Large language models on graphs: A comprehensive survey

B Jin, G Liu, C Han, M Jiang, H Ji, J Han - arXiv preprint arXiv:2312.02783, 2023 - arxiv.org
Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant
advancements in natural language processing, due to their strong text encoding/decoding …

Multi-modal molecule structure–text model for text-based retrieval and editing

S Liu, W Nie, C Wang, J Lu, Z Qiao, L Liu… - Nature Machine …, 2023 - nature.com
There is increasing adoption of artificial intelligence in drug discovery. However, existing
studies use machine learning to mainly utilize the chemical structures of molecules but …

Translation between molecules and natural language

C Edwards, T Lai, K Ros, G Honke, K Cho… - arXiv preprint arXiv …, 2022 - arxiv.org
We present $\textbf {MolT5} $$-$ a self-supervised learning framework for pretraining
models on a vast amount of unlabeled natural language text and molecule strings. $\textbf …

[HTML][HTML] Unraveling the mystery of efficacy in Chinese medicine formula: new approaches and technologies for research on pharmacodynamic substances

Y Li, Z Lin, Y Wang, S Ju, H Wu, H Jin, S Ma… - Arabian Journal of …, 2022 - Elsevier
Traditional Chinese medicine (TCM) is the key to unlock treasures of Chinese civilization.
TCM and its compound play a beneficial role in medical activities to cure diseases …

Mol-instructions: A large-scale biomolecular instruction dataset for large language models

Y Fang, X Liang, N Zhang, K Liu, R Huang… - arXiv preprint arXiv …, 2023 - arxiv.org
Large Language Models (LLMs), with their remarkable task-handling capabilities and
innovative outputs, have catalyzed significant advancements across a spectrum of fields …

Enhancing activity prediction models in drug discovery with the ability to understand human language

P Seidl, A Vall, S Hochreiter… - … on Machine Learning, 2023 - proceedings.mlr.press
Activity and property prediction models are the central workhorses in drug discovery and
materials sciences, but currently, they have to be trained or fine-tuned for new tasks. Without …

Artificial intelligence for science in quantum, atomistic, and continuum systems

X Zhang, L Wang, J Helwig, Y Luo, C Fu, Y Xie… - arXiv preprint arXiv …, 2023 - arxiv.org
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural
sciences. Today, AI has started to advance natural sciences by improving, accelerating, and …

Empowering molecule discovery for molecule-caption translation with large language models: A chatgpt perspective

J Li, Y Liu, W Fan, XY Wei, H Liu… - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
Molecule discovery plays a crucial role in various scientific fields, advancing the design of
tailored materials and drugs, which contributes to the development of society and human …

Git-mol: A multi-modal large language model for molecular science with graph, image, and text

P Liu, Y Ren, J Tao, Z Ren - Computers in biology and medicine, 2024 - Elsevier
Large language models have made significant strides in natural language processing,
enabling innovative applications in molecular science by processing textual representations …

MolCA: Molecular graph-language modeling with cross-modal projector and uni-modal adapter

Z Liu, S Li, Y Luo, H Fei, Y Cao, K Kawaguchi… - arXiv preprint arXiv …, 2023 - arxiv.org
Language Models (LMs) have demonstrated impressive molecule understanding ability on
various 1D text-related tasks. However, they inherently lack 2D graph perception-a critical …