Transformer technology in molecular science

J Jiang, L Ke, L Chen, B Dou, Y Zhu… - Wiley …, 2024 - Wiley Online Library
A transformer is the foundational architecture behind large language models designed to
handle sequential data by using mechanisms of self‐attention to weigh the importance of …

[HTML][HTML] Gotta be SAFE: a new framework for molecular design

E Noutahi, C Gabellini, M Craig, JSC Lim, P Tossou - Digital Discovery, 2024 - pubs.rsc.org
Traditional molecular string representations, such as SMILES, often pose challenges for AI-
driven molecular design due to their non-sequential depiction of molecular substructures. To …

Application of Transformers in Cheminformatics

KD Luong, A Singh - Journal of Chemical Information and …, 2024 - ACS Publications
By accelerating time-consuming processes with high efficiency, computing has become an
essential part of many modern chemical pipelines. Machine learning is a class of computing …

SALSA: Semantically-Aware Latent Space Autoencoder

KE Kirchoff, T Maxfield, A Tropsha… - Proceedings of the AAAI …, 2024 - ojs.aaai.org
In deep learning for drug discovery, molecular representations are often based on
sequences, known as SMILES, which allow for straightforward implementation of natural …

ChemSpaceAL: An efficient active learning methodology applied to protein-specific molecular generation

GW Kyro, A Morgunov, RI Brent, VS Batista - Biophysical Journal, 2024 - cell.com
The incredible capabilities of generative artificial intelligence models have inevitably led to
their application in the domain of drug discovery. It is therefore of tremendous interest to …

Composition based oxidation state prediction of materials using deep learning

N Fu, J Hu, Y Feng, G Morrison, HC Loye… - arXiv preprint arXiv …, 2022 - arxiv.org
Oxidation states are the charges of atoms after their ionic approximation of their bonds,
which have been widely used in charge-neutrality verification, crystal structure …

CardioGenAI: A Machine Learning-Based Framework for Re-Engineering Drugs for Reduced hERG Liability

GW Kyro, MT Martin, ED Watt, VS Batista - arXiv preprint arXiv:2403.07632, 2024 - arxiv.org
Drug-induced cardiotoxicity is a major health concern which can lead to serious adverse
effects including life-threatening cardiac arrhythmias via the blockade of the voltage-gated …

A Large Encoder-Decoder Family of Foundation Models For Chemical Language

E Soares, V Shirasuna, EV Brazil, R Cerqueira… - arXiv preprint arXiv …, 2024 - arxiv.org
Large-scale pre-training methodologies for chemical language models represent a
breakthrough in cheminformatics. These methods excel in tasks such as property prediction …

Empirical Evidence for the Fragment level Understanding on Drug Molecular Structure of LLMs

X Hu, G Liu, Y Zhao, H Zhang - arXiv preprint arXiv:2401.07657, 2024 - arxiv.org
AI for drug discovery has been a research hotspot in recent years, and SMILES-based
language models has been increasingly applied in drug molecular design. However, no …

Learning Improved Representations Through Informed Self-Supervision: Applications to Drug Discovery

KE Kirchoff - 2024 - search.proquest.com
In recent years, deep learning methodologies have afforded unparalleled computational
advancements, from artistic generation and self-driving cars, to voice assistants and …