BERTology of Molecular Property Prediction (Cross-validated Hyperparameter Search: Base-BERT)

Cross-validated Hyperparameter Search Base-BERT This record pertains to Cross-validated Hyperparameter Search Experiments involving Base-BERT. It includes the following files: HLM-fold0-base-binidx-0-ms-1234-ds-2345.tar.gz HLM-fold0-base-binidx-3-ms-1234-ds-1234.tar.gz HLM-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz HLM-fold1-base-binidx-0-ms-1234-ds-2345.tar.gz HLM-fold1-base-binidx-3-ms-1234-ds-1234.tar.gz HLM-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz HLM-fold2-base-binidx-0-ms-1234-ds-2345.tar.gz HLM-fold2-base-binidx-3-ms-1234-ds-1234.tar.gz HLM-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz hPPB-fold0-base-binidx-0-ms-1234-ds-2345.tar.gz hPPB-fold0-base-binidx-3-ms-1234-ds-1234.tar.gz hPPB-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz hPPB-fold1-base-binidx-0-ms-1234-ds-2345.tar.gzhPPB-fold1-base-binidx-3-ms-1234-ds-1234.tar.gz hPPB-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz hPPB-fold2-base-binidx-0-ms-1234-ds-2345.tar.gz hPPB-fold2-base-binidx-3-ms-1234-ds-1234.tar.gz hPPB-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz MDR1_ER-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz MDR1_ER-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz MDR1_ER-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz RLM-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz RLM-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz RLM-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz rPPB-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz rPPB-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz rPPB-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz SOL-fold0-base-binidx-0-ms-1234-ds-2345.tar.gz SOL-fold0-base-binidx-3-ms-1234-ds-1234.tar.gz SOL-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz SOL-fold1-base-binidx-0-ms-1234-ds-2345.tar.gz SOL-fold1-base-binidx-3-ms-1234-ds-1234.tar.gz SOL-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz SOL-fold2-base-binidx-0-ms-1234-ds-2345.tar.gz SOL-fold2-base-binidx-3-ms-1234-ds-1234.tar.gz SOL-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz NOTES: The hyperparameter search and finetuning scripts are based on Biogen's codebases. As a result, the program design and many software development choices were not based on our own preferences or recommended best practices. As Base-BERT checkpoint files are very large, we have removed them and their corresponding W&B artifact cache files from the compressed files. Users can find the best cross-validated model checkpoints and their re-fitted variants, used for testing, in their corresponding Zenodo records. Preprint: https://doi.org/10.48550/arXiv.2603.13627