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import ot
from sklearn.preprocessing import normalize
from lapjv import lapjv
from sklearn.neighbors import KNeighborsClassifier
from sklearn.metrics import euclidean_distances
from sklearn.externals.joblib import Parallel, delayed
from sklearn.utils import check_array
from sklearn.metrics.scorer import check_scoring
from pathos.multiprocessing import ProcessingPool as Pool
from sklearn.metrics import euclidean_distances
import numpy as np
from mosestokenizer import MosesTokenizer
class Wasserstein_Matcher(KNeighborsClassifier):
"""
Implements a nearest neighbors classifier for input distributions using the Wasserstein distance as metric.
Source and target distributions are l_1 normalized before computing the Wasserstein distance.
Wasserstein is parametrized by the distances between the individual points of the distributions.
"""
def __init__(self, W_embed, n_neighbors=1, n_jobs=1, verbose=False, sinkhorn= False, sinkhorn_reg=0.1):
"""
Initialization of the class.
Arguments
---------
W_embed: embeddings of the words, np.array
verbose: True/False
"""
self.sinkhorn = sinkhorn
self.sinkhorn_reg = sinkhorn_reg
self.W_embed = W_embed
self.verbose = verbose
super(Wasserstein_Matcher, self).__init__(n_neighbors=n_neighbors, n_jobs=n_jobs, metric='precomputed', algorithm='brute')
def _wmd(self, i, row, X_train):
union_idx = np.union1d(X_train[i].indices, row.indices)
W_minimal = self.W_embed[union_idx]
W_dist = euclidean_distances(W_minimal)
bow_i = X_train[i, union_idx].A.ravel()
bow_j = row[:, union_idx].A.ravel()
if self.sinkhorn:
return ot.sinkhorn2(bow_i, bow_j, W_dist, self.sinkhorn_reg, numItermax=50, method='sinkhorn_stabilized',)[0]
else:
return ot.emd2(bow_i, bow_j, W_dist)
def _wmd_row(self, row):
X_train = self._fit_X
n_samples_train = X_train.shape[0]
return [self._wmd(i, row, X_train) for i in range(n_samples_train)]
def _pairwise_wmd(self, X_test, X_train=None):
n_samples_test = X_test.shape[0]
if X_train is None:
X_train = self._fit_X
pool = Pool(nodes=self.n_jobs) # Parallelization of the calculation of the distances
dist = pool.map(self._wmd_row, X_test)
return np.array(dist)
def fit(self, X, y): # X_train_idf
X = check_array(X, accept_sparse='csr', copy=True) # check if array is sparse
X = normalize(X, norm='l1', copy=False)
return super(Wasserstein_Matcher, self).fit(X, y) # X_train_idf, np_ones(document collection size)
def predict(self, X):
X = check_array(X, accept_sparse='csr', copy=True)
X = normalize(X, norm='l1', copy=False)
dist = self._pairwise_wmd(X)
dist = dist * 1000 # for lapjv, small floating point numbers are evil
return super(Wasserstein_Matcher, self).predict(dist)
def kneighbors(self, X, n_neighbors=1): # X : X_train_idf
X = check_array(X, accept_sparse='csr', copy=True)
X = normalize(X, norm='l1', copy=False)
dist = self._pairwise_wmd(X)
dist = dist * 1000 # for lapjv, small floating point numbers are evil
return lapjv(dist) # and here is the matching part
class Wasserstein_Retriever(KNeighborsClassifier):
"""
Implements a nearest neighbors classifier for input distributions using the Wasserstein distance as metric.
Source and target distributions are l_1 normalized before computing the Wasserstein distance.
Wasserstein is parametrized by the distances between the individual points of the distributions.
"""
def __init__(self, W_embed, n_neighbors=1, n_jobs=1, verbose=False, sinkhorn= False, sinkhorn_reg=0.1):
"""
Initialization of the class.
Arguments
---------
W_embed: embeddings of the words, np.array
verbose: True/False
"""
self.sinkhorn = sinkhorn
self.sinkhorn_reg = sinkhorn_reg
self.W_embed = W_embed
self.verbose = verbose
super(Wasserstein_Retriever, self).__init__(n_neighbors=n_neighbors, n_jobs=n_jobs, metric='precomputed', algorithm='brute')
def _wmd(self, i, row, X_train):
union_idx = np.union1d(X_train[i].indices, row.indices)
W_minimal = self.W_embed[union_idx]
W_dist = euclidean_distances(W_minimal)
bow_i = X_train[i, union_idx].A.ravel()
bow_j = row[:, union_idx].A.ravel()
if self.sinkhorn:
return ot.sinkhorn2(bow_i, bow_j, W_dist, self.sinkhorn_reg, numItermax=50, method='sinkhorn_stabilized',)[0]
else:
return ot.emd2(bow_i, bow_j, W_dist)
def _wmd_row(self, row):
X_train = self._fit_X
n_samples_train = X_train.shape[0]
return [self._wmd(i, row, X_train) for i in range(n_samples_train)]
def _pairwise_wmd(self, X_test, X_train=None):
n_samples_test = X_test.shape[0]
if X_train is None:
X_train = self._fit_X
pool = Pool(nodes=self.n_jobs) # Parallelization of the calculation of the distances
dist = pool.map(self._wmd_row, X_test)
return np.array(dist)
def fit(self, X, y):
X = check_array(X, accept_sparse='csr', copy=True)
X = normalize(X, norm='l1', copy=False)
return super(Wasserstein_Retriever, self).fit(X, y)
def predict(self, X):
X = check_array(X, accept_sparse='csr', copy=True)
X = normalize(X, norm='l1', copy=False)
dist = self._pairwise_wmd(X)
return super(Wasserstein_Retriever, self).predict(dist)
def kneighbors(self, X, n_neighbors=1):
X = check_array(X, accept_sparse='csr', copy=True)
X = normalize(X, norm='l1', copy=False)
dist = self._pairwise_wmd(X)
return super(Wasserstein_Retriever, self).kneighbors(dist, n_neighbors)
def load_embeddings(path, dimension=300):
"""
Loads the embeddings from a word2vec formatted file.
word2vec format is one line per word and it's associated embedding
(dimension x floating numbers) separated by spaces
The first line may or may not include the word count and dimension
"""
vectors = {}
with open(path, mode='r', encoding='utf8') as fp:
first_line = fp.readline().rstrip('\n')
if first_line.count(' ') == 1:
# includes the "word_count dimension" information
(word_count, dimension) = map(int, first_line.split())
else:
# assume the file only contains vectors
fp.seek(0)
for line in fp:
elems = line.split()
vectors[" ".join(elems[:-dimension])] = " ".join(elems[-dimension:])
return vectors
def clean_corpus_using_embeddings_vocabulary(
embeddings_dictionary,
corpus,
vectors,
language,
):
'''
Cleans corpus using the dictionary of embeddings.
Any word without an associated embedding in the dictionary is ignored.
Adds '__target-language' and '__source-language' at the end of the words according to their language.
'''
clean_corpus, clean_vectors, keys = [], {}, []
words_we_want = set(embeddings_dictionary)
tokenize = MosesTokenizer(language)
for key, doc in enumerate(corpus):
clean_doc = []
words = tokenize(doc)
for word in words:
if word in words_we_want:
clean_doc.append(word + '__%s' % language)
clean_vectors[word + '__%s' % language] = np.array(vectors[word].split()).astype(np.float)
if len(clean_doc) > 3 and len(clean_doc) < 25:
keys.append(key)
clean_corpus.append(' '.join(clean_doc))
tokenize.close()
return np.array(clean_corpus), clean_vectors, keys
def mrr_precision_at_k(golden, preds, k_list=[1,]):
"""
Calculates Mean Reciprocal Error and Hits@1 == Precision@1
"""
my_score = 0
precision_at = np.zeros(len(k_list))
for key, elem in enumerate(golden):
if elem in preds[key]:
location = np.where(preds[key]==elem)[0][0]
my_score += 1/(1+ location)
for k_index, k_value in enumerate(k_list):
if location < k_value:
precision_at[k_index] += 1
return my_score/len(golden), (precision_at/len(golden))[0]
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