Literature DB >> 34283864

A community-powered search of machine learning strategy space to find NMR property prediction models.

Lars A Bratholm1,2, Will Gerrard1, Brandon Anderson3,4,5, Shaojie Bai6,7, Sunghwan Choi8, Lam Dang9, Pavel Hanchar10, Addison Howard11, Sanghoon Kim12, Zico Kolter6,7, Risi Kondor3,4,13, Mordechai Kornbluth14, Youhan Lee15, Youngsoo Lee16, Jonathan P Mailoa14, Thanh Tu Nguyen9, Milos Popovic17, Goran Rakocevic17, Walter Reade11, Wonho Song18, Luka Stojanovic17, Erik H Thiede3,13, Nebojsa Tijanic17, Andres Torrubia19, Devin Willmott6, Craig P Butts1, David R Glowacki1,20,21.   

Abstract

The rise of machine learning (ML) has created an explosion in the potential strategies for using data to make scientific predictions. For physical scientists wishing to apply ML strategies to a particular domain, it can be difficult to assess in advance what strategy to adopt within a vast space of possibilities. Here we outline the results of an online community-powered effort to swarm search the space of ML strategies and develop algorithms for predicting atomic-pairwise nuclear magnetic resonance (NMR) properties in molecules. Using an open-source dataset, we worked with Kaggle to design and host a 3-month competition which received 47,800 ML model predictions from 2,700 teams in 84 countries. Within 3 weeks, the Kaggle community produced models with comparable accuracy to our best previously published 'in-house' efforts. A meta-ensemble model constructed as a linear combination of the top predictions has a prediction accuracy which exceeds that of any individual model, 7-19x better than our previous state-of-the-art. The results highlight the potential of transformer architectures for predicting quantum mechanical (QM) molecular properties.

Entities:  

Year:  2021        PMID: 34283864     DOI: 10.1371/journal.pone.0253612

Source DB:  PubMed          Journal:  PLoS One        ISSN: 1932-6203            Impact factor:   3.240


  24 in total

1.  Generalized neural-network representation of high-dimensional potential-energy surfaces.

Authors:  Jörg Behler; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2007-04-02       Impact factor: 9.161

2.  Atom-centered symmetry functions for constructing high-dimensional neural network potentials.

Authors:  Jörg Behler
Journal:  J Chem Phys       Date:  2011-02-21       Impact factor: 3.488

3.  Opinion: Toward an international definition of citizen science.

Authors:  Florian Heigl; Barbara Kieslinger; Katharina T Paul; Julia Uhlik; Daniel Dörler
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-23       Impact factor: 11.205

4.  Alchemical and structural distribution based representation for universal quantum machine learning.

Authors:  Felix A Faber; Anders S Christensen; Bing Huang; O Anatole von Lilienfeld
Journal:  J Chem Phys       Date:  2018-06-28       Impact factor: 3.488

5.  Superhuman AI for multiplayer poker.

Authors:  Noam Brown; Tuomas Sandholm
Journal:  Science       Date:  2019-07-11       Impact factor: 47.728

6.  Choosing experiments to accelerate collective discovery.

Authors:  Andrey Rzhetsky; Jacob G Foster; Ian T Foster; James A Evans
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-09       Impact factor: 11.205

7.  Human-level performance in 3D multiplayer games with population-based reinforcement learning.

Authors:  Max Jaderberg; Wojciech M Czarnecki; Iain Dunning; Luke Marris; Guy Lever; Antonio Garcia Castañeda; Charles Beattie; Neil C Rabinowitz; Ari S Morcos; Avraham Ruderman; Nicolas Sonnerat; Tim Green; Louise Deason; Joel Z Leibo; David Silver; Demis Hassabis; Koray Kavukcuoglu; Thore Graepel
Journal:  Science       Date:  2019-05-31       Impact factor: 47.728

8.  Predicting protein structures with a multiplayer online game.

Authors:  Seth Cooper; Firas Khatib; Adrien Treuille; Janos Barbero; Jeehyung Lee; Michael Beenen; Andrew Leaver-Fay; David Baker; Zoran Popović; Foldit Players
Journal:  Nature       Date:  2010-08-05       Impact factor: 49.962

9.  Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space.

Authors:  Katja Hansen; Franziska Biegler; Raghunathan Ramakrishnan; Wiktor Pronobis; O Anatole von Lilienfeld; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  J Phys Chem Lett       Date:  2015-06-18       Impact factor: 6.475

10.  Remote optimization of an ultracold atoms experiment by experts and citizen scientists.

Authors:  Robert Heck; Oana Vuculescu; Jens Jakob Sørensen; Jonathan Zoller; Morten G Andreasen; Mark G Bason; Poul Ejlertsen; Ottó Elíasson; Pinja Haikka; Jens S Laustsen; Lærke L Nielsen; Andrew Mao; Romain Müller; Mario Napolitano; Mads K Pedersen; Aske R Thorsen; Carsten Bergenholtz; Tommaso Calarco; Simone Montangero; Jacob F Sherson
Journal:  Proc Natl Acad Sci U S A       Date:  2018-11-09       Impact factor: 11.205

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  2 in total

1.  Predicting chemical shifts with graph neural networks.

Authors:  Ziyue Yang; Maghesree Chakraborty; Andrew D White
Journal:  Chem Sci       Date:  2021-07-09       Impact factor: 9.825

Review 2.  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

  2 in total

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