Drug discovery with explainable artificial intelligence

J Jiménez-Luna, F Grisoni, G Schneider - Nature Machine Intelligence, 2020 - nature.com
Deep learning bears promise for drug discovery, including advanced image analysis,
prediction of molecular structure and function, and automated generation of innovative …

Autonomous discovery in the chemical sciences part I: Progress

CW Coley, NS Eyke, KF Jensen - … Chemie International Edition, 2020 - Wiley Online Library
This two‐part Review examines how automation has contributed to different aspects of
discovery in the chemical sciences. In this first part, we describe a classification for …

Interpretation of quantitative structure–activity relationship models: past, present, and future

P Polishchuk - Journal of Chemical Information and Modeling, 2017 - ACS Publications
This paper is an overview of the most significant and impactful interpretation approaches of
quantitative structure–activity relationship (QSAR) models, their development, and …

Explainable machine learning for property predictions in compound optimization: miniperspective

R Rodríguez-Pérez, J Bajorath - Journal of medicinal chemistry, 2021 - ACS Publications
The prediction of compound properties from chemical structure is a main task for machine
learning (ML) in medicinal chemistry. ML is often applied to large data sets in applications …

Coloring molecules with explainable artificial intelligence for preclinical relevance assessment

J Jiménez-Luna, M Skalic, N Weskamp… - Journal of Chemical …, 2021 - ACS Publications
Graph neural networks are able to solve certain drug discovery tasks such as molecular
property prediction and de novo molecule generation. However, these models are …

A perspective on explanations of molecular prediction models

GP Wellawatte, HA Gandhi, A Seshadri… - Journal of Chemical …, 2023 - ACS Publications
Chemists can be skeptical in using deep learning (DL) in decision making, due to the lack of
interpretability in “black-box” models. Explainable artificial intelligence (XAI) is a branch of …

Chemical-informatics approach to COVID-19 drug discovery: Exploration of important fragments and data mining based prediction of some hits from natural origins as …

K Ghosh, SA Amin, S Gayen, T Jha - Journal of Molecular Structure, 2021 - Elsevier
As the world struggles against current global pandemic of novel coronavirus disease
(COVID-19), it is challenging to trigger drug discovery efforts to search broad-spectrum …

Benchmarks for interpretation of QSAR models

M Matveieva, P Polishchuk - Journal of cheminformatics, 2021 - Springer
Abstract Interpretation of QSAR models is useful to understand the complex nature of
biological or physicochemical processes, guide structural optimization or perform …

Comparison of the predictive performance and interpretability of random forest and linear models on benchmark data sets

RL Marchese Robinson, A Palczewska… - Journal of chemical …, 2017 - ACS Publications
The ability to interpret the predictions made by quantitative structure–activity relationships
(QSARs) offers a number of advantages. While QSARs built using nonlinear modeling …

Benchmarking molecular feature attribution methods with activity cliffs

J Jiménez-Luna, M Skalic… - Journal of Chemical …, 2022 - ACS Publications
Feature attribution techniques are popular choices within the explainable artificial
intelligence toolbox, as they can help elucidate which parts of the provided inputs used by …