spaCy/spacy/syntax/nn_parser.pyx
Matthew Honnibal bede11b67c
Improve label management in parser and NER (#2108)
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]
2018-03-19 02:58:08 +01:00

1046 lines
42 KiB
Cython

# cython: infer_types=True
# cython: cdivision=True
# cython: boundscheck=False
# coding: utf-8
from __future__ import unicode_literals, print_function
from collections import OrderedDict
import ujson
import json
import numpy
cimport cython.parallel
import cytoolz
import numpy.random
cimport numpy as np
from cpython.ref cimport PyObject, Py_XDECREF
from cpython.exc cimport PyErr_CheckSignals, PyErr_SetFromErrno
from libc.math cimport exp
from libcpp.vector cimport vector
from libc.string cimport memset, memcpy
from libc.stdlib cimport calloc, free
from cymem.cymem cimport Pool
from thinc.typedefs cimport weight_t, class_t, hash_t
from thinc.extra.search cimport Beam
from thinc.api import chain, clone
from thinc.v2v import Model, Maxout, Affine
from thinc.misc import LayerNorm
from thinc.neural.ops import CupyOps
from thinc.neural.util import get_array_module
from thinc.linalg cimport Vec, VecVec
from thinc.linalg cimport MatVec, VecVec
from .._ml import zero_init, PrecomputableAffine, Tok2Vec, flatten
from .._ml import link_vectors_to_models, create_default_optimizer
from ..compat import json_dumps, copy_array
from ..tokens.doc cimport Doc
from ..gold cimport GoldParse
from .. import util
from .stateclass cimport StateClass
from ._state cimport StateC
from .transition_system cimport Transition
from . import _beam_utils, nonproj
def get_templates(*args, **kwargs):
return []
DEBUG = False
def set_debug(val):
global DEBUG
DEBUG = val
cdef class precompute_hiddens:
"""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.
"""
cdef int nF, nO, nP
cdef bint _is_synchronized
cdef public object ops
cdef np.ndarray _features
cdef np.ndarray _cached
cdef np.ndarray bias
cdef object _cuda_stream
cdef object _bp_hiddens
def __init__(self, batch_size, tokvecs, lower_model, cuda_stream=None,
drop=0.):
gpu_cached, bp_features = lower_model.begin_update(tokvecs, drop=drop)
cdef np.ndarray cached
if not isinstance(gpu_cached, numpy.ndarray):
# Note the passing of cuda_stream here: it lets
# cupy make the copy asynchronously.
# We then have to block before first use.
cached = gpu_cached.get(stream=cuda_stream)
else:
cached = gpu_cached
if not isinstance(lower_model.b, numpy.ndarray):
self.bias = lower_model.b.get()
else:
self.bias = lower_model.b
self.nF = cached.shape[1]
self.nP = getattr(lower_model, 'nP', 1)
self.nO = cached.shape[2]
self.ops = lower_model.ops
self._is_synchronized = False
self._cuda_stream = cuda_stream
self._cached = cached
self._bp_hiddens = bp_features
cdef const float* get_feat_weights(self) except NULL:
if not self._is_synchronized and self._cuda_stream is not None:
self._cuda_stream.synchronize()
self._is_synchronized = True
return <float*>self._cached.data
def __call__(self, X):
return self.begin_update(X)[0]
def begin_update(self, token_ids, drop=0.):
cdef np.ndarray state_vector = numpy.zeros(
(token_ids.shape[0], self.nO, self.nP), dtype='f')
# This is tricky, but (assuming GPU available);
# - Input to forward on CPU
# - Output from forward on CPU
# - Input to backward on GPU!
# - Output from backward on GPU
bp_hiddens = self._bp_hiddens
feat_weights = self.get_feat_weights()
cdef int[:, ::1] ids = token_ids
sum_state_features(<float*>state_vector.data,
feat_weights, &ids[0,0],
token_ids.shape[0], self.nF, self.nO*self.nP)
state_vector += self.bias
state_vector, bp_nonlinearity = self._nonlinearity(state_vector)
def backward(d_state_vector_ids, sgd=None):
d_state_vector, token_ids = d_state_vector_ids
d_state_vector = bp_nonlinearity(d_state_vector, sgd)
# This will usually be on GPU
if not isinstance(d_state_vector, self.ops.xp.ndarray):
d_state_vector = self.ops.xp.array(d_state_vector)
d_tokens = bp_hiddens((d_state_vector, token_ids), sgd)
return d_tokens
return state_vector, backward
def _nonlinearity(self, state_vector):
if self.nP == 1:
state_vector = state_vector.reshape(state_vector.shape[:-1])
mask = state_vector >= 0.
state_vector *= mask
else:
state_vector, mask = self.ops.maxout(state_vector)
def backprop_nonlinearity(d_best, sgd=None):
if self.nP == 1:
d_best *= mask
d_best = d_best.reshape((d_best.shape + (1,)))
return d_best
else:
return self.ops.backprop_maxout(d_best, mask, self.nP)
return state_vector, backprop_nonlinearity
cdef void sum_state_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
padding = cached
cached += F * O
for b in range(B):
for f in range(F):
if token_ids[f] < 0:
feature = &padding[f*O]
else:
idx = token_ids[f] * F * O + f*O
feature = &cached[idx]
VecVec.add_i(output,
feature, 1., O)
output += O
token_ids += F
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 _collect_states(beams):
cdef StateClass state
cdef Beam beam
states = []
for beam in beams:
state = StateClass.borrow(<StateC*>beam.at(0))
states.append(state)
return states
cdef class Parser:
"""
Base class of the DependencyParser and EntityRecognizer.
"""
@classmethod
def Model(cls, nr_class, **cfg):
depth = util.env_opt('parser_hidden_depth', cfg.get('hidden_depth', 1))
if depth != 1:
raise ValueError("Currently parser depth is hard-coded to 1.")
parser_maxout_pieces = util.env_opt('parser_maxout_pieces',
cfg.get('maxout_pieces', 2))
token_vector_width = util.env_opt('token_vector_width',
cfg.get('token_vector_width', 128))
hidden_width = util.env_opt('hidden_width', cfg.get('hidden_width', 200))
embed_size = util.env_opt('embed_size', cfg.get('embed_size', 7000))
hist_size = util.env_opt('history_feats', cfg.get('hist_size', 0))
hist_width = util.env_opt('history_width', cfg.get('hist_width', 0))
if hist_size != 0:
raise ValueError("Currently history size is hard-coded to 0")
if hist_width != 0:
raise ValueError("Currently history width is hard-coded to 0")
tok2vec = Tok2Vec(token_vector_width, embed_size,
pretrained_dims=cfg.get('pretrained_dims', 0))
tok2vec = chain(tok2vec, flatten)
lower = PrecomputableAffine(hidden_width,
nF=cls.nr_feature, nI=token_vector_width,
nP=parser_maxout_pieces)
lower.nP = parser_maxout_pieces
with Model.use_device('cpu'):
upper = chain(
clone(Maxout(hidden_width, hidden_width), depth-1),
zero_init(Affine(nr_class, hidden_width, drop_factor=0.0))
)
cfg = {
'nr_class': nr_class,
'hidden_depth': depth,
'token_vector_width': token_vector_width,
'hidden_width': hidden_width,
'maxout_pieces': parser_maxout_pieces,
'hist_size': hist_size,
'hist_width': hist_width
}
return (tok2vec, lower, upper), cfg
def create_optimizer(self):
return create_default_optimizer(self.model[0].ops,
**self.cfg.get('optimizer', {}))
def __init__(self, Vocab vocab, moves=True, model=True, **cfg):
"""Create a Parser.
vocab (Vocab): The vocabulary object. Must be shared with documents
to be processed. The value is set to the `.vocab` attribute.
moves (TransitionSystem): Defines how the parse-state is created,
updated and evaluated. The value is set to the .moves attribute
unless True (default), in which case a new instance is created with
`Parser.Moves()`.
model (object): Defines how the parse-state is created, updated and
evaluated. The value is set to the .model attribute unless True
(default), in which case a new instance is created with
`Parser.Model()`.
**cfg: Arbitrary configuration parameters. Set to the `.cfg` attribute
"""
self.vocab = vocab
if moves is True:
self.moves = self.TransitionSystem(self.vocab.strings)
else:
self.moves = moves
if 'beam_width' not in cfg:
cfg['beam_width'] = util.env_opt('beam_width', 1)
if 'beam_density' not in cfg:
cfg['beam_density'] = util.env_opt('beam_density', 0.0)
if 'pretrained_dims' not in cfg:
cfg['pretrained_dims'] = self.vocab.vectors.data.shape[1]
self.cfg = cfg
self.model = model
self._multitasks = []
def __reduce__(self):
return (Parser, (self.vocab, self.moves, self.model), None, None)
def __call__(self, Doc doc, beam_width=None, beam_density=None):
"""Apply the parser or entity recognizer, setting the annotations onto
the `Doc` object.
doc (Doc): The document to be processed.
"""
if beam_width is None:
beam_width = self.cfg.get('beam_width', 1)
if beam_density is None:
beam_density = self.cfg.get('beam_density', 0.0)
cdef Beam beam
if beam_width == 1:
states, tokvecs = self.parse_batch([doc])
self.set_annotations([doc], states, tensors=tokvecs)
return doc
else:
beams, tokvecs = self.beam_parse([doc],
beam_width=beam_width,
beam_density=beam_density)
beam = beams[0]
output = self.moves.get_beam_annot(beam)
state = StateClass.borrow(<StateC*>beam.at(0))
self.set_annotations([doc], [state], tensors=tokvecs)
_cleanup(beam)
return output
def pipe(self, docs, int batch_size=256, int n_threads=2,
beam_width=None, beam_density=None):
"""Process a stream of documents.
stream: The sequence of documents to process.
batch_size (int): 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.
"""
if beam_width is None:
beam_width = self.cfg.get('beam_width', 1)
if beam_density is None:
beam_density = self.cfg.get('beam_density', 0.0)
cdef Doc doc
for batch in cytoolz.partition_all(batch_size, docs):
batch_in_order = list(batch)
by_length = sorted(batch_in_order, key=lambda doc: len(doc))
batch_beams = []
for subbatch in cytoolz.partition_all(8, by_length):
subbatch = list(subbatch)
if beam_width == 1:
parse_states, tokvecs = self.parse_batch(subbatch)
beams = []
else:
beams, tokvecs = self.beam_parse(subbatch,
beam_width=beam_width,
beam_density=beam_density)
parse_states = _collect_states(beams)
self.set_annotations(subbatch, parse_states, tensors=None)
for beam in beams:
_cleanup(beam)
for doc in batch_in_order:
yield doc
def parse_batch(self, docs):
cdef:
precompute_hiddens state2vec
Pool mem
const float* feat_weights
StateC* st
StateClass stcls
vector[StateC*] states
int guess, nr_class, nr_feat, nr_piece, nr_dim, nr_state, nr_step
int j
if isinstance(docs, Doc):
docs = [docs]
cuda_stream = util.get_cuda_stream()
(tokvecs, bp_tokvecs), state2vec, vec2scores = self.get_batch_model(
docs, cuda_stream, 0.0)
nr_state = len(docs)
nr_class = self.moves.n_moves
nr_dim = tokvecs.shape[1]
nr_feat = self.nr_feature
nr_piece = state2vec.nP
state_objs = self.moves.init_batch(docs)
for stcls in state_objs:
if not stcls.c.is_final():
states.push_back(stcls.c)
feat_weights = state2vec.get_feat_weights()
cdef int i
cdef np.ndarray hidden_weights = numpy.ascontiguousarray(
vec2scores._layers[-1].W.T)
cdef np.ndarray hidden_bias = vec2scores._layers[-1].b
hW = <float*>hidden_weights.data
hb = <float*>hidden_bias.data
bias = <float*>state2vec.bias.data
cdef int nr_hidden = hidden_weights.shape[0]
cdef int nr_task = states.size()
with nogil:
self._parseC(&states[0], nr_task, feat_weights, bias, hW, hb,
nr_class, nr_hidden, nr_feat, nr_piece)
PyErr_CheckSignals()
tokvecs = self.model[0].ops.unflatten(tokvecs,
[len(doc) for doc in docs])
return state_objs, tokvecs
cdef void _parseC(self, StateC** states, int nr_task,
const float* feat_weights, const float* bias,
const float* hW, const float* hb,
int nr_class, int nr_hidden, int nr_feat, int nr_piece) nogil:
token_ids = <int*>calloc(nr_feat, sizeof(int))
is_valid = <int*>calloc(nr_class, sizeof(int))
vectors = <float*>calloc(nr_hidden * nr_task, sizeof(float))
unmaxed = <float*>calloc(nr_hidden * nr_piece, sizeof(float))
scores = <float*>calloc(nr_class*nr_task, sizeof(float))
if not (token_ids and is_valid and vectors and scores):
with gil:
PyErr_SetFromErrno(MemoryError)
PyErr_CheckSignals()
cdef int nr_todo = nr_task
cdef int i, j
cdef vector[StateC*] unfinished
while nr_todo >= 1:
memset(vectors, 0, nr_todo * nr_hidden * sizeof(float))
memset(scores, 0, nr_todo * nr_class * sizeof(float))
for i in range(nr_todo):
state = states[i]
state.set_context_tokens(token_ids, nr_feat)
memset(unmaxed, 0, nr_hidden * nr_piece * sizeof(float))
sum_state_features(unmaxed,
feat_weights, token_ids, 1, nr_feat, nr_hidden * nr_piece)
VecVec.add_i(unmaxed,
bias, 1., nr_hidden*nr_piece)
state_vector = &vectors[i*nr_hidden]
for j in range(nr_hidden):
index = j * nr_piece
which = Vec.arg_max(&unmaxed[index], nr_piece)
state_vector[j] = unmaxed[index + which]
# Compute hidden-to-output
# TODO: These methods in Thinc are confusing at the moment, and
# quite backwards. But this currently does what we need.
MatVec.batch_T_dot(scores,
hW, vectors, nr_hidden, nr_class, nr_todo)
# Add bias
for i in range(nr_todo):
VecVec.add_i(&scores[i*nr_class],
hb, 1., nr_class)
# Validate actions, argmax, take action.
for i in range(nr_todo):
state = states[i]
self.moves.set_valid(is_valid, state)
guess = arg_max_if_valid(&scores[i*nr_class], is_valid, nr_class)
action = self.moves.c[guess]
action.do(state, action.label)
state.push_hist(guess)
if not state.is_final():
unfinished.push_back(state)
for i in range(unfinished.size()):
states[i] = unfinished[i]
nr_todo = unfinished.size()
unfinished.clear()
free(token_ids)
free(is_valid)
free(vectors)
free(unmaxed)
free(scores)
def beam_parse(self, docs, int beam_width=3, float beam_density=0.001,
float drop=0.):
cdef Beam beam
cdef np.ndarray scores
cdef Doc doc
cdef int nr_class = self.moves.n_moves
cuda_stream = util.get_cuda_stream()
(tokvecs, bp_tokvecs), state2vec, vec2scores = self.get_batch_model(
docs, cuda_stream, drop)
cdef int offset = 0
cdef int j = 0
cdef int k
beams = []
for doc in docs:
beam = Beam(nr_class, beam_width, min_density=beam_density)
beam.initialize(self.moves.init_beam_state, doc.length, doc.c)
for i in range(beam.width):
state = <StateC*>beam.at(i)
state.offset = offset
offset += len(doc)
beam.check_done(_check_final_state, NULL)
beams.append(beam)
cdef np.ndarray token_ids
token_ids = numpy.zeros((len(docs) * beam_width, self.nr_feature),
dtype='i', order='C')
todo = [beam for beam in beams if not beam.is_done]
cdef int* c_ids
cdef int nr_feature = self.nr_feature
cdef int n_states
while todo:
todo = [beam for beam in beams if not beam.is_done]
token_ids.fill(-1)
c_ids = <int*>token_ids.data
n_states = 0
for beam in todo:
for i in range(beam.size):
state = <StateC*>beam.at(i)
# This way we avoid having to score finalized states
# We do have to take care to keep indexes aligned, though
if not state.is_final():
state.set_context_tokens(c_ids, nr_feature)
c_ids += nr_feature
n_states += 1
if n_states == 0:
break
vectors, _ = state2vec.begin_update(token_ids[:n_states], drop)
scores, _ = vec2scores.begin_update(vectors, drop=drop)
c_scores = <float*>scores.data
for beam in todo:
for i in range(beam.size):
state = <StateC*>beam.at(i)
if not state.is_final():
self.moves.set_valid(beam.is_valid[i], state)
memcpy(beam.scores[i], c_scores, nr_class * sizeof(float))
c_scores += nr_class
beam.advance(_transition_state, NULL, <void*>self.moves.c)
beam.check_done(_check_final_state, NULL)
tokvecs = self.model[0].ops.unflatten(tokvecs,
[len(doc) for doc in docs])
return beams, tokvecs
def update(self, docs, golds, drop=0., sgd=None, losses=None):
if not any(self.moves.has_gold(gold) for gold in golds):
return None
assert len(docs) == len(golds)
if self.cfg.get('beam_width', 1) >= 2 and numpy.random.random() >= 0.0:
return self.update_beam(docs, golds,
self.cfg['beam_width'], self.cfg['beam_density'],
drop=drop, sgd=sgd, losses=losses)
if losses is not None and self.name not in losses:
losses[self.name] = 0.
if isinstance(docs, Doc) and isinstance(golds, GoldParse):
docs = [docs]
golds = [golds]
for multitask in self._multitasks:
multitask.update(docs, golds, drop=drop, sgd=sgd)
cuda_stream = util.get_cuda_stream()
# Chop sequences into lengths of this many transitions, to make the
# batch uniform length.
cut_gold = numpy.random.choice(range(20, 100))
states, golds, max_steps = self._init_gold_batch(docs, golds, max_length=cut_gold)
(tokvecs, bp_tokvecs), state2vec, vec2scores = self.get_batch_model(docs, cuda_stream,
drop)
todo = [(s, g) for (s, g) in zip(states, golds)
if not s.is_final() and g is not None]
if not todo:
return None
backprops = []
# Add a padding vector to the d_tokvecs gradient, so that missing
# values don't affect the real gradient.
d_tokvecs = state2vec.ops.allocate((tokvecs.shape[0]+1, tokvecs.shape[1]))
cdef float loss = 0.
n_steps = 0
while todo:
states, golds = zip(*todo)
token_ids = self.get_token_ids(states)
vector, bp_vector = state2vec.begin_update(token_ids, drop=0.0)
if drop != 0:
mask = vec2scores.ops.get_dropout_mask(vector.shape, drop)
vector *= mask
hists = numpy.asarray([st.history for st in states], dtype='i')
if self.cfg.get('hist_size', 0):
scores, bp_scores = vec2scores.begin_update((vector, hists), drop=drop)
else:
scores, bp_scores = vec2scores.begin_update(vector, drop=drop)
d_scores = self.get_batch_loss(states, golds, scores)
d_scores /= len(docs)
d_vector = bp_scores(d_scores, sgd=sgd)
if drop != 0:
d_vector *= mask
if isinstance(self.model[0].ops, CupyOps) \
and not isinstance(token_ids, state2vec.ops.xp.ndarray):
# Move token_ids and d_vector to GPU, asynchronously
backprops.append((
util.get_async(cuda_stream, token_ids),
util.get_async(cuda_stream, d_vector),
bp_vector
))
else:
backprops.append((token_ids, d_vector, bp_vector))
self.transition_batch(states, scores)
todo = [(st, gold) for (st, gold) in todo
if not st.is_final()]
if losses is not None:
losses[self.name] += (d_scores**2).sum()
n_steps += 1
if n_steps >= max_steps:
break
self._make_updates(d_tokvecs,
bp_tokvecs, backprops, sgd, cuda_stream)
def update_beam(self, docs, golds, width=None, density=None,
drop=0., sgd=None, losses=None):
if not any(self.moves.has_gold(gold) for gold in golds):
return None
if not golds:
return None
if width is None:
width = self.cfg.get('beam_width', 2)
if density is None:
density = self.cfg.get('beam_density', 0.0)
if losses is not None and self.name not in losses:
losses[self.name] = 0.
lengths = [len(d) for d in docs]
assert min(lengths) >= 1
states = self.moves.init_batch(docs)
for gold in golds:
self.moves.preprocess_gold(gold)
cuda_stream = util.get_cuda_stream()
(tokvecs, bp_tokvecs), state2vec, vec2scores = self.get_batch_model(
docs, cuda_stream, drop)
states_d_scores, backprops, beams = _beam_utils.update_beam(
self.moves, self.nr_feature, 500, states, golds, state2vec,
vec2scores, width, density, self.cfg.get('hist_size', 0),
drop=drop, losses=losses)
backprop_lower = []
cdef float batch_size = len(docs)
for i, d_scores in enumerate(states_d_scores):
d_scores /= batch_size
if losses is not None:
losses[self.name] += (d_scores**2).sum()
ids, bp_vectors, bp_scores = backprops[i]
d_vector = bp_scores(d_scores, sgd=sgd)
if isinstance(self.model[0].ops, CupyOps) \
and not isinstance(ids, state2vec.ops.xp.ndarray):
backprop_lower.append((
util.get_async(cuda_stream, ids),
util.get_async(cuda_stream, d_vector),
bp_vectors))
else:
backprop_lower.append((ids, d_vector, bp_vectors))
# Add a padding vector to the d_tokvecs gradient, so that missing
# values don't affect the real gradient.
d_tokvecs = state2vec.ops.allocate((tokvecs.shape[0]+1, tokvecs.shape[1]))
self._make_updates(d_tokvecs, bp_tokvecs, backprop_lower, sgd,
cuda_stream)
cdef Beam beam
for beam in beams:
_cleanup(beam)
def _init_gold_batch(self, whole_docs, whole_golds, min_length=5, max_length=500):
"""Make a square batch, of length equal to the shortest doc. A long
doc will get multiple states. Let's say we have a doc of length 2*N,
where N is the shortest doc. We'll make two states, one representing
long_doc[:N], and another representing long_doc[N:]."""
cdef:
StateClass state
Transition action
whole_states = self.moves.init_batch(whole_docs)
max_length = max(min_length, min(max_length, min([len(doc) for doc in whole_docs])))
max_moves = 0
states = []
golds = []
for doc, state, gold in zip(whole_docs, whole_states, whole_golds):
gold = self.moves.preprocess_gold(gold)
if gold is None:
continue
oracle_actions = self.moves.get_oracle_sequence(doc, gold)
start = 0
while start < len(doc):
state = state.copy()
n_moves = 0
while state.B(0) < start and not state.is_final():
action = self.moves.c[oracle_actions.pop(0)]
action.do(state.c, action.label)
state.c.push_hist(action.clas)
n_moves += 1
has_gold = self.moves.has_gold(gold, start=start,
end=start+max_length)
if not state.is_final() and has_gold:
states.append(state)
golds.append(gold)
max_moves = max(max_moves, n_moves)
start += min(max_length, len(doc)-start)
max_moves = max(max_moves, len(oracle_actions))
return states, golds, max_moves
def _make_updates(self, d_tokvecs, bp_tokvecs, backprops, sgd, cuda_stream=None):
# Tells CUDA to block, so our async copies complete.
if cuda_stream is not None:
cuda_stream.synchronize()
xp = get_array_module(d_tokvecs)
for ids, d_vector, bp_vector in backprops:
d_state_features = bp_vector((d_vector, ids), sgd=sgd)
ids = ids.flatten()
d_state_features = d_state_features.reshape(
(ids.size, d_state_features.shape[2]))
self.model[0].ops.scatter_add(d_tokvecs, ids,
d_state_features)
# Padded -- see update()
bp_tokvecs(d_tokvecs[:-1], sgd=sgd)
@property
def move_names(self):
names = []
for i in range(self.moves.n_moves):
name = self.moves.move_name(self.moves.c[i].move, self.moves.c[i].label)
names.append(name)
return names
def get_batch_model(self, docs, stream, dropout):
tok2vec, lower, upper = self.model
tokvecs, bp_tokvecs = tok2vec.begin_update(docs, drop=dropout)
state2vec = precompute_hiddens(len(docs), tokvecs,
lower, stream, drop=0.0)
return (tokvecs, bp_tokvecs), state2vec, upper
nr_feature = 13
def get_token_ids(self, states):
cdef StateClass state
cdef int n_tokens = self.nr_feature
cdef np.ndarray ids = numpy.zeros((len(states), n_tokens),
dtype='i', order='C')
c_ids = <int*>ids.data
for i, state in enumerate(states):
if not state.is_final():
state.c.set_context_tokens(c_ids, n_tokens)
c_ids += ids.shape[1]
return ids
def transition_batch(self, states, float[:, ::1] scores):
cdef StateClass state
cdef int[500] is_valid # TODO: Unhack
cdef float* c_scores = &scores[0, 0]
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]
state.c.push_hist(guess)
def get_batch_loss(self, states, golds, float[:, ::1] scores):
cdef StateClass state
cdef GoldParse gold
cdef Pool mem = Pool()
cdef int i
is_valid = <int*>mem.alloc(self.moves.n_moves, sizeof(int))
costs = <float*>mem.alloc(self.moves.n_moves, sizeof(float))
cdef np.ndarray d_scores = numpy.zeros((len(states), self.moves.n_moves),
dtype='f', order='C')
c_d_scores = <float*>d_scores.data
for i, (state, gold) in enumerate(zip(states, golds)):
memset(is_valid, 0, self.moves.n_moves * sizeof(int))
memset(costs, 0, self.moves.n_moves * sizeof(float))
self.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
def set_annotations(self, docs, states, tensors=None):
cdef StateClass state
cdef Doc doc
for i, (state, doc) in enumerate(zip(states, docs)):
self.moves.finalize_state(state.c)
for j in range(doc.length):
doc.c[j] = state.c._sent[j]
if tensors is not None:
if isinstance(doc.tensor, numpy.ndarray) \
and not isinstance(tensors[i], numpy.ndarray):
doc.extend_tensor(tensors[i].get())
else:
doc.extend_tensor(tensors[i])
self.moves.finalize_doc(doc)
for hook in self.postprocesses:
for doc in docs:
hook(doc)
@property
def labels(self):
class_names = [self.moves.get_class_name(i) for i in range(self.moves.n_moves)]
return class_names
@property
def tok2vec(self):
'''Return the embedding and convolutional layer of the model.'''
if self.model in (None, True, False):
return None
else:
return self.model[0]
@property
def postprocesses(self):
# Available for subclasses, e.g. to deprojectivize
return []
def add_label(self, label):
resized = False
for action in self.moves.action_types:
added = self.moves.add_action(action, label)
if added:
resized = True
if self.model not in (True, False, None) and resized:
# Weights are stored in (nr_out, nr_in) format, so we're basically
# just adding rows here.
smaller = self.model[-1]._layers[-1]
larger = Affine(self.moves.n_moves, smaller.nI)
copy_array(larger.W[:smaller.nO], smaller.W)
copy_array(larger.b[:smaller.nO], smaller.b)
self.model[-1]._layers[-1] = larger
def begin_training(self, gold_tuples, pipeline=None, sgd=None, **cfg):
if 'model' in cfg:
self.model = cfg['model']
cfg.setdefault('min_action_freq', 30)
actions = self.moves.get_actions(gold_parses=gold_tuples,
min_freq=cfg.get('min_action_freq', 30))
self.moves.initialize_actions(actions)
cfg.setdefault('token_vector_width', 128)
if self.model is True:
cfg['pretrained_dims'] = self.vocab.vectors_length
self.model, cfg = self.Model(self.moves.n_moves, **cfg)
if sgd is None:
sgd = self.create_optimizer()
self.model[1].begin_training(
self.model[1].ops.allocate((5, cfg['token_vector_width'])))
if pipeline is not None:
self.init_multitask_objectives(gold_tuples, pipeline, sgd=sgd, **cfg)
link_vectors_to_models(self.vocab)
else:
if sgd is None:
sgd = self.create_optimizer()
self.model[1].begin_training(
self.model[1].ops.allocate((5, cfg['token_vector_width'])))
self.cfg.update(cfg)
return sgd
def add_multitask_objective(self, target):
# Defined in subclasses, to avoid circular import
raise NotImplementedError
def init_multitask_objectives(self, gold_tuples, pipeline, **cfg):
'''Setup models for secondary objectives, to benefit from multi-task
learning. This method is intended to be overridden by subclasses.
For instance, the dependency parser can benefit from sharing
an input representation with a label prediction model. These auxiliary
models are discarded after training.
'''
pass
def preprocess_gold(self, docs_golds):
for doc, gold in docs_golds:
yield doc, gold
def use_params(self, params):
# Can't decorate cdef class :(. Workaround.
with self.model[0].use_params(params):
with self.model[1].use_params(params):
yield
def to_disk(self, path, **exclude):
serializers = {
'tok2vec_model': lambda p: p.open('wb').write(
self.model[0].to_bytes()),
'lower_model': lambda p: p.open('wb').write(
self.model[1].to_bytes()),
'upper_model': lambda p: p.open('wb').write(
self.model[2].to_bytes()),
'vocab': lambda p: self.vocab.to_disk(p),
'moves': lambda p: self.moves.to_disk(p, strings=False),
'cfg': lambda p: p.open('w').write(json_dumps(self.cfg))
}
util.to_disk(path, serializers, exclude)
def from_disk(self, path, **exclude):
deserializers = {
'vocab': lambda p: self.vocab.from_disk(p),
'moves': lambda p: self.moves.from_disk(p, strings=False),
'cfg': lambda p: self.cfg.update(util.read_json(p)),
'model': lambda p: None
}
util.from_disk(path, deserializers, exclude)
if 'model' not in exclude:
path = util.ensure_path(path)
if self.model is True:
self.cfg.setdefault('pretrained_dims', self.vocab.vectors_length)
self.model, cfg = self.Model(**self.cfg)
else:
cfg = {}
with (path / 'tok2vec_model').open('rb') as file_:
bytes_data = file_.read()
self.model[0].from_bytes(bytes_data)
with (path / 'lower_model').open('rb') as file_:
bytes_data = file_.read()
self.model[1].from_bytes(bytes_data)
with (path / 'upper_model').open('rb') as file_:
bytes_data = file_.read()
self.model[2].from_bytes(bytes_data)
self.cfg.update(cfg)
return self
def to_bytes(self, **exclude):
serializers = OrderedDict((
('tok2vec_model', lambda: self.model[0].to_bytes()),
('lower_model', lambda: self.model[1].to_bytes()),
('upper_model', lambda: self.model[2].to_bytes()),
('vocab', lambda: self.vocab.to_bytes()),
('moves', lambda: self.moves.to_bytes(strings=False)),
('cfg', lambda: json.dumps(self.cfg, indent=2, sort_keys=True))
))
if 'model' in exclude:
exclude['tok2vec_model'] = True
exclude['lower_model'] = True
exclude['upper_model'] = True
exclude.pop('model')
return util.to_bytes(serializers, exclude)
def from_bytes(self, bytes_data, **exclude):
deserializers = OrderedDict((
('vocab', lambda b: self.vocab.from_bytes(b)),
('moves', lambda b: self.moves.from_bytes(b, strings=False)),
('cfg', lambda b: self.cfg.update(json.loads(b))),
('tok2vec_model', lambda b: None),
('lower_model', lambda b: None),
('upper_model', lambda b: None)
))
msg = util.from_bytes(bytes_data, deserializers, exclude)
if 'model' not in exclude:
if self.model is True:
self.model, cfg = self.Model(**self.cfg)
cfg['pretrained_dims'] = self.vocab.vectors_length
else:
cfg = {}
cfg['pretrained_dims'] = self.vocab.vectors_length
if 'tok2vec_model' in msg:
self.model[0].from_bytes(msg['tok2vec_model'])
if 'lower_model' in msg:
self.model[1].from_bytes(msg['lower_model'])
if 'upper_model' in msg:
self.model[2].from_bytes(msg['upper_model'])
self.cfg.update(cfg)
return self
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
# These are passed as callbacks to thinc.search.Beam
cdef int _transition_state(void* _dest, void* _src, class_t clas, void* _moves) except -1:
dest = <StateC*>_dest
src = <StateC*>_src
moves = <const Transition*>_moves
dest.clone(src)
moves[clas].do(dest, moves[clas].label)
dest.push_hist(clas)
cdef int _check_final_state(void* _state, void* extra_args) except -1:
state = <StateC*>_state
return state.is_final()
def _cleanup(Beam beam):
cdef StateC* state
# Once parsing has finished, states in beam may not be unique. Is this
# correct?
seen = set()
for i in range(beam.width):
addr = <size_t>beam._parents[i].content
if addr not in seen:
state = <StateC*>addr
del state
seen.add(addr)
else:
print(i, addr)
print(seen)
raise Exception
addr = <size_t>beam._states[i].content
if addr not in seen:
state = <StateC*>addr
del state
seen.add(addr)
else:
print(i, addr)
print(seen)
raise Exception