spaCy/spacy/syntax/parser.pyx
2017-05-13 17:18:27 -05:00

638 lines
22 KiB
Cython

# cython: infer_types=True
# cython: profile=True
# coding: utf-8
from __future__ import unicode_literals, print_function
from collections import Counter
import ujson
from cupy.cuda.stream import Stream
import cupy
from libc.math cimport exp
cimport cython
cimport cython.parallel
import cytoolz
import numpy.random
cimport numpy as np
from cpython.ref cimport PyObject, Py_INCREF, Py_XDECREF
from cpython.exc cimport PyErr_CheckSignals
from libc.stdint cimport uint32_t, uint64_t
from libc.string cimport memset, memcpy
from libc.stdlib cimport malloc, calloc, free
from thinc.typedefs cimport weight_t, class_t, feat_t, atom_t, hash_t
from thinc.linear.avgtron cimport AveragedPerceptron
from thinc.linalg cimport VecVec
from thinc.structs cimport SparseArrayC, FeatureC, ExampleC
from thinc.extra.eg cimport Example
from cymem.cymem cimport Pool, Address
from murmurhash.mrmr cimport hash64
from preshed.maps cimport MapStruct
from preshed.maps cimport map_get
from thinc.api import layerize, chain
from thinc.neural import Affine, Model, Maxout
from thinc.neural.ops import NumpyOps
from .._ml import zero_init, PrecomputableAffine, PrecomputableMaxouts
from . import _parse_features
from ._parse_features cimport CONTEXT_SIZE
from ._parse_features cimport fill_context
from .stateclass cimport StateClass
from ._state cimport StateC
from .nonproj import PseudoProjectivity
from .transition_system import OracleError
from .transition_system cimport TransitionSystem, Transition
from ..structs cimport TokenC
from ..tokens.doc cimport Doc
from ..strings cimport StringStore
from ..gold cimport GoldParse
from ..attrs cimport TAG, DEP
def get_templates(*args, **kwargs):
return []
USE_FTRL = True
DEBUG = False
def set_debug(val):
global DEBUG
DEBUG = val
def get_greedy_model_for_batch(batch_size, tokvecs, lower_model, cuda_stream=None):
'''Allow a model to be "primed" by pre-computing input features in bulk.
This is used for the parser, where we want to take a batch of documents,
and compute vectors for each (token, position) pair. These vectors can then
be reused, especially for beam-search.
Let's say we're using 12 features for each state, e.g. word at start of
buffer, three words on stack, their children, etc. In the normal arc-eager
system, a document of length N is processed in 2*N states. This means we'll
create 2*N*12 feature vectors --- but if we pre-compute, we only need
N*12 vector computations. The saving for beam-search is much better:
if we have a beam of k, we'll normally make 2*N*12*K computations --
so we can save the factor k. This also gives a nice CPU/GPU division:
we can do all our hard maths up front, packed into large multiplications,
and do the hard-to-program parsing on the CPU.
'''
gpu_cached, bp_features = lower_model.begin_update(tokvecs, drop=0.)
cdef np.ndarray cached
if not isinstance(gpu_cached, numpy.ndarray):
cached = gpu_cached.get(stream=cuda_stream)
else:
cached = gpu_cached
nF = gpu_cached.shape[1]
nP = gpu_cached.shape[3]
ops = lower_model.ops
features = numpy.zeros((batch_size, cached.shape[2], nP), dtype='f')
synchronized = False
def forward(token_ids, drop=0.):
nonlocal synchronized
if not synchronized and cuda_stream is not None:
cuda_stream.synchronize()
synchronized = True
# This is tricky, but:
# - Input to forward on CPU
# - Output from forward on CPU
# - Input to backward on GPU!
# - Output from backward on GPU
nonlocal features
features = features[:len(token_ids)]
features.fill(0)
cdef float[:, :, ::1] feats = features
cdef int[:, ::1] ids = token_ids
_sum_features(<float*>&feats[0,0,0],
<float*>cached.data, &ids[0,0],
token_ids.shape[0], nF, cached.shape[2]*nP)
if nP >= 2:
best, which = ops.maxout(features)
else:
best = features.reshape((features.shape[0], features.shape[1]))
which = None
def backward(d_best, sgd=None):
# This will usually be on GPU
if isinstance(d_best, numpy.ndarray):
d_best = ops.xp.array(d_best)
if nP >= 2:
d_features = ops.backprop_maxout(d_best, which, nP)
else:
d_features = d_best.reshape((d_best.shape[0], d_best.shape[1], 1))
d_tokens = bp_features((d_features, token_ids), sgd)
return d_tokens
return best, backward
return forward
cdef void _sum_features(float* output,
const float* cached, const int* token_ids, int B, int F, int O) nogil:
cdef int idx, b, f, i
cdef const float* feature
for b in range(B):
for f in range(F):
if token_ids[f] < 0:
continue
idx = token_ids[f] * F * O + f*O
feature = &cached[idx]
for i in range(O):
output[i] += feature[i]
output += O
token_ids += F
def get_batch_loss(TransitionSystem moves, states, golds, float[:, ::1] scores):
cdef StateClass state
cdef GoldParse gold
cdef Pool mem = Pool()
cdef int i
is_valid = <int*>mem.alloc(moves.n_moves, sizeof(int))
costs = <float*>mem.alloc(moves.n_moves, sizeof(float))
cdef np.ndarray d_scores = numpy.zeros((len(states), moves.n_moves), dtype='f')
c_d_scores = <float*>d_scores.data
for i, (state, gold) in enumerate(zip(states, golds)):
memset(is_valid, 0, moves.n_moves * sizeof(int))
memset(costs, 0, moves.n_moves * sizeof(float))
moves.set_costs(is_valid, costs, state, gold)
cpu_log_loss(c_d_scores, costs, is_valid, &scores[i, 0], d_scores.shape[1])
c_d_scores += d_scores.shape[1]
return d_scores
cdef void cpu_log_loss(float* d_scores,
const float* costs, const int* is_valid, const float* scores,
int O) nogil:
"""Do multi-label log loss"""
cdef double max_, gmax, Z, gZ
best = arg_max_if_gold(scores, costs, is_valid, O)
guess = arg_max_if_valid(scores, is_valid, O)
Z = 1e-10
gZ = 1e-10
max_ = scores[guess]
gmax = scores[best]
for i in range(O):
if is_valid[i]:
Z += exp(scores[i] - max_)
if costs[i] <= costs[best]:
gZ += exp(scores[i] - gmax)
for i in range(O):
if not is_valid[i]:
d_scores[i] = 0.
elif costs[i] <= costs[best]:
d_scores[i] = (exp(scores[i]-max_) / Z) - (exp(scores[i]-gmax)/gZ)
else:
d_scores[i] = exp(scores[i]-max_) / Z
cdef void cpu_regression_loss(float* d_scores,
const float* costs, const int* is_valid, const float* scores,
int O) nogil:
cdef float eps = 2.
best = arg_max_if_gold(scores, costs, is_valid, O)
for i in range(O):
if not is_valid[i]:
d_scores[i] = 0.
elif scores[i] < scores[best]:
d_scores[i] = 0.
else:
# I doubt this is correct?
# Looking for something like Huber loss
diff = scores[i] - -costs[i]
if diff > eps:
d_scores[i] = eps
elif diff < -eps:
d_scores[i] = -eps
else:
d_scores[i] = diff
def init_states(TransitionSystem moves, docs):
cdef Doc doc
cdef StateClass state
offsets = []
states = []
offset = 0
for i, doc in enumerate(docs):
state = StateClass.init(doc.c, doc.length)
moves.initialize_state(state.c)
states.append(state)
offsets.append(offset)
offset += len(doc)
return states, offsets
def extract_token_ids(states, offsets=None, nF=1, nB=0, nS=2, nL=0, nR=0):
cdef StateClass state
cdef int n_tokens = states[0].nr_context_tokens(nF, nB, nS, nL, nR)
ids = numpy.zeros((len(states), n_tokens), dtype='i')
if offsets is None:
offsets = [0] * len(states)
for i, (state, offset) in enumerate(zip(states, offsets)):
state.set_context_tokens(ids[i], nF, nB, nS, nL, nR)
ids[i] += (ids[i] >= 0) * offset
return ids
cdef class Parser:
"""
Base class of the DependencyParser and EntityRecognizer.
"""
@classmethod
def load(cls, path, Vocab vocab, TransitionSystem=None, require=False, **cfg):
"""
Load the statistical model from the supplied path.
Arguments:
path (Path):
The path to load from.
vocab (Vocab):
The vocabulary. Must be shared by the documents to be processed.
require (bool):
Whether to raise an error if the files are not found.
Returns (Parser):
The newly constructed object.
"""
with (path / 'config.json').open() as file_:
cfg = ujson.load(file_)
self = cls(vocab, TransitionSystem=TransitionSystem, model=None, **cfg)
if (path / 'model').exists():
self.model.load(str(path / 'model'))
elif require:
raise IOError(
"Required file %s/model not found when loading" % str(path))
return self
def __init__(self, Vocab vocab, TransitionSystem=None, model=None, **cfg):
"""
Create a Parser.
Arguments:
vocab (Vocab):
The vocabulary object. Must be shared with documents to be processed.
model (thinc Model):
The statistical model.
Returns (Parser):
The newly constructed object.
"""
if TransitionSystem is None:
TransitionSystem = self.TransitionSystem
self.vocab = vocab
cfg['actions'] = TransitionSystem.get_actions(**cfg)
self.moves = TransitionSystem(vocab.strings, cfg['actions'])
if model is None:
self.model, self.feature_maps = self.build_model(**cfg)
else:
self.model, self.feature_maps = model
self.cfg = cfg
def __reduce__(self):
return (Parser, (self.vocab, self.moves, self.model), None, None)
def build_model(self,
hidden_width=128, token_vector_width=96, nr_vector=1000,
nF=1, nB=1, nS=1, nL=1, nR=1, **cfg):
nr_context_tokens = StateClass.nr_context_tokens(nF, nB, nS, nL, nR)
with Model.use_device('cpu'):
upper = chain(
Maxout(token_vector_width),
zero_init(Affine(self.moves.n_moves, token_vector_width)))
assert isinstance(upper.ops, NumpyOps)
lower = PrecomputableMaxouts(token_vector_width, nF=nr_context_tokens, nI=token_vector_width,
pieces=cfg.get('maxout_pieces', 1))
upper.begin_training(upper.ops.allocate((500, token_vector_width)))
lower.begin_training(lower.ops.allocate((500, token_vector_width)))
return upper, lower
def __call__(self, Doc tokens):
"""
Apply the parser or entity recognizer, setting the annotations onto the Doc object.
Arguments:
doc (Doc): The document to be processed.
Returns:
None
"""
self.parse_batch([tokens])
def pipe(self, stream, int batch_size=1000, int n_threads=2):
"""
Process a stream of documents.
Arguments:
stream: The sequence of documents to process.
batch_size (int):
The number of documents to accumulate into a working set.
n_threads (int):
The number of threads with which to work on the buffer in parallel.
Yields (Doc): Documents, in order.
"""
queue = []
for doc in stream:
queue.append(doc)
if len(queue) == batch_size:
self.parse_batch(queue)
for doc in queue:
self.moves.finalize_doc(doc)
yield doc
queue = []
if queue:
self.parse_batch(queue)
for doc in queue:
self.moves.finalize_doc(doc)
yield doc
def parse_batch(self, docs_tokvecs):
cdef:
int nC
Doc doc
StateClass state
np.ndarray py_scores
int[500] is_valid # Hacks for now
cuda_stream = Stream()
docs, tokvecs = docs_tokvecs
lower_model = get_greedy_model_for_batch(len(docs), tokvecs, self.feature_maps,
cuda_stream)
upper_model = self.model
states, offsets = init_states(self.moves, docs)
all_states = list(states)
todo = [st for st in zip(states, offsets) if not st[0].py_is_final()]
while todo:
states, offsets = zip(*todo)
token_ids = extract_token_ids(states, offsets=offsets)
py_scores = upper_model(lower_model(token_ids)[0])
scores = <float*>py_scores.data
nC = py_scores.shape[1]
for state, offset in zip(states, offsets):
self.moves.set_valid(is_valid, state.c)
guess = arg_max_if_valid(scores, is_valid, nC)
action = self.moves.c[guess]
action.do(state.c, action.label)
scores += nC
todo = [st for st in todo if not st[0].py_is_final()]
for state, doc in zip(all_states, docs):
self.moves.finalize_state(state.c)
for i in range(doc.length):
doc.c[i] = state.c._sent[i]
self.moves.finalize_doc(doc)
def update(self, docs_tokvecs, golds, drop=0., sgd=None):
cdef:
int nC
int[500] is_valid # Hack for now
Doc doc
StateClass state
np.ndarray scores
docs, tokvecs = docs_tokvecs
cuda_stream = Stream()
if isinstance(docs, Doc) and isinstance(golds, GoldParse):
return self.update(([docs], tokvecs), [golds], drop=drop)
for gold in golds:
self.moves.preprocess_gold(gold)
states, offsets = init_states(self.moves, docs)
todo = zip(states, offsets, golds)
todo = filter(lambda sp: not sp[0].py_is_final(), todo)
lower_model = get_greedy_model_for_batch(len(todo),
tokvecs, self.feature_maps, cuda_stream=cuda_stream)
upper_model = self.model
d_tokens = self.feature_maps.ops.allocate(tokvecs.shape)
backprops = []
n_tokens = tokvecs.shape[0]
nF = self.feature_maps.nF
while todo:
states, offsets, golds = zip(*todo)
token_ids = extract_token_ids(states, offsets=offsets)
lower, bp_lower = lower_model(token_ids)
scores, bp_scores = upper_model.begin_update(lower)
d_scores = get_batch_loss(self.moves, states, golds, scores)
d_lower = bp_scores(d_scores, sgd=sgd)
gpu_tok_ids = cupy.ndarray(token_ids.shape, dtype='i')
gpu_d_lower = cupy.ndarray(d_lower.shape, dtype='f')
gpu_tok_ids.set(token_ids, stream=cuda_stream)
gpu_d_lower.set(d_lower, stream=cuda_stream)
backprops.append((gpu_tok_ids, gpu_d_lower, bp_lower))
c_scores = <float*>scores.data
for state in states:
self.moves.set_valid(is_valid, state.c)
guess = arg_max_if_valid(c_scores, is_valid, scores.shape[1])
action = self.moves.c[guess]
action.do(state.c, action.label)
c_scores += scores.shape[1]
todo = filter(lambda sp: not sp[0].py_is_final(), todo)
# This tells CUDA to block --- so we know our copies are complete.
cuda_stream.synchronize()
for token_ids, d_lower, bp_lower in backprops:
d_state_features = bp_lower(d_lower, sgd=sgd)
active_feats = token_ids * (token_ids >= 0)
active_feats = active_feats.reshape((token_ids.shape[0], token_ids.shape[1], 1))
if hasattr(self.feature_maps.ops.xp, 'scatter_add'):
self.feature_maps.ops.xp.scatter_add(d_tokens,
token_ids, d_state_features * active_feats)
else:
self.model.ops.xp.add.at(d_tokens,
token_ids, d_state_features * active_feats)
return d_tokens
def step_through(self, Doc doc, GoldParse gold=None):
"""
Set up a stepwise state, to introspect and control the transition sequence.
Arguments:
doc (Doc): The document to step through.
gold (GoldParse): Optional gold parse
Returns (StepwiseState):
A state object, to step through the annotation process.
"""
return StepwiseState(self, doc, gold=gold)
def from_transition_sequence(self, Doc doc, sequence):
"""Control the annotations on a document by specifying a transition sequence
to follow.
Arguments:
doc (Doc): The document to annotate.
sequence: A sequence of action names, as unicode strings.
Returns: None
"""
with self.step_through(doc) as stepwise:
for transition in sequence:
stepwise.transition(transition)
def add_label(self, label):
# Doesn't set label into serializer -- subclasses override it to do that.
for action in self.moves.action_types:
added = self.moves.add_action(action, label)
if added:
# Important that the labels be stored as a list! We need the
# order, or the model goes out of synch
self.cfg.setdefault('extra_labels', []).append(label)
cdef class StepwiseState:
cdef readonly StateClass stcls
cdef readonly Example eg
cdef readonly Doc doc
cdef readonly GoldParse gold
cdef readonly Parser parser
def __init__(self, Parser parser, Doc doc, GoldParse gold=None):
self.parser = parser
self.doc = doc
if gold is not None:
self.gold = gold
self.parser.moves.preprocess_gold(self.gold)
else:
self.gold = GoldParse(doc)
self.stcls = StateClass.init(doc.c, doc.length)
self.parser.moves.initialize_state(self.stcls.c)
self.eg = Example(
nr_class=self.parser.moves.n_moves,
nr_atom=CONTEXT_SIZE,
nr_feat=self.parser.model.nr_feat)
def __enter__(self):
return self
def __exit__(self, type, value, traceback):
self.finish()
@property
def is_final(self):
return self.stcls.is_final()
@property
def stack(self):
return self.stcls.stack
@property
def queue(self):
return self.stcls.queue
@property
def heads(self):
return [self.stcls.H(i) for i in range(self.stcls.c.length)]
@property
def deps(self):
return [self.doc.vocab.strings[self.stcls.c._sent[i].dep]
for i in range(self.stcls.c.length)]
@property
def costs(self):
"""
Find the action-costs for the current state.
"""
if not self.gold:
raise ValueError("Can't set costs: No GoldParse provided")
self.parser.moves.set_costs(self.eg.c.is_valid, self.eg.c.costs,
self.stcls, self.gold)
costs = {}
for i in range(self.parser.moves.n_moves):
if not self.eg.c.is_valid[i]:
continue
transition = self.parser.moves.c[i]
name = self.parser.moves.move_name(transition.move, transition.label)
costs[name] = self.eg.c.costs[i]
return costs
def predict(self):
self.eg.reset()
#self.eg.c.nr_feat = self.parser.model.set_featuresC(self.eg.c.atoms, self.eg.c.features,
# self.stcls.c)
self.parser.moves.set_valid(self.eg.c.is_valid, self.stcls.c)
#self.parser.model.set_scoresC(self.eg.c.scores,
# self.eg.c.features, self.eg.c.nr_feat)
cdef Transition action = self.parser.moves.c[self.eg.guess]
return self.parser.moves.move_name(action.move, action.label)
def transition(self, action_name=None):
if action_name is None:
action_name = self.predict()
moves = {'S': 0, 'D': 1, 'L': 2, 'R': 3}
if action_name == '_':
action_name = self.predict()
action = self.parser.moves.lookup_transition(action_name)
elif action_name == 'L' or action_name == 'R':
self.predict()
move = moves[action_name]
clas = _arg_max_clas(self.eg.c.scores, move, self.parser.moves.c,
self.eg.c.nr_class)
action = self.parser.moves.c[clas]
else:
action = self.parser.moves.lookup_transition(action_name)
action.do(self.stcls.c, action.label)
def finish(self):
if self.stcls.is_final():
self.parser.moves.finalize_state(self.stcls.c)
self.doc.set_parse(self.stcls.c._sent)
self.parser.moves.finalize_doc(self.doc)
class ParserStateError(ValueError):
def __init__(self, doc):
ValueError.__init__(self,
"Error analysing doc -- no valid actions available. This should "
"never happen, so please report the error on the issue tracker. "
"Here's the thread to do so --- reopen it if it's closed:\n"
"https://github.com/spacy-io/spaCy/issues/429\n"
"Please include the text that the parser failed on, which is:\n"
"%s" % repr(doc.text))
cdef int arg_max_if_gold(const weight_t* scores, const weight_t* costs, const int* is_valid, int n) nogil:
# Find minimum cost
cdef float cost = 1
for i in range(n):
if is_valid[i] and costs[i] < cost:
cost = costs[i]
# Now find best-scoring with that cost
cdef int best = -1
for i in range(n):
if costs[i] <= cost and is_valid[i]:
if best == -1 or scores[i] > scores[best]:
best = i
return best
cdef int arg_max_if_valid(const weight_t* scores, const int* is_valid, int n) nogil:
cdef int best = -1
for i in range(n):
if is_valid[i] >= 1:
if best == -1 or scores[i] > scores[best]:
best = i
return best
cdef int _arg_max_clas(const weight_t* scores, int move, const Transition* actions,
int nr_class) except -1:
cdef weight_t score = 0
cdef int mode = -1
cdef int i
for i in range(nr_class):
if actions[i].move == move and (mode == -1 or scores[i] >= score):
mode = i
score = scores[i]
return mode