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* Tmp commit of ner code

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This commit is contained in:
Matthew Honnibal 2014-11-14 18:27:47 +11:00
parent 33c421bcf8
commit 5c3016bac8
4 changed files with 72 additions and 114 deletions
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1
spacy/ner/_state.pxd
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@ -6,6 +6,7 @@ cdef int begin_entity(State* s, label) except -1
cdef int end_entity(State* s) except -1
cdef State* init_state(Pool mem, int sent_length) except NULL
cdef int copy_state(Pool mem, State* dest, State* source) except -1
cdef bint entity_is_open(State *s) except -1

54
spacy/ner/_state.pyx
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@ -1,44 +1,50 @@
from .bilou_moves cimport BEGIN, UNIT
cdef int begin_entity(State* s, label) except -1:
s.curr.start = s.i
s.curr.label = label
cdef int end_entity(State* s) except -1:
s.curr.end = s.i
s.ents[s.j] = s.curr
cdef void begin_entity(State* s, label):
s.j += 1
s.curr.start = 0
s.curr.label = -1
s.curr.end = 0
s.ents[s.j].start = s.i
s.ents[s.j].tag = label
s.ents[s.j].end = s.i + 1
cdef void end_entity(State* s):
s.ents[s.j].end = s.i + 1
cdef State* init_state(Pool mem, int sent_length) except NULL:
s = <State*>mem.alloc(1, sizeof(State))
s.j = 0
s.ents = <Entity*>mem.alloc(sent_length, sizeof(Entity))
for i in range(sent_length):
s.ents[i].label = -1
s.curr.label = -1
s.tags = <int*>mem.alloc(sent_length, sizeof(int))
s.length = sent_length
return s
cdef bint entity_is_open(State *s) except -1:
return s.curr.label != -1
cdef bint entity_is_open(State *s):
return s.ents[s.j].start != 0
cdef bint entity_is_sunk(State *s, Move* golds) except -1:
cdef bint entity_is_sunk(State *s, Move* golds):
if not entity_is_open(s):
return False
cdef Move* gold = &golds[s.curr.start]
cdef Entity* ent = &s.ents[s.j]
cdef Move* gold = &golds[ent.start]
if gold.action != BEGIN and gold.action != UNIT:
return True
elif gold.label != s.curr.label:
elif gold.label != ent.label:
return True
else:
return False
cdef int copy_state(Pool mem, State* dest, State* source) except -1:
'''Copy state source into state dest.'''
if source.length > dest.length:
dest.ents = <Entity*>mem.realloc(dest.ents, source.length * sizeof(Entity))
dest.tags = <int*>mem.realloc(dest.tags, source.length * sizeof(int))
memcpy(dest.ents, source.ents, source.length * sizeof(Entity))
memcpy(dest.tags, source.tags, source.length * sizeof(int))
dest.length = source.length
dest.i = source.i
dest.j = source.j
dest.curr = source.curr

118
spacy/ner/greedy_parser.pyx
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@ -1,6 +1,3 @@
from __future__ import division
from __future__ import unicode_literals
cimport cython
import random
import os
@ -10,56 +7,14 @@ import json
from thinc.features cimport ConjFeat
from .context cimport fill_context
from .context cimport N_FIELDS
from .structs cimport Move, State
from .io_moves cimport fill_moves, transition, best_accepted
from .io_moves cimport set_accept_if_valid, set_accept_if_oracle
from .io_moves import get_n_moves
from ..context cimport fill_context
from ..context cimport N_FIELDS
from .moves cimport Move
from .moves cimport fill_moves, transition, best_accepted
from .moves cimport set_accept_if_valid, set_accept_if_oracle
from .moves import get_n_moves
from ._state cimport State
from ._state cimport init_state
from ._state cimport entity_is_open
from ._state cimport end_entity
from .annot cimport NERAnnotation
def setup_model_dir(entity_types, templates, model_dir):
if path.exists(model_dir):
shutil.rmtree(model_dir)
os.mkdir(model_dir)
config = {
'templates': templates,
'entity_types': entity_types,
}
with open(path.join(model_dir, 'config.json'), 'w') as file_:
json.dump(config, file_)
def train(train_sents, model_dir, nr_iter=10):
cdef Tokens tokens
cdef NERAnnotation gold_ner
parser = NERParser(model_dir)
for _ in range(nr_iter):
tp = 0
fp = 0
fn = 0
for i, (tokens, gold_ner) in enumerate(train_sents):
#print [tokens[i].string for i in range(tokens.length)]
test_ents = set(parser.train(tokens, gold_ner))
#print 'Test', test_ents
gold_ents = set(gold_ner.entities)
#print 'Gold', set(gold_ner.entities)
tp += len(gold_ents.intersection(test_ents))
fp += len(test_ents - gold_ents)
fn += len(gold_ents - test_ents)
p = tp / (tp + fp)
r = tp / (tp + fn)
f = 2 * ((p * r) / (p + r))
print 'P: %.3f' % p,
print 'R: %.3f' % r,
print 'F: %.3f' % f
random.shuffle(train_sents)
parser.model.end_training()
parser.model.dump(path.join(model_dir, 'model'))
cdef class NERParser:
@ -67,12 +22,12 @@ cdef class NERParser:
self.mem = Pool()
cfg = json.load(open(path.join(model_dir, 'config.json')))
templates = cfg['templates']
self.extractor = Extractor(templates, [ConjFeat] * len(templates))
self.entity_types = cfg['entity_types']
self.extractor = Extractor(templates, [ConjFeat] * len(templates))
self.n_classes = get_n_moves(len(self.entity_types))
self._moves = <Move*>self.mem.alloc(self.n_classes, sizeof(Move))
fill_moves(self._moves, self.n_classes, self.entity_types)
self.model = LinearModel(self.n_classes)
fill_moves(self._moves, len(self.entity_types))
self.model = LinearModel(len(self.tag_names))
if path.exists(path.join(model_dir, 'model')):
self.model.load(path.join(model_dir, 'model'))
@ -81,59 +36,46 @@ cdef class NERParser:
self._values = <weight_t*>self.mem.alloc(self.extractor.n+1, sizeof(weight_t))
self._scores = <weight_t*>self.mem.alloc(self.model.nr_class, sizeof(weight_t))
cpdef list train(self, Tokens tokens, NERAnnotation annot):
cpdef int train(self, Tokens tokens, gold_classes):
cdef Pool mem = Pool()
cdef State* s = init_state(mem, tokens.length)
cdef Move* golds = <Move*>mem.alloc(len(gold_classes), sizeof(Move))
for i, clas in enumerate(gold_classes):
golds[i] = self.moves[clas - 1]
assert golds[i].id == clas
cdef Move* guess
cdef Move* oracle_move
n_correct = 0
cdef int f = 0
while s.i < tokens.length:
fill_context(self._context, s, tokens)
fill_context(self._context, s.i, tokens)
self.extractor.extract(self._feats, self._values, self._context, NULL)
self.model.score(self._scores, self._feats, self._values)
set_accept_if_valid(self._moves, self.n_classes, s)
guess = best_accepted(self._moves, self._scores, self.n_classes)
assert guess.clas != 0
set_accept_if_oracle(self._moves, self.n_classes, s,
annot.starts, annot.ends, annot.labels)
oracle_move = best_accepted(self._moves, self._scores, self.n_classes)
assert oracle_move.clas != 0
if guess.clas == oracle_move.clas:
counts = {}
n_correct += 1
else:
counts = {guess.clas: {}, oracle_move.clas: {}}
self.extractor.count(counts[oracle_move.clas], self._feats, 1)
self.extractor.count(counts[guess.clas], self._feats, -1)
set_accept_if_oracle(self._moves, golds, self.n_classes, s) # TODO
gold = best_accepted(self._moves, self._scores, self.n_classes)
if guess.clas == gold.clas:
self.model.update({})
return 0
counts = {guess.clas: {}, gold.clas: {}}
self.extractor.count(counts[gold.clas], self._feats, 1)
self.extractor.count(counts[guess.clas], self._feats, -1)
self.model.update(counts)
transition(s, guess)
tokens.ner[s.i-1] = s.tags[s.i-1]
if entity_is_open(s):
s.curr.label = annot.labels[s.curr.start]
end_entity(s)
entities = []
for i in range(s.j):
entities.append((s.ents[i].start, s.ents[i].end, s.ents[i].label))
return entities
cpdef list set_tags(self, Tokens tokens):
cpdef int set_tags(self, Tokens tokens) except -1:
cdef Pool mem = Pool()
cdef State* s = init_state(mem, tokens.length)
cdef Move* move
while s.i < tokens.length:
fill_context(self._context, s, tokens)
fill_context(self._context, s.i, tokens)
self.extractor.extract(self._feats, self._values, self._context, NULL)
self.model.score(self._scores, self._feats, self._values)
set_accept_if_valid(self._moves, self.n_classes, s)
move = best_accepted(self._moves, self._scores, self.n_classes)
transition(s, move)
tokens.ner[s.i-1] = s.tags[s.i-1]
if entity_is_open(s):
s.curr.label = move.label
end_entity(s)
entities = []
for i in range(s.j):
entities.append((s.ents[i].start, s.ents[i].end, s.ents[i].label))
return entities

13
spacy/ner/io_moves.pyx
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@ -77,11 +77,16 @@ cdef int set_accept_if_valid(Move* moves, int n, State* s) except 0:
moves[0].accept = False
for i in range(1, n):
if moves[i].action == SHIFT:
moves[i].accept = moves[i].label == s.curr.label or not entity_is_open(s)
if s.i >= s.length:
moves[i].accept = False
elif open_ent and moves[i].label != s.curr.label:
moves[i].accept = False
else:
moves[i].accept = True
elif moves[i].action == REDUCE:
moves[i].accept = open_ent
elif moves[i].action == OUT:
moves[i].accept = not open_ent
moves[i].accept = s.i < s.length and not open_ent
n_accept += moves[i].accept
return n_accept
@ -150,3 +155,7 @@ cdef int fill_moves(Move* moves, int n, list entity_types) except -1:
moves[i].clas = i
moves[i].label = 0
i += 1
cdef bint is_final(State* s):
return s.i == s.length and not entity_is_open(s)