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README.md

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ChEBai is a deep learning library designed for the integration of deep learning methods with chemical ontologies, particularly ChEBI.
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The library emphasizes the incorporation of the semantic qualities of the ontology into the learning process.
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## Note for developers
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If you have used ChEBai before PR #39, the file structure in which your ChEBI-data is saved has changed. This means that
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datasets will be freshly generated. The data however is the same. If you want to keep the old data (including the old
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splits), you can use a migration script. It copies the old data to the new location for a specific ChEBI class
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(including chebi version and other parameters). The script can be called by specifying the data module from a config
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```
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python chebai/preprocessing/migration/chebi_data_migration.py migrate --datamodule=[path-to-data-config]
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```
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or by specifying the class name (e.g. `ChEBIOver50`) and arguments separately
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```
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python chebai/preprocessing/migration/chebi_data_migration.py migrate --class_name=[data-class] [--chebi_version=[version]]
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```
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The new dataset will by default generate random data splits (with a given seed).
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To reuse a fixed data split, you have to provide the path of the csv file generated during the migration:
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`--data.init_args.splits_file_path=[path-to-processed_data]/splits.csv`
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## Installation
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To install ChEBai, follow these steps:
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```
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To train K models, you need to do K such calls, each with a different `fold_index`. On the first call with a given
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`inner_k_folds`, all folds will be created and stored in the data directory
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## Note for developers
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If you have used ChEBai before PR #39, the file structure in which your ChEBI-data is saved has changed. This means that
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datasets will be freshly generated. The data however is the same. If you want to keep the old data (including the old
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splits), you can use a migration script. It copies the old data to the new location for a specific ChEBI class
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(including chebi version and other parameters). The script can be called by specifying the data module from a config
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```
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python chebai/preprocessing/migration/chebi_data_migration.py migrate --datamodule=[path-to-data-config]
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```
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or by specifying the class name (e.g. `ChEBIOver50`) and arguments separately
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```
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python chebai/preprocessing/migration/chebi_data_migration.py migrate --class_name=[data-class] [--chebi_version=[version]]
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```
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The new dataset will by default generate random data splits (with a given seed).
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To reuse a fixed data split, you have to provide the path of the csv file generated during the migration:
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`--data.init_args.splits_file_path=[path-to-processed_data]/splits.csv`

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