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ad068f51be
The helper method state.B(1) gets the index of the first token of the buffer, or -1 if no such token exists. Normally this is safe because we pass this to functions like state.safe_get(), which returns an empty token. Here we used it directly as an array index, which is not okay! This error may have been the cause of out-of-bounds access errors during training. Similar errors may still be around, so much be hunted down. Hunting this one down took a long time...I printed out values across training runs and diffed, looking for points of divergence between runs, when no randomness should be allowed.
502 lines
16 KiB
Cython
502 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
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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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from ..errors import Errors
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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 = kwargs.get('actions', OrderedDict((
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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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)))
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seen_entities = set()
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for entity_type in kwargs.get('entity_types', []):
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if entity_type in seen_entities:
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continue
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seen_entities.add(entity_type)
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for action in (BEGIN, IN, LAST, UNIT):
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actions[action].append(entity_type)
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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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_, label = ner_tag.split('-', 1)
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if label not in seen_entities:
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seen_entities.add(label)
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for move_str in ('B', 'I', 'L', 'U'):
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actions[moves.index(move_str)].append(label)
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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(Errors.E022.format(name=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 ValueError(Errors.E019.format(action=move, src='ner'))
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return t
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def add_action(self, int action, label_name):
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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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self.n_moves += 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(1) >= 0 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:
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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 == UNIT:
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# U, Gold U --> True iff tag 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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# U, Gold B --> False
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# U, Gold I --> False
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# U, Gold L --> False
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# U, Gold O --> False
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return 1
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cdef class Out:
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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 == 3:
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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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return 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.set_ent_tag(st.B(0), 2, 0)
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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 == ISNT and g_tag == 0:
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return 1
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elif g_act == MISSING or g_act == ISNT:
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return 0
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elif g_act == BEGIN:
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# O, Gold B --> False
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return 1
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elif g_act == IN:
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# O, Gold I --> True
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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
|