AMPL: A Data-Driven Modeling Pipeline for Drug Discovery

11/13/2019 ∙ by Amanda J. Minnich, et al. ∙ 51

One of the key requirements for incorporating machine learning into the drug discovery process is complete reproducibility and traceability 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 machine learning 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 machine learning and molecular featurization tools. We have benchmarked AMPL on a large collection of pharmaceutical datasets covering a wide range of parameters. Our key findings include: Physicochemical descriptors and deep learning-based graph representations are significantly better than traditional fingerprints to characterize molecular features Dataset size is directly correlated to performance of prediction: single-task deep learning models only outperform shallow learners if there is enough data. Likewise, data set size has a direct impact of model predictivity independently of comprehensive hyperparameter model tuning. Our findings point to the need for public dataset integration or multi-task/transfer learning approaches. DeepChem uncertainty quantification (UQ) analysis may help identify model error; however, efficacy of UQ to filter predictions varies considerably between datasets and model types. This software is open source and available for download at



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Code Repositories


The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.

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