.. ATOM Data-Driven Modeling Pipeline documentation master file, created by sphinx-quickstart on Wed Jul 31 10:53:25 2019. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. ATOM Modeling PipeLine (AMPL) for Drug Discovery ================================================= .. include:: /_static/shared/links.rst `AMPL `_ is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery. The ATOM Modeling PipeLine (AMPL) extends the functionality of DeepChem and supports an array of machine learning and molecular featurization tools. AMPL is an end-to-end data-driven modeling pipeline to generate machine learning models that can predict key safety and pharmacokinetic-relevant parameters. AMPL has been benchmarked on a large collection of pharmaceutical datasets covering a wide range of parameters. Features -------- AMPL enables tasks for modeling and prediction from data ingestion to data analysis and can be broken down into the following stages: * Data ingestion and curation * Featurization * Model training and tuning * Prediction generation * Visualization and analysis * Details of running specific features are within the parameter (options) documentation. More detailed documentation is in the library documentation. Built with ---------- * `DeepChem `_: The basis for the graph convolution models * `RDKit `_: Molecular informatics library * `Mordred `_: Chemical descriptors * Other Python package dependencies .. toctree:: :maxdepth: 2 :caption: Getting Started get_started/introduction get_started/install get_started/install_with_docker get_started/running_ampl get_started/tests .. toctree:: :maxdepth: 2 :caption: Tutorials tutorials/ampl_tutorials_intro tutorials/01_data_curation tutorials/02_perform_a_split tutorials/03_train_regression_model tutorials/04_application_of_a_trained_model tutorials/05_hyperopt tutorials/06_compare_models tutorials/07_train_a_production_model tutorials/08_visualizations_of_model_performance .. toctree:: :maxdepth: 2 :caption: Advanced Concepts advanced/advanced_ampl_usage advanced/advanced_installation advanced/advanced_testing .. toctree:: :maxdepth: 1 :caption: API Package Reference modules .. toctree:: :maxdepth: 1 :caption: External Resources external/resources