6 papers
AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents
Edward De Brouwer, Carl Edwards, Alexander Wu +9
Recent advances in machine learning and large-scale biological data collections have revived the prospect of building a virtual cell, a computational model of cellular behavior tha…
oMeBench: Towards Robust Benchmarking of LLMs in Organic Mechanism Elucidation and Reasoning
Ruiling Xu, Yifan Zhang, Qingyun Wang +2
Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and d…
mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Molecules
Carl Edwards, Chi Han, Gawon Lee +11
Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-…
Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems
Xuan Zhang, Limei Wang, Jacob Helwig +60
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…
Invariant Tokenization of Crystalline Materials for Language Model Enabled Generation
Keqiang Yan, Xiner Li, Hongyi Ling +8
We consider the problem of crystal materials generation using language models (LMs). A key step is to convert 3D crystal structures into 1D sequences to be processed by LMs. Prior…
ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback
Henry W. Sprueill, Carl Edwards, Khushbu Agarwal +6
The discovery of new catalysts is essential for the design of new and more efficient chemical processes in order to transition to a sustainable future. We introduce an AI-guided co…