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Merge pull request #6045 from svlandeg/feature/more-layers-docs [ci skip]

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6
spacy/ml/models/tok2vec.py
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@ -165,7 +165,7 @@ def MultiHashEmbed(
@registry.architectures.register("spacy.CharacterEmbed.v1")
def CharacterEmbed(width: int, rows: int, nM: int, nC: int):
"""Construct an embedded representations based on character embeddings, using
"""Construct an embedded representation based on character embeddings, using
a feed-forward network. A fixed number of UTF-8 byte characters are used for
each word, taken from the beginning and end of the word equally. Padding is
used in the centre for words that are too short.
@ -176,8 +176,8 @@ def CharacterEmbed(width: int, rows: int, nM: int, nC: int):
ensures that the final character is always in the last position, instead
of being in an arbitrary position depending on the word length.
The characters are embedded in a embedding table with 256 rows, and the
vectors concatenated. A hash-embedded vector of the NORM of the word is
The characters are embedded in a embedding table with a given number of rows,
and the vectors concatenated. A hash-embedded vector of the NORM of the word is
also concatenated on, and the result is then passed through a feed-forward
network to construct a single vector to represent the information.

2
spacy/tokens/doc.pyx
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@ -576,7 +576,7 @@ cdef class Doc:
entity_type = 0
kb_id = 0
# Set ent_iob to Missing (0) bij default unless this token was nered before
# Set ent_iob to Missing (0) by default unless this token was nered before
ent_iob = 0
if self.c[i].ent_iob != 0:
ent_iob = 2

8
website/docs/api/architectures.md
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@ -181,10 +181,10 @@ characters would be `"jumpping"`: 4 from the start, 4 from the end. This ensures
that the final character is always in the last position, instead of being in an
arbitrary position depending on the word length.
The characters are embedded in a embedding table with 256 rows, and the vectors
concatenated. A hash-embedded vector of the `NORM` of the word is also
concatenated on, and the result is then passed through a feed-forward network to
construct a single vector to represent the information.
The characters are embedded in a embedding table with a given number of rows,
and the vectors concatenated. A hash-embedded vector of the `NORM` of the word
is also concatenated on, and the result is then passed through a feed-forward
network to construct a single vector to represent the information.
| Name | Description |
| ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------- |

25
website/docs/api/dependencyparser.md
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@ -293,7 +293,11 @@ context, the original parameters are restored.
## DependencyParser.add_label {#add_label tag="method"}
Add a new label to the pipe.
Add a new label to the pipe. Note that you don't have to call this method if you
provide a **representative data sample** to the
[`begin_training`](#begin_training) method. In this case, all labels found in
the sample will be automatically added to the model, and the output dimension
will be [inferred](/usage/layers-architectures#shape-inference) automatically.
> #### Example
>
@ -307,6 +311,25 @@ Add a new label to the pipe.
| `label` | The label to add. ~~str~~ |
| **RETURNS** | `0` if the label is already present, otherwise `1`. ~~int~~ |
## DependencyParser.set_output {#set_output tag="method"}
Change the output dimension of the component's model by calling the model's
attribute `resize_output`. This is a function that takes the original model and
the new output dimension `nO`, and changes the model in place. When resizing an
already trained model, care should be taken to avoid the "catastrophic
forgetting" problem.
> #### Example
>
> ```python
> parser = nlp.add_pipe("parser")
> parser.set_output(512)
> ```
| Name | Description |
| ---- | --------------------------------- |
| `nO` | The new output dimension. ~~int~~ |
## DependencyParser.to_disk {#to_disk tag="method"}
Serialize the pipe to disk.

25
website/docs/api/entityrecognizer.md
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@ -281,7 +281,11 @@ context, the original parameters are restored.
## EntityRecognizer.add_label {#add_label tag="method"}
Add a new label to the pipe.
Add a new label to the pipe. Note that you don't have to call this method if you
provide a **representative data sample** to the
[`begin_training`](#begin_training) method. In this case, all labels found in
the sample will be automatically added to the model, and the output dimension
will be [inferred](/usage/layers-architectures#shape-inference) automatically.
> #### Example
>
@ -295,6 +299,25 @@ Add a new label to the pipe.
| `label` | The label to add. ~~str~~ |
| **RETURNS** | `0` if the label is already present, otherwise `1`. ~~int~~ |
## EntityRecognizer.set_output {#set_output tag="method"}
Change the output dimension of the component's model by calling the model's
attribute `resize_output`. This is a function that takes the original model and
the new output dimension `nO`, and changes the model in place. When resizing an
already trained model, care should be taken to avoid the "catastrophic
forgetting" problem.
> #### Example
>
> ```python
> ner = nlp.add_pipe("ner")
> ner.set_output(512)
> ```
| Name | Description |
| ---- | --------------------------------- |
| `nO` | The new output dimension. ~~int~~ |
## EntityRecognizer.to_disk {#to_disk tag="method"}
Serialize the pipe to disk.

9
website/docs/api/language.md
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@ -205,9 +205,16 @@ examples can either be the full training data or a representative sample. They
are used to **initialize the models** of trainable pipeline components and are
passed each component's [`begin_training`](/api/pipe#begin_training) method, if
available. Initialization includes validating the network,
[inferring missing shapes](https://thinc.ai/docs/usage-models#validation) and
[inferring missing shapes](/usage/layers-architectures#shape-inference) and
setting up the label scheme based on the data.
If no `get_examples` function is provided when calling `nlp.begin_training`, the
pipeline components will be initialized with generic data. In this case, it is
crucial that the output dimension of each component has already been defined
either in the [config](/usage/training#config), or by calling
[`pipe.add_label`](/api/pipe#add_label) for each possible output label (e.g. for
the tagger or textcat).
<Infobox variant="warning" title="Changed in v3.0">
The `Language.update` method now takes a **function** that is called with no

6
website/docs/api/morphologizer.md
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@ -258,6 +258,12 @@ context, the original parameters are restored.
Add a new label to the pipe. If the `Morphologizer` should set annotations for
both `pos` and `morph`, the label should include the UPOS as the feature `POS`.
Raises an error if the output dimension is already set, or if the model has
already been fully [initialized](#begin_training). Note that you don't have to
call this method if you provide a **representative data sample** to the
[`begin_training`](#begin_training) method. In this case, all labels found in
the sample will be automatically added to the model, and the output dimension
will be [inferred](/usage/layers-architectures#shape-inference) automatically.
> #### Example
>

78
website/docs/api/pipe.md
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@ -286,9 +286,6 @@ context, the original parameters are restored.
## Pipe.add_label {#add_label tag="method"}
Add a new label to the pipe. It's possible to extend trained models with new
labels, but care should be taken to avoid the "catastrophic forgetting" problem.
> #### Example
>
> ```python
@ -296,10 +293,81 @@ labels, but care should be taken to avoid the "catastrophic forgetting" problem.
> pipe.add_label("MY_LABEL")
> ```
Add a new label to the pipe, to be predicted by the model. The actual
implementation depends on the specific component, but in general `add_label`
shouldn't be called if the output dimension is already set, or if the model has
already been fully [initialized](#begin_training). If these conditions are
violated, the function will raise an Error. The exception to this rule is when
the component is [resizable](#is_resizable), in which case
[`set_output`](#set_output) should be called to ensure that the model is
properly resized.
<Infobox variant="danger">
This method needs to be overwritten with your own custom `add_label` method.
</Infobox>
| Name | Description |
| ----------- | ----------------------------------------------------------- |
| ----------- | ------------------------------------------------------- |
| `label` | The label to add. ~~str~~ |
| **RETURNS** | `0` if the label is already present, otherwise `1`. ~~int~~ |
| **RETURNS** | 0 if the label is already present, otherwise 1. ~~int~~ |
Note that in general, you don't have to call `pipe.add_label` if you provide a
representative data sample to the [`begin_training`](#begin_training) method. In
this case, all labels found in the sample will be automatically added to the
model, and the output dimension will be
[inferred](/usage/layers-architectures#shape-inference) automatically.
## Pipe.is_resizable {#is_resizable tag="method"}
> #### Example
>
> ```python
> can_resize = pipe.is_resizable()
> ```
>
> ```python
> ### Custom resizing
> def custom_resize(model, new_nO):
> # adjust model
> return model
>
> custom_model.attrs["resize_output"] = custom_resize
> ```
Check whether or not the output dimension of the component's model can be
resized. If this method returns `True`, [`set_output`](#set_output) can be
called to change the model's output dimension.
For built-in components that are not resizable, you have to create and train a
new model from scratch with the appropriate architecture and output dimension.
For custom components, you can implement a `resize_output` function and add it
as an attribute to the component's model.
| Name | Description |
| ----------- | ---------------------------------------------------------------------------------------------- |
| **RETURNS** | Whether or not the output dimension of the model can be changed after initialization. ~~bool~~ |
## Pipe.set_output {#set_output tag="method"}
Change the output dimension of the component's model. If the component is not
[resizable](#is_resizable), this method will raise a `NotImplementedError`. If a
component is resizable, the model's attribute `resize_output` will be called.
This is a function that takes the original model and the new output dimension
`nO`, and changes the model in place. When resizing an already trained model,
care should be taken to avoid the "catastrophic forgetting" problem.
> #### Example
>
> ```python
> if pipe.is_resizable():
> pipe.set_output(512)
> ```
| Name | Description |
| ---- | --------------------------------- |
| `nO` | The new output dimension. ~~int~~ |
## Pipe.to_disk {#to_disk tag="method"}

10
website/docs/api/tagger.md
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@ -250,7 +250,7 @@ Score a batch of examples.
> ```
| Name | Description |
| ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
| ----------- | --------------------------------------------------------------------------------------------------------------------------------- |
| `examples` | The examples to score. ~~Iterable[Example]~~ |
| **RETURNS** | The scores, produced by [`Scorer.score_token_attr`](/api/scorer#score_token_attr) for the attribute `"tag"`. ~~Dict[str, float]~~ |
@ -288,7 +288,13 @@ context, the original parameters are restored.
## Tagger.add_label {#add_label tag="method"}
Add a new label to the pipe.
Add a new label to the pipe. Raises an error if the output dimension is already
set, or if the model has already been fully [initialized](#begin_training). Note
that you don't have to call this method if you provide a **representative data
sample** to the [`begin_training`](#begin_training) method. In this case, all
labels found in the sample will be automatically added to the model, and the
output dimension will be [inferred](/usage/layers-architectures#shape-inference)
automatically.
> #### Example
>

8
website/docs/api/textcategorizer.md
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@ -297,7 +297,13 @@ Modify the pipe's model, to use the given parameter values.
## TextCategorizer.add_label {#add_label tag="method"}
Add a new label to the pipe.
Add a new label to the pipe. Raises an error if the output dimension is already
set, or if the model has already been fully [initialized](#begin_training). Note
that you don't have to call this method if you provide a **representative data
sample** to the [`begin_training`](#begin_training) method. In this case, all
labels found in the sample will be automatically added to the model, and the
output dimension will be [inferred](/usage/layers-architectures#shape-inference)
automatically.
> #### Example
>

261
website/docs/usage/layers-architectures.md
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@ -5,7 +5,7 @@ menu:
- ['Type Signatures', 'type-sigs']
- ['Swapping Architectures', 'swap-architectures']
- ['PyTorch & TensorFlow', 'frameworks']
- ['Thinc Models', 'thinc']
- ['Custom Thinc Models', 'thinc']
- ['Trainable Components', 'components']
next: /usage/projects
---
@ -118,7 +118,7 @@ code.
If no model is specified for the [`TextCategorizer`](/api/textcategorizer), the
[TextCatEnsemble](/api/architectures#TextCatEnsemble) architecture is used by
default. This architecture combines a simpel bag-of-words model with a neural
default. This architecture combines a simple bag-of-words model with a neural
network, usually resulting in the most accurate results, but at the cost of
speed. The config file for this model would look something like this:
@ -225,28 +225,263 @@ you'll be able to try it out in any of the spaCy components. ​
Thinc allows you to [wrap models](https://thinc.ai/docs/usage-frameworks)
written in other machine learning frameworks like PyTorch, TensorFlow and MXNet
using a unified [`Model`](https://thinc.ai/docs/api-model) API. As well as
**wrapping whole models**, Thinc lets you call into an external framework for
just **part of your model**: you can have a model where you use PyTorch just for
the transformer layers, using "native" Thinc layers to do fiddly input and
output transformations and add on task-specific "heads", as efficiency is less
of a consideration for those parts of the network.
using a unified [`Model`](https://thinc.ai/docs/api-model) API. This makes it
easy to use a model implemented in a different framework to power a component in
your spaCy pipeline. For example, to wrap a PyTorch model as a Thinc `Model`,
you can use Thinc's
[`PyTorchWrapper`](https://thinc.ai/docs/api-layers#pytorchwrapper):
<!-- TODO: custom tagger implemented in PyTorch, wrapped as Thinc model, link off to project (with notebook?) -->
```python
from thinc.api import PyTorchWrapper
## Implementing models in Thinc {#thinc}
wrapped_pt_model = PyTorchWrapper(torch_model)
```
<!-- TODO: use same example as above, custom tagger, but implemented in Thinc, link off to Thinc docs where appropriate -->
Let's use PyTorch to define a very simple neural network consisting of two
hidden `Linear` layers with `ReLU` activation and dropout, and a
softmax-activated output layer:
## Models for trainable components {#components}
```python
### PyTorch model
from torch import nn
torch_model = nn.Sequential(
nn.Linear(width, hidden_width),
nn.ReLU(),
nn.Dropout2d(dropout),
nn.Linear(hidden_width, nO),
nn.ReLU(),
nn.Dropout2d(dropout),
nn.Softmax(dim=1)
)
```
The resulting wrapped `Model` can be used as a **custom architecture** as such,
or can be a **subcomponent of a larger model**. For instance, we can use Thinc's
[`chain`](https://thinc.ai/docs/api-layers#chain) combinator, which works like
`Sequential` in PyTorch, to combine the wrapped model with other components in a
larger network. This effectively means that you can easily wrap different
components from different frameworks, and "glue" them together with Thinc:
```python
from thinc.api import chain, with_array
from spacy.ml import CharacterEmbed
char_embed = CharacterEmbed(width, embed_size, nM, nC)
model = chain(char_embed, with_array(wrapped_pt_model))
```
In the above example, we have combined our custom PyTorch model with a character
embedding layer defined by spaCy.
[CharacterEmbed](/api/architectures#CharacterEmbed) returns a `Model` that takes
a ~~List[Doc]~~ as input, and outputs a ~~List[Floats2d]~~. To make sure that
the wrapped PyTorch model receives valid inputs, we use Thinc's
[`with_array`](https://thinc.ai/docs/api-layers#with_array) helper.
You could also implement a model that only uses PyTorch for the transformer
layers, and "native" Thinc layers to do fiddly input and output transformations
and add on task-specific "heads", as efficiency is less of a consideration for
those parts of the network.
### Using wrapped models {#frameworks-usage}
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
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:
```python
### Registering the architecture {highlight="9"}
from typing import List
from thinc.types import Floats2d
from thinc.api import Model, PyTorchWrapper, chain, with_array
import spacy
from spacy.tokens.doc import Doc
from spacy.ml import CharacterEmbed
from torch import nn
@spacy.registry.architectures("CustomTorchModel.v1")
def create_torch_model(
nO: int,
width: int,
hidden_width: int,
embed_size: int,
nM: int,
nC: int,
dropout: float,
) -> Model[List[Doc], List[Floats2d]]:
char_embed = CharacterEmbed(width, embed_size, nM, nC)
torch_model = nn.Sequential(
nn.Linear(width, hidden_width),
nn.ReLU(),
nn.Dropout2d(dropout),
nn.Linear(hidden_width, nO),
nn.ReLU(),
nn.Dropout2d(dropout),
nn.Softmax(dim=1)
)
wrapped_pt_model = PyTorchWrapper(torch_model)
model = chain(char_embed, with_array(wrapped_pt_model))
return model
```
The model definition can now be used in any existing trainable spaCy component,
by specifying it in the config file. In this configuration, all required
parameters for the various subcomponents of the custom architecture are passed
in as settings via the config.
```ini
### config.cfg (excerpt) {highlight="5-5"}
[components.tagger]
factory = "tagger"
[components.tagger.model]
@architectures = "CustomTorchModel.v1"
nO = 50
width = 96
hidden_width = 48
embed_size = 2000
nM = 64
nC = 8
dropout = 0.2
```
<Infobox variant="warning">
Remember that it is best not to rely on any (hidden) default values, to ensure
that training configs are complete and experiments fully reproducible.
</Infobox>
## Custom models with Thinc {#thinc}
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
[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:
```python
from thinc.api import chain, with_array, Model, Relu, Dropout, Softmax
from spacy.ml import CharacterEmbed
char_embed = CharacterEmbed(width, embed_size, nM, nC)
with Model.define_operators({">>": chain}):
layers = (
Relu(hidden_width, width)
>> Dropout(dropout)
>> Relu(hidden_width, hidden_width)
>> Dropout(dropout)
>> Softmax(nO, hidden_width)
)
model = char_embed >> with_array(layers)
```
<Infobox variant="warning" title="Important note on inputs and outputs">
Note that Thinc layers define the output dimension (`nO`) as the first argument,
followed (optionally) by the input dimension (`nI`). This is in contrast to how
the PyTorch layers are defined, where `in_features` precedes `out_features`.
</Infobox>
### Shape inference in Thinc {#thinc-shape-inference}
It is **not** strictly necessary to define all the input and output dimensions
for each layer, as Thinc can perform
[shape inference](https://thinc.ai/docs/usage-models#validation) between
sequential layers by matching up the output dimensionality of one layer to the
input dimensionality of the next. This means that we can simplify the `layers`
definition:
> #### Diff
>
> ```diff
> layers = (
> Relu(hidden_width, width)
> >> Dropout(dropout)
> - >> Relu(hidden_width, hidden_width)
> + >> Relu(hidden_width)
> >> Dropout(dropout)
> - >> Softmax(nO, hidden_width)
> + >> Softmax(nO)
> )
> ```
```python
with Model.define_operators({">>": chain}):
layers = (
Relu(hidden_width, width)
>> Dropout(dropout)
>> Relu(hidden_width)
>> Dropout(dropout)
>> Softmax(nO)
)
```
Thinc can even go one step further and **deduce the correct input dimension** of
the first layer, and output dimension of the last. To enable this functionality,
you have to call
[`Model.initialize`](https://thinc.ai/docs/api-model#initialize) with an **input
sample** `X` and an **output sample** `Y` with the correct dimensions:
```python
### Shape inference with initialization {highlight="3,7,10"}
with Model.define_operators({">>": chain}):
layers = (
Relu(hidden_width)
>> Dropout(dropout)
>> Relu(hidden_width)
>> Dropout(dropout)
>> Softmax()
)
model = char_embed >> with_array(layers)
model.initialize(X=input_sample, Y=output_sample)
```
The built-in [pipeline components](/usage/processing-pipelines) in spaCy ensure
that their internal models are **always initialized** with appropriate sample
data. In this case, `X` is typically a ~~List[Doc]~~, while `Y` is typically a
~~List[Array1d]~~ or ~~List[Array2d]~~, depending on the specific task. This
functionality is triggered when
[`nlp.begin_training`](/api/language#begin_training) is called.
### Dropout and normalization in Thinc {#thinc-dropout-norm}
Many of the available Thinc [layers](https://thinc.ai/docs/api-layers) allow you
to define a `dropout` argument that will result in "chaining" an additional
[`Dropout`](https://thinc.ai/docs/api-layers#dropout) layer. Optionally, you can
often specify whether or not you want to add layer normalization, which would
result in an additional
[`LayerNorm`](https://thinc.ai/docs/api-layers#layernorm) layer. That means that
the following `layers` definition is equivalent to the previous:
```python
with Model.define_operators({">>": chain}):
layers = (
Relu(hidden_width, dropout=dropout, normalize=False)
>> Relu(hidden_width, dropout=dropout, normalize=False)
>> Softmax()
)
model = char_embed >> with_array(layers)
model.initialize(X=input_sample, Y=output_sample)
```
## Create new trainable components {#components}
<!-- TODO:
- Interaction with `predict`, `get_loss` and `set_annotations`
- Initialization life-cycle with `begin_training`.
- Initialization life-cycle with `begin_training`, correlation with add_label
Example: relation extraction component (implemented as project template)
Avoid duplication with usage/processing-pipelines#trainable-components ?
-->
![Diagram of a pipeline component with its model](../images/layers-architectures.svg)

17
website/docs/usage/processing-pipelines.md
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@ -1028,11 +1028,11 @@ 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 [layers](https://thinc.ai/docs/api-layers) implemented
in Thinc, or a [wrapped model](https://thinc.ai/docs/usage-frameworks)
implemented in PyTorch, TensorFlow, MXNet or a fully custom solution. The
model must take a list of [`Doc`](/api/doc) objects as input and can have any
type of output.
can be a model using 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
list of [`Doc`](/api/doc) objects as input and can have any type of output.
2. **Pipe subclass:** A subclass of [`Pipe`](/api/pipe) that implements at least
two methods: [`Pipe.predict`](/api/pipe#predict) and
[`Pipe.set_annotations`](/api/pipe#set_annotations).
@ -1078,8 +1078,9 @@ _first_ create a `Model` from a [registered architecture](/api/architectures),
validate its arguments and _then_ pass the object forward to the component. This
means that the config can express very complex, nested trees of objects – but
the objects don't have to pass the model settings all the way down to the
components. It also makes the components more **modular** and lets you swap
different architectures in your config, and re-use model definitions.
components. It also makes the components more **modular** and lets you
[swap](/usage/layers-architectures#swap-architectures) different architectures
in your config, and re-use model definitions.
```ini
### config.cfg (excerpt)
@ -1134,7 +1135,7 @@ loss is calculated and to add evaluation scores to the training output.
For more details on how to implement your own trainable components and model
architectures, and plug existing models implemented in PyTorch or TensorFlow
into your spaCy pipeline, see the usage guide on
[layers and model architectures](/usage/layers-architectures#components).
[layers and model architectures](/usage/layers-architectures).
</Infobox>

2
website/meta/type-annotations.json
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@ -34,6 +34,8 @@
"Floats2d": "https://thinc.ai/docs/api-types#types",
"Floats3d": "https://thinc.ai/docs/api-types#types",
"FloatsXd": "https://thinc.ai/docs/api-types#types",
"Array1d": "https://thinc.ai/docs/api-types#types",
"Array2d": "https://thinc.ai/docs/api-types#types",
"Ops": "https://thinc.ai/docs/api-backends#ops",
"cymem.Pool": "https://github.com/explosion/cymem",
"preshed.BloomFilter": "https://github.com/explosion/preshed",