diff --git a/website/docs/api/pipe.md b/website/docs/api/pipe.md index 4f5ac6f61..de35f9eb4 100644 --- a/website/docs/api/pipe.md +++ b/website/docs/api/pipe.md @@ -226,6 +226,12 @@ the "catastrophic forgetting" problem. This feature is experimental. Find the loss and gradient of loss for the batch of documents and their predicted scores. + + +This method needs to be overwritten with your own custom `get_loss` method. + + + > #### Example > > ```python diff --git a/website/docs/usage/layers-architectures.md b/website/docs/usage/layers-architectures.md index b65c3d903..414562d6d 100644 --- a/website/docs/usage/layers-architectures.md +++ b/website/docs/usage/layers-architectures.md @@ -288,7 +288,7 @@ those parts of the network. To use our custom model including the PyTorch subnetwork, all we need to do is register the architecture using the -[`architectures` registry](/api/top-level#registry). This will assign the +[`architectures` registry](/api/top-level#registry). This assigns the architecture a name so spaCy knows how to find it, and allows passing in arguments like hyperparameters via the [config](/usage/training#config). The full example then becomes: @@ -373,7 +373,7 @@ gpu_allocator = "pytorch" Of course it's also possible to define the `Model` from the previous section entirely in Thinc. The Thinc documentation provides details on the [various layers](https://thinc.ai/docs/api-layers) and helper functions -available. Combinators can also be used to +available. Combinators can be used to [overload operators](https://thinc.ai/docs/usage-models#operators) and a common usage pattern is to bind `chain` to `>>`. The "native" Thinc version of our simple neural network would then become: @@ -486,28 +486,314 @@ with Model.define_operators({">>": chain}): ## Create new trainable components {#components} - - +In addition to [swapping out](#swap-architectures) default models in built-in +components, you can also implement an entirely new, +[trainable pipeline component](/usage/processing-pipelines#trainable-components) +from scratch. This can be done by creating a new class inheriting from +[`Pipe`](/api/pipe), and linking it up to your custom model implementation. - +### Example: Pipeline component for relation extraction {#component-rel} - + +The first layer in this model will typically be an +[embedding layer](/usage/embeddings-transformers) such as a +[`Tok2Vec`](/api/tok2vec) component or a [`Transformer`](/api/transformer). This +layer is assumed to be of type ~~Model[List[Doc], List[Floats2d]]~~ as it +transforms each document into a list of tokens, with each token being +represented by its embedding in the vector space. + +Next, we need a method that generates pairs of entities that we want to classify +as being related or not. As these candidate pairs are typically formed within +one document, this function takes a `Doc` as input and outputs a `List` of +`Span` tuples. For instance, a very straightforward implementation would be to +just take any two entities from the same document: + +```python +def get_candidates(doc: "Doc") -> List[Tuple[Span, Span]]: + candidates = [] + for ent1 in doc.ents: + for ent2 in doc.ents: + candidates.append((ent1, ent2)) + return candidates +``` + +> ``` +> [model] +> @architectures = "rel_model.v1" +> +> [model.tok2vec] +> ... +> +> [model.get_candidates] +> @misc = "rel_cand_generator.v2" +> max_length = 20 +> ``` + +But we could also refine this further by excluding relations of an entity with +itself, and posing a maximum distance (in number of tokens) between two +entities. We register this function in the +[`@misc` registry](/api/top-level#registry) so we can refer to it from the +config, and easily swap it out for any other candidate generation function. + +```python +### {highlight="1,2,7,8"} +@registry.misc.register("rel_cand_generator.v2") +def create_candidate_indices(max_length: int) -> Callable[[Doc], List[Tuple[Span, Span]]]: + def get_candidates(doc: "Doc") -> List[Tuple[Span, Span]]: + candidates = [] + for ent1 in doc.ents: + for ent2 in doc.ents: + if ent1 != ent2: + if max_length and abs(ent2.start - ent1.start) <= max_length: + candidates.append((ent1, ent2)) + return candidates + return get_candidates +``` + +Finally, we require a method that transforms the candidate entity pairs into a +2D tensor using the specified `Tok2Vec` function. The resulting `Floats2d` +object will then be processed by a final `output_layer` of the network. Putting +all this together, we can define our relation model in a config file as such: + +``` +[model] +@architectures = "rel_model.v1" +... + +[model.tok2vec] +... + +[model.get_candidates] +@misc = "rel_cand_generator.v2" +max_length = 20 + +[model.create_candidate_tensor] +@misc = "rel_cand_tensor.v1" + +[model.output_layer] +@architectures = "rel_output_layer.v1" +... +``` + + + +When creating this model, we store the custom functions as +[attributes](https://thinc.ai/docs/api-model#properties) and the sublayers as +references, so we can access them easily: + +```python +tok2vec_layer = model.get_ref("tok2vec") +output_layer = model.get_ref("output_layer") +create_candidate_tensor = model.attrs["create_candidate_tensor"] +get_candidates = model.attrs["get_candidates"] +``` + +#### Step 2: Implementing the pipeline component {#component-rel-pipe} + +To use our new relation extraction model as part of a custom component, we +create a subclass of [`Pipe`](/api/pipe) that holds the model: + +```python +from spacy.pipeline import Pipe + +class RelationExtractor(Pipe): + def __init__(self, vocab, model, name="rel", labels=[]): + self.model = model + ... + + def update(self, examples, ...): + ... + + def predict(self, docs): + ... + + def set_annotations(self, docs, predictions): + ... +``` + +Before the model can be used, it needs to be +[initialized](/api/pipe#initialize). This function receives either the full +training data set, or a representative sample. This data set can be used to +deduce all relevant labels. Alternatively, a list of labels can be provided, or +a script can call `rel_component.add_label()` directly. + +The number of labels defines the output dimensionality of the network, and will +be used to do [shape inference](https://thinc.ai/docs/usage-models#validation) +throughout the layers of the neural network. This is triggered by calling +`model.initialize`. + +```python +### {highlight="12,18,22"} +from itertools import islice + +def initialize( + self, + get_examples: Callable[[], Iterable[Example]], + *, + nlp: Language = None, + labels: Optional[List[str]] = None, +): + if labels is not None: + for label in labels: + self.add_label(label) + else: + for example in get_examples(): + relations = example.reference._.rel + for indices, label_dict in relations.items(): + for label in label_dict.keys(): + self.add_label(label) + subbatch = list(islice(get_examples(), 10)) + doc_sample = [eg.reference for eg in subbatch] + label_sample = self._examples_to_truth(subbatch) + self.model.initialize(X=doc_sample, Y=label_sample) +``` + +The `initialize` method is triggered whenever this component is part of an `nlp` +pipeline, and [`nlp.initialize()`](/api/language#initialize) is invoked. After +doing so, the pipeline component and its internal model can be trained and used +to make predictions. + +During training, the function [`update`](/api/pipe#update) is invoked which +delegates to +[`self.model.begin_update`](https://thinc.ai/docs/api-model#begin_update) and a +[`get_loss`](/api/pipe#get_loss) function that calculate the loss for a batch of +examples, as well as the gradient of loss that will be used to update the +weights of the model layers. + +```python +### {highlight="12-14"} +def update( + self, + examples: Iterable[Example], + *, + drop: float = 0.0, + set_annotations: bool = False, + sgd: Optional[Optimizer] = None, + losses: Optional[Dict[str, float]] = None, +) -> Dict[str, float]: + ... + docs = [ex.predicted for ex in examples] + predictions, backprop = self.model.begin_update(docs) + loss, gradient = self.get_loss(examples, predictions) + backprop(gradient) + losses[self.name] += loss + ... + return losses +``` + +Thinc provides several [loss functions](https://thinc.ai/docs/api-loss) that can +be used for the implementation of the `get_loss` function. + +When the internal model is trained, the component can be used to make novel +predictions. The [`predict`](/api/pipe#predict) function needs to be implemented +for each subclass of `Pipe`. In our case, we can simply delegate to the internal +model's [predict](https://thinc.ai/docs/api-model#predict) function: + +```python +def predict(self, docs: Iterable[Doc]) -> Floats2d: + predictions = self.model.predict(docs) + return self.model.ops.asarray(predictions) +``` + +The final method that needs to be implemented, is +[`set_annotations`](/api/pipe#set_annotations). This function takes the +predictions, and modifies the given `Doc` object in place to store them. For our +relation extraction component, we store the data as a dictionary in a custom +extension attribute `doc._.rel`. As keys, we represent the candidate pair by the +start offsets of each entity, as this defines an entity pair uniquely within one +document. + +To interpret the scores predicted by the REL model correctly, we need to refer +to the model's `get_candidates` function that defined which pairs of entities +were relevant candidates, so that the predictions can be linked to those exact +entities: + +> #### Example output +> +> ```python +> doc = nlp("Amsterdam is the capital of the Netherlands.") +> print(f"spans: [(e.start, e.text, e.label_) for e in doc.ents]") +> for value, rel_dict in doc._.rel.items(): +> print(f"{value}: {rel_dict}") +> ``` + +> ``` +> spans [(0, 'Amsterdam', 'LOC'), (6, 'Netherlands', 'LOC')] +> (0, 6): {'CAPITAL_OF': 0.89, 'LOCATED_IN': 0.75, 'UNRELATED': 0.002} +> (6, 0): {'CAPITAL_OF': 0.01, 'LOCATED_IN': 0.13, 'UNRELATED': 0.017} +> ``` + +```python +### {highlight="5-6,10"} +def set_annotations(self, docs: Iterable[Doc], predictions: Floats2d): + c = 0 + get_candidates = self.model.attrs["get_candidates"] + for doc in docs: + for (e1, e2) in get_candidates(doc): + offset = (e1.start, e2.start) + if offset not in doc._.rel: + doc._.rel[offset] = {} + for j, label in enumerate(self.labels): + doc._.rel[offset][label] = predictions[c, j] + c += 1 +``` + +Under the hood, when the pipe is applied to a document, it delegates to the +`predict` and `set_annotations` functions: + +```python +def __call__(self, Doc doc): + predictions = self.predict([doc]) + self.set_annotations([doc], predictions) + return doc +``` + +Once our `Pipe` subclass is fully implemented, we can +[register](http://localhost:8000/usage/processing-pipelines#custom-components-factories) +the component with the `Language.factory` decorator. This enables the creation +of the component with `nlp.add_pipe`, or via the config. + +> ``` +> +> [components.relation_extractor] +> factory = "relation_extractor" +> labels = [] +> +> [components.relation_extractor.model] +> @architectures = "rel_model.v1" +> ... +> ``` + +```python +from spacy.language import Language + +@Language.factory("relation_extractor") +def make_relation_extractor(nlp, name, model, labels): + return RelationExtractor(nlp.vocab, model, name, labels=labels) +``` + + + + diff --git a/website/docs/usage/processing-pipelines.md b/website/docs/usage/processing-pipelines.md index 3d0c7b7e9..c8224dfc9 100644 --- a/website/docs/usage/processing-pipelines.md +++ b/website/docs/usage/processing-pipelines.md @@ -1176,7 +1176,7 @@ plug fully custom machine learning components into your pipeline. You'll need the following: 1. **Model:** A Thinc [`Model`](https://thinc.ai/docs/api-model) instance. This - can be a model using implemented in + can be a model implemented in [Thinc](/usage/layers-architectures#thinc), or a [wrapped model](/usage/layers-architectures#frameworks) implemented in PyTorch, TensorFlow, MXNet or a fully custom solution. The model must take a