Literature DB >> 29960353

Less is more: Sampling chemical space with active learning.

Justin S Smith1, Ben Nebgen2, Nicholas Lubbers2, Olexandr Isayev3, Adrian E Roitberg1.   

Abstract

The development of accurate and transferable machine learning (ML) potentials for predicting molecular energetics is a challenging task. The process of data generation to train such ML potentials is a task neither well understood nor researched in detail. In this work, we present a fully automated approach for the generation of datasets with the intent of training universal ML potentials. It is based on the concept of active learning (AL) via Query by Committee (QBC), which uses the disagreement between an ensemble of ML potentials to infer the reliability of the ensemble's prediction. QBC allows the presented AL algorithm to automatically sample regions of chemical space where the ML potential fails to accurately predict the potential energy. AL improves the overall fitness of ANAKIN-ME (ANI) deep learning potentials in rigorous test cases by mitigating human biases in deciding what new training data to use. AL also reduces the training set size to a fraction of the data required when using naive random sampling techniques. To provide validation of our AL approach, we develop the COmprehensive Machine-learning Potential (COMP6) benchmark (publicly available on GitHub) which contains a diverse set of organic molecules. Active learning-based ANI potentials outperform the original random sampled ANI-1 potential with only 10% of the data, while the final active learning-based model vastly outperforms ANI-1 on the COMP6 benchmark after training to only 25% of the data. Finally, we show that our proposed AL technique develops a universal ANI potential (ANI-1x) that provides accurate energy and force predictions on the entire COMP6 benchmark. This universal ML potential achieves a level of accuracy on par with the best ML potentials for single molecules or materials, while remaining applicable to the general class of organic molecules composed of the elements CHNO.

Entities:  

Year:  2018        PMID: 29960353     DOI: 10.1063/1.5023802

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  41 in total

Review 1.  QSAR without borders.

Authors:  Eugene N Muratov; Jürgen Bajorath; Robert P Sheridan; Igor V Tetko; Dmitry Filimonov; Vladimir Poroikov; Tudor I Oprea; Igor I Baskin; Alexandre Varnek; Adrian Roitberg; Olexandr Isayev; Stefano Curtarolo; Denis Fourches; Yoram Cohen; Alan Aspuru-Guzik; David A Winkler; Dimitris Agrafiotis; Artem Cherkasov; Alexander Tropsha
Journal:  Chem Soc Rev       Date:  2020-05-01       Impact factor: 54.564

2.  Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease.

Authors:  Troy W Whitfield; Debra A Ragland; Konstantin B Zeldovich; Celia A Schiffer
Journal:  J Chem Theory Comput       Date:  2020-01-16       Impact factor: 6.006

3.  Transforming Computational Drug Discovery with Machine Learning and AI.

Authors:  Justin S Smith; Adrian E Roitberg; Olexandr Isayev
Journal:  ACS Med Chem Lett       Date:  2018-10-08       Impact factor: 4.345

4.  Predicting Molecular Energy Using Force-Field Optimized Geometries and Atomic Vector Representations Learned from an Improved Deep Tensor Neural Network.

Authors:  Jianing Lu; Cheng Wang; Yingkai Zhang
Journal:  J Chem Theory Comput       Date:  2019-06-12       Impact factor: 6.006

5.  Machine Learning for Electronically Excited States of Molecules.

Authors:  Julia Westermayr; Philipp Marquetand
Journal:  Chem Rev       Date:  2020-11-19       Impact factor: 60.622

6.  Learning to Make Chemical Predictions: the Interplay of Feature Representation, Data, and Machine Learning Methods.

Authors:  Mojtaba Haghighatlari; Jie Li; Farnaz Heidar-Zadeh; Yuchen Liu; Xingyi Guan; Teresa Head-Gordon
Journal:  Chem       Date:  2020-06-16       Impact factor: 22.804

7.  Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2019-09-17       Impact factor: 6.006

8.  Use of Interaction Energies in QM/MM Free Energy Simulations.

Authors:  Phillip S Hudson; H Lee Woodcock; Stefan Boresch
Journal:  J Chem Theory Comput       Date:  2019-07-02       Impact factor: 6.006

Review 9.  Ab Initio Machine Learning in Chemical Compound Space.

Authors:  Bing Huang; O Anatole von Lilienfeld
Journal:  Chem Rev       Date:  2021-08-13       Impact factor: 60.622

10.  Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning.

Authors:  Jianing Lu; Song Xia; Jieyu Lu; Yingkai Zhang
Journal:  J Chem Inf Model       Date:  2021-03-08       Impact factor: 4.956

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