spaCy/website/docs/api/entitylinker.mdx
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* Convert Candidate from Cython to Python class.

* Format.

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* Change type for mentions to look up entity candidates for to SpanGroup from Iterable[Span].

* Update docs.

* Update spacy/kb/candidate.py

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* Update doc string of BaseCandidate.__init__().

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* Rename Candidate to InMemoryCandidate, BaseCandidate to Candidate.

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* Rename alias -> mention.

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* Rename 'alias' to 'mention'.

* Port Candidate and InMemoryCandidate to Cython.

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* Fix entity_id refactoring problems in docstrings.

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* Update docstrings.

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* Partially fix alias/mention terminology usage. Convert Candidate to interface.

* Remove prior_prob from supported properties in Candidate. Introduce KnowledgeBase.supports_prior_probs().

* Update docstrings related to prior_prob.

* Update alias/mention usage in doc(strings).

* Update spacy/ml/models/entity_linker.py

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* Update spacy/ml/models/entity_linker.py

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* Mention -> alias renaming. Drop Candidate.mentions(). Drop InMemoryLookupKB.get_alias_candidates() from docs.

* Update docstrings.

* Fix InMemoryCandidate attribute names.

* Update spacy/kb/kb.pyx

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* Update spacy/ml/models/entity_linker.py

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* Update W401 test.

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* Use Candidate output type for toy generators in the test suite to mimick best practices

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* Update spacy/kb/kb.pyx

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* Update website/docs/api/entitylinker.mdx

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* Update get_candidates() docstring.

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* Update factory functions for backwards compatibility.

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Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com>
Co-authored-by: svlandeg <svlandeg@github.com>
2024-04-09 11:39:18 +02:00

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---
title: EntityLinker
tag: class
source: spacy/pipeline/entity_linker.py
version: 2.2
teaser: 'Pipeline component for named entity linking and disambiguation'
api_base_class: /api/pipe
api_string_name: entity_linker
api_trainable: true
---
An `EntityLinker` component disambiguates textual mentions (tagged as named
entities) to unique identifiers, grounding the named entities into the "real
world". It requires a `KnowledgeBase`, as well as a function to generate
plausible candidates from that `KnowledgeBase` given a certain textual mention,
and a machine learning model to pick the right candidate, given the local
context of the mention. `EntityLinker` defaults to using the
[`InMemoryLookupKB`](/api/inmemorylookupkb) implementation.
## Assigned Attributes {id="assigned-attributes"}
Predictions, in the form of knowledge base IDs, will be assigned to
`Token.ent_kb_id_`.
| Location | Value |
| ------------------ | --------------------------------- |
| `Token.ent_kb_id` | Knowledge base ID (hash). ~~int~~ |
| `Token.ent_kb_id_` | Knowledge base ID. ~~str~~ |
## Config and implementation {id="config"}
The default config is defined by the pipeline component factory and describes
how the component should be configured. You can override its settings via the
`config` argument on [`nlp.add_pipe`](/api/language#add_pipe) or in your
[`config.cfg` for training](/usage/training#config). See the
[model architectures](/api/architectures) documentation for details on the
architectures and their arguments and hyperparameters.
> #### Example
>
> ```python
> from spacy.pipeline.entity_linker import DEFAULT_NEL_MODEL
> config = {
> "labels_discard": [],
> "n_sents": 0,
> "incl_prior": True,
> "incl_context": True,
> "model": DEFAULT_NEL_MODEL,
> "entity_vector_length": 64,
> "get_candidates": {'@misc': 'spacy.CandidateGenerator.v2'},
> "threshold": None,
> }
> nlp.add_pipe("entity_linker", config=config)
> ```
| Setting | Description |
| ------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `labels_discard` | NER labels that will automatically get an "NIL" prediction. Defaults to `[]`. ~~Iterable[str]~~ |
| `n_sents` | The number of neighbouring sentences to take into account. Defaults to `0`. ~~int~~ |
| `incl_prior` | Whether prior probabilities from the KB are included in the model. Defaults to `True`. ~~bool~~ |
| `incl_context` | Whether the local context is included in the model. Defaults to `True`. ~~bool~~ |
| `model` | The [`Model`](https://thinc.ai/docs/api-model) powering the pipeline component. Defaults to [`EntityLinker`](/api/architectures#EntityLinker). ~~Model~~ |
| `entity_vector_length` | Size of encoding vectors in the KB. Defaults to `64`. ~~int~~ |
| `use_gold_ents` | Whether entities are copied from the gold docs. Defaults to `True`. If `False`, entities must be set in the training data or by an annotating component in the pipeline. ~~int~~ |
| `get_candidates` <Tag variant="new">4.0</Tag> | Function that retrieves plausible candidates per entity mention in a given `Iterator[SpanGroup]` (one `SpanGroup` includes all mentions found in a given `Doc` instance). Defaults to [CandidateGenerator](/api/architectures#CandidateGenerator). ~~Callable[[KnowledgeBase, Iterator[SpanGroup]], Iterator[Iterable[Iterable[Candidate]]]]~~ |
| `generate_empty_kb` <Tag variant="new">3.6</Tag> | Function that generates an empty `KnowledgeBase` object. Defaults to [`spacy.EmptyKB.v2`](/api/architectures#EmptyKB), which generates an empty [`InMemoryLookupKB`](/api/inmemorylookupkb). ~~Callable[[Vocab, int], KnowledgeBase]~~ |
| `overwrite` <Tag variant="new">3.2</Tag> | Whether existing annotation is overwritten. Defaults to `True`. ~~bool~~ |
| `scorer` <Tag variant="new">3.2</Tag> | The scoring method. Defaults to [`Scorer.score_links`](/api/scorer#score_links). ~~Optional[Callable]~~ |
| `save_activations` <Tag variant="new">4.0</Tag> | Save activations in `Doc` when annotating. Saved activations are `"ents"` and `"scores"`. ~~Union[bool, list[str]]~~ |
| `threshold` <Tag variant="new">3.4</Tag> | Confidence threshold for entity predictions. The default of `None` implies that all predictions are accepted, otherwise those with a score beneath the treshold are discarded. If there are no predictions with scores above the threshold, the linked entity is `NIL`. ~~Optional[float]~~ |
<Infobox variant="warning">
Prior to spaCy v4.0 `get_candidates()` returns a single `Iterable` of candidates
for one specific mention, i. e. the function was typed as
`Callable[[KnowledgeBase, Span], Iterable[Candidate]]`. To retrieve candidates
batch-wise, spaCy >= 3.5 exposes `get_candidates_batched()`, which identifies
candidates for an arbitrary number of spans:
`Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]]`. The
main difference between `get_candidates_batched()` and `get_candidates()` in
spaCy >= 4.0 is that the latter considers the grouping of provided mention spans
per `Doc` instance.
</Infobox>
```python
%%GITHUB_SPACY/spacy/pipeline/entity_linker.py
```
## EntityLinker.\_\_init\_\_ {id="init",tag="method"}
> #### Example
>
> ```python
> # Construction via add_pipe with default model
> entity_linker = nlp.add_pipe("entity_linker")
>
> # Construction via add_pipe with custom model
> config = {"model": {"@architectures": "my_el.v1"}}
> entity_linker = nlp.add_pipe("entity_linker", config=config)
>
> # Construction from class
> from spacy.pipeline import EntityLinker
> entity_linker = EntityLinker(nlp.vocab, model)
> ```
Create a new pipeline instance. In your application, you would normally use a
shortcut for this and instantiate the component using its string name and
[`nlp.add_pipe`](/api/language#add_pipe).
Upon construction of the entity linker component, an empty knowledge base is
constructed with the provided `entity_vector_length`. If you want to use a
custom knowledge base, you should either call
[`set_kb`](/api/entitylinker#set_kb) or provide a `kb_loader` in the
[`initialize`](/api/entitylinker#initialize) call.
| Name | Description |
| ---------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `vocab` | The shared vocabulary. ~~Vocab~~ |
| `model` | The [`Model`](https://thinc.ai/docs/api-model) powering the pipeline component. ~~Model~~ |
| `name` | String name of the component instance. Used to add entries to the `losses` during training. ~~str~~ |
| _keyword-only_ | |
| `entity_vector_length` | Size of encoding vectors in the KB. ~~int~~ |
| `get_candidates` | Function that retrieves plausible candidates per entity mention in a given `SpanGroup`. Defaults to [CandidateGenerator](/api/architectures#CandidateGenerator). ~~Callable[[KnowledgeBase, Iterator[SpanGroup]], Iterator[Iterable[Iterable[Candidate]]]]~~ |
| `labels_discard` | NER labels that will automatically get a `"NIL"` prediction. ~~Iterable[str]~~ |
| `n_sents` | The number of neighbouring sentences to take into account. ~~int~~ |
| `incl_prior` | Whether or not to include prior probabilities from the KB in the model. ~~bool~~ |
| `incl_context` | Whether or not to include the local context in the model. ~~bool~~ |
| `overwrite` <Tag variant="new">3.2</Tag> | Whether existing annotation is overwritten. Defaults to `True`. ~~bool~~ |
| `scorer` <Tag variant="new">3.2</Tag> | The scoring method. Defaults to [`Scorer.score_links`](/api/scorer#score_links). ~~Optional[Callable]~~ |
| `threshold` <Tag variant="new">3.4</Tag> | Confidence threshold for entity predictions. The default of `None` implies that all predictions are accepted, otherwise those with a score beneath the treshold are discarded. If there are no predictions with scores above the threshold, the linked entity is `NIL`. ~~Optional[float]~~ |
## EntityLinker.\_\_call\_\_ {id="call",tag="method"}
Apply the pipe to one document. The document is modified in place and returned.
This usually happens under the hood when the `nlp` object is called on a text
and all pipeline components are applied to the `Doc` in order. Both
[`__call__`](/api/entitylinker#call) and [`pipe`](/api/entitylinker#pipe)
delegate to the [`predict`](/api/entitylinker#predict) and
[`set_annotations`](/api/entitylinker#set_annotations) methods.
> #### Example
>
> ```python
> doc = nlp("This is a sentence.")
> entity_linker = nlp.add_pipe("entity_linker")
> # This usually happens under the hood
> processed = entity_linker(doc)
> ```
| Name | Description |
| ----------- | -------------------------------- |
| `doc` | The document to process. ~~Doc~~ |
| **RETURNS** | The processed document. ~~Doc~~ |
## EntityLinker.pipe {id="pipe",tag="method"}
Apply the pipe to a stream of documents. This usually happens under the hood
when the `nlp` object is called on a text and all pipeline components are
applied to the `Doc` in order. Both [`__call__`](/api/entitylinker#call) and
[`pipe`](/api/entitylinker#pipe) delegate to the
[`predict`](/api/entitylinker#predict) and
[`set_annotations`](/api/entitylinker#set_annotations) methods.
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> for doc in entity_linker.pipe(docs, batch_size=50):
> pass
> ```
| Name | Description |
| -------------- | ------------------------------------------------------------- |
| `stream` | A stream of documents. ~~Iterable[Doc]~~ |
| _keyword-only_ | |
| `batch_size` | The number of documents to buffer. Defaults to `128`. ~~int~~ |
| **YIELDS** | The processed documents in order. ~~Doc~~ |
## EntityLinker.set_kb {id="set_kb",tag="method",version="3"}
The `kb_loader` should be a function that takes a `Vocab` instance and creates
the `KnowledgeBase`, ensuring that the strings of the knowledge base are synced
with the current vocab.
> #### Example
>
> ```python
> def create_kb(vocab):
> kb = InMemoryLookupKB(vocab, entity_vector_length=128)
> kb.add_entity(...)
> kb.add_alias(...)
> return kb
> entity_linker = nlp.add_pipe("entity_linker")
> entity_linker.set_kb(create_kb)
> ```
| Name | Description |
| ----------- | ---------------------------------------------------------------------------------------------------------------- |
| `kb_loader` | Function that creates a [`KnowledgeBase`](/api/kb) from a `Vocab` instance. ~~Callable[[Vocab], KnowledgeBase]~~ |
## EntityLinker.initialize {id="initialize",tag="method",version="3"}
Initialize the component for training. `get_examples` should be a function that
returns an iterable of [`Example`](/api/example) objects. **At least one example
should be supplied.** The data examples are used to **initialize the model** of
the component and can either be the full training data or a representative
sample. Initialization includes validating the network,
[inferring missing shapes](https://thinc.ai/docs/usage-models#validation) and
setting up the label scheme based on the data. This method is typically called
by [`Language.initialize`](/api/language#initialize).
Optionally, a `kb_loader` argument may be specified to change the internal
knowledge base. This argument should be a function that takes a `Vocab` instance
and creates the `KnowledgeBase`, ensuring that the strings of the knowledge base
are synced with the current vocab.
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> entity_linker.initialize(lambda: examples, nlp=nlp, kb_loader=my_kb)
> ```
| Name | Description |
| -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `get_examples` | Function that returns gold-standard annotations in the form of [`Example`](/api/example) objects. Must contain at least one `Example`. ~~Callable[[], Iterable[Example]]~~ |
| _keyword-only_ | |
| `nlp` | The current `nlp` object. Defaults to `None`. ~~Optional[Language]~~ |
| `kb_loader` | Function that creates a [`KnowledgeBase`](/api/kb) from a `Vocab` instance. ~~Callable[[Vocab], KnowledgeBase]~~ |
## EntityLinker.predict {id="predict",tag="method"}
Apply the component's model to a batch of [`Doc`](/api/doc) objects, without
modifying them. Returns the KB IDs for each entity in each doc, including `NIL`
if there is no prediction.
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> kb_ids = entity_linker.predict([doc1, doc2])
> ```
| Name | Description |
| ----------- | -------------------------------------------------------------------------- |
| `docs` | The documents to predict. ~~Iterable[Doc]~~ |
| **RETURNS** | The predicted KB identifiers for the entities in the `docs`. ~~List[str]~~ |
## EntityLinker.set_annotations {id="set_annotations",tag="method"}
Modify a batch of documents, using pre-computed entity IDs for a list of named
entities.
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> kb_ids = entity_linker.predict([doc1, doc2])
> entity_linker.set_annotations([doc1, doc2], kb_ids)
> ```
| Name | Description |
| -------- | --------------------------------------------------------------------------------------------------------------- |
| `docs` | The documents to modify. ~~Iterable[Doc]~~ |
| `kb_ids` | The knowledge base identifiers for the entities in the docs, predicted by `EntityLinker.predict`. ~~List[str]~~ |
## EntityLinker.update {id="update",tag="method"}
Learn from a batch of [`Example`](/api/example) objects, updating both the
pipe's entity linking model and context encoder. Delegates to
[`predict`](/api/entitylinker#predict).
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> optimizer = nlp.initialize()
> losses = entity_linker.update(examples, sgd=optimizer)
> ```
| Name | Description |
| -------------- | ------------------------------------------------------------------------------------------------------------------------ |
| `examples` | A batch of [`Example`](/api/example) objects to learn from. ~~Iterable[Example]~~ |
| _keyword-only_ | |
| `drop` | The dropout rate. ~~float~~ |
| `sgd` | An optimizer. Will be created via [`create_optimizer`](#create_optimizer) if not set. ~~Optional[Optimizer]~~ |
| `losses` | Optional record of the loss during training. Updated using the component name as the key. ~~Optional[Dict[str, float]]~~ |
| **RETURNS** | The updated `losses` dictionary. ~~Dict[str, float]~~ |
## EntityLinker.create_optimizer {id="create_optimizer",tag="method"}
Create an optimizer for the pipeline component.
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> optimizer = entity_linker.create_optimizer()
> ```
| Name | Description |
| ----------- | ---------------------------- |
| **RETURNS** | The optimizer. ~~Optimizer~~ |
## EntityLinker.use_params {id="use_params",tag="method, contextmanager"}
Modify the pipe's model, to use the given parameter values. At the end of the
context, the original parameters are restored.
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> with entity_linker.use_params(optimizer.averages):
> entity_linker.to_disk("/best_model")
> ```
| Name | Description |
| -------- | -------------------------------------------------- |
| `params` | The parameter values to use in the model. ~~dict~~ |
## EntityLinker.to_disk {id="to_disk",tag="method"}
Serialize the pipe to disk.
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> entity_linker.to_disk("/path/to/entity_linker")
> ```
| Name | Description |
| -------------- | ------------------------------------------------------------------------------------------------------------------------------------------ |
| `path` | A path to a directory, which will be created if it doesn't exist. Paths may be either strings or `Path`-like objects. ~~Union[str, Path]~~ |
| _keyword-only_ | |
| `exclude` | String names of [serialization fields](#serialization-fields) to exclude. ~~Iterable[str]~~ |
## EntityLinker.from_disk {id="from_disk",tag="method"}
Load the pipe from disk. Modifies the object in place and returns it.
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> entity_linker.from_disk("/path/to/entity_linker")
> ```
| Name | Description |
| -------------- | ----------------------------------------------------------------------------------------------- |
| `path` | A path to a directory. Paths may be either strings or `Path`-like objects. ~~Union[str, Path]~~ |
| _keyword-only_ | |
| `exclude` | String names of [serialization fields](#serialization-fields) to exclude. ~~Iterable[str]~~ |
| **RETURNS** | The modified `EntityLinker` object. ~~EntityLinker~~ |
## EntityLinker.to_bytes {id="to_bytes",tag="method"}
> #### Example
>
> ```python
> entity_linker = nlp.add_pipe("entity_linker")
> entity_linker_bytes = entity_linker.to_bytes()
> ```
Serialize the pipe to a bytestring, including the `KnowledgeBase`.
| Name | Description |
| -------------- | ------------------------------------------------------------------------------------------- |
| _keyword-only_ | |
| `exclude` | String names of [serialization fields](#serialization-fields) to exclude. ~~Iterable[str]~~ |
| **RETURNS** | The serialized form of the `EntityLinker` object. ~~bytes~~ |
## EntityLinker.from_bytes {id="from_bytes",tag="method"}
Load the pipe from a bytestring. Modifies the object in place and returns it.
> #### Example
>
> ```python
> entity_linker_bytes = entity_linker.to_bytes()
> entity_linker = nlp.add_pipe("entity_linker")
> entity_linker.from_bytes(entity_linker_bytes)
> ```
| Name | Description |
| -------------- | ------------------------------------------------------------------------------------------- |
| `bytes_data` | The data to load from. ~~bytes~~ |
| _keyword-only_ | |
| `exclude` | String names of [serialization fields](#serialization-fields) to exclude. ~~Iterable[str]~~ |
| **RETURNS** | The `EntityLinker` object. ~~EntityLinker~~ |
## Serialization fields {id="serialization-fields"}
During serialization, spaCy will export several data fields used to restore
different aspects of the object. If needed, you can exclude them from
serialization by passing in the string names via the `exclude` argument.
> #### Example
>
> ```python
> data = entity_linker.to_disk("/path", exclude=["vocab"])
> ```
| Name | Description |
| ------- | -------------------------------------------------------------- |
| `vocab` | The shared [`Vocab`](/api/vocab). |
| `cfg` | The config file. You usually don't want to exclude this. |
| `model` | The binary model data. You usually don't want to exclude this. |
| `kb` | The knowledge base. You usually don't want to exclude this. |