Update data_processing.py #3
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atabeyunlu
requested changes
Feb 13, 2025
| @@ -294,13 +306,85 @@ def create_act_inact_files_similarity_based_neg_enrichment_threshold(act_inact_f | |||
| act_inact_count_fl.close() | |||
| act_inact_comp_fl.close() | |||
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| def create_final_randomized_training_val_test_sets(activity_data,max_cores,targetid,target_prediction_dataset_path, pchembl_threshold=6): | |||
| def create_final_randomized_training_val_test_sets(activity_data,max_cores,scaffold,targetid,target_prediction_dataset_path,moleculenet ,pchembl_threshold=6): | |||
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Here we need to take another approach. Please first look at this code to understand how we did the moleculenet split in the SELFormer. https://github.com/HUBioDataLab/SELFormer/blob/65e686feb72185cc95f5b81176444e20586848e1/prepare_finetuning_data.py#L42
What you did is not wrong but a bit problematic. We can just choose the last column (-1) for the label for classification and regression, and we can select a slice (e.g. 1:17). Now please examine the above code and write the function again. Also you can use a flag for MoleculeNet at the main_training part to route the moleculenet datasets to the new train_test function.
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