L2G Model
gentropy.method.l2g.model.LocusToGeneModel
dataclass
¶
Wrapper for the Locus to Gene classifier.
Source code in src/gentropy/method/l2g/model.py
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hyperparameters_dict: dict[str, Any]
property
¶
Return hyperparameters as a dictionary.
Returns:
Type | Description |
---|---|
dict[str, Any]
|
dict[str, Any]: Hyperparameters |
Raises:
Type | Description |
---|---|
ValueError
|
If hyperparameters have not been set |
export_to_hugging_face_hub(model_path: str, hf_hub_token: str, data: pd_dataframe, commit_message: str, repo_id: str = 'opentargets/locus_to_gene', local_repo: str = 'locus_to_gene') -> None
¶
Share the model on Hugging Face Hub.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
model_path |
str
|
The path to the L2G model file. |
required |
hf_hub_token |
str
|
Hugging Face Hub token |
required |
data |
DataFrame
|
Data used to train the model. This is used to have an example input for the model and to store the column order. |
required |
commit_message |
str
|
Commit message for the push |
required |
repo_id |
str
|
The Hugging Face Hub repo id where the model will be stored. |
'opentargets/locus_to_gene'
|
local_repo |
str
|
Path to the folder where the contents of the model repo + the documentation are located. This is used to push the model to the Hugging Face Hub. |
'locus_to_gene'
|
Raises:
Type | Description |
---|---|
Exception
|
If the push to the Hugging Face Hub fails |
Source code in src/gentropy/method/l2g/model.py
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load_from_disk(path: str | Path) -> LocusToGeneModel
classmethod
¶
Load a fitted model from disk.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
path |
str | Path
|
Path to the model |
required |
Returns:
Name | Type | Description |
---|---|---|
LocusToGeneModel |
LocusToGeneModel
|
L2G model loaded from disk |
Raises:
Type | Description |
---|---|
ValueError
|
If the model has not been fitted yet |
Source code in src/gentropy/method/l2g/model.py
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load_from_hub(model_id: str, hf_token: str | None = None, model_name: str = 'classifier.skops') -> LocusToGeneModel
classmethod
¶
Load a model from the Hugging Face Hub. This will download the model from the hub and load it from disk.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
model_id |
str
|
Model ID on the Hugging Face Hub |
required |
hf_token |
str | None
|
Hugging Face Hub token to download the model (only required if private) |
None
|
model_name |
str
|
Name of the persisted model to load. Defaults to "classifier.skops". |
'classifier.skops'
|
Returns:
Name | Type | Description |
---|---|---|
LocusToGeneModel |
LocusToGeneModel
|
L2G model loaded from the Hugging Face Hub |
Source code in src/gentropy/method/l2g/model.py
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|
predict(feature_matrix: L2GFeatureMatrix, session: Session) -> L2GPrediction
¶
Apply the model to a given feature matrix dataframe. The feature matrix needs to be preprocessed first.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
feature_matrix |
L2GFeatureMatrix
|
Feature matrix to apply the model to. |
required |
session |
Session
|
Session object to convert data to Spark |
required |
Returns:
Name | Type | Description |
---|---|---|
L2GPrediction |
L2GPrediction
|
Dataset containing credible sets and their L2G scores |
Source code in src/gentropy/method/l2g/model.py
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save(path: str) -> None
¶
Saves fitted model to disk using the skops persistence format.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
path |
str
|
Path to save the persisted model. Should end with .skops |
required |
Raises:
Type | Description |
---|---|
ValueError
|
If the model has not been fitted yet |
ValueError
|
If the path does not end with .skops |
Source code in src/gentropy/method/l2g/model.py
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