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update REL model code

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@ -540,7 +540,8 @@ code to create the ML model and the pipeline component from scratch.
It contains two config files to train the model: It contains two config files to train the model:
one to run on CPU with a Tok2Vec layer, and one for the GPU using a transformer. one to run on CPU with a Tok2Vec layer, and one for the GPU using a transformer.
The project applies the relation extraction component to identify biomolecular The project applies the relation extraction component to identify biomolecular
interactions, but you can easily swap in your own dataset for your experiments. interactions, but you can easily swap in your own dataset for your experiments
in any other domain.
</Project> </Project>
#### Step 1: Implementing the Model {#component-rel-model} #### Step 1: Implementing the Model {#component-rel-model}
@ -558,40 +559,17 @@ matrix** (~~Floats2d~~) of predictions:
```python ```python
### Register the model architecture ### Register the model architecture
@registry.architectures.register("rel_model.v1") @spacy.registry.architectures.register("rel_model.v1")
def create_relation_model(...) -> Model[List[Doc], Floats2d]: def create_relation_model(...) -> Model[List[Doc], Floats2d]:
model = ... # 👈 model will go here model = ... # 👈 model will go here
return model return model
``` ```
The first layer in this model will typically be an We will adapt a **modular approach** to the definition of this relation model, and
[embedding layer](/usage/embeddings-transformers) such as a define it as chaining to layers together: the first layer that generates an
[`Tok2Vec`](/api/tok2vec) component or a [`Transformer`](/api/transformer). This instance tensor from a given set of documents, and the second layer that
layer is assumed to be of type ~~Model[List[Doc], List[Floats2d]]~~ as it transforms this tensor into a final tensor holding the predictions:
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`](/api/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
### Simple candiate generation
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
```
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.
> #### config.cfg (excerpt) > #### config.cfg (excerpt)
> >
@ -599,17 +577,151 @@ config, and easily swap it out for any other candidate generation function.
> [model] > [model]
> @architectures = "rel_model.v1" > @architectures = "rel_model.v1"
> >
> [model.tok2vec] > [model.create_instance_tensor]
> # ... > # ...
> >
> [model.get_candidates] > [model.classification_layer]
> @misc = "rel_cand_generator.v1" > ...
> max_length = 20
> ``` > ```
```python ```python
### Extended candidate generation {highlight="1,2,7,8"} ### Implement the model architecture
@registry.misc.register("rel_cand_generator.v1") @spacy.registry.architectures.register("rel_model.v1")
def create_relation_model(
create_instance_tensor: Model[List[Doc], Floats2d],
classification_layer: Model[Floats2d, Floats2d],
) -> Model[List[Doc], Floats2d]:
model = chain(create_instance_tensor, classification_layer)
return model
```
The `classification_layer` could be something simple like a Linear layer
followed by a logistic activation function:
> #### config.cfg (excerpt)
>
> ```ini
> [model.classification_layer]
> @architectures = "rel_classification_layer.v1"
> nI = null
> nO = null
> ```
```python
### Implement the classification layer
@spacy.registry.architectures.register("rel_classification_layer.v1")
def create_classification_layer(
nO: int = None, nI: int = None
) -> Model[Floats2d, Floats2d]:
return chain(Linear(nO=nO, nI=nI), Logistic())
```
The first layer that **creates the instance tensor** can be defined
by implementing a
[custom forward function](https://thinc.ai/docs/usage-models#weights-layers-forward)
with an appropriate backpropagation callback. We also define an
[initialization method](https://thinc.ai/docs/usage-models#weights-layers-init)
that ensures that the layer is properly set up for training.
```python
### Implement the custom forward function
def instance_forward(
model: Model[List[Doc], Floats2d],
docs: List[Doc],
is_train: bool
) -> Tuple[Floats2d, Callable]:
...
tok2vec = model.get_ref("tok2vec")
tokvecs, bp_tokvecs = tok2vec(docs, is_train)
relations = ...
def backprop(d_relations: Floats2d) -> List[Doc]:
d_tokvecs = ...
return bp_tokvecs(d_tokvecs)
return relations, backprop
### Implement the custom initialization method
def instance_init(
model: Model,
X: List[Doc] = None,
Y: Floats2d = None
) -> Model:
tok2vec = model.get_ref("tok2vec")
tok2vec.initialize(X)
return model
### Implement the layer that creates the instance tensor
@spacy.registry.architectures.register("rel_instance_tensor.v1")
def create_tensors(
tok2vec: Model[List[Doc], List[Floats2d]],
pooling: Model[Ragged, Floats2d],
get_instances: Callable[[Doc], List[Tuple[Span, Span]]],
) -> Model[List[Doc], Floats2d]:
return Model(
"instance_tensors",
instance_forward,
layers=[tok2vec, pooling],
refs={"tok2vec": tok2vec, "pooling": pooling},
attrs={"get_instances": get_instances},
init=instance_init,
)
```
> #### config.cfg (excerpt)
>
> ```ini
> [model.create_instance_tensor]
> @architectures = "rel_instance_tensor.v1"
>
> [model.create_instance_tensor.tok2vec]
> @architectures = "spacy.HashEmbedCNN.v1"
> ...
>
> [model.create_instance_tensor.pooling]
> @layers = "reduce_mean.v1"
>
> [model.create_instance_tensor.get_instances]
> ...
> `
This custom layer uses 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.
The **`pooling`** layer will be applied to summarize the token vectors into entity
vectors, as named entities (represented by `Span` objects) can consist of one
or multiple tokens. For instance, the pooling layer could resort to calculating
the average of all token vectors in an entity. Thinc provides several
[built-in pooling operators](https://thinc.ai/docs/api-layers#reduction-ops) for
this purpose.
> #### config.cfg (excerpt)
>
> ```ini
>
> [model.create_instance_tensor.get_instances]
> @misc = "rel_instance_generator.v1"
> max_length = 100
> ```
Finally, we need a `get_instances` 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`](/api/doc) as input and
outputs a `List` of `Span` tuples. For instance, this
implementation takes any two entities from the same document, as long as they
are within a **maximum distance** (in number of tokens) of eachother:
```python
### Simple candiate generation
@spacy.registry.misc.register("rel_instance_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 = []
@ -621,46 +733,19 @@ def create_candidate_indices(max_length: int) -> Callable[[Doc], List[Tuple[Span
return candidates return candidates
return get_candidates return get_candidates
``` ```
This function in added to 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.
Finally, we require a method that transforms the candidate entity pairs into a
2D tensor using the specified [`Tok2Vec`](/api/tok2vec) or
[`Transformer`](/api/transformer). The resulting ~~Floats2~~ 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:
```ini
### config.cfg
[model]
@architectures = "rel_model.v1"
# ...
[model.tok2vec]
# ...
[model.get_candidates]
@misc = "rel_cand_generator.v1"
max_length = 20
[model.create_candidate_tensor]
@misc = "rel_cand_tensor.v1"
[model.output_layer]
@architectures = "rel_output_layer.v1"
# ...
```
<!-- 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
references, so we can access them easily: references, so we can access them easily:
```python ```python
tok2vec_layer = model.get_ref("tok2vec") pooling = model.get_ref("pooling")
output_layer = model.get_ref("output_layer") tok2vec = model.get_ref("tok2vec")
create_candidate_tensor = model.attrs["create_candidate_tensor"] get_instances = model.attrs["get_instances"]
get_candidates = model.attrs["get_candidates"]
``` ```
#### Step 2: Implementing the pipeline component {#component-rel-pipe} #### Step 2: Implementing the pipeline component {#component-rel-pipe}
@ -935,5 +1020,6 @@ code to create the ML model and the pipeline component from scratch.
It contains two config files to train the model: It contains two config files to train the model:
one to run on CPU with a Tok2Vec layer, and one for the GPU using a transformer. one to run on CPU with a Tok2Vec layer, and one for the GPU using a transformer.
The project applies the relation extraction component to identify biomolecular The project applies the relation extraction component to identify biomolecular
interactions, but you can easily swap in your own dataset for your experiments. interactions, but you can easily swap in your own dataset for your experiments
in any other domain.
</Project> </Project>