Literature DB >> 33386095

On failure modes in molecule generation and optimization.

Philipp Renz1, Dries Van Rompaey2, Jörg Kurt Wegner2, Sepp Hochreiter1, Günter Klambauer1.   

Abstract

There has been a wave of generative models for molecules triggered by advances in the field of Deep Learning. These generative models are often used to optimize chemical compounds towards particular properties or a desired biological activity. The evaluation of generative models remains challenging and suggested performance metrics or scoring functions often do not cover all relevant aspects of drug design projects. In this work, we highlight some unintended failure modes in molecular generation and optimization and how these evade detection by current performance metrics.
Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Keywords:  De novo molecule generation; Generative models for molecules; Machine learning

Year:  2020        PMID: 33386095     DOI: 10.1016/j.ddtec.2020.09.003

Source DB:  PubMed          Journal:  Drug Discov Today Technol        ISSN: 1740-6749


  11 in total

1.  Systemic evolutionary chemical space exploration for drug discovery.

Authors:  Chong Lu; Shien Liu; Weihua Shi; Jun Yu; Zhou Zhou; Xiaoxiao Zhang; Xiaoli Lu; Faji Cai; Ning Xia; Yikai Wang
Journal:  J Cheminform       Date:  2022-04-01       Impact factor: 5.514

2.  Graph-based molecular Pareto optimisation.

Authors:  Jonas Verhellen
Journal:  Chem Sci       Date:  2022-06-02       Impact factor: 9.969

Review 3.  De novo molecular drug design benchmarking.

Authors:  Lauren L Grant; Clarissa S Sit
Journal:  RSC Med Chem       Date:  2021-06-03

4.  Language models can learn complex molecular distributions.

Authors:  Daniel Flam-Shepherd; Kevin Zhu; Alán Aspuru-Guzik
Journal:  Nat Commun       Date:  2022-06-07       Impact factor: 17.694

5.  Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study.

Authors:  Morgan Thomas; Robert T Smith; Noel M O'Boyle; Chris de Graaf; Andreas Bender
Journal:  J Cheminform       Date:  2021-05-13       Impact factor: 5.514

6.  Explaining and avoiding failure modes in goal-directed generation of small molecules.

Authors:  Maxime Langevin; Rodolphe Vuilleumier; Marc Bianciotto
Journal:  J Cheminform       Date:  2022-04-01       Impact factor: 5.514

7.  In silico proof of principle of machine learning-based antibody design at unconstrained scale.

Authors:  Rahmad Akbar; Philippe A Robert; Cédric R Weber; Michael Widrich; Robert Frank; Milena Pavlović; Lonneke Scheffer; Maria Chernigovskaya; Igor Snapkov; Andrei Slabodkin; Brij Bhushan Mehta; Enkelejda Miho; Fridtjof Lund-Johansen; Jan Terje Andersen; Sepp Hochreiter; Ingrid Hobæk Haff; Günter Klambauer; Geir Kjetil Sandve; Victor Greiff
Journal:  MAbs       Date:  2022 Jan-Dec       Impact factor: 5.857

Review 8.  Defining Levels of Automated Chemical Design.

Authors:  Brian Goldman; Steven Kearnes; Trevor Kramer; Patrick Riley; W Patrick Walters
Journal:  J Med Chem       Date:  2022-05-05       Impact factor: 8.039

Review 9.  Improving Few- and Zero-Shot Reaction Template Prediction Using Modern Hopfield Networks.

Authors:  Philipp Seidl; Philipp Renz; Natalia Dyubankova; Paulo Neves; Jonas Verhoeven; Jörg K Wegner; Marwin Segler; Sepp Hochreiter; Günter Klambauer
Journal:  J Chem Inf Model       Date:  2022-01-15       Impact factor: 6.162

10.  Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation.

Authors:  Morgan Thomas; Noel M O'Boyle; Andreas Bender; Chris de Graaf
Journal:  J Cheminform       Date:  2022-10-03       Impact factor: 8.489

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