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@ -86,7 +86,8 @@ see are: ​
| ~~Ragged~~ | A container to handle variable-length sequence data in an unpadded contiguous array. | | ~~Ragged~~ | A container to handle variable-length sequence data in an unpadded contiguous array. |
| ~~Padded~~ | A container to handle variable-length sequence data in a padded contiguous array. | | ~~Padded~~ | A container to handle variable-length sequence data in a padded contiguous array. |
The model type signatures help you figure out which model architectures and See the [Thinc type reference](https://thinc.ai/docs/api-types) for details. The
model type signatures help you figure out which model architectures and
components can **fit together**. For instance, the components can **fit together**. For instance, the
[`TextCategorizer`](/api/textcategorizer) class expects a model typed [`TextCategorizer`](/api/textcategorizer) class expects a model typed
~~Model[List[Doc], Floats2d]~~, because the model will predict one row of ~~Model[List[Doc], Floats2d]~~, because the model will predict one row of
@ -488,32 +489,57 @@ with Model.define_operators({">>": chain}):
In addition to [swapping out](#swap-architectures) default models in built-in In addition to [swapping out](#swap-architectures) default models in built-in
components, you can also implement an entirely new, components, you can also implement an entirely new,
[trainable pipeline component](/usage/processing-pipelines#trainable-components) [trainable](/usage/processing-pipelines#trainable-components) pipeline component
from scratch. This can be done by creating a new class inheriting from 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. [`Pipe`](/api/pipe), and linking it up to your custom model implementation.
### Example: Pipeline component for relation extraction {#component-rel} <Infobox title="Trainable component API" emoji="💡">
This section outlines an example use-case of implementing a novel relation For details on how to implement pipeline components, check out the usage guide
extraction component from scratch. We'll implement a binary relation extraction on [custom components](/usage/processing-pipelines#custom-component) and the
method that determines whether or not two entities in a document are related, overview of the `Pipe` methods used by
and if so, what type of relation. We'll allow multiple types of relations [trainable components](/usage/processing-pipelines#trainable-components).
between two such entities (multi-label setting).
There are two major steps required: first, we need to </Infobox>
[implement a machine learning model](#component-rel-model) specific to this
task, and subsequently we use this model to ### Example: Entity elation extraction component {#component-rel}
[implement a custom pipeline component](#component-rel-pipe).
This section outlines an example use-case of implementing a **novel relation
extraction component** from scratch. We'll implement a binary relation
extraction method that determines whether or not **two entities** in a document
are related, and if so, what type of relation. We'll allow multiple types of
relations between two such entities (multi-label setting). There are two major
steps required:
1. Implement a [machine learning model](#component-rel-model) specific to this
task. It will have to extract candidates from a [`Doc`](/api/doc) and predict
a relation for the available candidate pairs.
2. Implement a custom [pipeline component](#component-rel-pipe) powered by the
machine learning model that sets annotations on the [`Doc`](/api/doc) passing
through the pipeline.
<!-- TODO: <Project id="tutorials/ner-relations">
</Project> -->
#### Step 1: Implementing the Model {#component-rel-model} #### Step 1: Implementing the Model {#component-rel-model}
We need to implement a [`Model`](https://thinc.ai/docs/api-model) that takes a We need to implement a [`Model`](https://thinc.ai/docs/api-model) that takes a
list of documents as input, and outputs a two-dimensional matrix of predictions: **list of documents** (~~List[Doc]~~) as input, and outputs a **two-dimensional
matrix** (~~Floats2d~~) of predictions:
> #### Model type annotations
>
> The `Model` class is a generic type that can specify its input and output
> types, e.g. ~~Model[List[Doc], Floats2d]~~. Type hints are used for static
> type checks and validation. See the section on [type signatures](#type-sigs)
> for details.
```python ```python
### Register the model architecture
@registry.architectures.register("rel_model.v1") @registry.architectures.register("rel_model.v1")
def create_relation_model(...) -> Model[List[Doc], Floats2d]: def create_relation_model(...) -> Model[List[Doc], Floats2d]:
model = _create_my_model() model = ... # 👈 model will go here
return model return model
``` ```
@ -521,17 +547,18 @@ The first layer in this model will typically be an
[embedding layer](/usage/embeddings-transformers) such as a [embedding layer](/usage/embeddings-transformers) such as a
[`Tok2Vec`](/api/tok2vec) component or a [`Transformer`](/api/transformer). This [`Tok2Vec`](/api/tok2vec) component or a [`Transformer`](/api/transformer). This
layer is assumed to be of type ~~Model[List[Doc], List[Floats2d]]~~ as it 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 transforms each **document into a list of tokens**, with each token being
represented by its embedding in the vector space. represented by its embedding in the vector space.
Next, we need a method that generates pairs of entities that we want to classify Next, we need a method that **generates pairs of entities** that we want to
as being related or not. As these candidate pairs are typically formed within classify as being related or not. As these candidate pairs are typically formed
one document, this function takes a `Doc` as input and outputs a `List` of within one document, this function takes a [`Doc`](/api/doc) as input and
`Span` tuples. For instance, a very straightforward implementation would be to outputs a `List` of `Span` tuples. For instance, a very straightforward
just take any two entities from the same document: implementation would be to just take any two entities from the same document:
```python ```python
def get_candidates(doc: "Doc") -> List[Tuple[Span, Span]]: ### Simple candiate generation
def get_candidates(doc: Doc) -> List[Tuple[Span, Span]]:
candidates = [] candidates = []
for ent1 in doc.ents: for ent1 in doc.ents:
for ent2 in doc.ents: for ent2 in doc.ents:
@ -539,27 +566,29 @@ def get_candidates(doc: "Doc") -> List[Tuple[Span, Span]]:
return candidates return candidates
``` ```
> ``` But we could also refine this further by **excluding relations** of an entity
> [model] with itself, and posing a **maximum distance** (in number of tokens) between two
> @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 entities. We register this function in the
[`@misc` registry](/api/top-level#registry) so we can refer to it from 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. config, and easily swap it out for any other candidate generation function.
> #### config.cfg (excerpt)
>
> ```ini
> [model]
> @architectures = "rel_model.v1"
>
> [model.tok2vec]
> # ...
>
> [model.get_candidates]
> @misc = "rel_cand_generator.v1"
> max_length = 20
> ```
```python ```python
### {highlight="1,2,7,8"} ### Extended candidate generation {highlight="1,2,7,8"}
@registry.misc.register("rel_cand_generator.v2") @registry.misc.register("rel_cand_generator.v1")
def create_candidate_indices(max_length: int) -> Callable[[Doc], List[Tuple[Span, Span]]]: def create_candidate_indices(max_length: int) -> Callable[[Doc], List[Tuple[Span, Span]]]:
def get_candidates(doc: "Doc") -> List[Tuple[Span, Span]]: def get_candidates(doc: "Doc") -> List[Tuple[Span, Span]]:
candidates = [] candidates = []
@ -573,17 +602,19 @@ def create_candidate_indices(max_length: int) -> Callable[[Doc], List[Tuple[Span
``` ```
Finally, we require a method that transforms the candidate entity pairs into a Finally, we require a method that transforms the candidate entity pairs into a
2D tensor using the specified `Tok2Vec` function. The resulting `Floats2d` 2D tensor using the specified [`Tok2Vec`](/api/tok2vec) or
object will then be processed by a final `output_layer` of the network. Putting [`Transformer`](/api/transformer). The resulting ~~Floats2~~ object will then be
all this together, we can define our relation model in a config file as such: 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:
``` ```ini
### config.cfg
[model] [model]
@architectures = "rel_model.v1" @architectures = "rel_model.v1"
... # ...
[model.tok2vec] [model.tok2vec]
... # ...
[model.get_candidates] [model.get_candidates]
@misc = "rel_cand_generator.v2" @misc = "rel_cand_generator.v2"
@ -594,10 +625,11 @@ max_length = 20
[model.output_layer] [model.output_layer]
@architectures = "rel_output_layer.v1" @architectures = "rel_output_layer.v1"
... # ...
``` ```
<!-- TODO: Link to project for implementation details --> <!-- TODO: link to project for implementation details -->
<!-- TODO: maybe embed files from project that show the architectures? -->
When creating this model, we store the custom functions as When creating this model, we store the custom functions as
[attributes](https://thinc.ai/docs/api-model#properties) and the sublayers as [attributes](https://thinc.ai/docs/api-model#properties) and the sublayers as
@ -612,40 +644,55 @@ get_candidates = model.attrs["get_candidates"]
#### Step 2: Implementing the pipeline component {#component-rel-pipe} #### Step 2: Implementing the pipeline component {#component-rel-pipe}
To use our new relation extraction model as part of a custom component, we To use our new relation extraction model as part of a custom
[trainable component](/usage/processing-pipelines#trainable-components), we
create a subclass of [`Pipe`](/api/pipe) that holds the model: create a subclass of [`Pipe`](/api/pipe) that holds the model:
```python ```python
### Pipeline component skeleton
from spacy.pipeline import Pipe from spacy.pipeline import Pipe
class RelationExtractor(Pipe): class RelationExtractor(Pipe):
def __init__(self, vocab, model, name="rel", labels=[]): def __init__(self, vocab, model, name="rel"):
"""Create a component instance."""
self.model = model self.model = model
... self.vocab = vocab
self.name = name
def update(self, examples, ...): def update(self, examples, drop=0.0, set_annotations=False, sgd=None, losses=None):
"""Learn from a batch of Example objects."""
... ...
def predict(self, docs): def predict(self, docs):
"""Apply the model to a batch of Doc objects."""
... ...
def set_annotations(self, docs, predictions): def set_annotations(self, docs, predictions):
"""Modify a batch of Doc objects using the predictions."""
... ...
def initialize(self, get_examples, nlp=None, labels=None):
"""Initialize the model before training."""
...
def add_label(self, label):
"""Add a label to the component."""
...
``` ```
Before the model can be used, it needs to be Before the model can be used, it needs to be
[initialized](/api/pipe#initialize). This function receives either the full [initialized](/usage/training#initialization). This function receives a callback
training data set, or a representative sample. This data set can be used to to access the full **training data set**, or a representative sample. This data
deduce all relevant labels. Alternatively, a list of labels can be provided, or set can be used to deduce all **relevant labels**. Alternatively, a list of
a script can call `rel_component.add_label()` directly. labels can be provided to `initialize`, or you can call the
`RelationExtractoradd_label` directly. The number of labels defines the output
The number of labels defines the output dimensionality of the network, and will dimensionality of the network, and will be used to do
be used to do [shape inference](https://thinc.ai/docs/usage-models#validation) [shape inference](https://thinc.ai/docs/usage-models#validation) throughout the
throughout the layers of the neural network. This is triggered by calling layers of the neural network. This is triggered by calling
`model.initialize`. [`Model.initialize`](https://thinc.ai/api/model#initialize).
```python ```python
### {highlight="12,18,22"} ### The initialize method {highlight="12,18,22"}
from itertools import islice from itertools import islice
def initialize( def initialize(
@ -671,19 +718,22 @@ def initialize(
``` ```
The `initialize` method is triggered whenever this component is part of an `nlp` The `initialize` method is triggered whenever this component is part of an `nlp`
pipeline, and [`nlp.initialize()`](/api/language#initialize) is invoked. After pipeline, and [`nlp.initialize`](/api/language#initialize) is invoked.
doing so, the pipeline component and its internal model can be trained and used Typically, this happens when the pipeline is set up before training in
to make predictions. [`spacy train`](/api/cli#training). After initialization, 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 During training, the function [`update`](/api/pipe#update) is invoked which
delegates to delegates to
[`self.model.begin_update`](https://thinc.ai/docs/api-model#begin_update) and a [`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 [`get_loss`](/api/pipe#get_loss) function that **calculate the loss** for a
examples, as well as the gradient of loss that will be used to update the batch of examples, as well as the **gradient** of loss that will be used to
weights of the model layers. update the weights of the model layers. Thinc provides several
[loss functions](https://thinc.ai/docs/api-loss) that can be used for the
implementation of the `get_loss` function.
```python ```python
### {highlight="12-14"} ### The update method {highlight="12-14"}
def update( def update(
self, self,
examples: Iterable[Example], examples: Iterable[Example],
@ -703,15 +753,14 @@ def update(
return losses 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 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 **predictions**. The [`predict`](/api/pipe#predict) function needs to be
for each subclass of `Pipe`. In our case, we can simply delegate to the internal implemented for each subclass of `Pipe`. In our case, we can simply delegate to
model's [predict](https://thinc.ai/docs/api-model#predict) function: the internal model's [predict](https://thinc.ai/docs/api-model#predict) function
that takes a batch of `Doc` objects and returns a ~~Floats2d~~ array:
```python ```python
### The predict method
def predict(self, docs: Iterable[Doc]) -> Floats2d: def predict(self, docs: Iterable[Doc]) -> Floats2d:
predictions = self.model.predict(docs) predictions = self.model.predict(docs)
return self.model.ops.asarray(predictions) return self.model.ops.asarray(predictions)
@ -721,32 +770,36 @@ The final method that needs to be implemented, is
[`set_annotations`](/api/pipe#set_annotations). This function takes the [`set_annotations`](/api/pipe#set_annotations). This function takes the
predictions, and modifies the given `Doc` object in place to store them. For our 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 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 [extension attribute](/usage/processing-pipelines#custom-components-attributes)
start offsets of each entity, as this defines an entity pair uniquely within one `doc._.rel`. As keys, we represent the candidate pair by the **start offsets of
document. 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 interpret the scores predicted by the relation extraction model correctly, we
to the model's `get_candidates` function that defined which pairs of entities need to refer to the model's `get_candidates` function that defined which pairs
were relevant candidates, so that the predictions can be linked to those exact of entities were relevant candidates, so that the predictions can be linked to
entities: those exact entities:
> #### Example output > #### Example output
> >
> ```python > ```python
> doc = nlp("Amsterdam is the capital of the Netherlands.") > doc = nlp("Amsterdam is the capital of the Netherlands.")
> print(f"spans: [(e.start, e.text, e.label_) for e in doc.ents]") > print("spans", [(e.start, e.text, e.label_) for e in doc.ents])
> for value, rel_dict in doc._.rel.items(): > for value, rel_dict in doc._.rel.items():
> print(f"{value}: {rel_dict}") > 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}
> spans [(0, 'Amsterdam', 'LOC'), (6, 'Netherlands', 'LOC')] > # (6, 0): {'CAPITAL_OF': 0.01, 'LOCATED_IN': 0.13, 'UNRELATED': 0.017}
> (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 ```python
### {highlight="5-6,10"} ### Registering the extension attribute
from spacy.tokens import Doc
Doc.set_extension("rel", default={})
```
```python
### The set_annotations method {highlight="5-6,10"}
def set_annotations(self, docs: Iterable[Doc], predictions: Floats2d): def set_annotations(self, docs: Iterable[Doc], predictions: Floats2d):
c = 0 c = 0
get_candidates = self.model.attrs["get_candidates"] get_candidates = self.model.attrs["get_candidates"]
@ -761,9 +814,10 @@ def set_annotations(self, docs: Iterable[Doc], predictions: Floats2d):
``` ```
Under the hood, when the pipe is applied to a document, it delegates to the Under the hood, when the pipe is applied to a document, it delegates to the
`predict` and `set_annotations` functions: `predict` and `set_annotations` methods:
```python ```python
### The __call__ method
def __call__(self, Doc doc): def __call__(self, Doc doc):
predictions = self.predict([doc]) predictions = self.predict([doc])
self.set_annotations([doc], predictions) self.set_annotations([doc], predictions)
@ -771,29 +825,38 @@ def __call__(self, Doc doc):
``` ```
Once our `Pipe` subclass is fully implemented, we can Once our `Pipe` subclass is fully implemented, we can
[register](http://localhost:8000/usage/processing-pipelines#custom-components-factories) [register](/usage/processing-pipelines#custom-components-factories) the
the component with the `Language.factory` decorator. This enables the creation component with the [`@Language.factory`](/api/lnguage#factory) decorator. This
of the component with `nlp.add_pipe`, or via the config. assigns it a name and lets you create the component with
[`nlp.add_pipe`](/api/language#add_pipe) and via the
[config](/usage/training#config).
> ``` > #### config.cfg (excerpt)
> >
> ```ini
> [components.relation_extractor] > [components.relation_extractor]
> factory = "relation_extractor" > factory = "relation_extractor"
> labels = []
> >
> [components.relation_extractor.model] > [components.relation_extractor.model]
> @architectures = "rel_model.v1" > @architectures = "rel_model.v1"
> ... >
> [components.relation_extractor.model.tok2vec]
> # ...
>
> [components.relation_extractor.model.get_candidates]
> @misc = "rel_cand_generator.v1"
> max_length = 20
> ``` > ```
```python ```python
### Registering the pipeline component
from spacy.language import Language from spacy.language import Language
@Language.factory("relation_extractor") @Language.factory("relation_extractor")
def make_relation_extractor(nlp, name, model, labels): def make_relation_extractor(nlp, name, model):
return RelationExtractor(nlp.vocab, model, name, labels=labels) return RelationExtractor(nlp.vocab, model, name)
``` ```
<!-- TODO: refer once more to example project --> <!-- TODO: <Project id="tutorials/ner-relations">
<!-- ![Diagram of a pipeline component with its model](../images/layers-architectures.svg) --> </Project> -->