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"""All code taken from https://github.com/lucidrains/VN-transformer"""
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from collections import namedtuple
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from functools import wraps
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import torch
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import torch.nn.functional as F
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from einops import rearrange, reduce
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from einops.layers.torch import Rearrange
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from packaging import version
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from torch import einsum, nn
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FlashAttentionConfig = namedtuple(
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"FlashAttentionConfig", ["enable_flash", "enable_math", "enable_mem_efficient"]
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)
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def exists(val):
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return val is not None
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def once(fn):
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called = False
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@wraps(fn)
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def inner(x):
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nonlocal called
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if called:
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return
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called = True
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return fn(x)
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return inner
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print_once = once(print)
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class Attend(nn.Module):
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def __init__(self, dropout=0.0, flash=False, l2_dist=False):
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super().__init__()
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assert not (
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flash and l2_dist
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), "flash attention is not compatible with l2 distance"
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self.l2_dist = l2_dist
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self.dropout = dropout
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self.attn_dropout = nn.Dropout(dropout)
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self.flash = flash
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assert not (
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flash and version.parse(torch.__version__) < version.parse("2.0.0")
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), "in order to use flash attention, you must be using pytorch 2.0 or above"
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self.cpu_config = FlashAttentionConfig(True, True, True)
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self.cuda_config = None
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if not torch.cuda.is_available() or not flash:
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return
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device_properties = torch.cuda.get_device_properties(torch.device("cuda"))
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if device_properties.major == 8 and device_properties.minor == 0:
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print_once(
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"A100 GPU detected, using flash attention if input tensor is on cuda"
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)
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self.cuda_config = FlashAttentionConfig(True, False, False)
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else:
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print_once(
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"Non-A100 GPU detected, using math or mem efficient attention if input tensor is on cuda"
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)
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self.cuda_config = FlashAttentionConfig(False, True, True)
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def flash_attn(self, q, k, v, mask=None):
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_, heads, q_len, _, _, is_cuda = (
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*q.shape,
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k.shape[-2],
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q.is_cuda,
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)
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if exists(mask):
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mask = mask.expand(-1, heads, q_len, -1)
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config = self.cuda_config if is_cuda else self.cpu_config
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with torch.backends.cuda.sdp_kernel(**config._asdict()):
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out = F.scaled_dot_product_attention(
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q,
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k,
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v,
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attn_mask=mask,
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dropout_p=self.dropout if self.training else 0.0,
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)
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return out
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def forward(self, q, k, v, mask=None):
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"""
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einstein notation
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b - batch
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h - heads
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n, i, j - sequence length (base sequence length, source, target)
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d - feature dimension
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"""
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scale = q.shape[-1] ** -0.5
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if exists(mask) and mask.ndim != 4:
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mask = rearrange(mask, "b j -> b 1 1 j")
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if self.flash:
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return self.flash_attn(q, k, v, mask=mask)
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sim = einsum("b h i d, b h j d -> b h i j", q, k) * scale
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if self.l2_dist:
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q_squared = reduce(q**2, "b h i d -> b h i 1", "sum")
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k_squared = reduce(k**2, "b h j d -> b h 1 j", "sum")
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sim = sim * 2 - q_squared - k_squared
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if exists(mask):
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sim = sim.masked_fill(~mask, -torch.finfo(sim.dtype).max)
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attn = sim.softmax(dim=-1)
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attn = self.attn_dropout(attn)
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out = einsum("b h i j, b h j d -> b h i d", attn, v)
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return out
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def exists(val):
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return val is not None
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def default(val, d):
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return val if exists(val) else d
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def inner_dot_product(x, y, *, dim=-1, keepdim=True):
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return (x * y).sum(dim=dim, keepdim=keepdim)
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class LayerNorm(nn.Module):
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def __init__(self, dim):
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super().__init__()
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self.gamma = nn.Parameter(torch.ones(dim))
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self.register_buffer("beta", torch.zeros(dim))
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def forward(self, x):
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return F.layer_norm(x, x.shape[-1:], self.gamma, self.beta)
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class VNLinear(nn.Module):
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def __init__(self, dim_in, dim_out, bias_epsilon=0.0):
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super().__init__()
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self.weight = nn.Parameter(torch.randn(dim_out, dim_in))
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self.bias = None
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self.bias_epsilon = bias_epsilon
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if bias_epsilon > 0.0:
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self.bias = nn.Parameter(torch.randn(dim_out))
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def forward(self, x):
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out = einsum("... i c, o i -> ... o c", x, self.weight)
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if exists(self.bias):
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bias = F.normalize(self.bias, dim=-1) * self.bias_epsilon
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out = out + rearrange(bias, "... -> ... 1")
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return out
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class VNReLU(nn.Module):
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def __init__(self, dim, eps=1e-6):
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super().__init__()
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self.eps = eps
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self.W = nn.Parameter(torch.randn(dim, dim))
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self.U = nn.Parameter(torch.randn(dim, dim))
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def forward(self, x):
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q = einsum("... i c, o i -> ... o c", x, self.W)
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k = einsum("... i c, o i -> ... o c", x, self.U)
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qk = inner_dot_product(q, k)
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k_norm = k.norm(dim=-1, keepdim=True).clamp(min=self.eps)
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q_projected_on_k = q - inner_dot_product(q, k / k_norm) * k
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out = torch.where(qk >= 0.0, q, q_projected_on_k)
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return out
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class VNAttention(nn.Module):
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|
def __init__(
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|
self,
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dim,
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dim_head=64,
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heads=8,
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dim_coor=3,
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bias_epsilon=0.0,
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|
l2_dist_attn=False,
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flash=False,
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|
num_latents=None,
|
|
):
|
|
super().__init__()
|
|
assert not (
|
|
l2_dist_attn and flash
|
|
), "l2 distance attention is not compatible with flash attention"
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|
|
self.scale = (dim_coor * dim_head) ** -0.5
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dim_inner = dim_head * heads
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|
self.heads = heads
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self.to_q_input = None
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|
if exists(num_latents):
|
|
self.to_q_input = VNWeightedPool(
|
|
dim, num_pooled_tokens=num_latents, squeeze_out_pooled_dim=False
|
|
)
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self.to_q = VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon)
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self.to_k = VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon)
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self.to_v = VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon)
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self.to_out = VNLinear(dim_inner, dim, bias_epsilon=bias_epsilon)
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|
|
if l2_dist_attn and not exists(num_latents):
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|
|
self.to_k = self.to_q
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|
|
self.attend = Attend(flash=flash, l2_dist=l2_dist_attn)
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|
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def forward(self, x, mask=None):
|
|
"""
|
|
einstein notation
|
|
b - batch
|
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n - sequence
|
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h - heads
|
|
d - feature dimension (channels)
|
|
c - coordinate dimension (3 for 3d space)
|
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i - source sequence dimension
|
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j - target sequence dimension
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|
"""
|
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|
|
c = x.shape[-1]
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|
|
if exists(self.to_q_input):
|
|
q_input = self.to_q_input(x, mask=mask)
|
|
else:
|
|
q_input = x
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|
|
q, k, v = self.to_q(q_input), self.to_k(x), self.to_v(x)
|
|
q, k, v = map(
|
|
lambda t: rearrange(t, "b n (h d) c -> b h n (d c)", h=self.heads),
|
|
(q, k, v),
|
|
)
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|
|
out = self.attend(q, k, v, mask=mask)
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|
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out = rearrange(out, "b h n (d c) -> b n (h d) c", c=c)
|
|
return self.to_out(out)
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|
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|
|
def VNFeedForward(dim, mult=4, bias_epsilon=0.0):
|
|
dim_inner = int(dim * mult)
|
|
return nn.Sequential(
|
|
VNLinear(dim, dim_inner, bias_epsilon=bias_epsilon),
|
|
VNReLU(dim_inner),
|
|
VNLinear(dim_inner, dim, bias_epsilon=bias_epsilon),
|
|
)
|
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|
|
|
class VNLayerNorm(nn.Module):
|
|
def __init__(self, dim, eps=1e-6):
|
|
super().__init__()
|
|
self.eps = eps
|
|
self.ln = LayerNorm(dim)
|
|
|
|
def forward(self, x):
|
|
norms = x.norm(dim=-1)
|
|
x = x / rearrange(norms.clamp(min=self.eps), "... -> ... 1")
|
|
ln_out = self.ln(norms)
|
|
return x * rearrange(ln_out, "... -> ... 1")
|
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|
|
|
|
class VNWeightedPool(nn.Module):
|
|
def __init__(
|
|
self, dim, dim_out=None, num_pooled_tokens=1, squeeze_out_pooled_dim=True
|
|
):
|
|
super().__init__()
|
|
dim_out = default(dim_out, dim)
|
|
self.weight = nn.Parameter(torch.randn(num_pooled_tokens, dim, dim_out))
|
|
self.squeeze_out_pooled_dim = num_pooled_tokens == 1 and squeeze_out_pooled_dim
|
|
|
|
def forward(self, x, mask=None):
|
|
if exists(mask):
|
|
mask = rearrange(mask, "b n -> b n 1 1")
|
|
x = x.masked_fill(~mask, 0.0)
|
|
numer = reduce(x, "b n d c -> b d c", "sum")
|
|
denom = mask.sum(dim=1)
|
|
mean_pooled = numer / denom.clamp(min=1e-6)
|
|
else:
|
|
mean_pooled = reduce(x, "b n d c -> b d c", "mean")
|
|
|
|
out = einsum("b d c, m d e -> b m e c", mean_pooled, self.weight)
|
|
|
|
if not self.squeeze_out_pooled_dim:
|
|
return out
|
|
|
|
out = rearrange(out, "b 1 d c -> b d c")
|
|
return out
|
|
|
|
|
|
|
|
|
|
|
|
class VNTransformerEncoder(nn.Module):
|
|
def __init__(
|
|
self,
|
|
dim,
|
|
*,
|
|
depth,
|
|
dim_head=64,
|
|
heads=8,
|
|
dim_coor=3,
|
|
ff_mult=4,
|
|
final_norm=False,
|
|
bias_epsilon=0.0,
|
|
l2_dist_attn=False,
|
|
flash_attn=False,
|
|
):
|
|
super().__init__()
|
|
self.dim = dim
|
|
self.dim_coor = dim_coor
|
|
|
|
self.layers = nn.ModuleList([])
|
|
|
|
for _ in range(depth):
|
|
self.layers.append(
|
|
nn.ModuleList(
|
|
[
|
|
VNAttention(
|
|
dim=dim,
|
|
dim_head=dim_head,
|
|
heads=heads,
|
|
bias_epsilon=bias_epsilon,
|
|
l2_dist_attn=l2_dist_attn,
|
|
flash=flash_attn,
|
|
),
|
|
VNLayerNorm(dim),
|
|
VNFeedForward(dim=dim, mult=ff_mult, bias_epsilon=bias_epsilon),
|
|
VNLayerNorm(dim),
|
|
]
|
|
)
|
|
)
|
|
|
|
self.norm = VNLayerNorm(dim) if final_norm else nn.Identity()
|
|
|
|
def forward(self, x, mask=None):
|
|
*_, d, c = x.shape
|
|
|
|
assert (
|
|
x.ndim == 4 and d == self.dim and c == self.dim_coor
|
|
), "input needs to be in the shape of (batch, seq, dim ({self.dim}), coordinate dim ({self.dim_coor}))"
|
|
|
|
for attn, attn_post_ln, ff, ff_post_ln in self.layers:
|
|
x = attn_post_ln(attn(x, mask=mask)) + x
|
|
x = ff_post_ln(ff(x)) + x
|
|
|
|
return self.norm(x)
|
|
|
|
|
|
|
|
|
|
|
|
class VNInvariant(nn.Module):
|
|
def __init__(
|
|
self,
|
|
dim,
|
|
dim_coor=3,
|
|
):
|
|
super().__init__()
|
|
self.mlp = nn.Sequential(
|
|
VNLinear(dim, dim_coor), VNReLU(dim_coor), Rearrange("... d e -> ... e d")
|
|
)
|
|
|
|
def forward(self, x):
|
|
return einsum("b n d i, b n i o -> b n o", x, self.mlp(x))
|
|
|
|
|
|
|
|
|
|
|
|
class VNTransformer(nn.Module):
|
|
def __init__(
|
|
self,
|
|
*,
|
|
dim,
|
|
depth,
|
|
num_tokens=None,
|
|
dim_feat=None,
|
|
dim_head=64,
|
|
heads=8,
|
|
dim_coor=3,
|
|
reduce_dim_out=True,
|
|
bias_epsilon=0.0,
|
|
l2_dist_attn=False,
|
|
flash_attn=False,
|
|
translation_equivariance=False,
|
|
translation_invariant=False,
|
|
):
|
|
super().__init__()
|
|
self.token_emb = nn.Embedding(num_tokens, dim) if exists(num_tokens) else None
|
|
|
|
dim_feat = default(dim_feat, 0)
|
|
self.dim_feat = dim_feat
|
|
self.dim_coor_total = dim_coor + dim_feat
|
|
|
|
assert (int(translation_equivariance) + int(translation_invariant)) <= 1
|
|
self.translation_equivariance = translation_equivariance
|
|
self.translation_invariant = translation_invariant
|
|
|
|
self.vn_proj_in = nn.Sequential(
|
|
Rearrange("... c -> ... 1 c"), VNLinear(1, dim, bias_epsilon=bias_epsilon)
|
|
)
|
|
|
|
self.encoder = VNTransformerEncoder(
|
|
dim=dim,
|
|
depth=depth,
|
|
dim_head=dim_head,
|
|
heads=heads,
|
|
bias_epsilon=bias_epsilon,
|
|
dim_coor=self.dim_coor_total,
|
|
l2_dist_attn=l2_dist_attn,
|
|
flash_attn=flash_attn,
|
|
)
|
|
|
|
if reduce_dim_out:
|
|
self.vn_proj_out = nn.Sequential(
|
|
VNLayerNorm(dim),
|
|
VNLinear(dim, 1, bias_epsilon=bias_epsilon),
|
|
Rearrange("... 1 c -> ... c"),
|
|
)
|
|
else:
|
|
self.vn_proj_out = nn.Identity()
|
|
|
|
def forward(
|
|
self, coors, *, feats=None, mask=None, return_concatted_coors_and_feats=False
|
|
):
|
|
if self.translation_equivariance or self.translation_invariant:
|
|
coors_mean = reduce(coors, "... c -> c", "mean")
|
|
coors = coors - coors_mean
|
|
|
|
x = coors
|
|
|
|
if exists(feats):
|
|
if feats.dtype == torch.long:
|
|
assert exists(
|
|
self.token_emb
|
|
), "num_tokens must be given to the VNTransformer (to build the Embedding), if the features are to be given as indices"
|
|
feats = self.token_emb(feats)
|
|
|
|
assert (
|
|
feats.shape[-1] == self.dim_feat
|
|
), f"dim_feat should be set to {feats.shape[-1]}"
|
|
x = torch.cat((x, feats), dim=-1)
|
|
|
|
assert x.shape[-1] == self.dim_coor_total
|
|
|
|
x = self.vn_proj_in(x)
|
|
x = self.encoder(x, mask=mask)
|
|
x = self.vn_proj_out(x)
|
|
|
|
coors_out, feats_out = (
|
|
x[..., :3],
|
|
x[..., 3:],
|
|
)
|
|
|
|
if self.translation_equivariance:
|
|
coors_out = coors_out + coors_mean
|
|
|
|
if not exists(feats):
|
|
return coors_out
|
|
|
|
if return_concatted_coors_and_feats:
|
|
return torch.cat((coors_out, feats_out), dim=-1)
|
|
|
|
return coors_out, feats_out
|
|
|