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 …

Artificial intelligence for compound pharmacokinetics prediction

O Obrezanova - Current Opinion in Structural Biology, 2023 - Elsevier
Optimisation of compound pharmacokinetics (PK) is an integral part of drug discovery and
development. Animal in vivo PK data as well as human and animal in vitro systems are …

Explainable artificial intelligence: A taxonomy and guidelines for its application to drug discovery

I Ponzoni, JA Páez Prosper… - Wiley Interdisciplinary …, 2023 - Wiley Online Library
Artificial intelligence (AI) is having a growing impact in many areas related to drug discovery.
However, it is still critical for their adoption by the medicinal chemistry community to achieve …

Computational predictions of nonclinical pharmacokinetics at the drug design stage

R Stoyanova, PM Katzberger… - Journal of Chemical …, 2023 - ACS Publications
Although computational predictions of pharmacokinetics (PK) are desirable at the drug
design stage, existing approaches are often limited by prediction accuracy and human …

Explainable artificial intelligence for drug discovery and development-a comprehensive survey

R Alizadehsani, SS Oyelere, S Hussain… - IEEE …, 2024 - ieeexplore.ieee.org
The field of drug discovery has experienced a remarkable transformation with the advent of
artificial intelligence (AI) and machine learning (ML) technologies. However, as these AI and …

Explainability and white box in drug discovery

KK Kırboğa, S Abbasi… - Chemical Biology & Drug …, 2023 - Wiley Online Library
Recently, artificial intelligence (AI) techniques have been increasingly used to overcome the
challenges in drug discovery. Although traditional AI techniques generally have high …

General graph neural network-based model to accurately predict cocrystal density and insight from data quality and feature representation

J Guo, M Sun, X Zhao, C Shi, H Su… - Journal of Chemical …, 2023 - ACS Publications
Cocrystal engineering as an effective way to modify solid-state properties has inspired great
interest from diverse material fields while cocrystal density is an important property closely …

Enhancing property and activity prediction and interpretation using multiple molecular graph representations with MMGX

A Kengkanna, M Ohue - Communications Chemistry, 2024 - nature.com
Abstract Graph Neural Networks (GNNs) excel in compound property and activity prediction,
but the choice of molecular graph representations significantly influences model learning …

SmartCADD: AI-QM Empowered Drug Discovery Platform with Explainability

A Madushanka, E Laird, C Clark… - Journal of Chemical …, 2024 - ACS Publications
Artificial intelligence (AI) has emerged as a pivotal force in enhancing productivity across
various sectors, with its impact being profoundly felt within the pharmaceutical and …

Atom typing using graph representation learning: How do models learn chemistry?

J Zhang - The Journal of Chemical Physics, 2022 - pubs.aip.org
Atom typing is the first step for simulating molecules using a force field. Automatic atom
typing for an arbitrary molecule is often realized by rule-based algorithms, which have to …