Merge pull request #11089 from polm/coref/dimension-inference

Dimension inference in Coref

spacy/ml/models/coref.py

@@ -1,6 +1,6 @@
 from typing import List, Tuple, Callable, cast
 
-from thinc.api import Model, chain
+from thinc.api import Model, chain, get_width
 from thinc.api import PyTorchWrapper, ArgsKwargs
 from thinc.types import Floats2d, Ints2d
 from thinc.util import torch, xp2torch, torch2xp
@@ -22,13 +22,48 @@ def build_wl_coref_model(
     # pairs to keep per mention after rough scoring
     antecedent_limit: int = 50,
     antecedent_batch_size: int = 512,
-    tok2vec_size: int = 768,  # tok2vec size
+    nI=None,
 ) -> Model[List[Doc], Tuple[Floats2d, Ints2d]]:
 
     with Model.define_operators({">>": chain}):
-        coref_clusterer = PyTorchWrapper(
+        coref_clusterer: Model[List[Floats2d], Tuple[Floats2d, Ints2d]] = Model(
+            "coref_clusterer",
+            forward=coref_forward,
+            init=coref_init,
+            dims={"nI": nI},
+            attrs={
+                "distance_embedding_size": distance_embedding_size,
+                "hidden_size": hidden_size,
+                "depth": depth,
+                "dropout": dropout,
+                "antecedent_limit": antecedent_limit,
+                "antecedent_batch_size": antecedent_batch_size,
+            },
+        )
+
+        model = tok2vec >> coref_clusterer
+        model.set_ref("coref_clusterer", coref_clusterer)
+    return model
+
+
+def coref_init(model: Model, X=None, Y=None):
+    if model.layers:
+        return
+
+    if X is not None and model.has_dim("nI") is None:
+        model.set_dim("nI", get_width(X))
+
+    hidden_size = model.attrs["hidden_size"]
+    depth = model.attrs["depth"]
+    dropout = model.attrs["dropout"]
+    antecedent_limit = model.attrs["antecedent_limit"]
+    antecedent_batch_size = model.attrs["antecedent_batch_size"]
+    distance_embedding_size = model.attrs["distance_embedding_size"]
+
+    model._layers = [
+        PyTorchWrapper(
             CorefClusterer(
-                tok2vec_size,
+                model.get_dim("nI"),
                 distance_embedding_size,
                 hidden_size,
                 depth,
@@ -39,10 +74,13 @@ def build_wl_coref_model(
             convert_inputs=convert_coref_clusterer_inputs,
             convert_outputs=convert_coref_clusterer_outputs,
         )
-        coref_model = tok2vec >> coref_clusterer
+        # TODO maybe we need mixed precision and grad scaling?
-    return coref_model
+    ]
 
 
+def coref_forward(model: Model, X, is_train: bool):
+    return model.layers[0](X, is_train)
+
 def convert_coref_clusterer_inputs(model: Model, X: List[Floats2d], is_train: bool):
     # The input here is List[Floats2d], one for each doc
     # just use the first

spacy/ml/models/coref_util.py

@@ -147,7 +147,9 @@ def get_clusters_from_doc(doc) -> List[List[Tuple[int, int]]]:
     ints are char spans, to be tokenization independent.
     """
     out = []
-    for key, val in doc.spans.items():
+    keys = sorted(list(doc.spans.keys()))
+    for key in keys:
+        val = doc.spans[key]
         cluster = []
         for span in val:
 

spacy/ml/models/span_predictor.py

@@ -1,6 +1,6 @@
 from typing import List, Tuple, cast
 
-from thinc.api import Model, chain, tuplify
+from thinc.api import Model, chain, tuplify, get_width
 from thinc.api import PyTorchWrapper, ArgsKwargs
 from thinc.types import Floats2d, Ints1d
 from thinc.util import torch, xp2torch, torch2xp
@@ -13,7 +13,6 @@ from .coref_util import get_sentence_ids
 @registry.architectures("spacy.SpanPredictor.v1")
 def build_span_predictor(
     tok2vec: Model[List[Doc], List[Floats2d]],
-    tok2vec_size: int = 768,
     hidden_size: int = 1024,
     distance_embedding_size: int = 64,
     conv_channels: int = 4,
@@ -23,10 +22,46 @@ def build_span_predictor(
 ):
     # TODO add model return types
 
+    nI = None
+
     with Model.define_operators({">>": chain, "&": tuplify}):
-        span_predictor = PyTorchWrapper(
+        span_predictor: Model[List[Floats2d], List[Floats2d]] = Model(
+            "span_predictor",
+            forward=span_predictor_forward,
+            init=span_predictor_init,
+            dims={"nI": nI},
+            attrs={
+                "distance_embedding_size": distance_embedding_size,
+                "hidden_size": hidden_size,
+                "conv_channels": conv_channels,
+                "window_size": window_size,
+                "max_distance": max_distance,
+            },
+        )
+        head_info = build_get_head_metadata(prefix)
+        model = (tok2vec & head_info) >> span_predictor
+        model.set_ref("span_predictor", span_predictor)
+
+    return model
+
+
+def span_predictor_init(model: Model, X=None, Y=None):
+    if model.layers:
+        return
+
+    if X is not None and model.has_dim("nI") is None:
+        model.set_dim("nI", get_width(X))
+
+    hidden_size = model.attrs["hidden_size"]
+    distance_embedding_size = model.attrs["distance_embedding_size"]
+    conv_channels = model.attrs["conv_channels"]
+    window_size = model.attrs["window_size"]
+    max_distance = model.attrs["max_distance"]
+
+    model._layers = [
+        PyTorchWrapper(
             SpanPredictor(
-                tok2vec_size,
+                model.get_dim("nI"),
                 hidden_size,
                 distance_embedding_size,
                 conv_channels,
@@ -35,10 +70,12 @@ def build_span_predictor(
             ),
             convert_inputs=convert_span_predictor_inputs,
         )
-        head_info = build_get_head_metadata(prefix)
+        # TODO maybe we need mixed precision and grad scaling?
-        model = (tok2vec & head_info) >> span_predictor
+    ]
 
-    return model
+
+def span_predictor_forward(model: Model, X, is_train: bool):
+    return model.layers[0](X, is_train)
 
 
 def convert_span_predictor_inputs(
@@ -61,7 +98,9 @@ def convert_span_predictor_inputs(
     else:
         head_ids_tensor = xp2torch(head_ids[0], requires_grad=False)
 
-    argskwargs = ArgsKwargs(args=(sent_ids_tensor, word_features, head_ids_tensor), kwargs={})
+    argskwargs = ArgsKwargs(
+        args=(sent_ids_tensor, word_features, head_ids_tensor), kwargs={}
+    )
     return argskwargs, backprop
 
 

spacy/pipeline/coref.py

@@ -6,6 +6,7 @@ from thinc.api import Model, Config, Optimizer
 from thinc.api import set_dropout_rate, to_categorical
 from itertools import islice
 from statistics import mean
+import srsly
 
 from .trainable_pipe import TrainablePipe
 from ..language import Language
@@ -13,7 +14,7 @@ from ..training import Example, validate_examples, validate_get_examples
 from ..errors import Errors
 from ..tokens import Doc
 from ..vocab import Vocab
-from ..util import registry
+from ..util import registry, from_disk, from_bytes
 
 from ..ml.models.coref_util import (
     create_gold_scores,
@@ -30,7 +31,6 @@ from ..scorer import Scorer
 default_config = """
 [model]
 @architectures = "spacy.Coref.v1"
-tok2vec_size = 768
 distance_embedding_size = 20
 hidden_size = 1024
 depth = 1
@@ -340,3 +340,57 @@ class CoreferenceResolver(TrainablePipe):
 
         assert len(X) > 0, Errors.E923.format(name=self.name)
         self.model.initialize(X=X, Y=Y)
+
+        # Store the input dimensionality. nI and nO are not stored explicitly
+        # for PyTorch models. This makes it tricky to reconstruct the model
+        # during deserialization. So, besides storing the labels, we also
+        # store the number of inputs.
+        coref_clusterer = self.model.get_ref("coref_clusterer")
+        self.cfg["nI"] = coref_clusterer.get_dim("nI")
+
+    def from_bytes(self, bytes_data, *, exclude=tuple()):
+        deserializers = {
+            "cfg": lambda b: self.cfg.update(srsly.json_loads(b)),
+            "vocab": lambda b: self.vocab.from_bytes(b, exclude=exclude),
+        }
+        from_bytes(bytes_data, deserializers, exclude)
+
+        self._initialize_from_disk()
+
+        model_deserializers = {
+            "model": lambda b: self.model.from_bytes(b),
+        }
+        from_bytes(bytes_data, model_deserializers, exclude)
+
+        return self
+
+    def from_disk(self, path, exclude=tuple()):
+        def load_model(p):
+            try:
+                with open(p, "rb") as mfile:
+                    self.model.from_bytes(mfile.read())
+            except AttributeError:
+                raise ValueError(Errors.E149) from None
+
+        deserializers = {
+            "cfg": lambda p: self.cfg.update(srsly.read_json(p)),
+            "vocab": lambda p: self.vocab.from_disk(p, exclude=exclude),
+        }
+        from_disk(path, deserializers, exclude)
+
+        self._initialize_from_disk()
+
+        model_deserializers = {
+            "model": load_model,
+        }
+        from_disk(path, model_deserializers, exclude)
+
+        return self
+
+    def _initialize_from_disk(self):
+        # The PyTorch model is constructed lazily, so we need to
+        # explicitly initialize the model before deserialization.
+        model = self.model.get_ref("coref_clusterer")
+        if model.has_dim("nI") is None:
+            model.set_dim("nI", self.cfg["nI"])
+        self.model.initialize()

spacy/pipeline/span_predictor.py

@@ -5,6 +5,7 @@ from thinc.types import Floats2d, Floats3d, Ints2d
 from thinc.api import Model, Config, Optimizer, CategoricalCrossentropy
 from thinc.api import set_dropout_rate, to_categorical
 from itertools import islice
+import srsly
 
 from .trainable_pipe import TrainablePipe
 from ..language import Language
@@ -13,7 +14,7 @@ from ..errors import Errors
 from ..scorer import Scorer, doc2clusters
 from ..tokens import Doc
 from ..vocab import Vocab
-from ..util import registry
+from ..util import registry, from_bytes, from_disk
 
 from ..ml.models.coref_util import (
     MentionClusters,
@@ -23,7 +24,6 @@ from ..ml.models.coref_util import (
 default_span_predictor_config = """
 [model]
 @architectures = "spacy.SpanPredictor.v1"
-tok2vec_size = 768
 hidden_size = 1024
 distance_embedding_size = 64
 conv_channels = 4
@@ -346,3 +346,57 @@ class SpanPredictor(TrainablePipe):
 
         assert len(X) > 0, Errors.E923.format(name=self.name)
         self.model.initialize(X=X, Y=Y)
+
+        # Store the input dimensionality. nI and nO are not stored explicitly
+        # for PyTorch models. This makes it tricky to reconstruct the model
+        # during deserialization. So, besides storing the labels, we also
+        # store the number of inputs.
+        span_predictor = self.model.get_ref("span_predictor")
+        self.cfg["nI"] = span_predictor.get_dim("nI")
+
+    def from_bytes(self, bytes_data, *, exclude=tuple()):
+        deserializers = {
+            "cfg": lambda b: self.cfg.update(srsly.json_loads(b)),
+            "vocab": lambda b: self.vocab.from_bytes(b, exclude=exclude),
+        }
+        from_bytes(bytes_data, deserializers, exclude)
+
+        self._initialize_from_disk()
+
+        model_deserializers = {
+            "model": lambda b: self.model.from_bytes(b),
+        }
+        from_bytes(bytes_data, model_deserializers, exclude)
+
+        return self
+
+    def from_disk(self, path, exclude=tuple()):
+        def load_model(p):
+            try:
+                with open(p, "rb") as mfile:
+                    self.model.from_bytes(mfile.read())
+            except AttributeError:
+                raise ValueError(Errors.E149) from None
+
+        deserializers = {
+            "cfg": lambda p: self.cfg.update(srsly.read_json(p)),
+            "vocab": lambda p: self.vocab.from_disk(p, exclude=exclude),
+        }
+        from_disk(path, deserializers, exclude)
+
+        self._initialize_from_disk()
+
+        model_deserializers = {
+            "model": load_model,
+        }
+        from_disk(path, model_deserializers, exclude)
+
+        return self
+
+    def _initialize_from_disk(self):
+        # The PyTorch model is constructed lazily, so we need to
+        # explicitly initialize the model before deserialization.
+        model = self.model.get_ref("span_predictor")
+        if model.has_dim("nI") is None:
+            model.set_dim("nI", self.cfg["nI"])
+        self.model.initialize()

spacy/tests/pipeline/test_coref.py

@@ -36,9 +36,6 @@ TRAIN_DATA = [
 # fmt: on
 
 
-CONFIG = {"model": {"@architectures": "spacy.Coref.v1", "tok2vec_size": 64}}
-
-
 @pytest.fixture
 def nlp():
     return English()
@@ -67,7 +64,7 @@ def test_not_initialized(nlp):
 
 @pytest.mark.skipif(not has_torch, reason="Torch not available")
 def test_initialized(nlp):
-    nlp.add_pipe("coref", config=CONFIG)
+    nlp.add_pipe("coref")
     nlp.initialize()
     assert nlp.pipe_names == ["coref"]
     text = "She gave me her pen."
@@ -79,7 +76,7 @@ def test_initialized(nlp):
 
 @pytest.mark.skipif(not has_torch, reason="Torch not available")
 def test_initialized_short(nlp):
-    nlp.add_pipe("coref", config=CONFIG)
+    nlp.add_pipe("coref")
     nlp.initialize()
     assert nlp.pipe_names == ["coref"]
     text = "Hi there"
@@ -89,7 +86,7 @@ def test_initialized_short(nlp):
 @pytest.mark.skipif(not has_torch, reason="Torch not available")
 def test_coref_serialization(nlp):
     # Test that the coref component can be serialized
-    nlp.add_pipe("coref", last=True, config=CONFIG)
+    nlp.add_pipe("coref", last=True)
     nlp.initialize()
     assert nlp.pipe_names == ["coref"]
     text = "She gave me her pen."
@@ -111,7 +108,7 @@ def test_overfitting_IO(nlp):
     for text, annot in TRAIN_DATA:
         train_examples.append(Example.from_dict(nlp.make_doc(text), annot))
 
-    nlp.add_pipe("coref", config=CONFIG)
+    nlp.add_pipe("coref")
     optimizer = nlp.initialize()
     test_text = TRAIN_DATA[0][0]
     doc = nlp(test_text)
@@ -166,7 +163,7 @@ def test_tokenization_mismatch(nlp):
 
         train_examples.append(eg)
 
-    nlp.add_pipe("coref", config=CONFIG)
+    nlp.add_pipe("coref")
     optimizer = nlp.initialize()
     test_text = TRAIN_DATA[0][0]
     doc = nlp(test_text)
@@ -228,7 +225,7 @@ def test_whitespace_mismatch(nlp):
         eg.predicted = nlp.make_doc("  " + text)
         train_examples.append(eg)
 
-    nlp.add_pipe("coref", config=CONFIG)
+    nlp.add_pipe("coref")
     optimizer = nlp.initialize()
     test_text = TRAIN_DATA[0][0]
     doc = nlp(test_text)

spacy/tests/pipeline/test_span_predictor.py

@@ -44,8 +44,6 @@ TRAIN_DATA = [
 ]
 # fmt: on
 
-CONFIG = {"model": {"@architectures": "spacy.SpanPredictor.v1", "tok2vec_size": 64}}
-
 
 @pytest.fixture
 def nlp():
@@ -76,7 +74,7 @@ def test_not_initialized(nlp):
 @pytest.mark.skipif(not has_torch, reason="Torch not available")
 def test_span_predictor_serialization(nlp):
     # Test that the span predictor component can be serialized
-    nlp.add_pipe("span_predictor", last=True, config=CONFIG)
+    nlp.add_pipe("span_predictor", last=True)
     nlp.initialize()
     assert nlp.pipe_names == ["span_predictor"]
     text = "She gave me her pen."
@@ -109,7 +107,7 @@ def test_overfitting_IO(nlp):
                 pred.spans[key] = [pred[span.start : span.end] for span in spans]
 
         train_examples.append(eg)
-    nlp.add_pipe("span_predictor", config=CONFIG)
+    nlp.add_pipe("span_predictor")
     optimizer = nlp.initialize()
     test_text = TRAIN_DATA[0][0]
     doc = nlp(test_text)
@@ -173,7 +171,7 @@ def test_tokenization_mismatch(nlp):
 
         train_examples.append(eg)
 
-    nlp.add_pipe("span_predictor", config=CONFIG)
+    nlp.add_pipe("span_predictor")
     optimizer = nlp.initialize()
     test_text = TRAIN_DATA[0][0]
     doc = nlp(test_text)
@@ -218,7 +216,7 @@ def test_whitespace_mismatch(nlp):
         eg.predicted = nlp.make_doc("  " + text)
         train_examples.append(eg)
 
-    nlp.add_pipe("span_predictor", config=CONFIG)
+    nlp.add_pipe("span_predictor")
     optimizer = nlp.initialize()
     test_text = TRAIN_DATA[0][0]
     doc = nlp(test_text)