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3 | 3 | ChEBai is a deep learning library designed for the integration of deep learning methods with chemical ontologies, particularly ChEBI. |
4 | 4 | The library emphasizes the incorporation of the semantic qualities of the ontology into the learning process. |
5 | 5 |
|
6 | | -## Note for developers |
7 | | - |
8 | | -If you have used ChEBai before PR #39, the file structure in which your ChEBI-data is saved has changed. This means that |
9 | | -datasets will be freshly generated. The data however is the same. If you want to keep the old data (including the old |
10 | | -splits), you can use a migration script. It copies the old data to the new location for a specific ChEBI class |
11 | | -(including chebi version and other parameters). The script can be called by specifying the data module from a config |
12 | | -``` |
13 | | -python chebai/preprocessing/migration/chebi_data_migration.py migrate --datamodule=[path-to-data-config] |
14 | | -``` |
15 | | -or by specifying the class name (e.g. `ChEBIOver50`) and arguments separately |
16 | | -``` |
17 | | -python chebai/preprocessing/migration/chebi_data_migration.py migrate --class_name=[data-class] [--chebi_version=[version]] |
18 | | -``` |
19 | | -The new dataset will by default generate random data splits (with a given seed). |
20 | | -To reuse a fixed data split, you have to provide the path of the csv file generated during the migration: |
21 | | -`--data.init_args.splits_file_path=[path-to-processed_data]/splits.csv` |
22 | | - |
23 | 6 | ## Installation |
24 | 7 |
|
25 | 8 | To install ChEBai, follow these steps: |
@@ -87,3 +70,20 @@ and the fold to be used in the current optimisation run as |
87 | 70 | ``` |
88 | 71 | To train K models, you need to do K such calls, each with a different `fold_index`. On the first call with a given |
89 | 72 | `inner_k_folds`, all folds will be created and stored in the data directory |
| 73 | + |
| 74 | +## Note for developers |
| 75 | + |
| 76 | +If you have used ChEBai before PR #39, the file structure in which your ChEBI-data is saved has changed. This means that |
| 77 | +datasets will be freshly generated. The data however is the same. If you want to keep the old data (including the old |
| 78 | +splits), you can use a migration script. It copies the old data to the new location for a specific ChEBI class |
| 79 | +(including chebi version and other parameters). The script can be called by specifying the data module from a config |
| 80 | +``` |
| 81 | +python chebai/preprocessing/migration/chebi_data_migration.py migrate --datamodule=[path-to-data-config] |
| 82 | +``` |
| 83 | +or by specifying the class name (e.g. `ChEBIOver50`) and arguments separately |
| 84 | +``` |
| 85 | +python chebai/preprocessing/migration/chebi_data_migration.py migrate --class_name=[data-class] [--chebi_version=[version]] |
| 86 | +``` |
| 87 | +The new dataset will by default generate random data splits (with a given seed). |
| 88 | +To reuse a fixed data split, you have to provide the path of the csv file generated during the migration: |
| 89 | +`--data.init_args.splits_file_path=[path-to-processed_data]/splits.csv` |
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