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"""MLLM (Maui-like Lexical Matchin) model for Annif""" |
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import collections |
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import math |
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import joblib |
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from statistics import mean |
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from enum import IntEnum |
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import numpy as np |
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from rdflib.namespace import SKOS |
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from sklearn.feature_extraction.text import CountVectorizer |
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from sklearn.ensemble import BaggingClassifier |
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from sklearn.tree import DecisionTreeClassifier |
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import annif.util |
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import annif.parallel |
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from annif.exception import OperationFailedException |
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from annif.lexical.tokenset import TokenSet, TokenSetIndex |
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from annif.lexical.util import get_subject_labels |
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from annif.lexical.util import make_relation_matrix, make_collection_matrix |
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Term = collections.namedtuple('Term', 'subject_id label is_pref') |
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Match = collections.namedtuple( |
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'Match', 'subject_id is_pref n_tokens pos ambiguity') |
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Candidate = collections.namedtuple( |
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'Candidate', |
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'doc_length subject_id freq is_pref n_tokens ambiguity ' + |
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'first_occ last_occ spread') |
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ModelData = collections.namedtuple( |
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'ModelData', |
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'broader narrower related collection ' + |
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'doc_freq subj_freq idf') |
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Feature = IntEnum( |
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'Feature', |
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'freq doc_freq subj_freq tfidf is_pref n_tokens ambiguity ' + |
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'first_occ last_occ spread doc_length ' + |
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'broader narrower related collection', |
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start=0) |
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View Code Duplication |
def conflate_matches(matches, doc_length): |
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subj_matches = collections.defaultdict(list) |
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for match in matches: |
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subj_matches[match.subject_id].append(match) |
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return [ |
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Candidate( |
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doc_length=doc_length, |
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subject_id=subject_id, |
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freq=len(matches) / doc_length, |
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is_pref=mean((float(m.is_pref) for m in matches)), |
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n_tokens=mean((m.n_tokens for m in matches)), |
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ambiguity=mean((m.ambiguity for m in matches)), |
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first_occ=matches[0].pos / doc_length, |
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last_occ=matches[-1].pos / doc_length, |
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spread=(matches[-1].pos - matches[0].pos) / doc_length |
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) |
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for subject_id, matches in subj_matches.items()] |
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View Code Duplication |
def generate_candidates(text, analyzer, vectorizer, index): |
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sentences = analyzer.tokenize_sentences(text) |
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sent_tokens = vectorizer.transform(sentences) |
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matches = [] |
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for sent_idx, token_matrix in enumerate(sent_tokens): |
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tset = TokenSet(token_matrix.nonzero()[1]) |
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for ts, ambiguity in index.search(tset): |
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matches.append(Match(subject_id=ts.subject_id, |
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is_pref=ts.is_pref, |
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n_tokens=len(ts), |
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pos=sent_idx, |
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ambiguity=ambiguity)) |
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return conflate_matches(matches, len(sentences)) |
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View Code Duplication |
def candidates_to_features(candidates, mdata): |
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"""Convert a list of Candidates to a NumPy feature matrix""" |
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matrix = np.zeros((len(candidates), len(Feature)), dtype=np.float32) |
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c_ids = [c.subject_id for c in candidates] |
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c_vec = np.zeros(mdata.related.shape[0], dtype=bool) |
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c_vec[c_ids] = True |
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broader = mdata.broader.multiply(c_vec).sum(axis=1) |
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narrower = mdata.narrower.multiply(c_vec).sum(axis=1) |
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related = mdata.related.multiply(c_vec).sum(axis=1) |
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collection = mdata.collection.multiply(c_vec).T.dot( |
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mdata.collection).sum(axis=0) |
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for idx, c in enumerate(candidates): |
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subj = c.subject_id |
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matrix[idx, Feature.freq] = c.freq |
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matrix[idx, Feature.doc_freq] = mdata.doc_freq[subj] |
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matrix[idx, Feature.subj_freq] = mdata.subj_freq.get(subj, 1) - 1 |
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matrix[idx, Feature.tfidf] = c.freq * mdata.idf[subj] |
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matrix[idx, Feature.is_pref] = c.is_pref |
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matrix[idx, Feature.n_tokens] = c.n_tokens |
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matrix[idx, Feature.ambiguity] = c.ambiguity |
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matrix[idx, Feature.first_occ] = c.first_occ |
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matrix[idx, Feature.last_occ] = c.last_occ |
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matrix[idx, Feature.spread] = c.spread |
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matrix[idx, Feature.doc_length] = c.doc_length |
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matrix[idx, Feature.broader] = broader[subj, 0] / len(c_ids) |
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matrix[idx, Feature.narrower] = narrower[subj, 0] / len(c_ids) |
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matrix[idx, Feature.related] = related[subj, 0] / len(c_ids) |
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matrix[idx, Feature.collection] = collection[0, subj] / len(c_ids) |
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return matrix |
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class MLLMCandidateGenerator(annif.parallel.BaseWorker): |
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@classmethod |
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def generate_candidates(cls, doc_subject_ids, text): |
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candidates = generate_candidates(text, **cls.args) # pragma: no cover |
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return doc_subject_ids, candidates # pragma: no cover |
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class MLLMFeatureConverter(annif.parallel.BaseWorker): |
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@classmethod |
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def candidates_to_features(cls, candidates): |
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return candidates_to_features(candidates, |
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**cls.args) # pragma: no cover |
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View Code Duplication |
class MLLMModel: |
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"""Maui-like Lexical Matching model""" |
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def generate_candidates(self, text, analyzer): |
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return generate_candidates(text, analyzer, |
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self._vectorizer, self._index) |
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@property |
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def _model_data(self): |
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return ModelData(broader=self._broader_matrix, |
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narrower=self._narrower_matrix, |
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related=self._related_matrix, |
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collection=self._collection_matrix, |
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doc_freq=self._doc_freq, |
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subj_freq=self._subj_freq, |
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idf=self._idf) |
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def _candidates_to_features(self, candidates): |
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return candidates_to_features(candidates, self._model_data) |
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@staticmethod |
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def _get_label_props(params): |
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pref_label_props = [SKOS.prefLabel] |
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if annif.util.boolean(params['use_hidden_labels']): |
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nonpref_label_props = [SKOS.altLabel, SKOS.hiddenLabel] |
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else: |
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nonpref_label_props = [SKOS.altLabel] |
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return (pref_label_props, nonpref_label_props) |
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def _prepare_terms(self, graph, vocab, params): |
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pref_label_props, nonpref_label_props = self._get_label_props(params) |
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terms = [] |
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subject_ids = [] |
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for subj_id, uri, _, _ in vocab.subjects.active: |
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subject_ids.append(subj_id) |
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for label in get_subject_labels(graph, uri, pref_label_props, |
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params['language']): |
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terms.append(Term(subject_id=subj_id, |
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label=label, |
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is_pref=True)) |
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for label in get_subject_labels(graph, uri, nonpref_label_props, |
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params['language']): |
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terms.append(Term(subject_id=subj_id, |
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label=label, |
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is_pref=False)) |
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return (terms, subject_ids) |
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def _prepare_relations(self, graph, vocab): |
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self._broader_matrix = make_relation_matrix( |
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graph, vocab, SKOS.broader) |
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self._narrower_matrix = make_relation_matrix( |
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graph, vocab, SKOS.narrower) |
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self._related_matrix = make_relation_matrix( |
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graph, vocab, SKOS.related) |
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self._collection_matrix = make_collection_matrix(graph, vocab) |
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def _prepare_train_index(self, vocab, analyzer, params): |
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graph = vocab.as_graph() |
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terms, subject_ids = self._prepare_terms(graph, vocab, params) |
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self._prepare_relations(graph, vocab) |
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self._vectorizer = CountVectorizer( |
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binary=True, |
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tokenizer=analyzer.tokenize_words |
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) |
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label_corpus = self._vectorizer.fit_transform((t.label for t in terms)) |
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# frequency of each token used in labels - how rare each word is |
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token_freq = np.bincount(label_corpus.indices, |
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minlength=label_corpus.shape[1]) |
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self._index = TokenSetIndex() |
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for term, label_matrix in zip(terms, label_corpus): |
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tokens = label_matrix.nonzero()[1] |
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# sort tokens by frequency - use the rarest token as index key |
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tokens = sorted(tokens, key=token_freq.__getitem__) |
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tset = TokenSet(tokens, term.subject_id, term.is_pref) |
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self._index.add(tset) |
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return subject_ids |
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def _prepare_train_data(self, corpus, vocab, analyzer, n_jobs): |
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# frequency of subjects (by id) in the generated candidates |
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self._doc_freq = collections.Counter() |
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# frequency of manually assigned subjects ("domain keyphraseness") |
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self._subj_freq = collections.Counter() |
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train_x = [] |
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train_y = [] |
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jobs, pool_class = annif.parallel.get_pool(n_jobs) |
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cg_args = { |
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'analyzer': analyzer, |
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'vectorizer': self._vectorizer, |
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'index': self._index |
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} |
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with pool_class(jobs, |
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initializer=MLLMCandidateGenerator.init, |
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initargs=(cg_args,)) as pool: |
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params = (([vocab.subjects.by_uri(uri) for uri in doc.uris], |
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doc.text) |
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for doc in corpus.documents) |
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for doc_subject_ids, candidates in pool.starmap( |
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MLLMCandidateGenerator.generate_candidates, params, 10): |
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self._subj_freq.update(doc_subject_ids) |
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self._doc_freq.update([c.subject_id for c in candidates]) |
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train_x.append(candidates) |
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train_y += [(c.subject_id in doc_subject_ids) |
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for c in candidates] |
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return (train_x, train_y) |
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def _calculate_idf(self, subject_ids, doc_count): |
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idf = collections.defaultdict(float) |
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for subj_id in subject_ids: |
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idf[subj_id] = math.log((doc_count + 1) / |
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(self._doc_freq[subj_id] + 1)) + 1 |
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return idf |
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def _prepare_features(self, train_x, n_jobs): |
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fc_args = {'mdata': self._model_data} |
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jobs, pool_class = annif.parallel.get_pool(n_jobs) |
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with pool_class(jobs, |
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initializer=MLLMFeatureConverter.init, |
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initargs=(fc_args,)) as pool: |
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features = pool.map( |
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MLLMFeatureConverter.candidates_to_features, train_x, 10) |
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return features |
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def prepare_train(self, corpus, vocab, analyzer, params, n_jobs): |
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# create an index from the vocabulary terms |
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subject_ids = self._prepare_train_index(vocab, analyzer, params) |
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# convert the corpus into train data |
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train_x, train_y = self._prepare_train_data( |
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corpus, vocab, analyzer, n_jobs) |
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# precalculate idf values for all candidate subjects |
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self._idf = self._calculate_idf(subject_ids, len(train_x)) |
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# convert the train data into feature values |
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features = self._prepare_features(train_x, n_jobs) |
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return (np.vstack(features), np.array(train_y)) |
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def _create_classifier(self, params): |
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return BaggingClassifier( |
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DecisionTreeClassifier( |
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min_samples_leaf=int(params['min_samples_leaf']), |
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max_leaf_nodes=int(params['max_leaf_nodes']) |
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), max_samples=float(params['max_samples'])) |
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def train(self, train_x, train_y, params): |
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# fit the model on the training corpus |
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self._classifier = self._create_classifier(params) |
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self._classifier.fit(train_x, train_y) |
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# sanity check: verify that the classifier has seen both classes |
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if self._classifier.n_classes_ != 2: |
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raise OperationFailedException( |
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"Unable to create classifier: " + |
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"Not enough positive and negative examples " + |
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"in the training data. Please check that your training " + |
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"data matches your vocabulary.") |
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def _prediction_to_list(self, scores, candidates): |
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subj_scores = [(score[1], c.subject_id) |
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for score, c in zip(scores, candidates)] |
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return sorted(subj_scores, reverse=True) |
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def predict(self, candidates): |
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if not candidates: |
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return [] |
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features = self._candidates_to_features(candidates) |
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scores = self._classifier.predict_proba(features) |
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return self._prediction_to_list(scores, candidates) |
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def save(self, filename): |
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return joblib.dump(self, filename) |
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@staticmethod |
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def load(filename): |
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return joblib.load(filename) |
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