[HTML][HTML] Deep learning for low-data drug discovery: hurdles and opportunities

D van Tilborg, H Brinkmann, E Criscuolo… - Current Opinion in …, 2024 - Elsevier
Deep learning is becoming increasingly relevant in drug discovery, from de novo design to
protein structure prediction and synthesis planning. However, it is often challenged by the …

Exposing the limitations of molecular machine learning with activity cliffs

D Van Tilborg, A Alenicheva… - Journal of chemical …, 2022 - ACS Publications
Machine learning has become a crucial tool in drug discovery and chemistry at large, eg, to
predict molecular properties, such as bioactivity, with high accuracy. However, activity …

Effect of dataset size and train/test split ratios in QSAR/QSPR multiclass classification

A Rácz, D Bajusz, K Héberger - Molecules, 2021 - mdpi.com
Applied datasets can vary from a few hundred to thousands of samples in typical quantitative
structure-activity/property (QSAR/QSPR) relationships and classification. However, the size …

Understanding the limitations of deep models for molecular property prediction: Insights and solutions

J Xia, L Zhang, X Zhu, Y Liu, Z Gao… - Advances in …, 2023 - proceedings.neurips.cc
Abstract Molecular Property Prediction (MPP) is a crucial task in the AI-driven Drug
Discovery (AIDD) pipeline, which has recently gained considerable attention thanks to …

Oxy-fuel and air atmosphere combustions of Chinese medicine residues: performances, mechanisms, flue gas emission, and ash properties

Z Chen, J Liu, H Chen, Z Ding, X Tang, F Evrendilek - Renewable Energy, 2022 - Elsevier
This study aims to quantify the combustion performances, mechanisms, and ash
characteristics of Chinese medicine residues (CMR) in the air and oxy-fuel atmospheres …

Machine learning and computational chemistry for the endocannabinoid system

K Atz, W Guba, U Grether, G Schneider - … Signaling: Methods and …, 2022 - Springer
Computational methods in medicinal chemistry facilitate drug discovery and design. In
particular, machine learning methodologies have recently gained increasing attention. This …

CatNet: Sequence-based deep learning with cross-attention mechanism for identifying endocrine-disrupting chemicals

L Zhao, Q Xue, H Zhang, Y Hao, H Yi, X Liu… - Journal of Hazardous …, 2024 - Elsevier
Endocrine-disrupting chemicals (EDCs) pose significant environmental and health risks due
to their potential to interfere with nuclear receptors (NRs), key regulators of physiological …

Profiling prediction of nuclear receptor modulators with multi-task deep learning methods: toward the virtual screening

J Wang, C Lou, G Liu, W Li, Z Wu… - Briefings in …, 2022 - academic.oup.com
Nuclear receptors (NRs) are ligand-activated transcription factors, which constitute one of
the most important targets for drug discovery. Current computational strategies mainly focus …

Parsimonious optimization of multitask neural network hyperparameters

C Valsecchi, V Consonni, R Todeschini, ME Orlandi… - Molecules, 2021 - mdpi.com
Neural networks are rapidly gaining popularity in chemical modeling and Quantitative
Structure–Activity Relationship (QSAR) thanks to their ability to handle multitask problems …

Why Deep Models Often Cannot Beat Non-deep Counterparts on Molecular Property Prediction?

J Xia, L Zhang, X Zhu, SZ Li - arXiv preprint arXiv:2306.17702, 2023 - arxiv.org
Molecular property prediction (MPP) is a crucial task in the drug discovery pipeline, which
has recently gained considerable attention thanks to advances in deep neural networks …