Literature DB >> 30336670

Adversarial Controls for Scientific Machine Learning.

Kangway V Chuang1, Michael J Keiser1.   

Abstract

New machine learning methods to analyze raw chemical and biological data are now widely accessible as open-source toolkits. This positions researchers to leverage powerful, predictive models in their own domains. We caution, however, that the application of machine learning to experimental research merits careful consideration. Machine learning algorithms readily exploit confounding variables and experimental artifacts instead of relevant patterns, leading to overoptimistic performance and poor model generalization. In parallel to the strong control experiments that remain a cornerstone of experimental research, we advance the concept of adversarial controls for scientific machine learning: the design of exacting and purposeful experiments to ensure that predictive performance arises from meaningful models.

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Mesh:

Year:  2018        PMID: 30336670     DOI: 10.1021/acschembio.8b00881

Source DB:  PubMed          Journal:  ACS Chem Biol        ISSN: 1554-8929            Impact factor:   5.100


  11 in total

Review 1.  Big-Data Science in Porous Materials: Materials Genomics and Machine Learning.

Authors:  Kevin Maik Jablonka; Daniele Ongari; Seyed Mohamad Moosavi; Berend Smit
Journal:  Chem Rev       Date:  2020-06-10       Impact factor: 60.622

2.  Using attribution to decode binding mechanism in neural network models for chemistry.

Authors:  Kevin McCloskey; Ankur Taly; Federico Monti; Michael P Brenner; Lucy J Colwell
Journal:  Proc Natl Acad Sci U S A       Date:  2019-05-24       Impact factor: 11.205

3.  Exploiting machine learning for end-to-end drug discovery and development.

Authors:  Sean Ekins; Ana C Puhl; Kimberley M Zorn; Thomas R Lane; Daniel P Russo; Jennifer J Klein; Anthony J Hickey; Alex M Clark
Journal:  Nat Mater       Date:  2019-04-18       Impact factor: 43.841

4.  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

5.  Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes.

Authors:  Matthew G Durrant; Ami S Bhatt
Journal:  Cell Host Microbe       Date:  2020-12-07       Impact factor: 21.023

6.  Computationally guided high-throughput design of self-assembling drug nanoparticles.

Authors:  Daniel Reker; Yulia Rybakova; Ameya R Kirtane; Ruonan Cao; Jee Won Yang; Natsuda Navamajiti; Apolonia Gardner; Rosanna M Zhang; Tina Esfandiary; Johanna L'Heureux; Thomas von Erlach; Elena M Smekalova; Dominique Leboeuf; Kaitlyn Hess; Aaron Lopes; Jaimie Rogner; Joy Collins; Siddartha M Tamang; Keiko Ishida; Paul Chamberlain; DongSoo Yun; Abigail Lytton-Jean; Christian K Soule; Jaime H Cheah; Alison M Hayward; Robert Langer; Giovanni Traverso
Journal:  Nat Nanotechnol       Date:  2021-03-25       Impact factor: 40.523

7.  Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline.

Authors:  Ziqi Tang; Kangway V Chuang; Charles DeCarli; Lee-Way Jin; Laurel Beckett; Michael J Keiser; Brittany N Dugger
Journal:  Nat Commun       Date:  2019-05-15       Impact factor: 14.919

Review 8.  Deep Learning for Deep Chemistry: Optimizing the Prediction of Chemical Patterns.

Authors:  Tânia F G G Cova; Alberto A C C Pais
Journal:  Front Chem       Date:  2019-11-26       Impact factor: 5.221

9.  Exploring Novel Biologically-Relevant Chemical Space Through Artificial Intelligence: The NCATS ASPIRE Program.

Authors:  Katharine K Duncan; Dobrila D Rudnicki; Christopher P Austin; Danilo A Tagle
Journal:  Front Robot AI       Date:  2020-01-10

10.  Ten quick tips for deep learning in biology.

Authors:  Benjamin D Lee; Anthony Gitter; Casey S Greene; Sebastian Raschka; Finlay Maguire; Alexander J Titus; Michael D Kessler; Alexandra J Lee; Marc G Chevrette; Paul Allen Stewart; Thiago Britto-Borges; Evan M Cofer; Kun-Hsing Yu; Juan Jose Carmona; Elana J Fertig; Alexandr A Kalinin; Brandon Signal; Benjamin J Lengerich; Timothy J Triche; Simina M Boca
Journal:  PLoS Comput Biol       Date:  2022-03-24       Impact factor: 4.475

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