+
est.intercept_ = np.atleast_1d(intercept)
|
79 |
+
return est.score(self.X_val, self.y_val, self.sample_weight_val)
|
80 |
+
|
81 |
+
|
82 |
+
class BaseSGD(SparseCoefMixin, BaseEstimator, metaclass=ABCMeta):
|
83 |
+
"""Base class for SGD classification and regression."""
|
84 |
+
|
85 |
+
_parameter_constraints: dict = {
|
86 |
+
"fit_intercept": ["boolean"],
|
87 |
+
"max_iter": [Interval(Integral, 1, None, closed="left")],
|
88 |
+
"tol": [Interval(Real, 0, None, closed="left"), None],
|
89 |
+
"shuffle": ["boolean"],
|
90 |
+
"verbose": ["verbose"],
|
91 |
+
"random_state": ["random_state"],
|
92 |
+
"warm_start": ["boolean"],
|
93 |
+
"average": [Interval(Integral, 0, None, closed="left"), bool, np.bool_],
|
94 |
+
}
|
95 |
+
|
96 |
+
def __init__(
|
97 |
+
self,
|
98 |
+
loss,
|
99 |
+
*,
|
100 |
+
penalty="l2",
|
101 |
+
alpha=0.0001,
|
102 |
+
C=1.0,
|
103 |
+
l1_ratio=0.15,
|
104 |
+
fit_intercept=True,
|
105 |
+
max_iter=1000,
|
106 |
+
tol=1e-3,
|
107 |
+
shuffle=True,
|
108 |
+
verbose=0,
|
109 |
+
epsilon=0.1,
|
110 |
+
random_state=None,
|
111 |
+
learning_rate="optimal",
|
112 |
+
eta0=0.0,
|
113 |
+
power_t=0.5,
|
114 |
+
early_stopping=False,
|
115 |
+
validation_fraction=0.1,
|
116 |
+
n_iter_no_change=5,
|
117 |
+
warm_start=False,
|
118 |
+
average=False,
|
119 |
+
):
|
120 |
+
self.loss = loss
|
121 |
+
self.penalty = penalty
|
122 |
+
self.learning_rate = learning_rate
|
123 |
+
self.epsilon = epsilon
|
124 |
+
self.alpha = alpha
|
125 |
+
self.C = C
|
126 |
+
self.l1_ratio = l1_ratio
|
127 |
+
self.fit_intercept = fit_intercept
|
128 |
+
self.shuffle = shuffle
|
129 |
+
self.random_state = random_state
|
130 |
+
self.verbose = verbose
|
131 |
+
self.eta0 = eta0
|
132 |
+
self.power_t = power_t
|
133 |
+
self.early_stopping = early_stopping
|
134 |
+
self.validation_fraction = validation_fraction
|
135 |
+
self.n_iter_no_change = n_iter_no_change
|
136 |
+
self.warm_start = warm_start
|
137 |
+
self.average = average
|
138 |
+
self.max_iter = max_iter
|
139 |
+
self.tol = tol
|
140 |
+
|
141 |
+
@abstractmethod
|
142 |
+
def fit(self, X, y):
|
143 |
+
"""Fit model."""
|
144 |
+
|
145 |
+
def _more_validate_params(self, for_partial_fit=False):
|
146 |
+
"""Validate input params."""
|
147 |
+
if self.early_stopping and for_partial_fit:
|
148 |
+
raise ValueError("early_stopping should be False with partial_fit")
|
149 |
+
if (
|
150 |
+
self.learning_rate in ("constant", "invscaling", "adaptive")
|
151 |
+
and self.eta0 <= 0.0
|
152 |
+
):
|
153 |
+
raise ValueError("eta0 must be > 0")
|
154 |
+
if self.learning_rate == "optimal" and self.alpha == 0:
|
155 |
+
raise ValueError(
|
156 |
+
"alpha must be > 0 since "
|
157 |
+
"learning_rate is 'optimal'. alpha is used "
|
158 |
+
"to compute the optimal learning rate."
|
159 |
+
)
|
160 |
+
|
161 |
+
# raises ValueError if not registered
|
162 |
+
self._get_penalty_type(self.penalty)
|
163 |
+
self._get_learning_rate_type(self.learning_rate)
|
164 |
+
|
165 |
+
def _get_loss_function(self, loss):
|
166 |
+
"""Get concrete ``LossFunction`` object for str ``loss``."""
|
167 |
+
loss_ = self.loss_functions[loss]
|
168 |
+
loss_class, args = loss_[0], loss_[1:]
|
169 |
+
if loss in ("huber", "epsilon_insensitive", "squared_epsilon_insensitive"):
|
170 |
+
args = (self.epsilon,)
|
171 |
+
return loss_class(*args)
|
172 |
+
|
173 |
+
def _get_learning_rate_type(self, learning_rate):
|
174 |
+
return LEARNING_RATE_TYPES[learning_rate]
|
175 |
+
|
176 |
+
def _get_penalty_type(self, penalty):
|
177 |
+
penalty = str(penalty).lower()
|
178 |
+
return PENALTY_TYPES[penalty]
|
179 |
+
|
180 |
+
def _allocate_parameter_mem(
|
181 |
+
self,
|
182 |
+
n_classes,
|
183 |
+
n_features,
|
184 |
+
input_dtype,
|
185 |
+
coef_init=None,
|
186 |
+
intercept_init=None,
|
187 |
+
one_class=0,
|
188 |
+
):
|
189 |
+
"""Allocate mem for parameters; initialize if provided."""
|
190 |
+
if n_classes > 2:
|
191 |
+
# allocate coef_ for multi-class
|
192 |
+
if coef_init is not None:
|
193 |
+
coef_init = np.asarray(coef_init, dtype=input_dtype, order="C")
|
194 |
+
if coef_init.shape != (n_classes, n_features):
|
195 |
+
raise ValueError("Provided ``coef_`` does not match dataset. ")
|
196 |
+
self.coef_ = coef_init
|
197 |
+
else:
|
198 |
+
self.coef_ = np.zeros(
|
199 |
+
(n_classes, n_features), dtype=input_dtype, order="C"
|
200 |
+
)
|
201 |
+
|
202 |
+
# allocate intercept_ for multi-class
|
203 |
+
if intercept_init is not None:
|
204 |
+
intercept_init = np.asarray(
|
205 |
+
intercept_init, order="C", dtype=input_dtype
|
206 |
+
)
|
207 |
+
if intercept_init.shape != (n_classes,):
|
208 |
+
raise ValueError("Provided intercept_init does not match dataset.")
|
209 |
+
self.intercept_ = intercept_init
|
210 |
+
else:
|
211 |
+
self.intercept_ = np.zeros(n_classes, dtype=input_dtype, order="C")
|
212 |
+
else:
|
213 |
+
# allocate coef_
|
214 |
+
if coef_init is not None:
|
215 |
+
coef_init = np.asarray(coef_init, dtype=input_dtype, order="C")
|
216 |
+
coef_init = coef_init.ravel()
|
217 |
+
if coef_init.shape != (n_features,):
|
218 |
+
raise ValueError("Provided coef_init does not match dataset.")
|
219 |
+
self.coef_ = coef_init
|
220 |
+
else:
|
221 |
+
self.coef_ = np.zeros(n_features, dtype=input_dtype, order="C")
|
222 |
+
|
223 |
+
# allocate intercept_
|
224 |
+
if intercept_init is not None:
|
225 |
+
intercept_init = np.asarray(intercept_init, dtype=input_dtype)
|
226 |
+
if intercept_init.shape != (1,) and intercept_init.shape != ():
|
227 |
+
raise ValueError("Provided intercept_init does not match dataset.")
|
228 |
+
if one_class:
|
229 |
+
self.offset_ = intercept_init.reshape(
|
230 |
+
1,
|
231 |
+
)
|
232 |
+
else:
|
233 |
+
self.intercept_ = intercept_init.reshape(
|
234 |
+
1,
|
235 |
+
)
|
236 |
+
else:
|
237 |
+
if one_class:
|
238 |
+
self.offset_ = np.zeros(1, dtype=input_dtype, order="C")
|
239 |
+
else:
|
240 |
+
self.intercept_ = np.zeros(1, dtype=input_dtype, order="C")
|
241 |
+
|
242 |
+
# initialize average parameters
|
243 |
+
if self.average > 0:
|
244 |
+
self._standard_coef = self.coef_
|
245 |
+
self._average_coef = np.zeros(
|
246 |
+
self.coef_.shape, dtype=input_dtype, order="C"
|
247 |
+
)
|
248 |
+
if one_class:
|
249 |
+
self._standard_intercept = 1 - self.offset_
|
250 |
+
else:
|
251 |
+
self._standard_intercept = self.intercept_
|
252 |
+
|
253 |
+
self._average_intercept = np.zeros(
|
254 |
+
self._standard_intercept.shape, dtype=input_dtype, order="C"
|
255 |
+
)
|
256 |
+
|
257 |
+
def _make_validation_split(self, y, sample_mask):
|
258 |
+
"""Split the dataset between training set and validation set.
|
259 |
+
|
260 |
+
Parameters
|
261 |
+
----------
|
262 |
+
y : ndarray of shape (n_samples, )
|
263 |
+
Target values.
|
264 |
+
|
265 |
+
sample_mask : ndarray of shape (n_samples, )
|
266 |
+
A boolean array indicating whether each sample should be included
|
267 |
+
for validation set.
|
268 |
+
|
269 |
+
Returns
|
270 |
+
-------
|
271 |
+
validation_mask : ndarray of shape (n_samples, )
|
272 |
+
Equal to True on the validation set, False on the training set.
|
273 |
+
"""
|
274 |
+
n_samples = y.shape[0]
|
275 |
+
validation_mask = np.zeros(n_samples, dtype=np.bool_)
|
276 |
+
if not self.early_stopping:
|
277 |
+
# use the full set for training, with an empty validation set
|
278 |
+
return validation_mask
|
279 |
+
|
280 |
+
if is_classifier(self):
|
281 |
+
splitter_type = StratifiedShuffleSplit
|
282 |
+
else:
|
283 |
+
splitter_type = ShuffleSplit
|
284 |
+
cv = splitter_type(
|
285 |
+
test_size=self.validation_fraction, random_state=self.random_state
|
286 |
+
)
|
287 |
+
idx_train, idx_val = next(cv.split(np.zeros(shape=(y.shape[0], 1)), y))
|
288 |
+
|
289 |
+
if not np.any(sample_mask[idx_val]):
|
290 |
+
raise ValueError(
|
291 |
+
"The sample weights for validation set are all zero, consider using a"
|
292 |
+
" different random state."
|
293 |
+
)
|
294 |
+
|
295 |
+
if idx_train.shape[0] == 0 or idx_val.shape[0] == 0:
|
296 |
+
raise ValueError(
|
297 |
+
"Splitting %d samples into a train set and a validation set "
|
298 |
+
"with validation_fraction=%r led to an empty set (%d and %d "
|
299 |
+
"samples). Please either change validation_fraction, increase "
|
300 |
+
"number of samples, or disable early_stopping."
|
301 |
+
% (
|
302 |
+
n_samples,
|
303 |
+
self.validation_fraction,
|
304 |
+
idx_train.shape[0],
|
305 |
+
idx_val.shape[0],
|
306 |
+
)
|
307 |
+
)
|
308 |
+
|
309 |
+
validation_mask[idx_val] = True
|
310 |
+
return validation_mask
|
311 |
+
|
312 |
+
def _make_validation_score_cb(
|
313 |
+
self, validation_mask, X, y, sample_weight, classes=None
|
314 |
+
):
|
315 |
+
if not self.early_stopping:
|
316 |
+
return None
|
317 |
+
|
318 |
+
return _ValidationScoreCallback(
|
319 |
+
self,
|
320 |
+
X[validation_mask],
|
321 |
+
y[validation_mask],
|
322 |
+
sample_weight[validation_mask],
|
323 |
+
classes=classes,
|
324 |
+
)
|
325 |
+
|
326 |
+
# TODO(1.6): Remove
|
327 |
+
# mypy error: Decorated property not supported
|
328 |
+
@deprecated( # type: ignore
|
329 |
+
"Attribute `loss_function_` was deprecated in version 1.4 and will be removed "
|
330 |
+
"in 1.6."
|
331 |
+
)
|
332 |
+
@property
|
333 |
+
def loss_function_(self):
|
334 |
+
return self._loss_function_
|
335 |
+
|
336 |
+
|
337 |
+
def _prepare_fit_binary(est, y, i, input_dtye):
|
338 |
+
"""Initialization for fit_binary.
|
339 |
+
|
340 |
+
Returns y, coef, intercept, average_coef, average_intercept.
|
341 |
+
"""
|
342 |
+
y_i = np.ones(y.shape, dtype=input_dtye, order="C")
|
343 |
+
y_i[y != est.classes_[i]] = -1.0
|
344 |
+
average_intercept = 0
|
345 |
+
average_coef = None
|
346 |
+
|
347 |
+
if len(est.classes_) == 2:
|
348 |
+
if not est.average:
|
349 |
+
coef = est.coef_.ravel()
|
350 |
+
intercept = est.intercept_[0]
|
351 |
+
else:
|
352 |
+
coef = est._standard_coef.ravel()
|
353 |
+
intercept = est._standard_intercept[0]
|
354 |
+
average_coef = est._average_coef.ravel()
|
355 |
+
average_intercept = est._average_intercept[0]
|
356 |
+
else:
|
357 |
+
if not est.average:
|
358 |
+
coef = est.coef_[i]
|
359 |
+
intercept = est.intercept_[i]
|
360 |
+
else:
|
361 |
+
coef = est._standard_coef[i]
|
362 |
+
intercept = est._standard_intercept[i]
|
363 |
+
average_coef = est._average_coef[i]
|
364 |
+
average_intercept = est._average_intercept[i]
|
365 |
+
|
366 |
+
return y_i, coef, intercept, average_coef, average_intercept
|
367 |
+
|
368 |
+
|
369 |
+
def fit_binary(
|
370 |
+
est,
|
371 |
+
i,
|
372 |
+
X,
|
373 |
+
y,
|
374 |
+
alpha,
|
375 |
+
C,
|
376 |
+
learning_rate,
|
377 |
+
max_iter,
|
378 |
+
pos_weight,
|
379 |
+
neg_weight,
|
380 |
+
sample_weight,
|
381 |
+
validation_mask=None,
|
382 |
+
random_state=None,
|
383 |
+
):
|
384 |
+
"""Fit a single binary classifier.
|
385 |
+
|
386 |
+
The i'th class is considered the "positive" class.
|
387 |
+
|
388 |
+
Parameters
|
389 |
+
----------
|
390 |
+
est : Estimator object
|
391 |
+
The estimator to fit
|
392 |
+
|
393 |
+
i : int
|
394 |
+
Index of the positive class
|
395 |
+
|
396 |
+
X : numpy array or sparse matrix of shape [n_samples,n_features]
|
397 |
+
Training data
|
398 |
+
|
399 |
+
y : numpy array of shape [n_samples, ]
|
400 |
+
Target values
|
401 |
+
|
402 |
+
alpha : float
|
403 |
+
The regularization parameter
|
404 |
+
|
405 |
+
C : float
|
406 |
+
Maximum step size for passive aggressive
|
407 |
+
|
408 |
+
learning_rate : str
|
409 |
+
The learning rate. Accepted values are 'constant', 'optimal',
|
410 |
+
'invscaling', 'pa1' and 'pa2'.
|
411 |
+
|
412 |
+
max_iter : int
|
413 |
+
The maximum number of iterations (epochs)
|
414 |
+
|
415 |
+
pos_weight : float
|
416 |
+
The weight of the positive class
|
417 |
+
|
418 |
+
neg_weight : float
|
419 |
+
The weight of the negative class
|
420 |
+
|
421 |
+
sample_weight : numpy array of shape [n_samples, ]
|
422 |
+
The weight of each sample
|
423 |
+
|
424 |
+
validation_mask : numpy array of shape [n_samples, ], default=None
|
425 |
+
Precomputed validation mask in case _fit_binary is called in the
|
426 |
+
context of a one-vs-rest reduction.
|
427 |
+
|
428 |
+
random_state : int, RandomState instance, default=None
|
429 |
+
If int, random_state is the seed used by the random number generator;
|
430 |
+
If RandomState instance, random_state is the random number generator;
|
431 |
+
If None, the random number generator is the RandomState instance used
|
432 |
+
by `np.random`.
|
433 |
+
"""
|
434 |
+
# if average is not true, average_coef, and average_intercept will be
|
435 |
+
# unused
|
436 |
+
y_i, coef, intercept, average_coef, average_intercept = _prepare_fit_binary(
|
437 |
+
est, y, i, input_dtye=X.dtype
|
438 |
+
)
|
439 |
+
assert y_i.shape[0] == y.shape[0] == sample_weight.shape[0]
|
440 |
+
|
441 |
+
random_state = check_random_state(random_state)
|
442 |
+
dataset, intercept_decay = make_dataset(
|
443 |
+
X, y_i, sample_weight, random_state=random_state
|
444 |
+
)
|
445 |
+
|
446 |
+
penalty_type = est._get_penalty_type(est.penalty)
|
447 |
+
learning_rate_type = est._get_learning_rate_type(learning_rate)
|
448 |
+
|
449 |
+
if validation_mask is None:
|
450 |
+
validation_mask = est._make_validation_split(y_i, sample_mask=sample_weight > 0)
|
451 |
+
classes = np.array([-1, 1], dtype=y_i.dtype)
|
452 |
+
validation_score_cb = est._make_validation_score_cb(
|
453 |
+
validation_mask, X, y_i, sample_weight, classes=classes
|
454 |
+
)
|
455 |
+
|
456 |
+
# numpy mtrand expects a C long which is a signed 32 bit integer under
|
457 |
+
# Windows
|
458 |
+
seed = random_state.randint(MAX_INT)
|
459 |
+
|
460 |
+
tol = est.tol if est.tol is not None else -np.inf
|
461 |
+
|
462 |
+
_plain_sgd = _get_plain_sgd_function(input_dtype=coef.dtype)
|
463 |
+
coef, intercept, average_coef, average_intercept, n_iter_ = _plain_sgd(
|
464 |
+
coef,
|
465 |
+
intercept,
|
466 |
+
average_coef,
|
467 |
+
average_intercept,
|
468 |
+
est._loss_function_,
|
469 |
+
penalty_type,
|
470 |
+
alpha,
|
471 |
+
C,
|
472 |
+
est.l1_ratio,
|
473 |
+
dataset,
|
474 |
+
validation_mask,
|
475 |
+
est.early_stopping,
|
476 |
+
validation_score_cb,
|
477 |
+
int(est.n_iter_no_change),
|
478 |
+
max_iter,
|
479 |
+
tol,
|
480 |
+
int(est.fit_intercept),
|
481 |
+
int(est.verbose),
|
482 |
+
int(est.shuffle),
|
483 |
+
seed,
|
484 |
+
pos_weight,
|
485 |
+
neg_weight,
|
486 |
+
learning_rate_type,
|
487 |
+
est.eta0,
|
488 |
+
est.power_t,
|
489 |
+
0,
|
490 |
+
est.t_,
|
491 |
+
intercept_decay,
|
492 |
+
est.average,
|
493 |
+
)
|
494 |
+
|
495 |
+
if est.average:
|
496 |
+
if len(est.classes_) == 2:
|
497 |
+
est._average_intercept[0] = average_intercept
|
498 |
+
else:
|
499 |
+
est._average_intercept[i] = average_intercept
|
500 |
+
|
501 |
+
return coef, intercept, n_iter_
|
502 |
+
|
503 |
+
|
504 |
+
def _get_plain_sgd_function(input_dtype):
|
505 |
+
return _plain_sgd32 if input_dtype == np.float32 else _plain_sgd64
|
506 |
+
|
507 |
+
|
508 |
+
class BaseSGDClassifier(LinearClassifierMixin, BaseSGD, metaclass=ABCMeta):
|
509 |
+
loss_functions = {
|
510 |
+
"hinge": (Hinge, 1.0),
|
511 |
+
"squared_hinge": (SquaredHinge, 1.0),
|
512 |
+
"perceptron": (Hinge, 0.0),
|
513 |
+
"log_loss": (Log,),
|
514 |
+
"modified_huber": (ModifiedHuber,),
|
515 |
+
"squared_error": (SquaredLoss,),
|
516 |
+
"huber": (Huber, DEFAULT_EPSILON),
|
517 |
+
"epsilon_insensitive": (EpsilonInsensitive, DEFAULT_EPSILON),
|
518 |
+
"squared_epsilon_insensitive": (SquaredEpsilonInsensitive, DEFAULT_EPSILON),
|
519 |
+
}
|
520 |
+
|
521 |
+
_parameter_constraints: dict = {
|
522 |
+
**BaseSGD._parameter_constraints,
|
523 |
+
"loss": [StrOptions(set(loss_functions))],
|
524 |
+
"early_stopping": ["boolean"],
|
525 |
+
"validation_fraction": [Interval(Real, 0, 1, closed="neither")],
|
526 |
+
"n_iter_no_change": [Interval(Integral, 1, None, closed="left")],
|
527 |
+
"n_jobs": [Integral, None],
|
528 |
+
"class_weight": [StrOptions({"balanced"}), dict, None],
|
529 |
+
}
|
530 |
+
|
531 |
+
@abstractmethod
|
532 |
+
def __init__(
|
533 |
+
self,
|
534 |
+
loss="hinge",
|
535 |
+
*,
|
536 |
+
penalty="l2",
|
537 |
+
alpha=0.0001,
|
538 |
+
l1_ratio=0.15,
|
539 |
+
fit_intercept=True,
|
540 |
+
max_iter=1000,
|
541 |
+
tol=1e-3,
|
542 |
+
shuffle=True,
|
543 |
+
verbose=0,
|
544 |
+
epsilon=DEFAULT_EPSILON,
|
545 |
+
n_jobs=None,
|
546 |
+
random_state=None,
|
547 |
+
learning_rate="optimal",
|
548 |
+
eta0=0.0,
|
549 |
+
power_t=0.5,
|
550 |
+
early_stopping=False,
|
551 |
+
validation_fraction=0.1,
|
552 |
+
n_iter_no_change=5,
|
553 |
+
class_weight=None,
|
554 |
+
warm_start=False,
|
555 |
+
average=False,
|
556 |
+
):
|
557 |
+
super().__init__(
|
558 |
+
loss=loss,
|
559 |
+
penalty=penalty,
|
560 |
+
alpha=alpha,
|
561 |
+
l1_ratio=l1_ratio,
|
562 |
+
fit_intercept=fit_intercept,
|
563 |
+
max_iter=max_iter,
|
564 |
+
tol=tol,
|
565 |
+
shuffle=shuffle,
|
566 |
+
verbose=verbose,
|
567 |
+
epsilon=epsilon,
|
568 |
+
random_state=random_state,
|
569 |
+
learning_rate=learning_rate,
|
570 |
+
eta0=eta0,
|
571 |
+
power_t=power_t,
|
572 |
+
early_stopping=early_stopping,
|
573 |
+
validation_fraction=validation_fraction,
|
574 |
+
n_iter_no_change=n_iter_no_change,
|
575 |
+
warm_start=warm_start,
|
576 |
+
average=average,
|
577 |
+
)
|
578 |
+
self.class_weight = class_weight
|
579 |
+
self.n_jobs = n_jobs
|
580 |
+
|
581 |
+
def _partial_fit(
|
582 |
+
self,
|
583 |
+
X,
|
584 |
+
y,
|
585 |
+
alpha,
|
586 |
+
C,
|
587 |
+
loss,
|
588 |
+
learning_rate,
|
589 |
+
max_iter,
|
590 |
+
classes,
|
591 |
+
sample_weight,
|
592 |
+
coef_init,
|
593 |
+
intercept_init,
|
594 |
+
):
|
595 |
+
first_call = not hasattr(self, "classes_")
|
596 |
+
X, y = self._validate_data(
|
597 |
+
X,
|
598 |
+
y,
|
599 |
+
accept_sparse="csr",
|
600 |
+
dtype=[np.float64, np.float32],
|
601 |
+
order="C",
|
602 |
+
accept_large_sparse=False,
|
603 |
+
reset=first_call,
|
604 |
+
)
|
605 |
+
|
606 |
+
n_samples, n_features = X.shape
|
607 |
+
|
608 |
+
_check_partial_fit_first_call(self, classes)
|
609 |
+
|
610 |
+
n_classes = self.classes_.shape[0]
|
611 |
+
|
612 |
+
# Allocate datastructures from input arguments
|
613 |
+
self._expanded_class_weight = compute_class_weight(
|
614 |
+
self.class_weight, classes=self.classes_, y=y
|
615 |
+
)
|
616 |
+
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
|
617 |
+
|
618 |
+
if getattr(self, "coef_", None) is None or coef_init is not None:
|
619 |
+
self._allocate_parameter_mem(
|
620 |
+
n_classes=n_classes,
|
621 |
+
n_features=n_features,
|
622 |
+
input_dtype=X.dtype,
|
623 |
+
coef_init=coef_init,
|
624 |
+
intercept_init=intercept_init,
|
625 |
+
)
|
626 |
+
elif n_features != self.coef_.shape[-1]:
|
627 |
+
raise ValueError(
|
628 |
+
"Number of features %d does not match previous data %d."
|
629 |
+
% (n_features, self.coef_.shape[-1])
|
630 |
+
)
|
631 |
+
|
632 |
+
self._loss_function_ = self._get_loss_function(loss)
|
633 |
+
if not hasattr(self, "t_"):
|
634 |
+
self.t_ = 1.0
|
635 |
+
|
636 |
+
# delegate to concrete training procedure
|
637 |
+
if n_classes > 2:
|
638 |
+
self._fit_multiclass(
|
639 |
+
X,
|
640 |
+
y,
|
641 |
+
alpha=alpha,
|
642 |
+
C=C,
|
643 |
+
learning_rate=learning_rate,
|
644 |
+
sample_weight=sample_weight,
|
645 |
+
max_iter=max_iter,
|
646 |
+
)
|
647 |
+
elif n_classes == 2:
|
648 |
+
self._fit_binary(
|
649 |
+
X,
|
650 |
+
y,
|
651 |
+
alpha=alpha,
|
652 |
+
C=C,
|
653 |
+
learning_rate=learning_rate,
|
654 |
+
sample_weight=sample_weight,
|
655 |
+
max_iter=max_iter,
|
656 |
+
)
|
657 |
+
else:
|
658 |
+
raise ValueError(
|
659 |
+
"The number of classes has to be greater than one; got %d class"
|
660 |
+
% n_classes
|
661 |
+
)
|
662 |
+
|
663 |
+
return self
|
664 |
+
|
665 |
+
def _fit(
|
666 |
+
self,
|
667 |
+
X,
|
668 |
+
y,
|
669 |
+
alpha,
|
670 |
+
C,
|
671 |
+
loss,
|
672 |
+
learning_rate,
|
673 |
+
coef_init=None,
|
674 |
+
intercept_init=None,
|
675 |
+
sample_weight=None,
|
676 |
+
):
|
677 |
+
if hasattr(self, "classes_"):
|
678 |
+
# delete the attribute otherwise _partial_fit thinks it's not the first call
|
679 |
+
delattr(self, "classes_")
|
680 |
+
|
681 |
+
# labels can be encoded as float, int, or string literals
|
682 |
+
# np.unique sorts in asc order; largest class id is positive class
|
683 |
+
y = self._validate_data(y=y)
|
684 |
+
classes = np.unique(y)
|
685 |
+
|
686 |
+
if self.warm_start and hasattr(self, "coef_"):
|
687 |
+
if coef_init is None:
|
688 |
+
coef_init = self.coef_
|
689 |
+
if intercept_init is None:
|
690 |
+
intercept_init = self.intercept_
|
691 |
+
else:
|
692 |
+
self.coef_ = None
|
693 |
+
self.intercept_ = None
|
694 |
+
|
695 |
+
if self.average > 0:
|
696 |
+
self._standard_coef = self.coef_
|
697 |
+
self._standard_intercept = self.intercept_
|
698 |
+
self._average_coef = None
|
699 |
+
self._average_intercept = None
|
700 |
+
|
701 |
+
# Clear iteration count for multiple call to fit.
|
702 |
+
self.t_ = 1.0
|
703 |
+
|
704 |
+
self._partial_fit(
|
705 |
+
X,
|
706 |
+
y,
|
707 |
+
alpha,
|
708 |
+
C,
|
709 |
+
loss,
|
710 |
+
learning_rate,
|
711 |
+
self.max_iter,
|
712 |
+
classes,
|
713 |
+
sample_weight,
|
714 |
+
coef_init,
|
715 |
+
intercept_init,
|
716 |
+
)
|
717 |
+
|
718 |
+
if (
|
719 |
+
self.tol is not None
|
720 |
+
and self.tol > -np.inf
|
721 |
+
and self.n_iter_ == self.max_iter
|
722 |
+
):
|
723 |
+
warnings.warn(
|
724 |
+
(
|
725 |
+
"Maximum number of iteration reached before "
|
726 |
+
"convergence. Consider increasing max_iter to "
|
727 |
+
"improve the fit."
|
728 |
+
),
|
729 |
+
ConvergenceWarning,
|
730 |
+
)
|
731 |
+
return self
|
732 |
+
|
733 |
+
def _fit_binary(self, X, y, alpha, C, sample_weight, learning_rate, max_iter):
|
734 |
+
"""Fit a binary classifier on X and y."""
|
735 |
+
coef, intercept, n_iter_ = fit_binary(
|
736 |
+
self,
|
737 |
+
1,
|
738 |
+
X,
|
739 |
+
y,
|
740 |
+
alpha,
|
741 |
+
C,
|
742 |
+
learning_rate,
|
743 |
+
max_iter,
|
744 |
+
self._expanded_class_weight[1],
|
745 |
+
self._expanded_class_weight[0],
|
746 |
+
sample_weight,
|
747 |
+
random_state=self.random_state,
|
748 |
+
)
|
749 |
+
|
750 |
+
self.t_ += n_iter_ * X.shape[0]
|
751 |
+
self.n_iter_ = n_iter_
|
752 |
+
|
753 |
+
# need to be 2d
|
754 |
+
if self.average > 0:
|
755 |
+
if self.average <= self.t_ - 1:
|
756 |
+
self.coef_ = self._average_coef.reshape(1, -1)
|
757 |
+
self.intercept_ = self._average_intercept
|
758 |
+
else:
|
759 |
+
self.coef_ = self._standard_coef.reshape(1, -1)
|
760 |
+
self._standard_intercept = np.atleast_1d(intercept)
|
761 |
+
self.intercept_ = self._standard_intercept
|
762 |
+
else:
|
763 |
+
self.coef_ = coef.reshape(1, -1)
|
764 |
+
# intercept is a float, need to convert it to an array of length 1
|
765 |
+
self.intercept_ = np.atleast_1d(intercept)
|
766 |
+
|
767 |
+
def _fit_multiclass(self, X, y, alpha, C, learning_rate, sample_weight, max_iter):
|
768 |
+
"""Fit a multi-class classifier by combining binary classifiers
|
769 |
+
|
770 |
+
Each binary classifier predicts one class versus all others. This
|
771 |
+
strategy is called OvA (One versus All) or OvR (One versus Rest).
|
772 |
+
"""
|
773 |
+
# Precompute the validation split using the multiclass labels
|
774 |
+
# to ensure proper balancing of the classes.
|
775 |
+
validation_mask = self._make_validation_split(y, sample_mask=sample_weight > 0)
|
776 |
+
|
777 |
+
# Use joblib to fit OvA in parallel.
|
778 |
+
# Pick the random seed for each job outside of fit_binary to avoid
|
779 |
+
# sharing the estimator random state between threads which could lead
|
780 |
+
# to non-deterministic behavior
|
781 |
+
random_state = check_random_state(self.random_state)
|
782 |
+
seeds = random_state.randint(MAX_INT, size=len(self.classes_))
|
783 |
+
result = Parallel(
|
784 |
+
n_jobs=self.n_jobs, verbose=self.verbose, require="sharedmem"
|
785 |
+
)(
|
786 |
+
delayed(fit_binary)(
|
787 |
+
self,
|
788 |
+
i,
|
789 |
+
X,
|
790 |
+
y,
|
791 |
+
alpha,
|
792 |
+
C,
|
793 |
+
learning_rate,
|
794 |
+
max_iter,
|
795 |
+
self._expanded_class_weight[i],
|
796 |
+
1.0,
|
797 |
+
sample_weight,
|
798 |
+
validation_mask=validation_mask,
|
799 |
+
random_state=seed,
|
800 |
+
)
|
801 |
+
for i, seed in enumerate(seeds)
|
802 |
+
)
|
803 |
+
|
804 |
+
# take the maximum of n_iter_ over every binary fit
|
805 |
+
n_iter_ = 0.0
|
806 |
+
for i, (_, intercept, n_iter_i) in enumerate(result):
|
807 |
+
self.intercept_[i] = intercept
|
808 |
+
n_iter_ = max(n_iter_, n_iter_i)
|
809 |
+
|
810 |
+
self.t_ += n_iter_ * X.shape[0]
|
811 |
+
self.n_iter_ = n_iter_
|
812 |
+
|
813 |
+
if self.average > 0:
|
814 |
+
if self.average <= self.t_ - 1.0:
|
815 |
+
self.coef_ = self._average_coef
|
816 |
+
self.intercept_ = self._average_intercept
|
817 |
+
else:
|
818 |
+
self.coef_ = self._standard_coef
|
819 |
+
self._standard_intercept = np.atleast_1d(self.intercept_)
|
820 |
+
self.intercept_ = self._standard_intercept
|
821 |
+
|
822 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
823 |
+
def partial_fit(self, X, y, classes=None, sample_weight=None):
|
824 |
+
"""Perform one epoch of stochastic gradient descent on given samples.
|
825 |
+
|
826 |
+
Internally, this method uses ``max_iter = 1``. Therefore, it is not
|
827 |
+
guaranteed that a minimum of the cost function is reached after calling
|
828 |
+
it once. Matters such as objective convergence, early stopping, and
|
829 |
+
learning rate adjustments should be handled by the user.
|
830 |
+
|
831 |
+
Parameters
|
832 |
+
----------
|
833 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
834 |
+
Subset of the training data.
|
835 |
+
|
836 |
+
y : ndarray of shape (n_samples,)
|
837 |
+
Subset of the target values.
|
838 |
+
|
839 |
+
classes : ndarray of shape (n_classes,), default=None
|
840 |
+
Classes across all calls to partial_fit.
|
841 |
+
Can be obtained by via `np.unique(y_all)`, where y_all is the
|
842 |
+
target vector of the entire dataset.
|
843 |
+
This argument is required for the first call to partial_fit
|
844 |
+
and can be omitted in the subsequent calls.
|
845 |
+
Note that y doesn't need to contain all labels in `classes`.
|
846 |
+
|
847 |
+
sample_weight : array-like, shape (n_samples,), default=None
|
848 |
+
Weights applied to individual samples.
|
849 |
+
If not provided, uniform weights are assumed.
|
850 |
+
|
851 |
+
Returns
|
852 |
+
-------
|
853 |
+
self : object
|
854 |
+
Returns an instance of self.
|
855 |
+
"""
|
856 |
+
if not hasattr(self, "classes_"):
|
857 |
+
self._more_validate_params(for_partial_fit=True)
|
858 |
+
|
859 |
+
if self.class_weight == "balanced":
|
860 |
+
raise ValueError(
|
861 |
+
"class_weight '{0}' is not supported for "
|
862 |
+
"partial_fit. In order to use 'balanced' weights,"
|
863 |
+
" use compute_class_weight('{0}', "
|
864 |
+
"classes=classes, y=y). "
|
865 |
+
"In place of y you can use a large enough sample "
|
866 |
+
"of the full training set target to properly "
|
867 |
+
"estimate the class frequency distributions. "
|
868 |
+
"Pass the resulting weights as the class_weight "
|
869 |
+
"parameter.".format(self.class_weight)
|
870 |
+
)
|
871 |
+
|
872 |
+
return self._partial_fit(
|
873 |
+
X,
|
874 |
+
y,
|
875 |
+
alpha=self.alpha,
|
876 |
+
C=1.0,
|
877 |
+
loss=self.loss,
|
878 |
+
learning_rate=self.learning_rate,
|
879 |
+
max_iter=1,
|
880 |
+
classes=classes,
|
881 |
+
sample_weight=sample_weight,
|
882 |
+
coef_init=None,
|
883 |
+
intercept_init=None,
|
884 |
+
)
|
885 |
+
|
886 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
887 |
+
def fit(self, X, y, coef_init=None, intercept_init=None, sample_weight=None):
|
888 |
+
"""Fit linear model with Stochastic Gradient Descent.
|
889 |
+
|
890 |
+
Parameters
|
891 |
+
----------
|
892 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
893 |
+
Training data.
|
894 |
+
|
895 |
+
y : ndarray of shape (n_samples,)
|
896 |
+
Target values.
|
897 |
+
|
898 |
+
coef_init : ndarray of shape (n_classes, n_features), default=None
|
899 |
+
The initial coefficients to warm-start the optimization.
|
900 |
+
|
901 |
+
intercept_init : ndarray of shape (n_classes,), default=None
|
902 |
+
The initial intercept to warm-start the optimization.
|
903 |
+
|
904 |
+
sample_weight : array-like, shape (n_samples,), default=None
|
905 |
+
Weights applied to individual samples.
|
906 |
+
If not provided, uniform weights are assumed. These weights will
|
907 |
+
be multiplied with class_weight (passed through the
|
908 |
+
constructor) if class_weight is specified.
|
909 |
+
|
910 |
+
Returns
|
911 |
+
-------
|
912 |
+
self : object
|
913 |
+
Returns an instance of self.
|
914 |
+
"""
|
915 |
+
self._more_validate_params()
|
916 |
+
|
917 |
+
return self._fit(
|
918 |
+
X,
|
919 |
+
y,
|
920 |
+
alpha=self.alpha,
|
921 |
+
C=1.0,
|
922 |
+
loss=self.loss,
|
923 |
+
learning_rate=self.learning_rate,
|
924 |
+
coef_init=coef_init,
|
925 |
+
intercept_init=intercept_init,
|
926 |
+
sample_weight=sample_weight,
|
927 |
+
)
|
928 |
+
|
929 |
+
|
930 |
+
class SGDClassifier(BaseSGDClassifier):
|
931 |
+
"""Linear classifiers (SVM, logistic regression, etc.) with SGD training.
|
932 |
+
|
933 |
+
This estimator implements regularized linear models with stochastic
|
934 |
+
gradient descent (SGD) learning: the gradient of the loss is estimated
|
935 |
+
each sample at a time and the model is updated along the way with a
|
936 |
+
decreasing strength schedule (aka learning rate). SGD allows minibatch
|
937 |
+
(online/out-of-core) learning via the `partial_fit` method.
|
938 |
+
For best results using the default learning rate schedule, the data should
|
939 |
+
have zero mean and unit variance.
|
940 |
+
|
941 |
+
This implementation works with data represented as dense or sparse arrays
|
942 |
+
of floating point values for the features. The model it fits can be
|
943 |
+
controlled with the loss parameter; by default, it fits a linear support
|
944 |
+
vector machine (SVM).
|
945 |
+
|
946 |
+
The regularizer is a penalty added to the loss function that shrinks model
|
947 |
+
parameters towards the zero vector using either the squared euclidean norm
|
948 |
+
L2 or the absolute norm L1 or a combination of both (Elastic Net). If the
|
949 |
+
parameter update crosses the 0.0 value because of the regularizer, the
|
950 |
+
update is truncated to 0.0 to allow for learning sparse models and achieve
|
951 |
+
online feature selection.
|
952 |
+
|
953 |
+
Read more in the :ref:`User Guide <sgd>`.
|
954 |
+
|
955 |
+
Parameters
|
956 |
+
----------
|
957 |
+
loss : {'hinge', 'log_loss', 'modified_huber', 'squared_hinge',\
|
958 |
+
'perceptron', 'squared_error', 'huber', 'epsilon_insensitive',\
|
959 |
+
'squared_epsilon_insensitive'}, default='hinge'
|
960 |
+
The loss function to be used.
|
961 |
+
|
962 |
+
- 'hinge' gives a linear SVM.
|
963 |
+
- 'log_loss' gives logistic regression, a probabilistic classifier.
|
964 |
+
- 'modified_huber' is another smooth loss that brings tolerance to
|
965 |
+
outliers as well as probability estimates.
|
966 |
+
- 'squared_hinge' is like hinge but is quadratically penalized.
|
967 |
+
- 'perceptron' is the linear loss used by the perceptron algorithm.
|
968 |
+
- The other losses, 'squared_error', 'huber', 'epsilon_insensitive' and
|
969 |
+
'squared_epsilon_insensitive' are designed for regression but can be useful
|
970 |
+
in classification as well; see
|
971 |
+
:class:`~sklearn.linear_model.SGDRegressor` for a description.
|
972 |
+
|
973 |
+
More details about the losses formulas can be found in the
|
974 |
+
:ref:`User Guide <sgd_mathematical_formulation>`.
|
975 |
+
|
976 |
+
penalty : {'l2', 'l1', 'elasticnet', None}, default='l2'
|
977 |
+
The penalty (aka regularization term) to be used. Defaults to 'l2'
|
978 |
+
which is the standard regularizer for linear SVM models. 'l1' and
|
979 |
+
'elasticnet' might bring sparsity to the model (feature selection)
|
980 |
+
not achievable with 'l2'. No penalty is added when set to `None`.
|
981 |
+
|
982 |
+
alpha : float, default=0.0001
|
983 |
+
Constant that multiplies the regularization term. The higher the
|
984 |
+
value, the stronger the regularization. Also used to compute the
|
985 |
+
learning rate when `learning_rate` is set to 'optimal'.
|
986 |
+
Values must be in the range `[0.0, inf)`.
|
987 |
+
|
988 |
+
l1_ratio : float, default=0.15
|
989 |
+
The Elastic Net mixing parameter, with 0 <= l1_ratio <= 1.
|
990 |
+
l1_ratio=0 corresponds to L2 penalty, l1_ratio=1 to L1.
|
991 |
+
Only used if `penalty` is 'elasticnet'.
|
992 |
+
Values must be in the range `[0.0, 1.0]`.
|
993 |
+
|
994 |
+
fit_intercept : bool, default=True
|
995 |
+
Whether the intercept should be estimated or not. If False, the
|
996 |
+
data is assumed to be already centered.
|
997 |
+
|
998 |
+
max_iter : int, default=1000
|
999 |
+
The maximum number of passes over the training data (aka epochs).
|
1000 |
+
It only impacts the behavior in the ``fit`` method, and not the
|
1001 |
+
:meth:`partial_fit` method.
|
1002 |
+
Values must be in the range `[1, inf)`.
|
1003 |
+
|
1004 |
+
.. versionadded:: 0.19
|
1005 |
+
|
1006 |
+
tol : float or None, default=1e-3
|
1007 |
+
The stopping criterion. If it is not None, training will stop
|
1008 |
+
when (loss > best_loss - tol) for ``n_iter_no_change`` consecutive
|
1009 |
+
epochs.
|
1010 |
+
Convergence is checked against the training loss or the
|
1011 |
+
validation loss depending on the `early_stopping` parameter.
|
1012 |
+
Values must be in the range `[0.0, inf)`.
|
1013 |
+
|
1014 |
+
.. versionadded:: 0.19
|
1015 |
+
|
1016 |
+
shuffle : bool, default=True
|
1017 |
+
Whether or not the training data should be shuffled after each epoch.
|
1018 |
+
|
1019 |
+
verbose : int, default=0
|
1020 |
+
The verbosity level.
|
1021 |
+
Values must be in the range `[0, inf)`.
|
1022 |
+
|
1023 |
+
epsilon : float, default=0.1
|
1024 |
+
Epsilon in the epsilon-insensitive loss functions; only if `loss` is
|
1025 |
+
'huber', 'epsilon_insensitive', or 'squared_epsilon_insensitive'.
|
1026 |
+
For 'huber', determines the threshold at which it becomes less
|
1027 |
+
important to get the prediction exactly right.
|
1028 |
+
For epsilon-insensitive, any differences between the current prediction
|
1029 |
+
and the correct label are ignored if they are less than this threshold.
|
1030 |
+
Values must be in the range `[0.0, inf)`.
|
1031 |
+
|
1032 |
+
n_jobs : int, default=None
|
1033 |
+
The number of CPUs to use to do the OVA (One Versus All, for
|
1034 |
+
multi-class problems) computation.
|
1035 |
+
``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
|
1036 |
+
``-1`` means using all processors. See :term:`Glossary <n_jobs>`
|
1037 |
+
for more details.
|
1038 |
+
|
1039 |
+
random_state : int, RandomState instance, default=None
|
1040 |
+
Used for shuffling the data, when ``shuffle`` is set to ``True``.
|
1041 |
+
Pass an int for reproducible output across multiple function calls.
|
1042 |
+
See :term:`Glossary <random_state>`.
|
1043 |
+
Integer values must be in the range `[0, 2**32 - 1]`.
|
1044 |
+
|
1045 |
+
learning_rate : str, default='optimal'
|
1046 |
+
The learning rate schedule:
|
1047 |
+
|
1048 |
+
- 'constant': `eta = eta0`
|
1049 |
+
- 'optimal': `eta = 1.0 / (alpha * (t + t0))`
|
1050 |
+
where `t0` is chosen by a heuristic proposed by Leon Bottou.
|
1051 |
+
- 'invscaling': `eta = eta0 / pow(t, power_t)`
|
1052 |
+
- 'adaptive': `eta = eta0`, as long as the training keeps decreasing.
|
1053 |
+
Each time n_iter_no_change consecutive epochs fail to decrease the
|
1054 |
+
training loss by tol or fail to increase validation score by tol if
|
1055 |
+
`early_stopping` is `True`, the current learning rate is divided by 5.
|
1056 |
+
|
1057 |
+
.. versionadded:: 0.20
|
1058 |
+
Added 'adaptive' option
|
1059 |
+
|
1060 |
+
eta0 : float, default=0.0
|
1061 |
+
The initial learning rate for the 'constant', 'invscaling' or
|
1062 |
+
'adaptive' schedules. The default value is 0.0 as eta0 is not used by
|
1063 |
+
the default schedule 'optimal'.
|
1064 |
+
Values must be in the range `[0.0, inf)`.
|
1065 |
+
|
1066 |
+
power_t : float, default=0.5
|
1067 |
+
The exponent for inverse scaling learning rate.
|
1068 |
+
Values must be in the range `(-inf, inf)`.
|
1069 |
+
|
1070 |
+
early_stopping : bool, default=False
|
1071 |
+
Whether to use early stopping to terminate training when validation
|
1072 |
+
score is not improving. If set to `True`, it will automatically set aside
|
1073 |
+
a stratified fraction of training data as validation and terminate
|
1074 |
+
training when validation score returned by the `score` method is not
|
1075 |
+
improving by at least tol for n_iter_no_change consecutive epochs.
|
1076 |
+
|
1077 |
+
.. versionadded:: 0.20
|
1078 |
+
Added 'early_stopping' option
|
1079 |
+
|
1080 |
+
validation_fraction : float, default=0.1
|
1081 |
+
The proportion of training data to set aside as validation set for
|
1082 |
+
early stopping. Must be between 0 and 1.
|
1083 |
+
Only used if `early_stopping` is True.
|
1084 |
+
Values must be in the range `(0.0, 1.0)`.
|
1085 |
+
|
1086 |
+
.. versionadded:: 0.20
|
1087 |
+
Added 'validation_fraction' option
|
1088 |
+
|
1089 |
+
n_iter_no_change : int, default=5
|
1090 |
+
Number of iterations with no improvement to wait before stopping
|
1091 |
+
fitting.
|
1092 |
+
Convergence is checked against the training loss or the
|
1093 |
+
validation loss depending on the `early_stopping` parameter.
|
1094 |
+
Integer values must be in the range `[1, max_iter)`.
|
1095 |
+
|
1096 |
+
.. versionadded:: 0.20
|
1097 |
+
Added 'n_iter_no_change' option
|
1098 |
+
|
1099 |
+
class_weight : dict, {class_label: weight} or "balanced", default=None
|
1100 |
+
Preset for the class_weight fit parameter.
|
1101 |
+
|
1102 |
+
Weights associated with classes. If not given, all classes
|
1103 |
+
are supposed to have weight one.
|
1104 |
+
|
1105 |
+
The "balanced" mode uses the values of y to automatically adjust
|
1106 |
+
weights inversely proportional to class frequencies in the input data
|
1107 |
+
as ``n_samples / (n_classes * np.bincount(y))``.
|
1108 |
+
|
1109 |
+
warm_start : bool, default=False
|
1110 |
+
When set to True, reuse the solution of the previous call to fit as
|
1111 |
+
initialization, otherwise, just erase the previous solution.
|
1112 |
+
See :term:`the Glossary <warm_start>`.
|
1113 |
+
|
1114 |
+
Repeatedly calling fit or partial_fit when warm_start is True can
|
1115 |
+
result in a different solution than when calling fit a single time
|
1116 |
+
because of the way the data is shuffled.
|
1117 |
+
If a dynamic learning rate is used, the learning rate is adapted
|
1118 |
+
depending on the number of samples already seen. Calling ``fit`` resets
|
1119 |
+
this counter, while ``partial_fit`` will result in increasing the
|
1120 |
+
existing counter.
|
1121 |
+
|
1122 |
+
average : bool or int, default=False
|
1123 |
+
When set to `True`, computes the averaged SGD weights across all
|
1124 |
+
updates and stores the result in the ``coef_`` attribute. If set to
|
1125 |
+
an int greater than 1, averaging will begin once the total number of
|
1126 |
+
samples seen reaches `average`. So ``average=10`` will begin
|
1127 |
+
averaging after seeing 10 samples.
|
1128 |
+
Integer values must be in the range `[1, n_samples]`.
|
1129 |
+
|
1130 |
+
Attributes
|
1131 |
+
----------
|
1132 |
+
coef_ : ndarray of shape (1, n_features) if n_classes == 2 else \
|
1133 |
+
(n_classes, n_features)
|
1134 |
+
Weights assigned to the features.
|
1135 |
+
|
1136 |
+
intercept_ : ndarray of shape (1,) if n_classes == 2 else (n_classes,)
|
1137 |
+
Constants in decision function.
|
1138 |
+
|
1139 |
+
n_iter_ : int
|
1140 |
+
The actual number of iterations before reaching the stopping criterion.
|
1141 |
+
For multiclass fits, it is the maximum over every binary fit.
|
1142 |
+
|
1143 |
+
loss_function_ : concrete ``LossFunction``
|
1144 |
+
|
1145 |
+
.. deprecated:: 1.4
|
1146 |
+
Attribute `loss_function_` was deprecated in version 1.4 and will be
|
1147 |
+
removed in 1.6.
|
1148 |
+
|
1149 |
+
classes_ : array of shape (n_classes,)
|
1150 |
+
|
1151 |
+
t_ : int
|
1152 |
+
Number of weight updates performed during training.
|
1153 |
+
Same as ``(n_iter_ * n_samples + 1)``.
|
1154 |
+
|
1155 |
+
n_features_in_ : int
|
1156 |
+
Number of features seen during :term:`fit`.
|
1157 |
+
|
1158 |
+
.. versionadded:: 0.24
|
1159 |
+
|
1160 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
1161 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
1162 |
+
has feature names that are all strings.
|
1163 |
+
|
1164 |
+
.. versionadded:: 1.0
|
1165 |
+
|
1166 |
+
See Also
|
1167 |
+
--------
|
1168 |
+
sklearn.svm.LinearSVC : Linear support vector classification.
|
1169 |
+
LogisticRegression : Logistic regression.
|
1170 |
+
Perceptron : Inherits from SGDClassifier. ``Perceptron()`` is equivalent to
|
1171 |
+
``SGDClassifier(loss="perceptron", eta0=1, learning_rate="constant",
|
1172 |
+
penalty=None)``.
|
1173 |
+
|
1174 |
+
Examples
|
1175 |
+
--------
|
1176 |
+
>>> import numpy as np
|
1177 |
+
>>> from sklearn.linear_model import SGDClassifier
|
1178 |
+
>>> from sklearn.preprocessing import StandardScaler
|
1179 |
+
>>> from sklearn.pipeline import make_pipeline
|
1180 |
+
>>> X = np.array([[-1, -1], [-2, -1], [1, 1], [2, 1]])
|
1181 |
+
>>> Y = np.array([1, 1, 2, 2])
|
1182 |
+
>>> # Always scale the input. The most convenient way is to use a pipeline.
|
1183 |
+
>>> clf = make_pipeline(StandardScaler(),
|
1184 |
+
... SGDClassifier(max_iter=1000, tol=1e-3))
|
1185 |
+
>>> clf.fit(X, Y)
|
1186 |
+
Pipeline(steps=[('standardscaler', StandardScaler()),
|
1187 |
+
('sgdclassifier', SGDClassifier())])
|
1188 |
+
>>> print(clf.predict([[-0.8, -1]]))
|
1189 |
+
[1]
|
1190 |
+
"""
|
1191 |
+
|
1192 |
+
_parameter_constraints: dict = {
|
1193 |
+
**BaseSGDClassifier._parameter_constraints,
|
1194 |
+
"penalty": [StrOptions({"l2", "l1", "elasticnet"}), None],
|
1195 |
+
"alpha": [Interval(Real, 0, None, closed="left")],
|
1196 |
+
"l1_ratio": [Interval(Real, 0, 1, closed="both")],
|
1197 |
+
"power_t": [Interval(Real, None, None, closed="neither")],
|
1198 |
+
"epsilon": [Interval(Real, 0, None, closed="left")],
|
1199 |
+
"learning_rate": [
|
1200 |
+
StrOptions({"constant", "optimal", "invscaling", "adaptive"}),
|
1201 |
+
Hidden(StrOptions({"pa1", "pa2"})),
|
1202 |
+
],
|
1203 |
+
"eta0": [Interval(Real, 0, None, closed="left")],
|
1204 |
+
}
|
1205 |
+
|
1206 |
+
def __init__(
|
1207 |
+
self,
|
1208 |
+
loss="hinge",
|
1209 |
+
*,
|
1210 |
+
penalty="l2",
|
1211 |
+
alpha=0.0001,
|
1212 |
+
l1_ratio=0.15,
|
1213 |
+
fit_intercept=True,
|
1214 |
+
max_iter=1000,
|
1215 |
+
tol=1e-3,
|
1216 |
+
shuffle=True,
|
1217 |
+
verbose=0,
|
1218 |
+
epsilon=DEFAULT_EPSILON,
|
1219 |
+
n_jobs=None,
|
1220 |
+
random_state=None,
|
1221 |
+
learning_rate="optimal",
|
1222 |
+
eta0=0.0,
|
1223 |
+
power_t=0.5,
|
1224 |
+
early_stopping=False,
|
1225 |
+
validation_fraction=0.1,
|
1226 |
+
n_iter_no_change=5,
|
1227 |
+
class_weight=None,
|
1228 |
+
warm_start=False,
|
1229 |
+
average=False,
|
1230 |
+
):
|
1231 |
+
super().__init__(
|
1232 |
+
loss=loss,
|
1233 |
+
penalty=penalty,
|
1234 |
+
alpha=alpha,
|
1235 |
+
l1_ratio=l1_ratio,
|
1236 |
+
fit_intercept=fit_intercept,
|
1237 |
+
max_iter=max_iter,
|
1238 |
+
tol=tol,
|
1239 |
+
shuffle=shuffle,
|
1240 |
+
verbose=verbose,
|
1241 |
+
epsilon=epsilon,
|
1242 |
+
n_jobs=n_jobs,
|
1243 |
+
random_state=random_state,
|
1244 |
+
learning_rate=learning_rate,
|
1245 |
+
eta0=eta0,
|
1246 |
+
power_t=power_t,
|
1247 |
+
early_stopping=early_stopping,
|
1248 |
+
validation_fraction=validation_fraction,
|
1249 |
+
n_iter_no_change=n_iter_no_change,
|
1250 |
+
class_weight=class_weight,
|
1251 |
+
warm_start=warm_start,
|
1252 |
+
average=average,
|
1253 |
+
)
|
1254 |
+
|
1255 |
+
def _check_proba(self):
|
1256 |
+
if self.loss not in ("log_loss", "modified_huber"):
|
1257 |
+
raise AttributeError(
|
1258 |
+
"probability estimates are not available for loss=%r" % self.loss
|
1259 |
+
)
|
1260 |
+
return True
|
1261 |
+
|
1262 |
+
@available_if(_check_proba)
|
1263 |
+
def predict_proba(self, X):
|
1264 |
+
"""Probability estimates.
|
1265 |
+
|
1266 |
+
This method is only available for log loss and modified Huber loss.
|
1267 |
+
|
1268 |
+
Multiclass probability estimates are derived from binary (one-vs.-rest)
|
1269 |
+
estimates by simple normalization, as recommended by Zadrozny and
|
1270 |
+
Elkan.
|
1271 |
+
|
1272 |
+
Binary probability estimates for loss="modified_huber" are given by
|
1273 |
+
(clip(decision_function(X), -1, 1) + 1) / 2. For other loss functions
|
1274 |
+
it is necessary to perform proper probability calibration by wrapping
|
1275 |
+
the classifier with
|
1276 |
+
:class:`~sklearn.calibration.CalibratedClassifierCV` instead.
|
1277 |
+
|
1278 |
+
Parameters
|
1279 |
+
----------
|
1280 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
1281 |
+
Input data for prediction.
|
1282 |
+
|
1283 |
+
Returns
|
1284 |
+
-------
|
1285 |
+
ndarray of shape (n_samples, n_classes)
|
1286 |
+
Returns the probability of the sample for each class in the model,
|
1287 |
+
where classes are ordered as they are in `self.classes_`.
|
1288 |
+
|
1289 |
+
References
|
1290 |
+
----------
|
1291 |
+
Zadrozny and Elkan, "Transforming classifier scores into multiclass
|
1292 |
+
probability estimates", SIGKDD'02,
|
1293 |
+
https://dl.acm.org/doi/pdf/10.1145/775047.775151
|
1294 |
+
|
1295 |
+
The justification for the formula in the loss="modified_huber"
|
1296 |
+
case is in the appendix B in:
|
1297 |
+
http://jmlr.csail.mit.edu/papers/volume2/zhang02c/zhang02c.pdf
|
1298 |
+
"""
|
1299 |
+
check_is_fitted(self)
|
1300 |
+
|
1301 |
+
if self.loss == "log_loss":
|
1302 |
+
return self._predict_proba_lr(X)
|
1303 |
+
|
1304 |
+
elif self.loss == "modified_huber":
|
1305 |
+
binary = len(self.classes_) == 2
|
1306 |
+
scores = self.decision_function(X)
|
1307 |
+
|
1308 |
+
if binary:
|
1309 |
+
prob2 = np.ones((scores.shape[0], 2))
|
1310 |
+
prob = prob2[:, 1]
|
1311 |
+
else:
|
1312 |
+
prob = scores
|
1313 |
+
|
1314 |
+
np.clip(scores, -1, 1, prob)
|
1315 |
+
prob += 1.0
|
1316 |
+
prob /= 2.0
|
1317 |
+
|
1318 |
+
if binary:
|
1319 |
+
prob2[:, 0] -= prob
|
1320 |
+
prob = prob2
|
1321 |
+
else:
|
1322 |
+
# the above might assign zero to all classes, which doesn't
|
1323 |
+
# normalize neatly; work around this to produce uniform
|
1324 |
+
# probabilities
|
1325 |
+
prob_sum = prob.sum(axis=1)
|
1326 |
+
all_zero = prob_sum == 0
|
1327 |
+
if np.any(all_zero):
|
1328 |
+
prob[all_zero, :] = 1
|
1329 |
+
prob_sum[all_zero] = len(self.classes_)
|
1330 |
+
|
1331 |
+
# normalize
|
1332 |
+
prob /= prob_sum.reshape((prob.shape[0], -1))
|
1333 |
+
|
1334 |
+
return prob
|
1335 |
+
|
1336 |
+
else:
|
1337 |
+
raise NotImplementedError(
|
1338 |
+
"predict_(log_)proba only supported when"
|
1339 |
+
" loss='log_loss' or loss='modified_huber' "
|
1340 |
+
"(%r given)"
|
1341 |
+
% self.loss
|
1342 |
+
)
|
1343 |
+
|
1344 |
+
@available_if(_check_proba)
|
1345 |
+
def predict_log_proba(self, X):
|
1346 |
+
"""Log of probability estimates.
|
1347 |
+
|
1348 |
+
This method is only available for log loss and modified Huber loss.
|
1349 |
+
|
1350 |
+
When loss="modified_huber", probability estimates may be hard zeros
|
1351 |
+
and ones, so taking the logarithm is not possible.
|
1352 |
+
|
1353 |
+
See ``predict_proba`` for details.
|
1354 |
+
|
1355 |
+
Parameters
|
1356 |
+
----------
|
1357 |
+
X : {array-like, sparse matrix} of shape (n_samples, n_features)
|
1358 |
+
Input data for prediction.
|
1359 |
+
|
1360 |
+
Returns
|
1361 |
+
-------
|
1362 |
+
T : array-like, shape (n_samples, n_classes)
|
1363 |
+
Returns the log-probability of the sample for each class in the
|
1364 |
+
model, where classes are ordered as they are in
|
1365 |
+
`self.classes_`.
|
1366 |
+
"""
|
1367 |
+
return np.log(self.predict_proba(X))
|
1368 |
+
|
1369 |
+
def _more_tags(self):
|
1370 |
+
return {
|
1371 |
+
"_xfail_checks": {
|
1372 |
+
"check_sample_weights_invariance": (
|
1373 |
+
"zero sample_weight is not equivalent to removing samples"
|
1374 |
+
),
|
1375 |
+
},
|
1376 |
+
"preserves_dtype": [np.float64, np.float32],
|
1377 |
+
}
|
1378 |
+
|
1379 |
+
|
1380 |
+
class BaseSGDRegressor(RegressorMixin, BaseSGD):
|
1381 |
+
loss_functions = {
|
1382 |
+
"squared_error": (SquaredLoss,),
|
1383 |
+
"huber": (Huber, DEFAULT_EPSILON),
|
1384 |
+
"epsilon_insensitive": (EpsilonInsensitive, DEFAULT_EPSILON),
|
1385 |
+
"squared_epsilon_insensitive": (SquaredEpsilonInsensitive, DEFAULT_EPSILON),
|
1386 |
+
}
|
1387 |
+
|
1388 |
+
_parameter_constraints: dict = {
|
1389 |
+
**BaseSGD._parameter_constraints,
|
1390 |
+
"loss": [StrOptions(set(loss_functions))],
|
1391 |
+
"early_stopping": ["boolean"],
|
1392 |
+
"validation_fraction": [Interval(Real, 0, 1, closed="neither")],
|
1393 |
+
"n_iter_no_change": [Interval(Integral, 1, None, closed="left")],
|
1394 |
+
}
|
1395 |
+
|
1396 |
+
@abstractmethod
|
1397 |
+
def __init__(
|
1398 |
+
self,
|
1399 |
+
loss="squared_error",
|
1400 |
+
*,
|
1401 |
+
penalty="l2",
|
1402 |
+
alpha=0.0001,
|
1403 |
+
l1_ratio=0.15,
|
1404 |
+
fit_intercept=True,
|
1405 |
+
max_iter=1000,
|
1406 |
+
tol=1e-3,
|
1407 |
+
shuffle=True,
|
1408 |
+
verbose=0,
|
1409 |
+
epsilon=DEFAULT_EPSILON,
|
1410 |
+
random_state=None,
|
1411 |
+
learning_rate="invscaling",
|
1412 |
+
eta0=0.01,
|
1413 |
+
power_t=0.25,
|
1414 |
+
early_stopping=False,
|
1415 |
+
validation_fraction=0.1,
|
1416 |
+
n_iter_no_change=5,
|
1417 |
+
warm_start=False,
|
1418 |
+
average=False,
|
1419 |
+
):
|
1420 |
+
super().__init__(
|
1421 |
+
loss=loss,
|
1422 |
+
penalty=penalty,
|
1423 |
+
alpha=alpha,
|
1424 |
+
l1_ratio=l1_ratio,
|
1425 |
+
fit_intercept=fit_intercept,
|
1426 |
+
max_iter=max_iter,
|
1427 |
+
tol=tol,
|
1428 |
+
shuffle=shuffle,
|
1429 |
+
verbose=verbose,
|
1430 |
+
epsilon=epsilon,
|
1431 |
+
random_state=random_state,
|
1432 |
+
learning_rate=learning_rate,
|
1433 |
+
eta0=eta0,
|
1434 |
+
power_t=power_t,
|
1435 |
+
early_stopping=early_stopping,
|
1436 |
+
validation_fraction=validation_fraction,
|
1437 |
+
n_iter_no_change=n_iter_no_change,
|
1438 |
+
warm_start=warm_start,
|
1439 |
+
average=average,
|
1440 |
+
)
|
1441 |
+
|
1442 |
+
def _partial_fit(
|
1443 |
+
self,
|
1444 |
+
X,
|
1445 |
+
y,
|
1446 |
+
alpha,
|
1447 |
+
C,
|
1448 |
+
loss,
|
1449 |
+
learning_rate,
|
1450 |
+
max_iter,
|
1451 |
+
sample_weight,
|
1452 |
+
coef_init,
|
1453 |
+
intercept_init,
|
1454 |
+
):
|
1455 |
+
first_call = getattr(self, "coef_", None) is None
|
1456 |
+
X, y = self._validate_data(
|
1457 |
+
X,
|
1458 |
+
y,
|
1459 |
+
accept_sparse="csr",
|
1460 |
+
copy=False,
|
1461 |
+
order="C",
|
1462 |
+
dtype=[np.float64, np.float32],
|
1463 |
+
accept_large_sparse=False,
|
1464 |
+
reset=first_call,
|
1465 |
+
)
|
1466 |
+
y = y.astype(X.dtype, copy=False)
|
1467 |
+
|
1468 |
+
n_samples, n_features = X.shape
|
1469 |
+
|
1470 |
+
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
|
1471 |
+
|
1472 |
+
# Allocate datastructures from input arguments
|
1473 |
+
if first_call:
|
1474 |
+
self._allocate_parameter_mem(
|
1475 |
+
n_classes=1,
|
1476 |
+
n_features=n_features,
|
1477 |
+
input_dtype=X.dtype,
|
1478 |
+
coef_init=coef_init,
|
1479 |
+
intercept_init=intercept_init,
|
1480 |
+
)
|
1481 |
+
if self.average > 0 and getattr(self, "_average_coef", None) is None:
|
1482 |
+
self._average_coef = np.zeros(n_features, dtype=X.dtype, order="C")
|
1483 |
+
self._average_intercept = np.zeros(1, dtype=X.dtype, order="C")
|
1484 |
+
|
1485 |
+
self._fit_regressor(
|
1486 |
+
X, y, alpha, C, loss, learning_rate, sample_weight, max_iter
|
1487 |
+
)
|
1488 |
+
|
1489 |
+
return self
|
1490 |
+
|
1491 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
1492 |
+
def partial_fit(self, X, y, sample_weight=None):
|
1493 |
+
"""Perform one epoch of stochastic gradient descent on given samples.
|
1494 |
+
|
1495 |
+
Internally, this method uses ``max_iter = 1``. Therefore, it is not
|
1496 |
+
guaranteed that a minimum of the cost function is reached after calling
|
1497 |
+
it once. Matters such as objective convergence and early stopping
|
1498 |
+
should be handled by the user.
|
1499 |
+
|
1500 |
+
Parameters
|
1501 |
+
----------
|
1502 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
1503 |
+
Subset of training data.
|
1504 |
+
|
1505 |
+
y : numpy array of shape (n_samples,)
|
1506 |
+
Subset of target values.
|
1507 |
+
|
1508 |
+
sample_weight : array-like, shape (n_samples,), default=None
|
1509 |
+
Weights applied to individual samples.
|
1510 |
+
If not provided, uniform weights are assumed.
|
1511 |
+
|
1512 |
+
Returns
|
1513 |
+
-------
|
1514 |
+
self : object
|
1515 |
+
Returns an instance of self.
|
1516 |
+
"""
|
1517 |
+
if not hasattr(self, "coef_"):
|
1518 |
+
self._more_validate_params(for_partial_fit=True)
|
1519 |
+
|
1520 |
+
return self._partial_fit(
|
1521 |
+
X,
|
1522 |
+
y,
|
1523 |
+
self.alpha,
|
1524 |
+
C=1.0,
|
1525 |
+
loss=self.loss,
|
1526 |
+
learning_rate=self.learning_rate,
|
1527 |
+
max_iter=1,
|
1528 |
+
sample_weight=sample_weight,
|
1529 |
+
coef_init=None,
|
1530 |
+
intercept_init=None,
|
1531 |
+
)
|
1532 |
+
|
1533 |
+
def _fit(
|
1534 |
+
self,
|
1535 |
+
X,
|
1536 |
+
y,
|
1537 |
+
alpha,
|
1538 |
+
C,
|
1539 |
+
loss,
|
1540 |
+
learning_rate,
|
1541 |
+
coef_init=None,
|
1542 |
+
intercept_init=None,
|
1543 |
+
sample_weight=None,
|
1544 |
+
):
|
1545 |
+
if self.warm_start and getattr(self, "coef_", None) is not None:
|
1546 |
+
if coef_init is None:
|
1547 |
+
coef_init = self.coef_
|
1548 |
+
if intercept_init is None:
|
1549 |
+
intercept_init = self.intercept_
|
1550 |
+
else:
|
1551 |
+
self.coef_ = None
|
1552 |
+
self.intercept_ = None
|
1553 |
+
|
1554 |
+
# Clear iteration count for multiple call to fit.
|
1555 |
+
self.t_ = 1.0
|
1556 |
+
|
1557 |
+
self._partial_fit(
|
1558 |
+
X,
|
1559 |
+
y,
|
1560 |
+
alpha,
|
1561 |
+
C,
|
1562 |
+
loss,
|
1563 |
+
learning_rate,
|
1564 |
+
self.max_iter,
|
1565 |
+
sample_weight,
|
1566 |
+
coef_init,
|
1567 |
+
intercept_init,
|
1568 |
+
)
|
1569 |
+
|
1570 |
+
if (
|
1571 |
+
self.tol is not None
|
1572 |
+
and self.tol > -np.inf
|
1573 |
+
and self.n_iter_ == self.max_iter
|
1574 |
+
):
|
1575 |
+
warnings.warn(
|
1576 |
+
(
|
1577 |
+
"Maximum number of iteration reached before "
|
1578 |
+
"convergence. Consider increasing max_iter to "
|
1579 |
+
"improve the fit."
|
1580 |
+
),
|
1581 |
+
ConvergenceWarning,
|
1582 |
+
)
|
1583 |
+
|
1584 |
+
return self
|
1585 |
+
|
1586 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
1587 |
+
def fit(self, X, y, coef_init=None, intercept_init=None, sample_weight=None):
|
1588 |
+
"""Fit linear model with Stochastic Gradient Descent.
|
1589 |
+
|
1590 |
+
Parameters
|
1591 |
+
----------
|
1592 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
1593 |
+
Training data.
|
1594 |
+
|
1595 |
+
y : ndarray of shape (n_samples,)
|
1596 |
+
Target values.
|
1597 |
+
|
1598 |
+
coef_init : ndarray of shape (n_features,), default=None
|
1599 |
+
The initial coefficients to warm-start the optimization.
|
1600 |
+
|
1601 |
+
intercept_init : ndarray of shape (1,), default=None
|
1602 |
+
The initial intercept to warm-start the optimization.
|
1603 |
+
|
1604 |
+
sample_weight : array-like, shape (n_samples,), default=None
|
1605 |
+
Weights applied to individual samples (1. for unweighted).
|
1606 |
+
|
1607 |
+
Returns
|
1608 |
+
-------
|
1609 |
+
self : object
|
1610 |
+
Fitted `SGDRegressor` estimator.
|
1611 |
+
"""
|
1612 |
+
self._more_validate_params()
|
1613 |
+
|
1614 |
+
return self._fit(
|
1615 |
+
X,
|
1616 |
+
y,
|
1617 |
+
alpha=self.alpha,
|
1618 |
+
C=1.0,
|
1619 |
+
loss=self.loss,
|
1620 |
+
learning_rate=self.learning_rate,
|
1621 |
+
coef_init=coef_init,
|
1622 |
+
intercept_init=intercept_init,
|
1623 |
+
sample_weight=sample_weight,
|
1624 |
+
)
|
1625 |
+
|
1626 |
+
def _decision_function(self, X):
|
1627 |
+
"""Predict using the linear model
|
1628 |
+
|
1629 |
+
Parameters
|
1630 |
+
----------
|
1631 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
1632 |
+
|
1633 |
+
Returns
|
1634 |
+
-------
|
1635 |
+
ndarray of shape (n_samples,)
|
1636 |
+
Predicted target values per element in X.
|
1637 |
+
"""
|
1638 |
+
check_is_fitted(self)
|
1639 |
+
|
1640 |
+
X = self._validate_data(X, accept_sparse="csr", reset=False)
|
1641 |
+
|
1642 |
+
scores = safe_sparse_dot(X, self.coef_.T, dense_output=True) + self.intercept_
|
1643 |
+
return scores.ravel()
|
1644 |
+
|
1645 |
+
def predict(self, X):
|
1646 |
+
"""Predict using the linear model.
|
1647 |
+
|
1648 |
+
Parameters
|
1649 |
+
----------
|
1650 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
1651 |
+
Input data.
|
1652 |
+
|
1653 |
+
Returns
|
1654 |
+
-------
|
1655 |
+
ndarray of shape (n_samples,)
|
1656 |
+
Predicted target values per element in X.
|
1657 |
+
"""
|
1658 |
+
return self._decision_function(X)
|
1659 |
+
|
1660 |
+
def _fit_regressor(
|
1661 |
+
self, X, y, alpha, C, loss, learning_rate, sample_weight, max_iter
|
1662 |
+
):
|
1663 |
+
loss_function = self._get_loss_function(loss)
|
1664 |
+
penalty_type = self._get_penalty_type(self.penalty)
|
1665 |
+
learning_rate_type = self._get_learning_rate_type(learning_rate)
|
1666 |
+
|
1667 |
+
if not hasattr(self, "t_"):
|
1668 |
+
self.t_ = 1.0
|
1669 |
+
|
1670 |
+
validation_mask = self._make_validation_split(y, sample_mask=sample_weight > 0)
|
1671 |
+
validation_score_cb = self._make_validation_score_cb(
|
1672 |
+
validation_mask, X, y, sample_weight
|
1673 |
+
)
|
1674 |
+
|
1675 |
+
random_state = check_random_state(self.random_state)
|
1676 |
+
# numpy mtrand expects a C long which is a signed 32 bit integer under
|
1677 |
+
# Windows
|
1678 |
+
seed = random_state.randint(0, MAX_INT)
|
1679 |
+
|
1680 |
+
dataset, intercept_decay = make_dataset(
|
1681 |
+
X, y, sample_weight, random_state=random_state
|
1682 |
+
)
|
1683 |
+
|
1684 |
+
tol = self.tol if self.tol is not None else -np.inf
|
1685 |
+
|
1686 |
+
if self.average:
|
1687 |
+
coef = self._standard_coef
|
1688 |
+
intercept = self._standard_intercept
|
1689 |
+
average_coef = self._average_coef
|
1690 |
+
average_intercept = self._average_intercept
|
1691 |
+
else:
|
1692 |
+
coef = self.coef_
|
1693 |
+
intercept = self.intercept_
|
1694 |
+
average_coef = None # Not used
|
1695 |
+
average_intercept = [0] # Not used
|
1696 |
+
|
1697 |
+
_plain_sgd = _get_plain_sgd_function(input_dtype=coef.dtype)
|
1698 |
+
coef, intercept, average_coef, average_intercept, self.n_iter_ = _plain_sgd(
|
1699 |
+
coef,
|
1700 |
+
intercept[0],
|
1701 |
+
average_coef,
|
1702 |
+
average_intercept[0],
|
1703 |
+
loss_function,
|
1704 |
+
penalty_type,
|
1705 |
+
alpha,
|
1706 |
+
C,
|
1707 |
+
self.l1_ratio,
|
1708 |
+
dataset,
|
1709 |
+
validation_mask,
|
1710 |
+
self.early_stopping,
|
1711 |
+
validation_score_cb,
|
1712 |
+
int(self.n_iter_no_change),
|
1713 |
+
max_iter,
|
1714 |
+
tol,
|
1715 |
+
int(self.fit_intercept),
|
1716 |
+
int(self.verbose),
|
1717 |
+
int(self.shuffle),
|
1718 |
+
seed,
|
1719 |
+
1.0,
|
1720 |
+
1.0,
|
1721 |
+
learning_rate_type,
|
1722 |
+
self.eta0,
|
1723 |
+
self.power_t,
|
1724 |
+
0,
|
1725 |
+
self.t_,
|
1726 |
+
intercept_decay,
|
1727 |
+
self.average,
|
1728 |
+
)
|
1729 |
+
|
1730 |
+
self.t_ += self.n_iter_ * X.shape[0]
|
1731 |
+
|
1732 |
+
if self.average > 0:
|
1733 |
+
self._average_intercept = np.atleast_1d(average_intercept)
|
1734 |
+
self._standard_intercept = np.atleast_1d(intercept)
|
1735 |
+
|
1736 |
+
if self.average <= self.t_ - 1.0:
|
1737 |
+
# made enough updates for averaging to be taken into account
|
1738 |
+
self.coef_ = average_coef
|
1739 |
+
self.intercept_ = np.atleast_1d(average_intercept)
|
1740 |
+
else:
|
1741 |
+
self.coef_ = coef
|
1742 |
+
self.intercept_ = np.atleast_1d(intercept)
|
1743 |
+
|
1744 |
+
else:
|
1745 |
+
self.intercept_ = np.atleast_1d(intercept)
|
1746 |
+
|
1747 |
+
|
1748 |
+
class SGDRegressor(BaseSGDRegressor):
|
1749 |
+
"""Linear model fitted by minimizing a regularized empirical loss with SGD.
|
1750 |
+
|
1751 |
+
SGD stands for Stochastic Gradient Descent: the gradient of the loss is
|
1752 |
+
estimated each sample at a time and the model is updated along the way with
|
1753 |
+
a decreasing strength schedule (aka learning rate).
|
1754 |
+
|
1755 |
+
The regularizer is a penalty added to the loss function that shrinks model
|
1756 |
+
parameters towards the zero vector using either the squared euclidean norm
|
1757 |
+
L2 or the absolute norm L1 or a combination of both (Elastic Net). If the
|
1758 |
+
parameter update crosses the 0.0 value because of the regularizer, the
|
1759 |
+
update is truncated to 0.0 to allow for learning sparse models and achieve
|
1760 |
+
online feature selection.
|
1761 |
+
|
1762 |
+
This implementation works with data represented as dense numpy arrays of
|
1763 |
+
floating point values for the features.
|
1764 |
+
|
1765 |
+
Read more in the :ref:`User Guide <sgd>`.
|
1766 |
+
|
1767 |
+
Parameters
|
1768 |
+
----------
|
1769 |
+
loss : str, default='squared_error'
|
1770 |
+
The loss function to be used. The possible values are 'squared_error',
|
1771 |
+
'huber', 'epsilon_insensitive', or 'squared_epsilon_insensitive'
|
1772 |
+
|
1773 |
+
The 'squared_error' refers to the ordinary least squares fit.
|
1774 |
+
'huber' modifies 'squared_error' to focus less on getting outliers
|
1775 |
+
correct by switching from squared to linear loss past a distance of
|
1776 |
+
epsilon. 'epsilon_insensitive' ignores errors less than epsilon and is
|
1777 |
+
linear past that; this is the loss function used in SVR.
|
1778 |
+
'squared_epsilon_insensitive' is the same but becomes squared loss past
|
1779 |
+
a tolerance of epsilon.
|
1780 |
+
|
1781 |
+
More details about the losses formulas can be found in the
|
1782 |
+
:ref:`User Guide <sgd_mathematical_formulation>`.
|
1783 |
+
|
1784 |
+
penalty : {'l2', 'l1', 'elasticnet', None}, default='l2'
|
1785 |
+
The penalty (aka regularization term) to be used. Defaults to 'l2'
|
1786 |
+
which is the standard regularizer for linear SVM models. 'l1' and
|
1787 |
+
'elasticnet' might bring sparsity to the model (feature selection)
|
1788 |
+
not achievable with 'l2'. No penalty is added when set to `None`.
|
1789 |
+
|
1790 |
+
alpha : float, default=0.0001
|
1791 |
+
Constant that multiplies the regularization term. The higher the
|
1792 |
+
value, the stronger the regularization. Also used to compute the
|
1793 |
+
learning rate when `learning_rate` is set to 'optimal'.
|
1794 |
+
Values must be in the range `[0.0, inf)`.
|
1795 |
+
|
1796 |
+
l1_ratio : float, default=0.15
|
1797 |
+
The Elastic Net mixing parameter, with 0 <= l1_ratio <= 1.
|
1798 |
+
l1_ratio=0 corresponds to L2 penalty, l1_ratio=1 to L1.
|
1799 |
+
Only used if `penalty` is 'elasticnet'.
|
1800 |
+
Values must be in the range `[0.0, 1.0]`.
|
1801 |
+
|
1802 |
+
fit_intercept : bool, default=True
|
1803 |
+
Whether the intercept should be estimated or not. If False, the
|
1804 |
+
data is assumed to be already centered.
|
1805 |
+
|
1806 |
+
max_iter : int, default=1000
|
1807 |
+
The maximum number of passes over the training data (aka epochs).
|
1808 |
+
It only impacts the behavior in the ``fit`` method, and not the
|
1809 |
+
:meth:`partial_fit` method.
|
1810 |
+
Values must be in the range `[1, inf)`.
|
1811 |
+
|
1812 |
+
.. versionadded:: 0.19
|
1813 |
+
|
1814 |
+
tol : float or None, default=1e-3
|
1815 |
+
The stopping criterion. If it is not None, training will stop
|
1816 |
+
when (loss > best_loss - tol) for ``n_iter_no_change`` consecutive
|
1817 |
+
epochs.
|
1818 |
+
Convergence is checked against the training loss or the
|
1819 |
+
validation loss depending on the `early_stopping` parameter.
|
1820 |
+
Values must be in the range `[0.0, inf)`.
|
1821 |
+
|
1822 |
+
.. versionadded:: 0.19
|
1823 |
+
|
1824 |
+
shuffle : bool, default=True
|
1825 |
+
Whether or not the training data should be shuffled after each epoch.
|
1826 |
+
|
1827 |
+
verbose : int, default=0
|
1828 |
+
The verbosity level.
|
1829 |
+
Values must be in the range `[0, inf)`.
|
1830 |
+
|
1831 |
+
epsilon : float, default=0.1
|
1832 |
+
Epsilon in the epsilon-insensitive loss functions; only if `loss` is
|
1833 |
+
'huber', 'epsilon_insensitive', or 'squared_epsilon_insensitive'.
|
1834 |
+
For 'huber', determines the threshold at which it becomes less
|
1835 |
+
important to get the prediction exactly right.
|
1836 |
+
For epsilon-insensitive, any differences between the current prediction
|
1837 |
+
and the correct label are ignored if they are less than this threshold.
|
1838 |
+
Values must be in the range `[0.0, inf)`.
|
1839 |
+
|
1840 |
+
random_state : int, RandomState instance, default=None
|
1841 |
+
Used for shuffling the data, when ``shuffle`` is set to ``True``.
|
1842 |
+
Pass an int for reproducible output across multiple function calls.
|
1843 |
+
See :term:`Glossary <random_state>`.
|
1844 |
+
|
1845 |
+
learning_rate : str, default='invscaling'
|
1846 |
+
The learning rate schedule:
|
1847 |
+
|
1848 |
+
- 'constant': `eta = eta0`
|
1849 |
+
- 'optimal': `eta = 1.0 / (alpha * (t + t0))`
|
1850 |
+
where t0 is chosen by a heuristic proposed by Leon Bottou.
|
1851 |
+
- 'invscaling': `eta = eta0 / pow(t, power_t)`
|
1852 |
+
- 'adaptive': eta = eta0, as long as the training keeps decreasing.
|
1853 |
+
Each time n_iter_no_change consecutive epochs fail to decrease the
|
1854 |
+
training loss by tol or fail to increase validation score by tol if
|
1855 |
+
early_stopping is True, the current learning rate is divided by 5.
|
1856 |
+
|
1857 |
+
.. versionadded:: 0.20
|
1858 |
+
Added 'adaptive' option
|
1859 |
+
|
1860 |
+
eta0 : float, default=0.01
|
1861 |
+
The initial learning rate for the 'constant', 'invscaling' or
|
1862 |
+
'adaptive' schedules. The default value is 0.01.
|
1863 |
+
Values must be in the range `[0.0, inf)`.
|
1864 |
+
|
1865 |
+
power_t : float, default=0.25
|
1866 |
+
The exponent for inverse scaling learning rate.
|
1867 |
+
Values must be in the range `(-inf, inf)`.
|
1868 |
+
|
1869 |
+
early_stopping : bool, default=False
|
1870 |
+
Whether to use early stopping to terminate training when validation
|
1871 |
+
score is not improving. If set to True, it will automatically set aside
|
1872 |
+
a fraction of training data as validation and terminate
|
1873 |
+
training when validation score returned by the `score` method is not
|
1874 |
+
improving by at least `tol` for `n_iter_no_change` consecutive
|
1875 |
+
epochs.
|
1876 |
+
|
1877 |
+
.. versionadded:: 0.20
|
1878 |
+
Added 'early_stopping' option
|
1879 |
+
|
1880 |
+
validation_fraction : float, default=0.1
|
1881 |
+
The proportion of training data to set aside as validation set for
|
1882 |
+
early stopping. Must be between 0 and 1.
|
1883 |
+
Only used if `early_stopping` is True.
|
1884 |
+
Values must be in the range `(0.0, 1.0)`.
|
1885 |
+
|
1886 |
+
.. versionadded:: 0.20
|
1887 |
+
Added 'validation_fraction' option
|
1888 |
+
|
1889 |
+
n_iter_no_change : int, default=5
|
1890 |
+
Number of iterations with no improvement to wait before stopping
|
1891 |
+
fitting.
|
1892 |
+
Convergence is checked against the training loss or the
|
1893 |
+
validation loss depending on the `early_stopping` parameter.
|
1894 |
+
Integer values must be in the range `[1, max_iter)`.
|
1895 |
+
|
1896 |
+
.. versionadded:: 0.20
|
1897 |
+
Added 'n_iter_no_change' option
|
1898 |
+
|
1899 |
+
warm_start : bool, default=False
|
1900 |
+
When set to True, reuse the solution of the previous call to fit as
|
1901 |
+
initialization, otherwise, just erase the previous solution.
|
1902 |
+
See :term:`the Glossary <warm_start>`.
|
1903 |
+
|
1904 |
+
Repeatedly calling fit or partial_fit when warm_start is True can
|
1905 |
+
result in a different solution than when calling fit a single time
|
1906 |
+
because of the way the data is shuffled.
|
1907 |
+
If a dynamic learning rate is used, the learning rate is adapted
|
1908 |
+
depending on the number of samples already seen. Calling ``fit`` resets
|
1909 |
+
this counter, while ``partial_fit`` will result in increasing the
|
1910 |
+
existing counter.
|
1911 |
+
|
1912 |
+
average : bool or int, default=False
|
1913 |
+
When set to True, computes the averaged SGD weights across all
|
1914 |
+
updates and stores the result in the ``coef_`` attribute. If set to
|
1915 |
+
an int greater than 1, averaging will begin once the total number of
|
1916 |
+
samples seen reaches `average`. So ``average=10`` will begin
|
1917 |
+
averaging after seeing 10 samples.
|
1918 |
+
|
1919 |
+
Attributes
|
1920 |
+
----------
|
1921 |
+
coef_ : ndarray of shape (n_features,)
|
1922 |
+
Weights assigned to the features.
|
1923 |
+
|
1924 |
+
intercept_ : ndarray of shape (1,)
|
1925 |
+
The intercept term.
|
1926 |
+
|
1927 |
+
n_iter_ : int
|
1928 |
+
The actual number of iterations before reaching the stopping criterion.
|
1929 |
+
|
1930 |
+
t_ : int
|
1931 |
+
Number of weight updates performed during training.
|
1932 |
+
Same as ``(n_iter_ * n_samples + 1)``.
|
1933 |
+
|
1934 |
+
n_features_in_ : int
|
1935 |
+
Number of features seen during :term:`fit`.
|
1936 |
+
|
1937 |
+
.. versionadded:: 0.24
|
1938 |
+
|
1939 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
1940 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
1941 |
+
has feature names that are all strings.
|
1942 |
+
|
1943 |
+
.. versionadded:: 1.0
|
1944 |
+
|
1945 |
+
See Also
|
1946 |
+
--------
|
1947 |
+
HuberRegressor : Linear regression model that is robust to outliers.
|
1948 |
+
Lars : Least Angle Regression model.
|
1949 |
+
Lasso : Linear Model trained with L1 prior as regularizer.
|
1950 |
+
RANSACRegressor : RANSAC (RANdom SAmple Consensus) algorithm.
|
1951 |
+
Ridge : Linear least squares with l2 regularization.
|
1952 |
+
sklearn.svm.SVR : Epsilon-Support Vector Regression.
|
1953 |
+
TheilSenRegressor : Theil-Sen Estimator robust multivariate regression model.
|
1954 |
+
|
1955 |
+
Examples
|
1956 |
+
--------
|
1957 |
+
>>> import numpy as np
|
1958 |
+
>>> from sklearn.linear_model import SGDRegressor
|
1959 |
+
>>> from sklearn.pipeline import make_pipeline
|
1960 |
+
>>> from sklearn.preprocessing import StandardScaler
|
1961 |
+
>>> n_samples, n_features = 10, 5
|
1962 |
+
>>> rng = np.random.RandomState(0)
|
1963 |
+
>>> y = rng.randn(n_samples)
|
1964 |
+
>>> X = rng.randn(n_samples, n_features)
|
1965 |
+
>>> # Always scale the input. The most convenient way is to use a pipeline.
|
1966 |
+
>>> reg = make_pipeline(StandardScaler(),
|
1967 |
+
... SGDRegressor(max_iter=1000, tol=1e-3))
|
1968 |
+
>>> reg.fit(X, y)
|
1969 |
+
Pipeline(steps=[('standardscaler', StandardScaler()),
|
1970 |
+
('sgdregressor', SGDRegressor())])
|
1971 |
+
"""
|
1972 |
+
|
1973 |
+
_parameter_constraints: dict = {
|
1974 |
+
**BaseSGDRegressor._parameter_constraints,
|
1975 |
+
"penalty": [StrOptions({"l2", "l1", "elasticnet"}), None],
|
1976 |
+
"alpha": [Interval(Real, 0, None, closed="left")],
|
1977 |
+
"l1_ratio": [Interval(Real, 0, 1, closed="both")],
|
1978 |
+
"power_t": [Interval(Real, None, None, closed="neither")],
|
1979 |
+
"learning_rate": [
|
1980 |
+
StrOptions({"constant", "optimal", "invscaling", "adaptive"}),
|
1981 |
+
Hidden(StrOptions({"pa1", "pa2"})),
|
1982 |
+
],
|
1983 |
+
"epsilon": [Interval(Real, 0, None, closed="left")],
|
1984 |
+
"eta0": [Interval(Real, 0, None, closed="left")],
|
1985 |
+
}
|
1986 |
+
|
1987 |
+
def __init__(
|
1988 |
+
self,
|
1989 |
+
loss="squared_error",
|
1990 |
+
*,
|
1991 |
+
penalty="l2",
|
1992 |
+
alpha=0.0001,
|
1993 |
+
l1_ratio=0.15,
|
1994 |
+
fit_intercept=True,
|
1995 |
+
max_iter=1000,
|
1996 |
+
tol=1e-3,
|
1997 |
+
shuffle=True,
|
1998 |
+
verbose=0,
|
1999 |
+
epsilon=DEFAULT_EPSILON,
|
2000 |
+
random_state=None,
|
2001 |
+
learning_rate="invscaling",
|
2002 |
+
eta0=0.01,
|
2003 |
+
power_t=0.25,
|
2004 |
+
early_stopping=False,
|
2005 |
+
validation_fraction=0.1,
|
2006 |
+
n_iter_no_change=5,
|
2007 |
+
warm_start=False,
|
2008 |
+
average=False,
|
2009 |
+
):
|
2010 |
+
super().__init__(
|
2011 |
+
loss=loss,
|
2012 |
+
penalty=penalty,
|
2013 |
+
alpha=alpha,
|
2014 |
+
l1_ratio=l1_ratio,
|
2015 |
+
fit_intercept=fit_intercept,
|
2016 |
+
max_iter=max_iter,
|
2017 |
+
tol=tol,
|
2018 |
+
shuffle=shuffle,
|
2019 |
+
verbose=verbose,
|
2020 |
+
epsilon=epsilon,
|
2021 |
+
random_state=random_state,
|
2022 |
+
learning_rate=learning_rate,
|
2023 |
+
eta0=eta0,
|
2024 |
+
power_t=power_t,
|
2025 |
+
early_stopping=early_stopping,
|
2026 |
+
validation_fraction=validation_fraction,
|
2027 |
+
n_iter_no_change=n_iter_no_change,
|
2028 |
+
warm_start=warm_start,
|
2029 |
+
average=average,
|
2030 |
+
)
|
2031 |
+
|
2032 |
+
def _more_tags(self):
|
2033 |
+
return {
|
2034 |
+
"_xfail_checks": {
|
2035 |
+
"check_sample_weights_invariance": (
|
2036 |
+
"zero sample_weight is not equivalent to removing samples"
|
2037 |
+
),
|
2038 |
+
},
|
2039 |
+
"preserves_dtype": [np.float64, np.float32],
|
2040 |
+
}
|
2041 |
+
|
2042 |
+
|
2043 |
+
class SGDOneClassSVM(BaseSGD, OutlierMixin):
|
2044 |
+
"""Solves linear One-Class SVM using Stochastic Gradient Descent.
|
2045 |
+
|
2046 |
+
This implementation is meant to be used with a kernel approximation
|
2047 |
+
technique (e.g. `sklearn.kernel_approximation.Nystroem`) to obtain results
|
2048 |
+
similar to `sklearn.svm.OneClassSVM` which uses a Gaussian kernel by
|
2049 |
+
default.
|
2050 |
+
|
2051 |
+
Read more in the :ref:`User Guide <sgd_online_one_class_svm>`.
|
2052 |
+
|
2053 |
+
.. versionadded:: 1.0
|
2054 |
+
|
2055 |
+
Parameters
|
2056 |
+
----------
|
2057 |
+
nu : float, default=0.5
|
2058 |
+
The nu parameter of the One Class SVM: an upper bound on the
|
2059 |
+
fraction of training errors and a lower bound of the fraction of
|
2060 |
+
support vectors. Should be in the interval (0, 1]. By default 0.5
|
2061 |
+
will be taken.
|
2062 |
+
|
2063 |
+
fit_intercept : bool, default=True
|
2064 |
+
Whether the intercept should be estimated or not. Defaults to True.
|
2065 |
+
|
2066 |
+
max_iter : int, default=1000
|
2067 |
+
The maximum number of passes over the training data (aka epochs).
|
2068 |
+
It only impacts the behavior in the ``fit`` method, and not the
|
2069 |
+
`partial_fit`. Defaults to 1000.
|
2070 |
+
Values must be in the range `[1, inf)`.
|
2071 |
+
|
2072 |
+
tol : float or None, default=1e-3
|
2073 |
+
The stopping criterion. If it is not None, the iterations will stop
|
2074 |
+
when (loss > previous_loss - tol). Defaults to 1e-3.
|
2075 |
+
Values must be in the range `[0.0, inf)`.
|
2076 |
+
|
2077 |
+
shuffle : bool, default=True
|
2078 |
+
Whether or not the training data should be shuffled after each epoch.
|
2079 |
+
Defaults to True.
|
2080 |
+
|
2081 |
+
verbose : int, default=0
|
2082 |
+
The verbosity level.
|
2083 |
+
|
2084 |
+
random_state : int, RandomState instance or None, default=None
|
2085 |
+
The seed of the pseudo random number generator to use when shuffling
|
2086 |
+
the data. If int, random_state is the seed used by the random number
|
2087 |
+
generator; If RandomState instance, random_state is the random number
|
2088 |
+
generator; If None, the random number generator is the RandomState
|
2089 |
+
instance used by `np.random`.
|
2090 |
+
|
2091 |
+
learning_rate : {'constant', 'optimal', 'invscaling', 'adaptive'}, default='optimal'
|
2092 |
+
The learning rate schedule to use with `fit`. (If using `partial_fit`,
|
2093 |
+
learning rate must be controlled directly).
|
2094 |
+
|
2095 |
+
- 'constant': `eta = eta0`
|
2096 |
+
- 'optimal': `eta = 1.0 / (alpha * (t + t0))`
|
2097 |
+
where t0 is chosen by a heuristic proposed by Leon Bottou.
|
2098 |
+
- 'invscaling': `eta = eta0 / pow(t, power_t)`
|
2099 |
+
- 'adaptive': eta = eta0, as long as the training keeps decreasing.
|
2100 |
+
Each time n_iter_no_change consecutive epochs fail to decrease the
|
2101 |
+
training loss by tol or fail to increase validation score by tol if
|
2102 |
+
early_stopping is True, the current learning rate is divided by 5.
|
2103 |
+
|
2104 |
+
eta0 : float, default=0.0
|
2105 |
+
The initial learning rate for the 'constant', 'invscaling' or
|
2106 |
+
'adaptive' schedules. The default value is 0.0 as eta0 is not used by
|
2107 |
+
the default schedule 'optimal'.
|
2108 |
+
Values must be in the range `[0.0, inf)`.
|
2109 |
+
|
2110 |
+
power_t : float, default=0.5
|
2111 |
+
The exponent for inverse scaling learning rate.
|
2112 |
+
Values must be in the range `(-inf, inf)`.
|
2113 |
+
|
2114 |
+
warm_start : bool, default=False
|
2115 |
+
When set to True, reuse the solution of the previous call to fit as
|
2116 |
+
initialization, otherwise, just erase the previous solution.
|
2117 |
+
See :term:`the Glossary <warm_start>`.
|
2118 |
+
|
2119 |
+
Repeatedly calling fit or partial_fit when warm_start is True can
|
2120 |
+
result in a different solution than when calling fit a single time
|
2121 |
+
because of the way the data is shuffled.
|
2122 |
+
If a dynamic learning rate is used, the learning rate is adapted
|
2123 |
+
depending on the number of samples already seen. Calling ``fit`` resets
|
2124 |
+
this counter, while ``partial_fit`` will result in increasing the
|
2125 |
+
existing counter.
|
2126 |
+
|
2127 |
+
average : bool or int, default=False
|
2128 |
+
When set to True, computes the averaged SGD weights and stores the
|
2129 |
+
result in the ``coef_`` attribute. If set to an int greater than 1,
|
2130 |
+
averaging will begin once the total number of samples seen reaches
|
2131 |
+
average. So ``average=10`` will begin averaging after seeing 10
|
2132 |
+
samples.
|
2133 |
+
|
2134 |
+
Attributes
|
2135 |
+
----------
|
2136 |
+
coef_ : ndarray of shape (1, n_features)
|
2137 |
+
Weights assigned to the features.
|
2138 |
+
|
2139 |
+
offset_ : ndarray of shape (1,)
|
2140 |
+
Offset used to define the decision function from the raw scores.
|
2141 |
+
We have the relation: decision_function = score_samples - offset.
|
2142 |
+
|
2143 |
+
n_iter_ : int
|
2144 |
+
The actual number of iterations to reach the stopping criterion.
|
2145 |
+
|
2146 |
+
t_ : int
|
2147 |
+
Number of weight updates performed during training.
|
2148 |
+
Same as ``(n_iter_ * n_samples + 1)``.
|
2149 |
+
|
2150 |
+
loss_function_ : concrete ``LossFunction``
|
2151 |
+
|
2152 |
+
.. deprecated:: 1.4
|
2153 |
+
``loss_function_`` was deprecated in version 1.4 and will be removed in
|
2154 |
+
1.6.
|
2155 |
+
|
2156 |
+
n_features_in_ : int
|
2157 |
+
Number of features seen during :term:`fit`.
|
2158 |
+
|
2159 |
+
.. versionadded:: 0.24
|
2160 |
+
|
2161 |
+
feature_names_in_ : ndarray of shape (`n_features_in_`,)
|
2162 |
+
Names of features seen during :term:`fit`. Defined only when `X`
|
2163 |
+
has feature names that are all strings.
|
2164 |
+
|
2165 |
+
.. versionadded:: 1.0
|
2166 |
+
|
2167 |
+
See Also
|
2168 |
+
--------
|
2169 |
+
sklearn.svm.OneClassSVM : Unsupervised Outlier Detection.
|
2170 |
+
|
2171 |
+
Notes
|
2172 |
+
-----
|
2173 |
+
This estimator has a linear complexity in the number of training samples
|
2174 |
+
and is thus better suited than the `sklearn.svm.OneClassSVM`
|
2175 |
+
implementation for datasets with a large number of training samples (say
|
2176 |
+
> 10,000).
|
2177 |
+
|
2178 |
+
Examples
|
2179 |
+
--------
|
2180 |
+
>>> import numpy as np
|
2181 |
+
>>> from sklearn import linear_model
|
2182 |
+
>>> X = np.array([[-1, -1], [-2, -1], [1, 1], [2, 1]])
|
2183 |
+
>>> clf = linear_model.SGDOneClassSVM(random_state=42)
|
2184 |
+
>>> clf.fit(X)
|
2185 |
+
SGDOneClassSVM(random_state=42)
|
2186 |
+
|
2187 |
+
>>> print(clf.predict([[4, 4]]))
|
2188 |
+
[1]
|
2189 |
+
"""
|
2190 |
+
|
2191 |
+
loss_functions = {"hinge": (Hinge, 1.0)}
|
2192 |
+
|
2193 |
+
_parameter_constraints: dict = {
|
2194 |
+
**BaseSGD._parameter_constraints,
|
2195 |
+
"nu": [Interval(Real, 0.0, 1.0, closed="right")],
|
2196 |
+
"learning_rate": [
|
2197 |
+
StrOptions({"constant", "optimal", "invscaling", "adaptive"}),
|
2198 |
+
Hidden(StrOptions({"pa1", "pa2"})),
|
2199 |
+
],
|
2200 |
+
"eta0": [Interval(Real, 0, None, closed="left")],
|
2201 |
+
"power_t": [Interval(Real, None, None, closed="neither")],
|
2202 |
+
}
|
2203 |
+
|
2204 |
+
def __init__(
|
2205 |
+
self,
|
2206 |
+
nu=0.5,
|
2207 |
+
fit_intercept=True,
|
2208 |
+
max_iter=1000,
|
2209 |
+
tol=1e-3,
|
2210 |
+
shuffle=True,
|
2211 |
+
verbose=0,
|
2212 |
+
random_state=None,
|
2213 |
+
learning_rate="optimal",
|
2214 |
+
eta0=0.0,
|
2215 |
+
power_t=0.5,
|
2216 |
+
warm_start=False,
|
2217 |
+
average=False,
|
2218 |
+
):
|
2219 |
+
self.nu = nu
|
2220 |
+
super(SGDOneClassSVM, self).__init__(
|
2221 |
+
loss="hinge",
|
2222 |
+
penalty="l2",
|
2223 |
+
C=1.0,
|
2224 |
+
l1_ratio=0,
|
2225 |
+
fit_intercept=fit_intercept,
|
2226 |
+
max_iter=max_iter,
|
2227 |
+
tol=tol,
|
2228 |
+
shuffle=shuffle,
|
2229 |
+
verbose=verbose,
|
2230 |
+
epsilon=DEFAULT_EPSILON,
|
2231 |
+
random_state=random_state,
|
2232 |
+
learning_rate=learning_rate,
|
2233 |
+
eta0=eta0,
|
2234 |
+
power_t=power_t,
|
2235 |
+
early_stopping=False,
|
2236 |
+
validation_fraction=0.1,
|
2237 |
+
n_iter_no_change=5,
|
2238 |
+
warm_start=warm_start,
|
2239 |
+
average=average,
|
2240 |
+
)
|
2241 |
+
|
2242 |
+
def _fit_one_class(self, X, alpha, C, sample_weight, learning_rate, max_iter):
|
2243 |
+
"""Uses SGD implementation with X and y=np.ones(n_samples)."""
|
2244 |
+
|
2245 |
+
# The One-Class SVM uses the SGD implementation with
|
2246 |
+
# y=np.ones(n_samples).
|
2247 |
+
n_samples = X.shape[0]
|
2248 |
+
y = np.ones(n_samples, dtype=X.dtype, order="C")
|
2249 |
+
|
2250 |
+
dataset, offset_decay = make_dataset(X, y, sample_weight)
|
2251 |
+
|
2252 |
+
penalty_type = self._get_penalty_type(self.penalty)
|
2253 |
+
learning_rate_type = self._get_learning_rate_type(learning_rate)
|
2254 |
+
|
2255 |
+
# early stopping is set to False for the One-Class SVM. thus
|
2256 |
+
# validation_mask and validation_score_cb will be set to values
|
2257 |
+
# associated to early_stopping=False in _make_validation_split and
|
2258 |
+
# _make_validation_score_cb respectively.
|
2259 |
+
validation_mask = self._make_validation_split(y, sample_mask=sample_weight > 0)
|
2260 |
+
validation_score_cb = self._make_validation_score_cb(
|
2261 |
+
validation_mask, X, y, sample_weight
|
2262 |
+
)
|
2263 |
+
|
2264 |
+
random_state = check_random_state(self.random_state)
|
2265 |
+
# numpy mtrand expects a C long which is a signed 32 bit integer under
|
2266 |
+
# Windows
|
2267 |
+
seed = random_state.randint(0, np.iinfo(np.int32).max)
|
2268 |
+
|
2269 |
+
tol = self.tol if self.tol is not None else -np.inf
|
2270 |
+
|
2271 |
+
one_class = 1
|
2272 |
+
# There are no class weights for the One-Class SVM and they are
|
2273 |
+
# therefore set to 1.
|
2274 |
+
pos_weight = 1
|
2275 |
+
neg_weight = 1
|
2276 |
+
|
2277 |
+
if self.average:
|
2278 |
+
coef = self._standard_coef
|
2279 |
+
intercept = self._standard_intercept
|
2280 |
+
average_coef = self._average_coef
|
2281 |
+
average_intercept = self._average_intercept
|
2282 |
+
else:
|
2283 |
+
coef = self.coef_
|
2284 |
+
intercept = 1 - self.offset_
|
2285 |
+
average_coef = None # Not used
|
2286 |
+
average_intercept = [0] # Not used
|
2287 |
+
|
2288 |
+
_plain_sgd = _get_plain_sgd_function(input_dtype=coef.dtype)
|
2289 |
+
coef, intercept, average_coef, average_intercept, self.n_iter_ = _plain_sgd(
|
2290 |
+
coef,
|
2291 |
+
intercept[0],
|
2292 |
+
average_coef,
|
2293 |
+
average_intercept[0],
|
2294 |
+
self._loss_function_,
|
2295 |
+
penalty_type,
|
2296 |
+
alpha,
|
2297 |
+
C,
|
2298 |
+
self.l1_ratio,
|
2299 |
+
dataset,
|
2300 |
+
validation_mask,
|
2301 |
+
self.early_stopping,
|
2302 |
+
validation_score_cb,
|
2303 |
+
int(self.n_iter_no_change),
|
2304 |
+
max_iter,
|
2305 |
+
tol,
|
2306 |
+
int(self.fit_intercept),
|
2307 |
+
int(self.verbose),
|
2308 |
+
int(self.shuffle),
|
2309 |
+
seed,
|
2310 |
+
neg_weight,
|
2311 |
+
pos_weight,
|
2312 |
+
learning_rate_type,
|
2313 |
+
self.eta0,
|
2314 |
+
self.power_t,
|
2315 |
+
one_class,
|
2316 |
+
self.t_,
|
2317 |
+
offset_decay,
|
2318 |
+
self.average,
|
2319 |
+
)
|
2320 |
+
|
2321 |
+
self.t_ += self.n_iter_ * n_samples
|
2322 |
+
|
2323 |
+
if self.average > 0:
|
2324 |
+
self._average_intercept = np.atleast_1d(average_intercept)
|
2325 |
+
self._standard_intercept = np.atleast_1d(intercept)
|
2326 |
+
|
2327 |
+
if self.average <= self.t_ - 1.0:
|
2328 |
+
# made enough updates for averaging to be taken into account
|
2329 |
+
self.coef_ = average_coef
|
2330 |
+
self.offset_ = 1 - np.atleast_1d(average_intercept)
|
2331 |
+
else:
|
2332 |
+
self.coef_ = coef
|
2333 |
+
self.offset_ = 1 - np.atleast_1d(intercept)
|
2334 |
+
|
2335 |
+
else:
|
2336 |
+
self.offset_ = 1 - np.atleast_1d(intercept)
|
2337 |
+
|
2338 |
+
def _partial_fit(
|
2339 |
+
self,
|
2340 |
+
X,
|
2341 |
+
alpha,
|
2342 |
+
C,
|
2343 |
+
loss,
|
2344 |
+
learning_rate,
|
2345 |
+
max_iter,
|
2346 |
+
sample_weight,
|
2347 |
+
coef_init,
|
2348 |
+
offset_init,
|
2349 |
+
):
|
2350 |
+
first_call = getattr(self, "coef_", None) is None
|
2351 |
+
X = self._validate_data(
|
2352 |
+
X,
|
2353 |
+
None,
|
2354 |
+
accept_sparse="csr",
|
2355 |
+
dtype=[np.float64, np.float32],
|
2356 |
+
order="C",
|
2357 |
+
accept_large_sparse=False,
|
2358 |
+
reset=first_call,
|
2359 |
+
)
|
2360 |
+
|
2361 |
+
n_features = X.shape[1]
|
2362 |
+
|
2363 |
+
# Allocate datastructures from input arguments
|
2364 |
+
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
|
2365 |
+
|
2366 |
+
# We use intercept = 1 - offset where intercept is the intercept of
|
2367 |
+
# the SGD implementation and offset is the offset of the One-Class SVM
|
2368 |
+
# optimization problem.
|
2369 |
+
if getattr(self, "coef_", None) is None or coef_init is not None:
|
2370 |
+
self._allocate_parameter_mem(
|
2371 |
+
n_classes=1,
|
2372 |
+
n_features=n_features,
|
2373 |
+
input_dtype=X.dtype,
|
2374 |
+
coef_init=coef_init,
|
2375 |
+
intercept_init=offset_init,
|
2376 |
+
one_class=1,
|
2377 |
+
)
|
2378 |
+
elif n_features != self.coef_.shape[-1]:
|
2379 |
+
raise ValueError(
|
2380 |
+
"Number of features %d does not match previous data %d."
|
2381 |
+
% (n_features, self.coef_.shape[-1])
|
2382 |
+
)
|
2383 |
+
|
2384 |
+
if self.average and getattr(self, "_average_coef", None) is None:
|
2385 |
+
self._average_coef = np.zeros(n_features, dtype=X.dtype, order="C")
|
2386 |
+
self._average_intercept = np.zeros(1, dtype=X.dtype, order="C")
|
2387 |
+
|
2388 |
+
self._loss_function_ = self._get_loss_function(loss)
|
2389 |
+
if not hasattr(self, "t_"):
|
2390 |
+
self.t_ = 1.0
|
2391 |
+
|
2392 |
+
# delegate to concrete training procedure
|
2393 |
+
self._fit_one_class(
|
2394 |
+
X,
|
2395 |
+
alpha=alpha,
|
2396 |
+
C=C,
|
2397 |
+
learning_rate=learning_rate,
|
2398 |
+
sample_weight=sample_weight,
|
2399 |
+
max_iter=max_iter,
|
2400 |
+
)
|
2401 |
+
|
2402 |
+
return self
|
2403 |
+
|
2404 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
2405 |
+
def partial_fit(self, X, y=None, sample_weight=None):
|
2406 |
+
"""Fit linear One-Class SVM with Stochastic Gradient Descent.
|
2407 |
+
|
2408 |
+
Parameters
|
2409 |
+
----------
|
2410 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
2411 |
+
Subset of the training data.
|
2412 |
+
y : Ignored
|
2413 |
+
Not used, present for API consistency by convention.
|
2414 |
+
|
2415 |
+
sample_weight : array-like, shape (n_samples,), optional
|
2416 |
+
Weights applied to individual samples.
|
2417 |
+
If not provided, uniform weights are assumed.
|
2418 |
+
|
2419 |
+
Returns
|
2420 |
+
-------
|
2421 |
+
self : object
|
2422 |
+
Returns a fitted instance of self.
|
2423 |
+
"""
|
2424 |
+
if not hasattr(self, "coef_"):
|
2425 |
+
self._more_validate_params(for_partial_fit=True)
|
2426 |
+
|
2427 |
+
alpha = self.nu / 2
|
2428 |
+
return self._partial_fit(
|
2429 |
+
X,
|
2430 |
+
alpha,
|
2431 |
+
C=1.0,
|
2432 |
+
loss=self.loss,
|
2433 |
+
learning_rate=self.learning_rate,
|
2434 |
+
max_iter=1,
|
2435 |
+
sample_weight=sample_weight,
|
2436 |
+
coef_init=None,
|
2437 |
+
offset_init=None,
|
2438 |
+
)
|
2439 |
+
|
2440 |
+
def _fit(
|
2441 |
+
self,
|
2442 |
+
X,
|
2443 |
+
alpha,
|
2444 |
+
C,
|
2445 |
+
loss,
|
2446 |
+
learning_rate,
|
2447 |
+
coef_init=None,
|
2448 |
+
offset_init=None,
|
2449 |
+
sample_weight=None,
|
2450 |
+
):
|
2451 |
+
if self.warm_start and hasattr(self, "coef_"):
|
2452 |
+
if coef_init is None:
|
2453 |
+
coef_init = self.coef_
|
2454 |
+
if offset_init is None:
|
2455 |
+
offset_init = self.offset_
|
2456 |
+
else:
|
2457 |
+
self.coef_ = None
|
2458 |
+
self.offset_ = None
|
2459 |
+
|
2460 |
+
# Clear iteration count for multiple call to fit.
|
2461 |
+
self.t_ = 1.0
|
2462 |
+
|
2463 |
+
self._partial_fit(
|
2464 |
+
X,
|
2465 |
+
alpha,
|
2466 |
+
C,
|
2467 |
+
loss,
|
2468 |
+
learning_rate,
|
2469 |
+
self.max_iter,
|
2470 |
+
sample_weight,
|
2471 |
+
coef_init,
|
2472 |
+
offset_init,
|
2473 |
+
)
|
2474 |
+
|
2475 |
+
if (
|
2476 |
+
self.tol is not None
|
2477 |
+
and self.tol > -np.inf
|
2478 |
+
and self.n_iter_ == self.max_iter
|
2479 |
+
):
|
2480 |
+
warnings.warn(
|
2481 |
+
(
|
2482 |
+
"Maximum number of iteration reached before "
|
2483 |
+
"convergence. Consider increasing max_iter to "
|
2484 |
+
"improve the fit."
|
2485 |
+
),
|
2486 |
+
ConvergenceWarning,
|
2487 |
+
)
|
2488 |
+
|
2489 |
+
return self
|
2490 |
+
|
2491 |
+
@_fit_context(prefer_skip_nested_validation=True)
|
2492 |
+
def fit(self, X, y=None, coef_init=None, offset_init=None, sample_weight=None):
|
2493 |
+
"""Fit linear One-Class SVM with Stochastic Gradient Descent.
|
2494 |
+
|
2495 |
+
This solves an equivalent optimization problem of the
|
2496 |
+
One-Class SVM primal optimization problem and returns a weight vector
|
2497 |
+
w and an offset rho such that the decision function is given by
|
2498 |
+
<w, x> - rho.
|
2499 |
+
|
2500 |
+
Parameters
|
2501 |
+
----------
|
2502 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
2503 |
+
Training data.
|
2504 |
+
y : Ignored
|
2505 |
+
Not used, present for API consistency by convention.
|
2506 |
+
|
2507 |
+
coef_init : array, shape (n_classes, n_features)
|
2508 |
+
The initial coefficients to warm-start the optimization.
|
2509 |
+
|
2510 |
+
offset_init : array, shape (n_classes,)
|
2511 |
+
The initial offset to warm-start the optimization.
|
2512 |
+
|
2513 |
+
sample_weight : array-like, shape (n_samples,), optional
|
2514 |
+
Weights applied to individual samples.
|
2515 |
+
If not provided, uniform weights are assumed. These weights will
|
2516 |
+
be multiplied with class_weight (passed through the
|
2517 |
+
constructor) if class_weight is specified.
|
2518 |
+
|
2519 |
+
Returns
|
2520 |
+
-------
|
2521 |
+
self : object
|
2522 |
+
Returns a fitted instance of self.
|
2523 |
+
"""
|
2524 |
+
self._more_validate_params()
|
2525 |
+
|
2526 |
+
alpha = self.nu / 2
|
2527 |
+
self._fit(
|
2528 |
+
X,
|
2529 |
+
alpha=alpha,
|
2530 |
+
C=1.0,
|
2531 |
+
loss=self.loss,
|
2532 |
+
learning_rate=self.learning_rate,
|
2533 |
+
coef_init=coef_init,
|
2534 |
+
offset_init=offset_init,
|
2535 |
+
sample_weight=sample_weight,
|
2536 |
+
)
|
2537 |
+
|
2538 |
+
return self
|
2539 |
+
|
2540 |
+
def decision_function(self, X):
|
2541 |
+
"""Signed distance to the separating hyperplane.
|
2542 |
+
|
2543 |
+
Signed distance is positive for an inlier and negative for an
|
2544 |
+
outlier.
|
2545 |
+
|
2546 |
+
Parameters
|
2547 |
+
----------
|
2548 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
2549 |
+
Testing data.
|
2550 |
+
|
2551 |
+
Returns
|
2552 |
+
-------
|
2553 |
+
dec : array-like, shape (n_samples,)
|
2554 |
+
Decision function values of the samples.
|
2555 |
+
"""
|
2556 |
+
|
2557 |
+
check_is_fitted(self, "coef_")
|
2558 |
+
|
2559 |
+
X = self._validate_data(X, accept_sparse="csr", reset=False)
|
2560 |
+
decisions = safe_sparse_dot(X, self.coef_.T, dense_output=True) - self.offset_
|
2561 |
+
|
2562 |
+
return decisions.ravel()
|
2563 |
+
|
2564 |
+
def score_samples(self, X):
|
2565 |
+
"""Raw scoring function of the samples.
|
2566 |
+
|
2567 |
+
Parameters
|
2568 |
+
----------
|
2569 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
2570 |
+
Testing data.
|
2571 |
+
|
2572 |
+
Returns
|
2573 |
+
-------
|
2574 |
+
score_samples : array-like, shape (n_samples,)
|
2575 |
+
Unshiffted scoring function values of the samples.
|
2576 |
+
"""
|
2577 |
+
score_samples = self.decision_function(X) + self.offset_
|
2578 |
+
return score_samples
|
2579 |
+
|
2580 |
+
def predict(self, X):
|
2581 |
+
"""Return labels (1 inlier, -1 outlier) of the samples.
|
2582 |
+
|
2583 |
+
Parameters
|
2584 |
+
----------
|
2585 |
+
X : {array-like, sparse matrix}, shape (n_samples, n_features)
|
2586 |
+
Testing data.
|
2587 |
+
|
2588 |
+
Returns
|
2589 |
+
-------
|
2590 |
+
y : array, shape (n_samples,)
|
2591 |
+
Labels of the samples.
|
2592 |
+
"""
|
2593 |
+
y = (self.decision_function(X) >= 0).astype(np.int32)
|
2594 |
+
y[y == 0] = -1 # for consistency with outlier detectors
|
2595 |
+
return y
|
2596 |
+
|
2597 |
+
def _more_tags(self):
|
2598 |
+
return {
|
2599 |
+
"_xfail_checks": {
|
2600 |
+
"check_sample_weights_invariance": (
|
2601 |
+
"zero sample_weight is not equivalent to removing samples"
|
2602 |
+
)
|
2603 |
+
},
|
2604 |
+
"preserves_dtype": [np.float64, np.float32],
|
2605 |
+
}
|
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