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570 lines
20 KiB
570 lines
20 KiB
# cython: profile=True
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# coding: utf8
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from __future__ import unicode_literals, print_function
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import re
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import ujson
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import random
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import cytoolz
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import itertools
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from .syntax import nonproj
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from .tokens import Doc
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from .errors import Errors
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from . import util
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from .util import minibatch
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def tags_to_entities(tags):
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entities = []
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start = None
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for i, tag in enumerate(tags):
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if tag is None:
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continue
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if tag.startswith('O'):
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# TODO: We shouldn't be getting these malformed inputs. Fix this.
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if start is not None:
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start = None
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continue
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elif tag == '-':
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continue
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elif tag.startswith('I'):
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if start is None:
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raise ValueError(Errors.E067.format(tags=tags[:i+1]))
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continue
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if tag.startswith('U'):
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entities.append((tag[2:], i, i))
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elif tag.startswith('B'):
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start = i
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elif tag.startswith('L'):
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entities.append((tag[2:], start, i))
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start = None
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else:
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raise ValueError(Errors.E068.format(tag=tag))
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return entities
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def merge_sents(sents):
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m_deps = [[], [], [], [], [], []]
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m_brackets = []
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i = 0
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for (ids, words, tags, heads, labels, ner), brackets in sents:
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m_deps[0].extend(id_ + i for id_ in ids)
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m_deps[1].extend(words)
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m_deps[2].extend(tags)
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m_deps[3].extend(head + i for head in heads)
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m_deps[4].extend(labels)
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m_deps[5].extend(ner)
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m_brackets.extend((b['first'] + i, b['last'] + i, b['label'])
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for b in brackets)
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i += len(ids)
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return [(m_deps, m_brackets)]
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def align(cand_words, gold_words):
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cost, edit_path = _min_edit_path(cand_words, gold_words)
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alignment = []
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i_of_gold = 0
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for move in edit_path:
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if move == 'M':
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alignment.append(i_of_gold)
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i_of_gold += 1
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elif move == 'S':
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alignment.append(None)
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i_of_gold += 1
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elif move == 'D':
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alignment.append(None)
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elif move == 'I':
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i_of_gold += 1
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else:
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raise Exception(move)
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return alignment
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punct_re = re.compile(r'\W')
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def _min_edit_path(cand_words, gold_words):
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cdef:
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Pool mem
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int i, j, n_cand, n_gold
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int* curr_costs
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int* prev_costs
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# TODO: Fix this --- just do it properly, make the full edit matrix and
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# then walk back over it...
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# Preprocess inputs
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cand_words = [punct_re.sub('', w).lower() for w in cand_words]
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gold_words = [punct_re.sub('', w).lower() for w in gold_words]
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if cand_words == gold_words:
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return 0, ''.join(['M' for _ in gold_words])
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mem = Pool()
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n_cand = len(cand_words)
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n_gold = len(gold_words)
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# Levenshtein distance, except we need the history, and we may want
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# different costs. Mark operations with a string, and score the history
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# using _edit_cost.
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previous_row = []
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prev_costs = <int*>mem.alloc(n_gold + 1, sizeof(int))
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curr_costs = <int*>mem.alloc(n_gold + 1, sizeof(int))
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for i in range(n_gold + 1):
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cell = ''
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for j in range(i):
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cell += 'I'
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previous_row.append('I' * i)
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prev_costs[i] = i
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for i, cand in enumerate(cand_words):
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current_row = ['D' * (i + 1)]
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curr_costs[0] = i+1
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for j, gold in enumerate(gold_words):
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if gold.lower() == cand.lower():
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s_cost = prev_costs[j]
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i_cost = curr_costs[j] + 1
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d_cost = prev_costs[j + 1] + 1
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else:
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s_cost = prev_costs[j] + 1
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i_cost = curr_costs[j] + 1
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d_cost = prev_costs[j + 1] + (1 if cand else 0)
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if s_cost <= i_cost and s_cost <= d_cost:
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best_cost = s_cost
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best_hist = previous_row[j] + ('M' if gold == cand else 'S')
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elif i_cost <= s_cost and i_cost <= d_cost:
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best_cost = i_cost
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best_hist = current_row[j] + 'I'
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else:
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best_cost = d_cost
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best_hist = previous_row[j + 1] + 'D'
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current_row.append(best_hist)
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curr_costs[j+1] = best_cost
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previous_row = current_row
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for j in range(len(gold_words) + 1):
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prev_costs[j] = curr_costs[j]
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curr_costs[j] = 0
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return prev_costs[n_gold], previous_row[-1]
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class GoldCorpus(object):
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"""An annotated corpus, using the JSON file format. Manages
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annotations for tagging, dependency parsing and NER."""
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def __init__(self, train_path, dev_path, gold_preproc=True, limit=None):
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"""Create a GoldCorpus.
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train_path (unicode or Path): File or directory of training data.
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dev_path (unicode or Path): File or directory of development data.
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RETURNS (GoldCorpus): The newly created object.
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"""
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self.train_path = util.ensure_path(train_path)
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self.dev_path = util.ensure_path(dev_path)
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self.limit = limit
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self.train_locs = self.walk_corpus(self.train_path)
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self.dev_locs = self.walk_corpus(self.dev_path)
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@property
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def train_tuples(self):
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i = 0
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for loc in self.train_locs:
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gold_tuples = read_json_file(loc)
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for item in gold_tuples:
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yield item
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i += len(item[1])
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if self.limit and i >= self.limit:
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break
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@property
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def dev_tuples(self):
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i = 0
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for loc in self.dev_locs:
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gold_tuples = read_json_file(loc)
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for item in gold_tuples:
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yield item
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i += len(item[1])
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if self.limit and i >= self.limit:
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break
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def count_train(self):
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n = 0
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i = 0
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for raw_text, paragraph_tuples in self.train_tuples:
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n += sum([len(s[0][1]) for s in paragraph_tuples])
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if self.limit and i >= self.limit:
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break
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i += len(paragraph_tuples)
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return n
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def train_docs(self, nlp, gold_preproc=False,
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projectivize=False, max_length=None,
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noise_level=0.0):
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train_tuples = self.train_tuples
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if projectivize:
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train_tuples = nonproj.preprocess_training_data(
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self.train_tuples, label_freq_cutoff=100)
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random.shuffle(train_tuples)
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gold_docs = self.iter_gold_docs(nlp, train_tuples, gold_preproc,
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max_length=max_length,
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noise_level=noise_level)
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yield from gold_docs
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def dev_docs(self, nlp, gold_preproc=False):
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gold_docs = self.iter_gold_docs(nlp, self.dev_tuples, gold_preproc)
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yield from gold_docs
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@classmethod
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def iter_gold_docs(cls, nlp, tuples, gold_preproc, max_length=None,
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noise_level=0.0):
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for raw_text, paragraph_tuples in tuples:
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if gold_preproc:
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raw_text = None
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else:
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paragraph_tuples = merge_sents(paragraph_tuples)
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docs = cls._make_docs(nlp, raw_text, paragraph_tuples,
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gold_preproc, noise_level=noise_level)
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golds = cls._make_golds(docs, paragraph_tuples)
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for doc, gold in zip(docs, golds):
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if (not max_length) or len(doc) < max_length:
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yield doc, gold
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@classmethod
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def _make_docs(cls, nlp, raw_text, paragraph_tuples, gold_preproc,
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noise_level=0.0):
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if raw_text is not None:
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raw_text = add_noise(raw_text, noise_level)
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return [nlp.make_doc(raw_text)]
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else:
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return [Doc(nlp.vocab,
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words=add_noise(sent_tuples[1], noise_level))
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for (sent_tuples, brackets) in paragraph_tuples]
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@classmethod
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def _make_golds(cls, docs, paragraph_tuples):
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if len(docs) != len(paragraph_tuples):
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raise ValueError(Errors.E070.format(n_docs=len(docs),
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n_annots=len(paragraph_tuples)))
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if len(docs) == 1:
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return [GoldParse.from_annot_tuples(docs[0],
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paragraph_tuples[0][0])]
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else:
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return [GoldParse.from_annot_tuples(doc, sent_tuples)
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for doc, (sent_tuples, brackets)
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in zip(docs, paragraph_tuples)]
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@staticmethod
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def walk_corpus(path):
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if not path.is_dir():
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return [path]
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paths = [path]
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locs = []
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seen = set()
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for path in paths:
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if str(path) in seen:
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continue
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seen.add(str(path))
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if path.parts[-1].startswith('.'):
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continue
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elif path.is_dir():
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paths.extend(path.iterdir())
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elif path.parts[-1].endswith('.json'):
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locs.append(path)
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return locs
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def add_noise(orig, noise_level):
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if random.random() >= noise_level:
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return orig
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elif type(orig) == list:
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corrupted = [_corrupt(word, noise_level) for word in orig]
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corrupted = [w for w in corrupted if w]
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return corrupted
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else:
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return ''.join(_corrupt(c, noise_level) for c in orig)
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def _corrupt(c, noise_level):
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if random.random() >= noise_level:
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return c
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elif c == ' ':
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return '\n'
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elif c == '\n':
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return ' '
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elif c in ['.', "'", "!", "?"]:
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return ''
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else:
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return c.lower()
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def read_json_file(loc, docs_filter=None, limit=None):
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loc = util.ensure_path(loc)
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if loc.is_dir():
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for filename in loc.iterdir():
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yield from read_json_file(loc / filename, limit=limit)
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else:
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with loc.open('r', encoding='utf8') as file_:
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docs = ujson.load(file_)
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if limit is not None:
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docs = docs[:limit]
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for doc in docs:
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if docs_filter is not None and not docs_filter(doc):
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continue
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paragraphs = []
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for paragraph in doc['paragraphs']:
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sents = []
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for sent in paragraph['sentences']:
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words = []
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ids = []
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tags = []
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heads = []
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labels = []
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ner = []
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for i, token in enumerate(sent['tokens']):
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words.append(token['orth'])
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ids.append(i)
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tags.append(token.get('tag', '-'))
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heads.append(token.get('head', 0) + i)
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labels.append(token.get('dep', ''))
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# Ensure ROOT label is case-insensitive
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if labels[-1].lower() == 'root':
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labels[-1] = 'ROOT'
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ner.append(token.get('ner', '-'))
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sents.append([
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[ids, words, tags, heads, labels, ner],
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sent.get('brackets', [])])
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if sents:
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yield [paragraph.get('raw', None), sents]
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def iob_to_biluo(tags):
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out = []
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curr_label = None
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tags = list(tags)
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while tags:
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out.extend(_consume_os(tags))
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out.extend(_consume_ent(tags))
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return out
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def _consume_os(tags):
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while tags and tags[0] == 'O':
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yield tags.pop(0)
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def _consume_ent(tags):
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if not tags:
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return []
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tag = tags.pop(0)
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target_in = 'I' + tag[1:]
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target_last = 'L' + tag[1:]
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length = 1
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while tags and tags[0] in {target_in, target_last}:
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length += 1
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tags.pop(0)
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label = tag[2:]
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if length == 1:
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return ['U-' + label]
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else:
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start = 'B-' + label
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end = 'L-' + label
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middle = ['I-%s' % label for _ in range(1, length - 1)]
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return [start] + middle + [end]
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cdef class GoldParse:
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"""Collection for training annotations."""
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@classmethod
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def from_annot_tuples(cls, doc, annot_tuples, make_projective=False):
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_, words, tags, heads, deps, entities = annot_tuples
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return cls(doc, words=words, tags=tags, heads=heads, deps=deps,
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entities=entities, make_projective=make_projective)
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def __init__(self, doc, annot_tuples=None, words=None, tags=None,
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heads=None, deps=None, entities=None, make_projective=False,
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cats=None):
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"""Create a GoldParse.
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doc (Doc): The document the annotations refer to.
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words (iterable): A sequence of unicode word strings.
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tags (iterable): A sequence of strings, representing tag annotations.
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heads (iterable): A sequence of integers, representing syntactic
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head offsets.
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deps (iterable): A sequence of strings, representing the syntactic
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relation types.
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entities (iterable): A sequence of named entity annotations, either as
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BILUO tag strings, or as `(start_char, end_char, label)` tuples,
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representing the entity positions.
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cats (dict): Labels for text classification. Each key in the dictionary
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may be a string or an int, or a `(start_char, end_char, label)`
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tuple, indicating that the label is applied to only part of the
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document (usually a sentence). Unlike entity annotations, label
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annotations can overlap, i.e. a single word can be covered by
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multiple labelled spans. The TextCategorizer component expects
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true examples of a label to have the value 1.0, and negative
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examples of a label to have the value 0.0. Labels not in the
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dictionary are treated as missing - the gradient for those labels
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will be zero.
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RETURNS (GoldParse): The newly constructed object.
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"""
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if words is None:
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words = [token.text for token in doc]
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if tags is None:
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tags = [None for _ in doc]
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if heads is None:
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heads = [None for token in doc]
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if deps is None:
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deps = [None for _ in doc]
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if entities is None:
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entities = [None for _ in doc]
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elif len(entities) == 0:
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entities = ['O' for _ in doc]
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elif not isinstance(entities[0], basestring):
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# Assume we have entities specified by character offset.
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entities = biluo_tags_from_offsets(doc, entities)
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self.mem = Pool()
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self.loss = 0
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self.length = len(doc)
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# These are filled by the tagger/parser/entity recogniser
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self.c.tags = <int*>self.mem.alloc(len(doc), sizeof(int))
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self.c.heads = <int*>self.mem.alloc(len(doc), sizeof(int))
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self.c.labels = <attr_t*>self.mem.alloc(len(doc), sizeof(attr_t))
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self.c.has_dep = <int*>self.mem.alloc(len(doc), sizeof(int))
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self.c.sent_start = <int*>self.mem.alloc(len(doc), sizeof(int))
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self.c.ner = <Transition*>self.mem.alloc(len(doc), sizeof(Transition))
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self.cats = {} if cats is None else dict(cats)
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self.words = [None] * len(doc)
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self.tags = [None] * len(doc)
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self.heads = [None] * len(doc)
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self.labels = [None] * len(doc)
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self.ner = [None] * len(doc)
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self.cand_to_gold = align([t.orth_ for t in doc], words)
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self.gold_to_cand = align(words, [t.orth_ for t in doc])
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annot_tuples = (range(len(words)), words, tags, heads, deps, entities)
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self.orig_annot = list(zip(*annot_tuples))
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for i, gold_i in enumerate(self.cand_to_gold):
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if doc[i].text.isspace():
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self.words[i] = doc[i].text
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self.tags[i] = '_SP'
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self.heads[i] = None
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self.labels[i] = None
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self.ner[i] = 'O'
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if gold_i is None:
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pass
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else:
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self.words[i] = words[gold_i]
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self.tags[i] = tags[gold_i]
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if heads[gold_i] is None:
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self.heads[i] = None
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else:
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self.heads[i] = self.gold_to_cand[heads[gold_i]]
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self.labels[i] = deps[gold_i]
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self.ner[i] = entities[gold_i]
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cycle = nonproj.contains_cycle(self.heads)
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if cycle is not None:
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raise ValueError(Errors.E069.format(cycle=cycle))
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if make_projective:
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proj_heads, _ = nonproj.projectivize(self.heads, self.labels)
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self.heads = proj_heads
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def __len__(self):
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"""Get the number of gold-standard tokens.
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RETURNS (int): The number of gold-standard tokens.
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"""
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return self.length
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@property
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def is_projective(self):
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"""Whether the provided syntactic annotations form a projective
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dependency tree.
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"""
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return not nonproj.is_nonproj_tree(self.heads)
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@property
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def sent_starts(self):
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return [self.c.sent_start[i] for i in range(self.length)]
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def biluo_tags_from_offsets(doc, entities, missing='O'):
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"""Encode labelled spans into per-token tags, using the
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Begin/In/Last/Unit/Out scheme (BILUO).
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doc (Doc): The document that the entity offsets refer to. The output tags
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will refer to the token boundaries within the document.
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entities (iterable): A sequence of `(start, end, label)` triples. `start`
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and `end` should be character-offset integers denoting the slice into
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the original string.
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RETURNS (list): A list of unicode strings, describing the tags. Each tag
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string will be of the form either "", "O" or "{action}-{label}", where
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action is one of "B", "I", "L", "U". The string "-" is used where the
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entity offsets don't align with the tokenization in the `Doc` object.
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The training algorithm will view these as missing values. "O" denotes a
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non-entity token. "B" denotes the beginning of a multi-token entity,
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"I" the inside of an entity of three or more tokens, and "L" the end
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of an entity of two or more tokens. "U" denotes a single-token entity.
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EXAMPLE:
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>>> text = 'I like London.'
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>>> entities = [(len('I like '), len('I like London'), 'LOC')]
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>>> doc = nlp.tokenizer(text)
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>>> tags = biluo_tags_from_offsets(doc, entities)
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>>> assert tags == ['O', 'O', 'U-LOC', 'O']
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"""
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starts = {token.idx: token.i for token in doc}
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ends = {token.idx+len(token): token.i for token in doc}
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biluo = ['-' for _ in doc]
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# Handle entity cases
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for start_char, end_char, label in entities:
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start_token = starts.get(start_char)
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end_token = ends.get(end_char)
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# Only interested if the tokenization is correct
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if start_token is not None and end_token is not None:
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if start_token == end_token:
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biluo[start_token] = 'U-%s' % label
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else:
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biluo[start_token] = 'B-%s' % label
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for i in range(start_token+1, end_token):
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biluo[i] = 'I-%s' % label
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biluo[end_token] = 'L-%s' % label
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# Now distinguish the O cases from ones where we miss the tokenization
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entity_chars = set()
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for start_char, end_char, label in entities:
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for i in range(start_char, end_char):
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entity_chars.add(i)
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for token in doc:
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for i in range(token.idx, token.idx+len(token)):
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if i in entity_chars:
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break
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else:
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biluo[token.i] = missing
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return biluo
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def offsets_from_biluo_tags(doc, tags):
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"""Encode per-token tags following the BILUO scheme into entity offsets.
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doc (Doc): The document that the BILUO tags refer to.
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entities (iterable): A sequence of BILUO tags with each tag describing one
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token. Each tags string will be of the form of either "", "O" or
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"{action}-{label}", where action is one of "B", "I", "L", "U".
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RETURNS (list): A sequence of `(start, end, label)` triples. `start` and
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`end` will be character-offset integers denoting the slice into the
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original string.
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"""
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token_offsets = tags_to_entities(tags)
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offsets = []
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for label, start_idx, end_idx in token_offsets:
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span = doc[start_idx : end_idx + 1]
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offsets.append((span.start_char, span.end_char, label))
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return offsets
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def is_punct_label(label):
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return label == 'P' or label.lower() == 'punct'
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