Large language models on graphs: A comprehensive survey

B Jin, G Liu, C Han, M Jiang, H Ji… - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
Large language models (LLMs), such as GPT4 and LLaMA, are creating significant
advancements in natural language processing, due to their strong text encoding/decoding …

Geometric deep learning on molecular representations

K Atz, F Grisoni, G Schneider - Nature Machine Intelligence, 2021 - nature.com
Geometric deep learning (GDL) is based on neural network architectures that incorporate
and process symmetry information. GDL bears promise for molecular modelling applications …

MolGPT: molecular generation using a transformer-decoder model

V Bagal, R Aggarwal, PK Vinod… - Journal of Chemical …, 2021 - ACS Publications
Application of deep learning techniques for de novo generation of molecules, termed as
inverse molecular design, has been gaining enormous traction in drug design. The …

Structure-based drug design with geometric deep learning

C Isert, K Atz, G Schneider - Current Opinion in Structural Biology, 2023 - Elsevier
Abstract Structure-based drug design uses three-dimensional geometric information of
macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric …

Molecular representations in AI-driven drug discovery: a review and practical guide

L David, A Thakkar, R Mercado, O Engkvist - Journal of Cheminformatics, 2020 - Springer
The technological advances of the past century, marked by the computer revolution and the
advent of high-throughput screening technologies in drug discovery, opened the path to the …

Deep generative molecular design reshapes drug discovery

X Zeng, F Wang, Y Luo, S Kang, J Tang… - Cell Reports …, 2022 - cell.com
Recent advances and accomplishments of artificial intelligence (AI) and deep generative
models have established their usefulness in medicinal applications, especially in drug …

Language models can learn complex molecular distributions

D Flam-Shepherd, K Zhu, A Aspuru-Guzik - Nature Communications, 2022 - nature.com
Deep generative models of molecules have grown immensely in popularity, trained on
relevant datasets, these models are used to search through chemical space. The …

[HTML][HTML] De novo molecular design and generative models

J Meyers, B Fabian, N Brown - Drug discovery today, 2021 - Elsevier
Molecular design strategies are integral to therapeutic progress in drug discovery.
Computational approaches for de novo molecular design have been developed over 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 …

SELFIES and the future of molecular string representations

M Krenn, Q Ai, S Barthel, N Carson, A Frei, NC Frey… - Patterns, 2022 - cell.com
Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad
applications to challenging tasks in chemistry and materials science. Examples include the …