Dataset Information

AMPL: A Data-Driven Modeling Pipeline for Drug Discovery.

ABSTRACT: One of the key requirements for incorporating machine learning (ML) into the drug discovery process is complete traceability and reproducibility of the model building and evaluation process. With this in mind, we have developed an end-to-end modular and extensible software pipeline for building and sharing ML models that predict key pharma-relevant parameters. The ATOM Modeling PipeLine, or AMPL, extends the functionality of the open source library DeepChem and supports an array of ML and molecular featurization tools. We have benchmarked AMPL on a large collection of pharmaceutical data sets covering a wide range of parameters. Our key findings indicate that traditional molecular fingerprints underperform other feature representation methods. We also find that data set size correlates directly with prediction performance, which points to the need to expand public data sets. Uncertainty quantification can help predict model error, but correlation with error varies considerably between data sets and model types. Our findings point to the need for an extensible pipeline that can be shared to make model building more widely accessible and reproducible. This software is open source and available at: https://github.com/ATOMconsortium/AMPL.

SUBMITTER: Minnich AJ

PROVIDER: S-EPMC7189366 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Publications

AMPL: A Data-Driven Modeling Pipeline for Drug Discovery.

Minnich Amanda J AJ McLoughlin Kevin K Tse Margaret M Deng Jason J Weber Andrew A Murad Neha N Madej Benjamin D BD Ramsundar Bharath B Rush Tom T Calad-Thomson Stacie S Brase Jim J Allen Jonathan E JE

Journal of chemical information and modeling 20200416 4

One of the key requirements for incorporating machine learning (ML) into the drug discovery process is complete traceability and reproducibility of the model building and evaluation process. With this in mind, we have developed an end-to-end modular and extensible software pipeline for building and sharing ML models that predict key pharma-relevant parameters. The ATOM Modeling PipeLine, or AMPL, extends the functionality of the open source library DeepChem and supports an array of ML and molecu ...[more]

PMID: 32243153

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Dataset Information

AMPL: A Data-Driven Modeling Pipeline for Drug Discovery.

Publications

AMPL: A Data-Driven Modeling Pipeline for Drug Discovery.

Similar Datasets

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