Literature DB >> 32695924

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

Mojtaba Haghighatlari1, Jie Li1, Farnaz Heidar-Zadeh1,2,3, Yuchen Liu1, Xingyi Guan1, Teresa Head-Gordon1,4,5.   

Abstract

Recently supervised machine learning has been ascending in providing new predictive approaches for chemical, biological and materials sciences applications. In this Perspective we focus on the interplay of machine learning method with the chemically motivated descriptors and the size and type of data sets needed for molecular property prediction. Using Nuclear Magnetic Resonance chemical shift prediction as an example, we demonstrate that success is predicated on the choice of feature extracted or real-space representations of chemical structures, whether the molecular property data is abundant and/or experimentally or computationally derived, and how these together will influence the correct choice of popular machine learning methods drawn from deep learning, random forests, or kernel methods.

Entities:  

Year:  2020        PMID: 32695924      PMCID: PMC7373218          DOI: 10.1016/j.chempr.2020.05.014

Source DB:  PubMed          Journal:  Chem            Impact factor:   22.804


  41 in total

1.  Random forest: a classification and regression tool for compound classification and QSAR modeling.

Authors:  Vladimir Svetnik; Andy Liaw; Christopher Tong; J Christopher Culberson; Robert P Sheridan; Bradley P Feuston
Journal:  J Chem Inf Comput Sci       Date:  2003 Nov-Dec

Review 2.  Prediction of physicochemical properties based on neural network modelling.

Authors:  Jyrki Taskinen; Jouko Yliruusi
Journal:  Adv Drug Deliv Rev       Date:  2003-09-12       Impact factor: 15.470

3.  Solid harmonic wavelet scattering for predictions of molecule properties.

Authors:  Michael Eickenberg; Georgios Exarchakis; Matthew Hirn; Stéphane Mallat; Louis Thiry
Journal:  J Chem Phys       Date:  2018-06-28       Impact factor: 3.488

4.  NMR Crystallography: Evaluation of Hydrogen Positions in Hydromagnesite by 13 C{1 H} REDOR Solid-State NMR and Density Functional Theory Calculation of Chemical Shielding Tensors.

Authors:  Jinlei Cui; David L Olmsted; Anil K Mehta; Mark Asta; Sophia E Hayes
Journal:  Angew Chem Int Ed Engl       Date:  2019-02-20       Impact factor: 15.336

5.  SHIFTX2: significantly improved protein chemical shift prediction.

Authors:  Beomsoo Han; Yifeng Liu; Simon W Ginzinger; David S Wishart
Journal:  J Biomol NMR       Date:  2011-03-30       Impact factor: 2.835

Review 6.  Machine learning approaches for analyzing and enhancing molecular dynamics simulations.

Authors:  Yihang Wang; João Marcelo Lamim Ribeiro; Pratyush Tiwary
Journal:  Curr Opin Struct Biol       Date:  2020-01-20       Impact factor: 6.809

7.  End-to-End Differentiable Learning of Protein Structure.

Authors:  Mohammed AlQuraishi
Journal:  Cell Syst       Date:  2019-04-17       Impact factor: 10.304

8.  3D deep convolutional neural networks for amino acid environment similarity analysis.

Authors:  Wen Torng; Russ B Altman
Journal:  BMC Bioinformatics       Date:  2017-06-14       Impact factor: 3.169

9.  EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation.

Authors:  Afshine Amidi; Shervine Amidi; Dimitrios Vlachakis; Vasileios Megalooikonomou; Nikos Paragios; Evangelia I Zacharaki
Journal:  PeerJ       Date:  2018-05-04       Impact factor: 2.984

10.  Enhancing materials property prediction by leveraging computational and experimental data using deep transfer learning.

Authors:  Dipendra Jha; Kamal Choudhary; Francesca Tavazza; Wei-Keng Liao; Alok Choudhary; Carelyn Campbell; Ankit Agrawal
Journal:  Nat Commun       Date:  2019-11-22       Impact factor: 14.919

View more
  7 in total

1.  Machine Learning for Electronically Excited States of Molecules.

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

2.  Mechanisms, Challenges, and Opportunities of Dual Ni/Photoredox-Catalyzed C(sp2)-C(sp3) Cross-Couplings.

Authors:  Mingbin Yuan; Osvaldo Gutierrez
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2021-09-21

3.  A benchmark dataset for Hydrogen Combustion.

Authors:  Xingyi Guan; Akshaya Das; Christopher J Stein; Farnaz Heidar-Zadeh; Luke Bertels; Meili Liu; Mojtaba Haghighatlari; Jie Li; Oufan Zhang; Hongxia Hao; Itai Leven; Martin Head-Gordon; Teresa Head-Gordon
Journal:  Sci Data       Date:  2022-05-17       Impact factor: 8.501

Review 4.  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

5.  Pushing the limits of solubility prediction via quality-oriented data selection.

Authors:  Murat Cihan Sorkun; J M Vianney A Koelman; Süleyman Er
Journal:  iScience       Date:  2020-12-17

Review 6.  Artificial intelligence and machine learning approaches for drug design: challenges and opportunities for the pharmaceutical industries.

Authors:  Chandrabose Selvaraj; Ishwar Chandra; Sanjeev Kumar Singh
Journal:  Mol Divers       Date:  2021-10-23       Impact factor: 2.943

Review 7.  Machine learning models for classification tasks related to drug safety.

Authors:  Anita Rácz; Dávid Bajusz; Ramón Alain Miranda-Quintana; Károly Héberger
Journal:  Mol Divers       Date:  2021-06-10       Impact factor: 3.364

  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.