From intuition to AI: evolution of small molecule representations in drug discovery

M McGibbon, S Shave, J Dong, Y Gao… - Briefings in …, 2024 - academic.oup.com
Within drug discovery, the goal of AI scientists and cheminformaticians is to help identify
molecular starting points that will develop into safe and efficacious drugs while reducing …

A knowledge-guided pre-training framework for improving molecular representation learning

H Li, R Zhang, Y Min, D Ma, D Zhao, J Zeng - Nature Communications, 2023 - nature.com
Learning effective molecular feature representation to facilitate molecular property prediction
is of great significance for drug discovery. Recently, there has been a surge of interest in pre …

Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey

T Kuang, P Liu, Z Ren - Big Data Mining and Analytics, 2024 - ieeexplore.ieee.org
The precise prediction of molecular properties is essential for advancements in drug
development, particularly in virtual screening and compound optimization. The recent …

GCNSA: DNA storage encoding with a graph convolutional network and self-attention

B Cao, B Wang, Q Zhang - Iscience, 2023 - cell.com
DNA Encoding, as a key step in DNA storage, plays an important role in reading and writing
accuracy and the storage error rate. However, currently, the encoding efficiency is not high …

Synthetic pre-training for neural-network interatomic potentials

JLA Gardner, KT Baker… - Machine Learning: Science …, 2024 - iopscience.iop.org
Abstract Machine learning (ML) based interatomic potentials have transformed the field of
atomistic materials modelling. However, ML potentials depend critically on the quality and …

Molshap: Interpreting quantitative structure–activity relationships using shapley values of r-groups

T Tian, S Li, M Fang, D Zhao, J Zeng - Journal of Chemical …, 2023 - ACS Publications
Optimizing the activities and properties of lead compounds is an essential step in the drug
discovery process. Despite recent advances in machine learning-aided drug discovery, most …

Fast and effective molecular property prediction with transferability map

S Yao, J Song, L Jia, L Cheng, Z Zhong… - Communications …, 2024 - nature.com
Effective transfer learning for molecular property prediction has shown considerable strength
in addressing insufficient labeled molecules. Many existing methods either disregard the …

Quantifying the hardness of bioactivity prediction tasks for transfer learning

H Fooladi, S Hirte, J Kirchmair - Journal of Chemical Information …, 2024 - ACS Publications
Today, machine learning methods are widely employed in drug discovery. However, the
chronic lack of data continues to hamper their further development, validation, and …

A Review on Transferability Estimation in Deep Transfer Learning

Y Xue, R Yang, X Chen, W Liu… - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
Deep transfer learning has become increasingly prevalent in various fields such as industry
and medical science in recent years. To ensure the successful implementation of target …

Advanced deep learning methods for molecular property prediction

C Pang, HHY Tong, L Wei - Quantitative Biology, 2023 - Wiley Online Library
The prediction of molecular properties is a crucial task in the field of drug discovery.
Computational methods that can accurately predict molecular properties can significantly …