Literature DB >> 30976107

Applications of machine learning in drug discovery and development.

Jessica Vamathevan1, Dominic Clark2, Paul Czodrowski3, Ian Dunham4, Edgardo Ferran2, George Lee5, Bin Li6, Anant Madabhushi7,8, Parantu Shah9, Michaela Spitzer4, Shanrong Zhao10.   

Abstract

Drug discovery and development pipelines are long, complex and depend on numerous factors. Machine learning (ML) approaches provide a set of tools that can improve discovery and decision making for well-specified questions with abundant, high-quality data. Opportunities to apply ML occur in all stages of drug discovery. Examples include target validation, identification of prognostic biomarkers and analysis of digital pathology data in clinical trials. Applications have ranged in context and methodology, with some approaches yielding accurate predictions and insights. The challenges of applying ML lie primarily with the lack of interpretability and repeatability of ML-generated results, which may limit their application. In all areas, systematic and comprehensive high-dimensional data still need to be generated. With ongoing efforts to tackle these issues, as well as increasing awareness of the factors needed to validate ML approaches, the application of ML can promote data-driven decision making and has the potential to speed up the process and reduce failure rates in drug discovery and development.

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Mesh:

Year:  2019        PMID: 30976107      PMCID: PMC6552674          DOI: 10.1038/s41573-019-0024-5

Source DB:  PubMed          Journal:  Nat Rev Drug Discov        ISSN: 1474-1776            Impact factor:   84.694


  106 in total

1.  MR fingerprinting Deep RecOnstruction NEtwork (DRONE).

Authors:  Ouri Cohen; Bo Zhu; Matthew S Rosen
Journal:  Magn Reson Med       Date:  2018-04-06       Impact factor: 4.668

2.  Deep neural nets as a method for quantitative structure-activity relationships.

Authors:  Junshui Ma; Robert P Sheridan; Andy Liaw; George E Dahl; Vladimir Svetnik
Journal:  J Chem Inf Model       Date:  2015-02-17       Impact factor: 4.956

3.  Fréchet ChemNet Distance: A Metric for Generative Models for Molecules in Drug Discovery.

Authors:  Kristina Preuer; Philipp Renz; Thomas Unterthiner; Sepp Hochreiter; Günter Klambauer
Journal:  J Chem Inf Model       Date:  2018-08-28       Impact factor: 4.956

4.  Deep Learning-A Technology With the Potential to Transform Health Care.

Authors:  Geoffrey Hinton
Journal:  JAMA       Date:  2018-09-18       Impact factor: 56.272

5.  Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy.

Authors:  Elena Sotillo; David M Barrett; Kathryn L Black; Asen Bagashev; Derek Oldridge; Glendon Wu; Robyn Sussman; Claudia Lanauze; Marco Ruella; Matthew R Gazzara; Nicole M Martinez; Colleen T Harrington; Elaine Y Chung; Jessica Perazzelli; Ted J Hofmann; Shannon L Maude; Pichai Raman; Alejandro Barrera; Saar Gill; Simon F Lacey; Jan J Melenhorst; David Allman; Elad Jacoby; Terry Fry; Crystal Mackall; Yoseph Barash; Kristen W Lynch; John M Maris; Stephan A Grupp; Andrei Thomas-Tikhonenko
Journal:  Cancer Discov       Date:  2015-10-29       Impact factor: 39.397

6.  Count on kappa.

Authors:  Paul Czodrowski
Journal:  J Comput Aided Mol Des       Date:  2014-07-11       Impact factor: 3.686

7.  Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.

Authors:  Joel Saltz; Rajarsi Gupta; Le Hou; Tahsin Kurc; Pankaj Singh; Vu Nguyen; Dimitris Samaras; Kenneth R Shroyer; Tianhao Zhao; Rebecca Batiste; John Van Arnam; Ilya Shmulevich; Arvind U K Rao; Alexander J Lazar; Ashish Sharma; Vésteinn Thorsson
Journal:  Cell Rep       Date:  2018-04-03       Impact factor: 9.423

8.  Maximum entropy methods for extracting the learned features of deep neural networks.

Authors:  Alex Finnegan; Jun S Song
Journal:  PLoS Comput Biol       Date:  2017-10-30       Impact factor: 4.475

9.  Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning.

Authors:  Nicolas Coudray; Paolo Santiago Ocampo; Theodore Sakellaropoulos; Navneet Narula; Matija Snuderl; David Fenyö; Andre L Moreira; Narges Razavian; Aristotelis Tsirigos
Journal:  Nat Med       Date:  2018-09-17       Impact factor: 53.440

10.  Deep Learning for Classification of Colorectal Polyps on Whole-slide Images.

Authors:  Bruno Korbar; Andrea M Olofson; Allen P Miraflor; Catherine M Nicka; Matthew A Suriawinata; Lorenzo Torresani; Arief A Suriawinata; Saeed Hassanpour
Journal:  J Pathol Inform       Date:  2017-07-25
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  204 in total

Review 1.  Opportunities and Challenges for Biosensors and Nanoscale Analytical Tools for Pandemics: COVID-19.

Authors:  Nikhil Bhalla; Yuwei Pan; Zhugen Yang; Amir Farokh Payam
Journal:  ACS Nano       Date:  2020-06-26       Impact factor: 15.881

2.  Machine Learning Attempts for Predicting Human Subcutaneous Bioavailability of Monoclonal Antibodies.

Authors:  Hao Lou; Michael J Hageman
Journal:  Pharm Res       Date:  2021-03-12       Impact factor: 4.200

Review 3.  Designing deep learning studies in cancer diagnostics.

Authors:  Andreas Kleppe; Ole-Johan Skrede; Sepp De Raedt; Knut Liestøl; David J Kerr; Håvard E Danielsen
Journal:  Nat Rev Cancer       Date:  2021-01-29       Impact factor: 60.716

Review 4.  Generative chemistry: drug discovery with deep learning generative models.

Authors:  Yuemin Bian; Xiang-Qun Xie
Journal:  J Mol Model       Date:  2021-02-04       Impact factor: 1.810

Review 5.  Recent advances in bioelectronics chemistry.

Authors:  Yin Fang; Lingyuan Meng; Aleksander Prominski; Erik N Schaumann; Matthew Seebald; Bozhi Tian
Journal:  Chem Soc Rev       Date:  2020-07-16       Impact factor: 54.564

6.  DOME: recommendations for supervised machine learning validation in biology.

Authors:  Ian Walsh; Dmytro Fishman; Dario Garcia-Gasulla; Tiina Titma; Gianluca Pollastri; Jennifer Harrow; Fotis E Psomopoulos; Silvio C E Tosatto
Journal:  Nat Methods       Date:  2021-07-27       Impact factor: 28.547

7.  Data Set Augmentation Allows Deep Learning-Based Virtual Screening to Better Generalize to Unseen Target Classes and Highlight Important Binding Interactions.

Authors:  Jack Scantlebury; Nathan Brown; Frank Von Delft; Charlotte M Deane
Journal:  J Chem Inf Model       Date:  2020-08-04       Impact factor: 4.956

Review 8.  Application of machine learning in the management of acute myeloid leukemia: current practice and future prospects.

Authors:  Jan-Niklas Eckardt; Martin Bornhäuser; Karsten Wendt; Jan Moritz Middeke
Journal:  Blood Adv       Date:  2020-12-08

9.  NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism.

Authors:  Anush Chiappino-Pepe; Kiandokht Haddadi; Homa MohammadiPeyhani; Jasmin Hafner; Noushin Hadadi; Vassily Hatzimanikatis
Journal:  Elife       Date:  2021-08-03       Impact factor: 8.140

10.  Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression.

Authors:  João Conde; Ruth A Pumroy; Charlotte Baker; Tiago Rodrigues; Ana Guerreiro; Bárbara B Sousa; Marta C Marques; Bernardo P de Almeida; Sohyon Lee; Elvira P Leites; Daniel Picard; Amrita Samanta; Sandra H Vaz; Florian Sieglitz; Maike Langini; Marc Remke; Rafael Roque; Tobias Weiss; Michael Weller; Yuhang Liu; Seungil Han; Francisco Corzana; Vanessa A Morais; Cláudia C Faria; Tânia Carvalho; Panagis Filippakopoulos; Berend Snijder; Nuno L Barbosa-Morais; Vera Y Moiseenkova-Bell; Gonçalo J L Bernardes
Journal:  ACS Cent Sci       Date:  2021-04-14       Impact factor: 14.553

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