Add geneformer #7
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lazappi
approved these changes
Dec 19, 2024
src/methods/geneformer/script.py
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| output_prefix="classifier", | ||
| ) | ||
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| import datasets |
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Can this be moved with the other imports?
src/methods/geneformer/script.py
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| classifier_fine_tuned_dir = os.path.join(work_dir.name, "classifier_fine_tuned") | ||
| os.makedirs(classifier_fine_tuned_dir) |
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Maybe do this with the other directories just so everything is in one place?
src/methods/geneformer/script.py
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| print('Generate predictions', flush=True) | ||
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| import pickle |
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Also move this to the start of the file
src/methods/geneformer/script.py
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| # cc_eval = Classifier( | ||
| # classifier="cell", | ||
| # cell_state_dict = {"state_key": "celltype", "states": "all"}, | ||
| # nproc=n_processors, | ||
| # token_dictionary_file=dictionary_files["token"], | ||
| # num_crossval_splits=1, | ||
| # ) | ||
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| # all_metrics_test = cc_eval.evaluate_model( | ||
| # model=model, | ||
| # id_class_dict=id_class_dict, | ||
| # eval_data=test_data, | ||
| # num_classes=num_types, | ||
| # output_directory="classifier_predictions", | ||
| # output_prefix="predictions", | ||
| # ) |
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Proposed changes are described in the CHANGELOG.md
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