Merge branch 'develop' of https://github.com/explosion/spaCy into develop

examples/training/train_new_entity_type.py

@@ -25,7 +25,7 @@ For more details, see the documentation:
 * Saving and loading models: https://spacy.io/docs/usage/saving-loading
 
 Developed for: spaCy 1.7.6
-Last tested for: spaCy 1.7.6
+Last updated for: spaCy 2.0.0a13
 """
 from __future__ import unicode_literals, print_function
 
@@ -34,55 +34,41 @@ from pathlib import Path
 import random
 
 import spacy
-from spacy.gold import GoldParse
-from spacy.tagger import Tagger
+from spacy.gold import GoldParse, minibatch
+from spacy.pipeline import NeuralEntityRecognizer
+from spacy.pipeline import TokenVectorEncoder
+
+
+def get_gold_parses(tokenizer, train_data):
+    '''Shuffle and create GoldParse objects'''
+    random.shuffle(train_data)
+    for raw_text, entity_offsets in train_data:
+        doc = tokenizer(raw_text)
+        gold = GoldParse(doc, entities=entity_offsets)
+        yield doc, gold
 
  
 def train_ner(nlp, train_data, output_dir):
-    # Add new words to vocab
-    for raw_text, _ in train_data:
-        doc = nlp.make_doc(raw_text)
-        for word in doc:
-            _ = nlp.vocab[word.orth]
     random.seed(0)
-    # You may need to change the learning rate. It's generally difficult to
-    # guess what rate you should set, especially when you have limited data.
-    nlp.entity.model.learn_rate = 0.001
-    for itn in range(1000):
-        random.shuffle(train_data)
-        loss = 0.
-        for raw_text, entity_offsets in train_data:
-            gold = GoldParse(doc, entities=entity_offsets)
-            # By default, the GoldParse class assumes that the entities
-            # described by offset are complete, and all other words should
-            # have the tag 'O'. You can tell it to make no assumptions
-            # about the tag of a word by giving it the tag '-'.
-            # However, this allows a trivial solution to the current
-            # learning problem: if words are either 'any tag' or 'ANIMAL',
-            # the model can learn that all words can be tagged 'ANIMAL'.
-            #for i in range(len(gold.ner)):
-                #if not gold.ner[i].endswith('ANIMAL'):
-                #    gold.ner[i] = '-'
-            doc = nlp.make_doc(raw_text)
-            nlp.tagger(doc)
-            # As of 1.9, spaCy's parser now lets you supply a dropout probability
-            # This might help the model generalize better from only a few
-            # examples.
-            loss += nlp.entity.update(doc, gold, drop=0.9)
-        if loss == 0:
-            break
-    # This step averages the model's weights. This may or may not be good for
-    # your situation --- it's empirical.
-    nlp.end_training()
-    if output_dir:
-        if not output_dir.exists():
-            output_dir.mkdir()
-        nlp.save_to_directory(output_dir)
+    optimizer = nlp.begin_training(lambda: [])
+    nlp.meta['name'] = 'en_ent_animal'
+    for itn in range(50):
+        losses = {}
+        for batch in minibatch(get_gold_parses(nlp.make_doc, train_data), size=3):
+            docs, golds = zip(*batch)
+            nlp.update(docs, golds, losses=losses, sgd=optimizer, update_shared=True,
+                       drop=0.35)
+        print(losses)
+    if not output_dir:
+        return
+    elif not output_dir.exists():
+        output_dir.mkdir()
+    nlp.to_disk(output_dir)
 
 
 def main(model_name, output_directory=None):
-    print("Loading initial model", model_name)
-    nlp = spacy.load(model_name)
+    print("Creating initial model", model_name)
+    nlp = spacy.blank(model_name)
     if output_directory is not None:
         output_directory = Path(output_directory)
 
@@ -91,6 +77,11 @@ def main(model_name, output_directory=None):
             "Horses are too tall and they pretend to care about your feelings",
             [(0, 6, 'ANIMAL')],
         ),
+        (
+            "Do they bite?", 
+            [],
+        ),
+ 
         (
             "horses are too tall and they pretend to care about your feelings",
             [(0, 6, 'ANIMAL')]
@@ -109,18 +100,20 @@ def main(model_name, output_directory=None):
         )
 
     ]
-    nlp.entity.add_label('ANIMAL')
+    nlp.pipeline.append(TokenVectorEncoder(nlp.vocab))
+    nlp.pipeline.append(NeuralEntityRecognizer(nlp.vocab))
+    nlp.pipeline[-1].add_label('ANIMAL')
     train_ner(nlp, train_data, output_directory)
 
     # Test that the entity is recognized
-    doc = nlp('Do you like horses?')
+    text = 'Do you like horses?'
     print("Ents in 'Do you like horses?':")
+    doc = nlp(text)
     for ent in doc.ents:
         print(ent.label_, ent.text)
     if output_directory:
         print("Loading from", output_directory)
-        nlp2 = spacy.load('en', path=output_directory)
-        nlp2.entity.add_label('ANIMAL')
+        nlp2 = spacy.load(output_directory)
         doc2 = nlp2('Do you like horses?')
         for ent in doc2.ents:
             print(ent.label_, ent.text)

spacy/_ml.py

@@ -229,20 +229,18 @@ def drop_layer(layer, factor=2.):
 def Tok2Vec(width, embed_size, preprocess=None):
     cols = [ID, NORM, PREFIX, SUFFIX, SHAPE, ORTH]
     with Model.define_operators({'>>': chain, '|': concatenate, '**': clone, '+': add}):
-        norm = get_col(cols.index(NORM))     >> HashEmbed(width, embed_size, name='embed_lower')
-        prefix = get_col(cols.index(PREFIX)) >> HashEmbed(width, embed_size//2, name='embed_prefix')
-        suffix = get_col(cols.index(SUFFIX)) >> HashEmbed(width, embed_size//2, name='embed_suffix')
-        shape = get_col(cols.index(SHAPE))   >> HashEmbed(width, embed_size//2, name='embed_shape')
+        norm = HashEmbed(width, embed_size, column=cols.index(NORM), name='embed_norm')
+        prefix = HashEmbed(width, embed_size//2, column=cols.index(PREFIX), name='embed_prefix')
+        suffix = HashEmbed(width, embed_size//2, column=cols.index(SUFFIX), name='embed_suffix')
+        shape = HashEmbed(width, embed_size//2, column=cols.index(SHAPE), name='embed_shape')
 
         embed = (norm | prefix | suffix | shape ) >> LN(Maxout(width, width*4, pieces=3))
         tok2vec = (
             with_flatten(
                 asarray(Model.ops, dtype='uint64')
                 >> uniqued(embed, column=5)
-                >> drop_layer(
-                    Residual(
-                        (ExtractWindow(nW=1) >> LN(Maxout(width, width*3)))
-                    )
+                >> Residual(
+                    (ExtractWindow(nW=1) >> LN(Maxout(width, width*3)))
                 ) ** 4, pad=4
             )
         )
@@ -372,6 +370,7 @@ def fine_tune(embedding, combine=None):
             "fine_tune currently only supports addition. Set combine=None")
     def fine_tune_fwd(docs_tokvecs, drop=0.):
         docs, tokvecs = docs_tokvecs
+
         lengths = model.ops.asarray([len(doc) for doc in docs], dtype='i')
 
         vecs, bp_vecs = embedding.begin_update(docs, drop=drop)

spacy/about.py

@@ -3,7 +3,7 @@
 # https://github.com/pypa/warehouse/blob/master/warehouse/__about__.py
 
 __title__ = 'spacy-nightly'
-__version__ = '2.0.0a13'
+__version__ = '2.0.0a14'
 __summary__ = 'Industrial-strength Natural Language Processing (NLP) with Python and Cython'
 __uri__ = 'https://spacy.io'
 __author__ = 'Explosion AI'

spacy/cli/train.py

@@ -72,8 +72,8 @@ def train(cmd, lang, output_dir, train_data, dev_data, n_iter=20, n_sents=0,
                                    util.env_opt('batch_compound', 1.001))
 
     if resume:
-        prints(output_path / 'model19.pickle', title="Resuming training")
-        nlp = dill.load((output_path / 'model19.pickle').open('rb'))
+        prints(output_path / 'model9.pickle', title="Resuming training")
+        nlp = dill.load((output_path / 'model9.pickle').open('rb'))
     else:
         nlp = lang_class(pipeline=pipeline)
     corpus = GoldCorpus(train_path, dev_path, limit=n_sents)
@@ -88,7 +88,7 @@ def train(cmd, lang, output_dir, train_data, dev_data, n_iter=20, n_sents=0,
             if resume:
                 i += 20
             with tqdm.tqdm(total=n_train_words, leave=False) as pbar:
-                train_docs = corpus.train_docs(nlp, projectivize=True,
+                train_docs = corpus.train_docs(nlp, projectivize=True, noise_level=0.0,
                                                gold_preproc=gold_preproc, max_length=0)
                 losses = {}
                 for batch in minibatch(train_docs, size=batch_sizes):

spacy/gold.pyx

@@ -7,6 +7,7 @@ import re
 import ujson
 import random
 import cytoolz
+import itertools
 
 from .syntax import nonproj
 from .util import ensure_path
@@ -146,9 +147,13 @@ def minibatch(items, size=8):
     '''Iterate over batches of items. `size` may be an iterator,
     so that batch-size can vary on each step.
     '''
+    if isinstance(size, int):
+        size_ = itertools.repeat(8)
+    else:
+        size_ = size
     items = iter(items)
     while True:
-        batch_size = next(size) #if hasattr(size, '__next__') else size
+        batch_size = next(size_)
         batch = list(cytoolz.take(int(batch_size), items))
         if len(batch) == 0:
             break

spacy/language.py

@@ -347,15 +347,9 @@ class Language(object):
         """Allocate models, pre-process training data and acquire a trainer and
         optimizer. Used as a contextmanager.
 
-        gold_tuples (iterable): Gold-standard training data.
+        get_gold_tuples (function): Function returning gold data
         **cfg: Config parameters.
-        YIELDS (tuple): A trainer and an optimizer.
-
-        EXAMPLE:
-            >>> with nlp.begin_training(gold, use_gpu=True) as (trainer, optimizer):
-            >>>    for epoch in trainer.epochs(gold):
-            >>>        for docs, golds in epoch:
-            >>>            state = nlp.update(docs, golds, sgd=optimizer)
+        returns: An optimizer
         """
         if self.parser:
             self.pipeline.append(NeuralLabeller(self.vocab))

spacy/lemmatizer.py

@@ -38,7 +38,8 @@ class Lemmatizer(object):
         avoid lemmatization entirely.
         """
         morphology = {} if morphology is None else morphology
-        others = [key for key in morphology if key not in (POS, 'number', 'pos', 'verbform')]
+        others = [key for key in morphology
+                  if key not in (POS, 'Number', 'POS', 'VerbForm', 'Tense')]
         true_morph_key = morphology.get('morph', 0)
         if univ_pos == 'noun' and morphology.get('Number') == 'sing':
             return True
@@ -47,7 +48,9 @@ class Lemmatizer(object):
         # This maps 'VBP' to base form -- probably just need 'IS_BASE'
         # morphology
         elif univ_pos == 'verb' and (morphology.get('VerbForm') == 'fin' and \
-                                     morphology.get('Tense') == 'pres'):
+                                     morphology.get('Tense') == 'pres' and \
+                                     morphology.get('Number') is None and \
+                                     not others):
             return True
         elif univ_pos == 'adj' and morphology.get('Degree') == 'pos':
             return True

spacy/syntax/_state.pxd

@@ -101,9 +101,10 @@ cdef cppclass StateC:
         elif n == 6:
             if this.B(0) >= 0:
                 ids[0] = this.B(0)
+                ids[1] = this.B(0)-1
             else:
                 ids[0] = -1
-            ids[1] = this.B(0)
+                ids[1] = -1
             ids[2] = this.B(1)
             ids[3] = this.E(0)
             if ids[3] >= 1:
@@ -118,8 +119,12 @@ cdef cppclass StateC:
             # TODO error =/
             pass
         for i in range(n):
+            # Token vectors should be padded, so that there's a vector for
+            # missing values at the start.
             if ids[i] >= 0:
-                ids[i] += this.offset
+                ids[i] += this.offset + 1
+            else:
+                ids[i] = 0
 
     int S(int i) nogil const:
         if i >= this._s_i:
@@ -162,9 +167,9 @@ cdef cppclass StateC:
 
     int E(int i) nogil const:
         if this._e_i <= 0 or this._e_i >= this.length:
-            return 0
+            return -1
         if i < 0 or i >= this._e_i:
-            return 0
+            return -1
         return this._ents[this._e_i - (i+1)].start
 
     int L(int i, int idx) nogil const:

spacy/syntax/ner.pyx

@@ -220,6 +220,31 @@ cdef class BiluoPushDown(TransitionSystem):
             raise Exception(move)
         return t
 
+    def add_action(self, int action, label_name):
+        cdef attr_t label_id
+        if not isinstance(label_name, (int, long)):
+            label_id = self.strings.add(label_name)
+        else:
+            label_id = label_name
+        if action == OUT and label_id != 0:
+            return
+        if action == MISSING or action == ISNT:
+            return
+        # Check we're not creating a move we already have, so that this is
+        # idempotent
+        for trans in self.c[:self.n_moves]:
+            if trans.move == action and trans.label == label_id:
+                return 0
+        if self.n_moves >= self._size:
+            self._size *= 2
+            self.c = <Transition*>self.mem.realloc(self.c, self._size * sizeof(self.c[0]))
+        self.c[self.n_moves] = self.init_transition(self.n_moves, action, label_id)
+        assert self.c[self.n_moves].label == label_id
+        self.n_moves += 1
+        return 1
+
+
+
     cdef int initialize_state(self, StateC* st) nogil:
         # This is especially necessary when we use limited training data.
         for i in range(st.length):

spacy/syntax/nn_parser.pyx

@@ -393,9 +393,8 @@ cdef class Parser:
 
         tokvecs = self.model[0].ops.flatten(tokvecses)
         if USE_FINE_TUNE:
-            # TODO: This is incorrect! Unhack when training next model
-            tokvecs += self.model[0].ops.flatten(self.model[0]((docs, tokvecses)))
-
+            tokvecs = self.model[0].ops.flatten(self.model[0]((docs, tokvecses)))
+        tokvecs = self._pad_tokvecs(tokvecs)
         nr_state = len(docs)
         nr_class = self.moves.n_moves
         nr_dim = tokvecs.shape[1]
@@ -455,6 +454,7 @@ cdef class Parser:
         tokvecs = self.model[0].ops.flatten(tokvecses)
         if USE_FINE_TUNE:
             tokvecs = self.model[0].ops.flatten(self.model[0]((docs, tokvecses)))
+        tokvecs = self._pad_tokvecs(tokvecs)
         cuda_stream = get_cuda_stream()
         state2vec, vec2scores = self.get_batch_model(len(docs), tokvecs,
                                                      cuda_stream, 0.0)
@@ -532,8 +532,10 @@ cdef class Parser:
             docs = [docs]
             golds = [golds]
         if USE_FINE_TUNE:
-            my_tokvecs, bp_my_tokvecs = self.model[0].begin_update(docs_tokvecs, drop=drop)
-            tokvecs += self.model[0].ops.flatten(my_tokvecs)
+            tokvecs, bp_my_tokvecs = self.model[0].begin_update(docs_tokvecs, drop=drop)
+            tokvecs = self.model[0].ops.flatten(tokvecs)
+
+        tokvecs = self._pad_tokvecs(tokvecs)
 
         cuda_stream = get_cuda_stream()
 
@@ -584,6 +586,7 @@ cdef class Parser:
                 break
         self._make_updates(d_tokvecs,
             backprops, sgd, cuda_stream)
+        d_tokvecs = self._unpad_tokvecs(d_tokvecs)
         d_tokvecs = self.model[0].ops.unflatten(d_tokvecs, [len(d) for d in docs])
         if USE_FINE_TUNE:
             d_tokvecs = bp_my_tokvecs(d_tokvecs, sgd=sgd)
@@ -606,8 +609,8 @@ cdef class Parser:
         assert min(lengths) >= 1
         tokvecs = self.model[0].ops.flatten(tokvecs)
         if USE_FINE_TUNE:
-            my_tokvecs, bp_my_tokvecs = self.model[0].begin_update(docs_tokvecs, drop=drop)
-            tokvecs += self.model[0].ops.flatten(my_tokvecs)
+            tokvecs, bp_my_tokvecs = self.model[0].begin_update(docs_tokvecs, drop=drop)
+            tokvecs = self.model[0].ops.flatten(tokvecs)
 
         states = self.moves.init_batch(docs)
         for gold in golds:
@@ -640,10 +643,20 @@ cdef class Parser:
         d_tokvecs = self.model[0].ops.allocate(tokvecs.shape)
         self._make_updates(d_tokvecs, backprop_lower, sgd, cuda_stream)
         d_tokvecs = self.model[0].ops.unflatten(d_tokvecs, lengths)
+        d_tokvecs = self._unpad_tokvecs(d_tokvecs)
         if USE_FINE_TUNE:
             d_tokvecs = bp_my_tokvecs(d_tokvecs, sgd=sgd)
         return d_tokvecs
 
+    def _pad_tokvecs(self, tokvecs):
+        # Add a vector for missing values at the start of tokvecs
+        xp = get_array_module(tokvecs)
+        pad = xp.zeros((1, tokvecs.shape[1]), dtype=tokvecs.dtype)
+        return xp.vstack((pad, tokvecs))
+
+    def _unpad_tokvecs(self, d_tokvecs):
+        return d_tokvecs[1:]
+
     def _init_gold_batch(self, whole_docs, whole_golds):
         """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,
@@ -706,7 +719,7 @@ cdef class Parser:
                         lower, stream, drop=dropout)
         return state2vec, upper
 
-    nr_feature = 13
+    nr_feature = 8
 
     def get_token_ids(self, states):
         cdef StateClass state

spacy/syntax/transition_system.pyx

@@ -148,7 +148,7 @@ cdef class TransitionSystem:
 
     def add_action(self, int action, label_name):
         cdef attr_t label_id
-        if not isinstance(label_name, int):
+        if not isinstance(label_name, (int, long)):
             label_id = self.strings.add(label_name)
         else:
             label_id = label_name

spacy/tests/regression/test_issue1305.py

@@ -0,0 +1,8 @@
+import pytest
+
+@pytest.mark.models('en')
+def test_issue1305(EN):
+    '''Test lemmatization of English VBZ'''
+    assert EN.vocab.morphology.lemmatizer('works', 'verb') == set(['work'])
+    doc = EN(u'This app works well')
+    assert doc[2].lemma_ == 'work'

spacy/tests/regression/test_issue429.py

@@ -9,11 +9,14 @@ import pytest
 @pytest.mark.models('en')
 def test_issue429(EN):
     def merge_phrases(matcher, doc, i, matches):
-      if i != len(matches) - 1:
-        return None
-      spans = [(ent_id, ent_id, doc[start:end]) for ent_id, start, end in matches]
-      for ent_id, label, span in spans:
-        span.merge('NNP' if label else span.root.tag_, span.text, EN.vocab.strings[label])
+        if i != len(matches) - 1:
+            return None
+        spans = [(ent_id, ent_id, doc[start:end]) for ent_id, start, end in matches]
+        for ent_id, label, span in spans:
+            span.merge(
+                tag=('NNP' if label else span.root.tag_),
+                lemma=span.text,
+                label='PERSON')
 
     doc = EN('a')
     matcher = Matcher(EN.vocab)

website/docs/usage/customizing-tokenizer.jade

@@ -282,7 +282,7 @@ p
         def __call__(self, text):
             words = text.split(' ')
             # All tokens 'own' a subsequent space character in this tokenizer
-            spaces = [True] * len(word)
+            spaces = [True] * len(words)
             return Doc(self.vocab, words=words, spaces=spaces)
 
 p