""" Adapted from BigCode project: https://github.com/bigcode-project/bigcode-dataset/tree/main/near_deduplication """ from __future__ import annotations import gc import hashlib import multiprocessing as mp import os import random import re import struct import time from collections import defaultdict from itertools import tee from typing import Any, Dict, Iterable, List, Tuple import numpy as np from scipy.integrate import quad as integrate from tqdm import tqdm from chat_data_pipeline.pipeline import logger SEED = 42 NON_ALPHA = re.compile("[^A-Za-z_0-9]") RNG = np.random.RandomState(SEED) MAX_HASH = np.uint64((1 << 32) - 1) MERSENNE_PRIME = np.uint64((1 << 61) - 1) def ngrams(sequence: List[str], n: int, min_ngram_size: int) -> Iterable: """ Directly taken from nltk package to avoid dependency. Parameters ---------- sequence : list The sequence of items to be n-grammed. n : int The order of the n-grams to be extracted. min_ngram_size : int The minimum size of n-grams. Returns ------- Iterable The n-grams generated from the sequence. """ if len(sequence) < min_ngram_size: return [] iterables = tee(sequence, n) for i, sub_iterable in enumerate(iterables): for _ in range(i): next(sub_iterable, None) return zip(*iterables) def sha1_hash32(data): """ Directly taken from datasketch package to avoid dependency. Parameters ---------- data : bytes Returns ------- int """ return struct.unpack(" Dict[str, Any]: """ Combined with some datasketch code to better parallelize computation. Parameters ---------- content : str The content to be embedded. idx : int The index of the content. num_perm : int The number of permutations. ngram_size : int The size of n-grams. hashranges : List[Tuple[int, int]] The ranges of hash values. permutations : np.ndarray The permutations for the minhash. min_ngram_size : int The minimum size of n-grams. Returns ------- Dict[str, Any] The hash values in each range and the index. """ hashvalues = np.ones(num_perm, dtype=np.uint64) * MAX_HASH tokens = {" ".join(t) for t in ngrams(NON_ALPHA.split(content), ngram_size, min_ngram_size)} hv = np.array([sha1_hash32(token.encode("utf-8")) for token in tokens], dtype=np.uint64) # noqa: E501 a, b = permutations phv = np.bitwise_and(((hv * np.tile(a, (len(hv), 1)).T).T + b) % MERSENNE_PRIME, MAX_HASH) # noqa: E501 hashvalues = np.vstack([phv, hashvalues]).min(axis=0) Hs = [bytes(hashvalues[start:end].byteswap().data) for start, end in hashranges] return {"__signatures__": Hs, "__id__": idx} def optimal_param( threshold: float, num_perm: int, false_positive_weight: float = 0.5, false_negative_weight: float = 0.5, ): """ Compute the optimal `MinHashLSH` parameter that minimizes the weighted sum of probabilities of false positive and false negative, taken from datasketch. Parameters ---------- threshold : float The threshold for similarity. num_perm : int The number of permutations. false_positive_weight : float The weight of false positive. false_negative_weight : float The weight of false negative. Returns ------- Tuple[int, int] The optimal `b` and `r` parameters. The number of bands, and the number of rows per band respectively. """ def false_positive_probability(threshold: float, b: int, r: int): """Source: `datasketch.lsh`""" def proba(s): return 1 - (1 - s ** float(r)) ** float(b) a, _ = integrate(proba, 0.0, threshold) return a def false_negative_probability(threshold: float, b: int, r: int): """Source: `datasketch.lsh`""" def proba(s): return 1 - (1 - (1 - s ** float(r)) ** float(b)) a, _ = integrate(proba, threshold, 1.0) return a min_error = float("inf") opt = (0, 0) for b in range(1, num_perm + 1): max_r = int(num_perm / b) for r in range(1, max_r + 1): fp = false_positive_probability(threshold, b, r) fn = false_negative_probability(threshold, b, r) error = fp * false_positive_weight + fn * false_negative_weight if error < min_error: min_error = error opt = (b, r) return opt class UnionFind: def __init__(self): self.parent: Dict[int, int] = {} def find(self, x): if x not in self.parent: self.parent[x] = x if self.parent[x] != x: self.parent[x] = self.find(self.parent[x]) return self.parent[x] def union(self, x, y): px = self.find(x) py = self.find(y) self.parent[px] = self.parent[py] = min(px, py) def prepare_dataset(dataset): def map_func(example): text = "" for message in example["conversation"]: if message["do_train"]: text += message["content"] + "\n\n" return { "text": text.strip() } dedup_ready_dataset = dataset.map( map_func, num_proc=os.cpu_count(), desc="Preparing..." ) return dedup_ready_dataset def deduplicate( dataset, # noqa: E501 column="text", ngram_size=5, num_perm=256, threshold=0.7, min_ngram_size=5, ): mp.set_start_method("fork", force=True) uf = UnionFind() time_measures = {} start_time = time.time() B, R = optimal_param(threshold, num_perm) HASH_RANGES = [(i * R, (i + 1) * R) for i in range(B)] HASH_TABLES = [defaultdict(set) for _ in range(B)] time_measures["load_dataset"] = time.time() time_measures["load_dataset"] = time.time() - time_measures["load_dataset"] DATA_SIZE = len(dataset) PERMUTATIONS = np.array( [ ( RNG.randint(1, MERSENNE_PRIME, dtype=np.uint64), RNG.randint(0, MERSENNE_PRIME, dtype=np.uint64), ) for _ in range(num_perm) ], dtype=np.uint64, ).T time_measures["minhash"] = time.time() embedded = dataset.map( function=embed_func, fn_kwargs={ "num_perm": num_perm, "hashranges": HASH_RANGES, "ngram_size": ngram_size, "permutations": PERMUTATIONS, "min_ngram_size": min_ngram_size, }, input_columns=[column], remove_columns=dataset.column_names, num_proc=os.cpu_count(), with_indices=True, desc="Fingerprinting...", ) time_measures["minhash"] = time.time() - time_measures["minhash"] time_measures["clustering"] = time.time() batch_size: int = 10000 for i in tqdm( range(0, len(embedded), batch_size), dynamic_ncols=True, desc="Iterating MinHashes..." # noqa: E501 ): batch = embedded[i: i + batch_size] for key, Hs in zip(batch["__id__"], batch["__signatures__"]): for H, hashtable in zip(Hs, HASH_TABLES): hashtable[H].add(key) for table in tqdm(HASH_TABLES, dynamic_ncols=True, desc="Clustering..."): for cluster in table.values(): if len(cluster) <= 1: continue idx = min(cluster) for x in cluster: uf.union(x, idx) time_measures["clustering"] = time.time() - time_measures["clustering"] time_measures["filtering"] = time.time() gc.freeze() gc.disable() dataset = dataset.map( function=lambda _, idx: {"__cluster__": uf.find(idx)}, with_indices=True, num_proc=os.cpu_count(), new_fingerprint=str(random.getrandbits(128)), desc="Finding clusters...", ) gc.enable() gc.collect() # This is where the deduplication happens # Since there is no easy groupby in datasets # I will use this simple filter for now final_data = dataset.filter( function=lambda record, idx: record["__cluster__"] == idx, with_indices=True, num_proc=os.cpu_count(), desc="Filtering clusters...", ) time_measures["filtering"] = time.time() - time_measures["filtering"] FINAL_DATA_SIZE = len(final_data) DUP_SIZE = DATA_SIZE - FINAL_DATA_SIZE PAD = 32 for key, value in time_measures.items(): logger.info(f"{key:<{PAD}}: {value:.2f} seconds") logger.info(f"{'Data Number (before)':<{PAD}}: {DATA_SIZE}") logger.info( f"{'Data Number (after)':<{PAD}}: {FINAL_DATA_SIZE} ({FINAL_DATA_SIZE / DATA_SIZE:.2%})" # noqa: E501 ) logger.info(f"{'Duplicate Number':<{PAD}}: {DUP_SIZE} ({DUP_SIZE / DATA_SIZE:.2%})") # noqa: E501 logger.info(f"{'Total Time':<{PAD}}: {time.time() - start_time:.2f} seconds") logger.info("🤗 Happy Deduplicating 🤗") return final_data