Literature DB >> 32091880

What Does the Machine Learn? Knowledge Representations of Chemical Reactivity.

Joshua A Kammeraad1, Jack Goetz2, Eric A Walker1, Ambuj Tewari2, Paul M Zimmerman1.   

Abstract

In a departure from conventional chemical approaches, data-driven models of chemical reactions have recently been shown to be statistically successful using machine learning. These models, however, are largely black box in character and have not provided the kind of chemical insights that historically advanced the field of chemistry. To examine the knowledgebase of machine-learning models-what does the machine learn-this article deconstructs black-box machine-learning models of a diverse chemical reaction data set. Through experimentation with chemical representations and modeling techniques, the analysis provides insights into the nature of how statistical accuracy can arise, even when the model lacks informative physical principles. By peeling back the layers of these complicated models we arrive at a minimal, chemically intuitive model (and no machine learning involved). This model is based on systematic reaction-type classification and Evans-Polanyi relationships within reaction types which are easily visualized and interpreted. Through exploring this simple model, we gain deeper understanding of the data set and uncover a means for expert interactions to improve the model's reliability.

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Mesh:

Year:  2020        PMID: 32091880      PMCID: PMC7166311          DOI: 10.1021/acs.jcim.9b00721

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  54 in total

1.  GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations.

Authors:  Julio Daniel Carvalho Maia; Gabriel Aires Urquiza Carvalho; Carlos Peixoto Mangueira; Sidney Ramos Santana; Lucidio Anjos Formiga Cabral; Gerd B Rocha
Journal:  J Chem Theory Comput       Date:  2012-08-13       Impact factor: 6.006

2.  Computer-aided molecular design of solvents for accelerated reaction kinetics.

Authors:  Heiko Struebing; Zara Ganase; Panagiotis G Karamertzanis; Eirini Siougkrou; Peter Haycock; Patrick M Piccione; Alan Armstrong; Amparo Galindo; Claire S Adjiman
Journal:  Nat Chem       Date:  2013-09-22       Impact factor: 24.427

3.  Development of a novel fingerprint for chemical reactions and its application to large-scale reaction classification and similarity.

Authors:  Nadine Schneider; Daniel M Lowe; Roger A Sayle; Gregory A Landrum
Journal:  J Chem Inf Model       Date:  2015-01-13       Impact factor: 4.956

4.  "Found in Translation": predicting outcomes of complex organic chemistry reactions using neural sequence-to-sequence models.

Authors:  Philippe Schwaller; Théophile Gaudin; Dávid Lányi; Costas Bekas; Teodoro Laino
Journal:  Chem Sci       Date:  2018-06-22       Impact factor: 9.825

5.  Many-Body Descriptors for Predicting Molecular Properties with Machine Learning: Analysis of Pairwise and Three-Body Interactions in Molecules.

Authors:  Wiktor Pronobis; Alexandre Tkatchenko; Klaus-Robert Müller
Journal:  J Chem Theory Comput       Date:  2018-05-31       Impact factor: 6.006

6.  Neural Networks for the Prediction of Organic Chemistry Reactions.

Authors:  Jennifer N Wei; David Duvenaud; Alán Aspuru-Guzik
Journal:  ACS Cent Sci       Date:  2016-10-14       Impact factor: 14.553

7.  Prediction of Organic Reaction Outcomes Using Machine Learning.

Authors:  Connor W Coley; Regina Barzilay; Tommi S Jaakkola; William H Green; Klavs F Jensen
Journal:  ACS Cent Sci       Date:  2017-04-18       Impact factor: 14.553

8.  ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost.

Authors:  J S Smith; O Isayev; A E Roitberg
Journal:  Chem Sci       Date:  2017-02-08       Impact factor: 9.825

9.  Database fingerprint (DFP): an approach to represent molecular databases.

Authors:  Eli Fernández-de Gortari; César R García-Jacas; Karina Martinez-Mayorga; José L Medina-Franco
Journal:  J Cheminform       Date:  2017-02-06       Impact factor: 5.514

10.  Controlling an organic synthesis robot with machine learning to search for new reactivity.

Authors:  Jarosław M Granda; Liva Donina; Vincenza Dragone; De-Liang Long; Leroy Cronin
Journal:  Nature       Date:  2018-07-18       Impact factor: 49.962

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  1 in total

1.  Predicting reaction conditions from limited data through active transfer learning.

Authors:  Eunjae Shim; Joshua A Kammeraad; Ziping Xu; Ambuj Tewari; Tim Cernak; Paul M Zimmerman
Journal:  Chem Sci       Date:  2022-05-11       Impact factor: 9.969

  1 in total

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