mirror of
https://github.com/explosion/spaCy.git
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bede11b67c
This patch does a few smallish things that tighten up the training workflow a little, and allow memory use during training to be reduced by letting the GoldCorpus stream data properly. Previously, the parser and entity recognizer read and saved labels as lists, with extra labels noted separately. Lists were used becaue ordering is very important, to ensure that the label-to-class mapping is stable. We now manage labels as nested dictionaries, first keyed by the action, and then keyed by the label. Values are frequencies. The trick is, how do we save new labels? We need to make sure we iterate over these in the same order they're added. Otherwise, we'll get different class IDs, and the model's predictions won't make sense. To allow stable sorting, we map the new labels to negative values. If we have two new labels, they'll be noted as having "frequency" -1 and -2. The next new label will then have "frequency" -3. When we sort by (frequency, label), we then get a stable sort. Storing frequencies then allows us to make the next nice improvement. Previously we had to iterate over the whole training set, to pre-process it for the deprojectivisation. This led to storing the whole training set in memory. This was most of the required memory during training. To prevent this, we now store the frequencies as we stream in the data, and deprojectivize as we go. Once we've built the frequencies, we can then apply a frequency cut-off when we decide how many classes to make. Finally, to allow proper data streaming, we also have to have some way of shuffling the iterator. This is awkward if the training files have multiple documents in them. To solve this, the GoldCorpus class now writes the training data to disk in msgpack files, one per document. We can then shuffle the data by shuffling the paths. This is a squash merge, as I made a lot of very small commits. Individual commit messages below. * Simplify label management for TransitionSystem and its subclasses * Fix serialization for new label handling format in parser * Simplify and improve GoldCorpus class. Reduce memory use, write to temp dir * Set actions in transition system * Require thinc 6.11.1.dev4 * Fix error in parser init * Add unicode declaration * Fix unicode declaration * Update textcat test * Try to get model training on less memory * Print json loc for now * Try rapidjson to reduce memory use * Remove rapidjson requirement * Try rapidjson for reduced mem usage * Handle None heads when projectivising * Stream json docs * Fix train script * Handle projectivity in GoldParse * Fix projectivity handling * Add minibatch_by_words util from ud_train * Minibatch by number of words in spacy.cli.train * Move minibatch_by_words util to spacy.util * Fix label handling * More hacking at label management in parser * Fix encoding in msgpack serialization in GoldParse * Adjust batch sizes in parser training * Fix minibatch_by_words * Add merge_subtokens function to pipeline.pyx * Register merge_subtokens factory * Restore use of msgpack tmp directory * Use minibatch-by-words in train * Handle retokenization in scorer * Change back-off approach for missing labels. Use 'dep' label * Update NER for new label management * Set NER tags for over-segmented words * Fix label alignment in gold * Fix label back-off for infrequent labels * Fix int type in labels dict key * Fix int type in labels dict key * Update feature definition for 8 feature set * Update ud-train script for new label stuff * Fix json streamer * Print the line number if conll eval fails * Update children and sentence boundaries after deprojectivisation * Export set_children_from_heads from doc.pxd * Render parses during UD training * Remove print statement * Require thinc 6.11.1.dev6. Try adding wheel as install_requires * Set different dev version, to flush pip cache * Update thinc version * Update GoldCorpus docs * Remove print statements * Fix formatting and links [ci skip]
505 lines
16 KiB
Cython
505 lines
16 KiB
Cython
# coding: utf-8
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from __future__ import unicode_literals
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from thinc.typedefs cimport weight_t
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from thinc.extra.search cimport Beam
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from collections import OrderedDict, Counter
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from .stateclass cimport StateClass
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from ._state cimport StateC
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from .transition_system cimport Transition
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from .transition_system cimport do_func_t
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from ..gold cimport GoldParseC, GoldParse
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cdef enum:
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MISSING
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BEGIN
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IN
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LAST
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UNIT
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OUT
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ISNT
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N_MOVES
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MOVE_NAMES = [None] * N_MOVES
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MOVE_NAMES[MISSING] = 'M'
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MOVE_NAMES[BEGIN] = 'B'
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MOVE_NAMES[IN] = 'I'
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MOVE_NAMES[LAST] = 'L'
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MOVE_NAMES[UNIT] = 'U'
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MOVE_NAMES[OUT] = 'O'
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MOVE_NAMES[ISNT] = 'x'
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cdef do_func_t[N_MOVES] do_funcs
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cdef bint _entity_is_sunk(StateClass st, Transition* golds) nogil:
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if not st.entity_is_open():
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return False
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cdef const Transition* gold = &golds[st.E(0)]
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if gold.move != BEGIN and gold.move != UNIT:
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return True
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elif gold.label != st.E_(0).ent_type:
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return True
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else:
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return False
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cdef class BiluoPushDown(TransitionSystem):
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def __init__(self, *args, **kwargs):
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TransitionSystem.__init__(self, *args, **kwargs)
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def __reduce__(self):
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labels_by_action = OrderedDict()
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cdef Transition t
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for trans in self.c[:self.n_moves]:
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label_str = self.strings[trans.label]
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labels_by_action.setdefault(trans.move, []).append(label_str)
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return (BiluoPushDown, (self.strings, labels_by_action),
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None, None)
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@classmethod
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def get_actions(cls, **kwargs):
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actions = {
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MISSING: Counter(),
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BEGIN: Counter(),
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IN: Counter(),
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LAST: Counter(),
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UNIT: Counter(),
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OUT: Counter()
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}
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actions[OUT][''] = 1
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for entity_type in kwargs.get('entity_types', []):
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for action in (BEGIN, IN, LAST, UNIT):
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actions[action][entity_type] = 1
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moves = ('M', 'B', 'I', 'L', 'U')
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for raw_text, sents in kwargs.get('gold_parses', []):
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for (ids, words, tags, heads, labels, biluo), _ in sents:
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for i, ner_tag in enumerate(biluo):
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if ner_tag != 'O' and ner_tag != '-':
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if ner_tag.count('-') != 1:
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raise ValueError(ner_tag)
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_, label = ner_tag.split('-')
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for action in (BEGIN, IN, LAST, UNIT):
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actions[action][label] += 1
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return actions
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property action_types:
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def __get__(self):
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return (BEGIN, IN, LAST, UNIT, OUT)
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def move_name(self, int move, attr_t label):
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if move == OUT:
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return 'O'
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elif move == MISSING:
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return 'M'
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else:
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return MOVE_NAMES[move] + '-' + self.strings[label]
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def has_gold(self, GoldParse gold, start=0, end=None):
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end = end or len(gold.ner)
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if all([tag in ('-', None) for tag in gold.ner[start:end]]):
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return False
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else:
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return True
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def preprocess_gold(self, GoldParse gold):
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if not self.has_gold(gold):
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return None
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for i in range(gold.length):
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gold.c.ner[i] = self.lookup_transition(gold.ner[i])
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return gold
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def get_beam_annot(self, Beam beam):
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entities = {}
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probs = beam.probs
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for i in range(beam.size):
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state = <StateC*>beam.at(i)
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if state.is_final():
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self.finalize_state(state)
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prob = probs[i]
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for j in range(state._e_i):
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start = state._ents[j].start
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end = state._ents[j].end
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label = state._ents[j].label
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entities.setdefault((start, end, label), 0.0)
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entities[(start, end, label)] += prob
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return entities
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def get_beam_parses(self, Beam beam):
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parses = []
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probs = beam.probs
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for i in range(beam.size):
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state = <StateC*>beam.at(i)
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if state.is_final():
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self.finalize_state(state)
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prob = probs[i]
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parse = []
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for j in range(state._e_i):
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start = state._ents[j].start
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end = state._ents[j].end
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label = state._ents[j].label
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parse.append((start, end, self.strings[label]))
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parses.append((prob, parse))
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return parses
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cdef Transition lookup_transition(self, object name) except *:
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cdef attr_t label
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if name == '-' or name is None:
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return Transition(clas=0, move=MISSING, label=0, score=0)
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elif name == '!O':
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return Transition(clas=0, move=ISNT, label=0, score=0)
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elif '-' in name:
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move_str, label_str = name.split('-', 1)
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# Hacky way to denote 'not this entity'
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if label_str.startswith('!'):
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label_str = label_str[1:]
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move_str = 'x'
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label = self.strings.add(label_str)
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else:
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move_str = name
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label = 0
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move = MOVE_NAMES.index(move_str)
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if move == ISNT:
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return Transition(clas=0, move=ISNT, label=label, score=0)
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for i in range(self.n_moves):
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if self.c[i].move == move and self.c[i].label == label:
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return self.c[i]
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else:
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raise KeyError(name)
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cdef Transition init_transition(self, int clas, int move, attr_t label) except *:
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# TODO: Apparent Cython bug here when we try to use the Transition()
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# constructor with the function pointers
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cdef Transition t
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t.score = 0
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t.clas = clas
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t.move = move
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t.label = label
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if move == MISSING:
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t.is_valid = Missing.is_valid
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t.do = Missing.transition
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t.get_cost = Missing.cost
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elif move == BEGIN:
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t.is_valid = Begin.is_valid
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t.do = Begin.transition
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t.get_cost = Begin.cost
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elif move == IN:
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t.is_valid = In.is_valid
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t.do = In.transition
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t.get_cost = In.cost
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elif move == LAST:
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t.is_valid = Last.is_valid
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t.do = Last.transition
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t.get_cost = Last.cost
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elif move == UNIT:
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t.is_valid = Unit.is_valid
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t.do = Unit.transition
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t.get_cost = Unit.cost
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elif move == OUT:
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t.is_valid = Out.is_valid
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t.do = Out.transition
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t.get_cost = Out.cost
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else:
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raise Exception(move)
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return t
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def add_action(self, int action, label_name, freq=None):
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cdef attr_t label_id
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if not isinstance(label_name, (int, long)):
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label_id = self.strings.add(label_name)
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else:
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label_id = label_name
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if action == OUT and label_id != 0:
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return
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if action == MISSING or action == ISNT:
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return
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# Check we're not creating a move we already have, so that this is
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# idempotent
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for trans in self.c[:self.n_moves]:
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if trans.move == action and trans.label == label_id:
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return 0
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if self.n_moves >= self._size:
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self._size *= 2
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self.c = <Transition*>self.mem.realloc(self.c, self._size * sizeof(self.c[0]))
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self.c[self.n_moves] = self.init_transition(self.n_moves, action, label_id)
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assert self.c[self.n_moves].label == label_id
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self.n_moves += 1
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if self.labels.get(action, []):
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freq = min(0, min(self.labels[action].values()))
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self.labels[action][label_name] = freq-1
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else:
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self.labels[action] = Counter()
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self.labels[action][label_name] = -1
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return 1
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cdef int initialize_state(self, StateC* st) nogil:
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# This is especially necessary when we use limited training data.
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for i in range(st.length):
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if st._sent[i].ent_type != 0:
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with gil:
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self.add_action(BEGIN, st._sent[i].ent_type)
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self.add_action(IN, st._sent[i].ent_type)
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self.add_action(UNIT, st._sent[i].ent_type)
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self.add_action(LAST, st._sent[i].ent_type)
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cdef class Missing:
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@staticmethod
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cdef bint is_valid(const StateC* st, attr_t label) nogil:
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return False
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@staticmethod
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cdef int transition(StateC* s, attr_t label) nogil:
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pass
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@staticmethod
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cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
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return 9000
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cdef class Begin:
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@staticmethod
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cdef bint is_valid(const StateC* st, attr_t label) nogil:
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# Ensure we don't clobber preset entities. If no entity preset,
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# ent_iob is 0
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cdef int preset_ent_iob = st.B_(0).ent_iob
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if preset_ent_iob == 1:
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return False
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elif preset_ent_iob == 2:
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return False
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elif preset_ent_iob == 3 and st.B_(0).ent_type != label:
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return False
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# If the next word is B or O, we can't B now
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elif st.B_(1).ent_iob == 2 or st.B_(1).ent_iob == 3:
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return False
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# If the current word is B, and the next word isn't I, the current word
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# is really U
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elif preset_ent_iob == 3 and st.B_(1).ent_iob != 1:
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return False
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# Don't allow entities to extend across sentence boundaries
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elif st.B_(1).sent_start == 1:
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return False
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else:
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return label != 0 and not st.entity_is_open()
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@staticmethod
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cdef int transition(StateC* st, attr_t label) nogil:
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st.open_ent(label)
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st.set_ent_tag(st.B(0), 3, label)
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st.push()
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st.pop()
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@staticmethod
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cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
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cdef int g_act = gold.ner[s.B(0)].move
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cdef attr_t g_tag = gold.ner[s.B(0)].label
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if g_act == MISSING:
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return 0
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elif g_act == BEGIN:
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# B, Gold B --> Label match
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return label != g_tag
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# Support partial supervision in the form of "not this label"
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elif g_act == ISNT:
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return label == g_tag
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else:
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# B, Gold I --> False (P)
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# B, Gold L --> False (P)
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# B, Gold O --> False (P)
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# B, Gold U --> False (P)
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return 1
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cdef class In:
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@staticmethod
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cdef bint is_valid(const StateC* st, attr_t label) nogil:
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cdef int preset_ent_iob = st.B_(0).ent_iob
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if preset_ent_iob == 2:
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return False
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elif preset_ent_iob == 3:
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return False
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# TODO: Is this quite right? I think it's supposed to be ensuring the
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# gazetteer matches are maintained
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elif st.B_(1).ent_iob != preset_ent_iob:
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return False
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# Don't allow entities to extend across sentence boundaries
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elif st.B_(1).sent_start == 1:
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return False
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return st.entity_is_open() and label != 0 and st.E_(0).ent_type == label
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@staticmethod
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cdef int transition(StateC* st, attr_t label) nogil:
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st.set_ent_tag(st.B(0), 1, label)
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st.push()
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st.pop()
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@staticmethod
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cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
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move = IN
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cdef int next_act = gold.ner[s.B(1)].move if s.B(0) < s.c.length else OUT
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cdef int g_act = gold.ner[s.B(0)].move
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cdef attr_t g_tag = gold.ner[s.B(0)].label
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cdef bint is_sunk = _entity_is_sunk(s, gold.ner)
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if g_act == MISSING:
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return 0
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elif g_act == BEGIN:
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# I, Gold B --> True
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# (P of bad open entity sunk, R of this entity sunk)
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return 0
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elif g_act == IN:
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# I, Gold I --> True
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# (label forced by prev, if mismatch, P and R both sunk)
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return 0
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elif g_act == LAST:
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# I, Gold L --> True iff this entity sunk and next tag == O
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return not (is_sunk and (next_act == OUT or next_act == MISSING))
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elif g_act == OUT:
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# I, Gold O --> True iff next tag == O
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return not (next_act == OUT or next_act == MISSING)
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elif g_act == UNIT:
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# I, Gold U --> True iff next tag == O
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return next_act != OUT
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# Support partial supervision in the form of "not this label"
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elif g_act == ISNT:
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return 0
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else:
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return 1
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cdef class Last:
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@staticmethod
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cdef bint is_valid(const StateC* st, attr_t label) nogil:
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if st.B_(1).ent_iob == 1:
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return False
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return st.entity_is_open() and label != 0 and st.E_(0).ent_type == label
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@staticmethod
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cdef int transition(StateC* st, attr_t label) nogil:
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st.close_ent()
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st.set_ent_tag(st.B(0), 1, label)
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st.push()
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st.pop()
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@staticmethod
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cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
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move = LAST
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cdef int g_act = gold.ner[s.B(0)].move
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cdef attr_t g_tag = gold.ner[s.B(0)].label
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if g_act == MISSING:
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return 0
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elif g_act == BEGIN:
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# L, Gold B --> True
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return 0
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elif g_act == IN:
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# L, Gold I --> True iff this entity sunk
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return not _entity_is_sunk(s, gold.ner)
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elif g_act == LAST:
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# L, Gold L --> True
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return 0
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elif g_act == OUT:
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# L, Gold O --> True
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return 0
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elif g_act == UNIT:
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# L, Gold U --> True
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return 0
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# Support partial supervision in the form of "not this label"
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elif g_act == ISNT:
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return 0
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else:
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return 1
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cdef class Unit:
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@staticmethod
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cdef bint is_valid(const StateC* st, attr_t label) nogil:
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cdef int preset_ent_iob = st.B_(0).ent_iob
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if preset_ent_iob == 2:
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return False
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elif preset_ent_iob == 1:
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return False
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elif preset_ent_iob == 3 and st.B_(0).ent_type != label:
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return False
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elif st.B_(1).ent_iob == 1:
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return False
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return label != 0 and not st.entity_is_open()
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@staticmethod
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cdef int transition(StateC* st, attr_t label) nogil:
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st.open_ent(label)
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st.close_ent()
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st.set_ent_tag(st.B(0), 3, label)
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st.push()
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st.pop()
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@staticmethod
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cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
|
|
cdef int g_act = gold.ner[s.B(0)].move
|
|
cdef attr_t g_tag = gold.ner[s.B(0)].label
|
|
|
|
if g_act == MISSING:
|
|
return 0
|
|
elif g_act == UNIT:
|
|
# U, Gold U --> True iff tag match
|
|
return label != g_tag
|
|
# Support partial supervision in the form of "not this label"
|
|
elif g_act == ISNT:
|
|
return label == g_tag
|
|
else:
|
|
# U, Gold B --> False
|
|
# U, Gold I --> False
|
|
# U, Gold L --> False
|
|
# U, Gold O --> False
|
|
return 1
|
|
|
|
|
|
cdef class Out:
|
|
@staticmethod
|
|
cdef bint is_valid(const StateC* st, attr_t label) nogil:
|
|
cdef int preset_ent_iob = st.B_(0).ent_iob
|
|
if preset_ent_iob == 3:
|
|
return False
|
|
elif preset_ent_iob == 1:
|
|
return False
|
|
return not st.entity_is_open()
|
|
|
|
@staticmethod
|
|
cdef int transition(StateC* st, attr_t label) nogil:
|
|
st.set_ent_tag(st.B(0), 2, 0)
|
|
st.push()
|
|
st.pop()
|
|
|
|
@staticmethod
|
|
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
|
|
cdef int g_act = gold.ner[s.B(0)].move
|
|
cdef attr_t g_tag = gold.ner[s.B(0)].label
|
|
|
|
if g_act == ISNT and g_tag == 0:
|
|
return 1
|
|
elif g_act == MISSING or g_act == ISNT:
|
|
return 0
|
|
elif g_act == BEGIN:
|
|
# O, Gold B --> False
|
|
return 1
|
|
elif g_act == IN:
|
|
# O, Gold I --> True
|
|
return 0
|
|
elif g_act == LAST:
|
|
# O, Gold L --> True
|
|
return 0
|
|
elif g_act == OUT:
|
|
# O, Gold O --> True
|
|
return 0
|
|
elif g_act == UNIT:
|
|
# O, Gold U --> False
|
|
return 1
|
|
else:
|
|
return 1
|