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

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Autores principales:	Mostafanejad, Mohammad, Saxe, Paul, Crawford, T. Daniel
Formato:	Recurso digital
Lenguaje:	inglés
Publicado:	Zenodo 2026
Materias:	Molecular property prediction Masked language modeling BERT ADME Pretraining Finetuning Chemical language models
Acceso en línea:	Acceder al recurso
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author	Mostafanejad, Mohammad Saxe, Paul Crawford, T. Daniel
author_facet	Mostafanejad, Mohammad Saxe, Paul Crawford, T. Daniel
contents	<div> <h1>Cross-validated Hyperparameter Search</h1> <h2>Base-BERT</h2> This record pertains to Cross-validated Hyperparameter Search Experiments involving Base-BERT.</div> <div>It includes the following files:</div> <div> <ul> <li>HLM-fold0-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>HLM-fold0-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold1-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>HLM-fold1-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold2-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>HLM-fold2-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold0-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>hPPB-fold0-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold1-base-binidx-0-ms-1234-ds-2345.tar.gz<br>hPPB-fold1-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold2-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>hPPB-fold2-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>MDR1_ER-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>MDR1_ER-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>MDR1_ER-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>RLM-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>RLM-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>RLM-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>rPPB-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>rPPB-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>rPPB-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold0-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>SOL-fold0-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold1-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>SOL-fold1-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold2-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>SOL-fold2-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> </ul> <p><strong>NOTES: </strong> </p> <ul> <li>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.</li> <li>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.</li> </ul> <p> </p> </div> <div> <div> <div><strong>Preprint: </strong>https://doi.org/10.48550/arXiv.2603.13627</div> </div> </div>
format	Recurso digital
id	zenodo_https___doi_org_10_5281_zenodo_19371494
institution	Zenodo
language	eng
publishDate	2026
publisher	Zenodo
record_format	zenodo
spellingShingle	BERTology of Molecular Property Prediction (Cross-validated Hyperparameter Search: Base-BERT) Mostafanejad, Mohammad Saxe, Paul Crawford, T. Daniel Molecular property prediction Masked language modeling BERT ADME Pretraining Finetuning Chemical language models <div> <h1>Cross-validated Hyperparameter Search</h1> <h2>Base-BERT</h2> This record pertains to Cross-validated Hyperparameter Search Experiments involving Base-BERT.</div> <div>It includes the following files:</div> <div> <ul> <li>HLM-fold0-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>HLM-fold0-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold1-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>HLM-fold1-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold2-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>HLM-fold2-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>HLM-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold0-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>hPPB-fold0-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold1-base-binidx-0-ms-1234-ds-2345.tar.gz<br>hPPB-fold1-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold2-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>hPPB-fold2-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>hPPB-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>MDR1_ER-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>MDR1_ER-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>MDR1_ER-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>RLM-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>RLM-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>RLM-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>rPPB-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>rPPB-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>rPPB-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold0-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>SOL-fold0-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold0-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold1-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>SOL-fold1-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold1-base-binidx-5-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold2-base-binidx-0-ms-1234-ds-2345.tar.gz</li> <li>SOL-fold2-base-binidx-3-ms-1234-ds-1234.tar.gz</li> <li>SOL-fold2-base-binidx-5-ms-1234-ds-1234.tar.gz</li> </ul> <p><strong>NOTES: </strong> </p> <ul> <li>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.</li> <li>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.</li> </ul> <p> </p> </div> <div> <div> <div><strong>Preprint: </strong>https://doi.org/10.48550/arXiv.2603.13627</div> </div> </div>
title	BERTology of Molecular Property Prediction (Cross-validated Hyperparameter Search: Base-BERT)
topic	Molecular property prediction Masked language modeling BERT ADME Pretraining Finetuning Chemical language models
url	https://doi.org/10.5281/zenodo.19371494