6 papers
From Answers to States: Verifiable Process-Level Evaluation of Chemical Reasoning in Large Language Models
Hongyu Guo, Hao Li, He Cao +2
Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers. This masks a critical failure mode: a model may o…
Plausibility Is Not Prediction: Contrastive Evidence for LLM-Based Cellular Perturbation Reasoning
Xinyu Yuan, Xixian Liu, Jianan Zhao +3
Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved condition…
GeneZip: Region-Aware Compression for Long Context DNA Modeling
Jianan Zhao, Xixian Liu, Zhihao Zhan +3
Long-context DNA models are limited by token-mixing cost and by how compression allocates representational budget across the genome. Existing approaches operate close to base-pair…
PerturbDiff: Functional Diffusion for Single-Cell Perturbation Modeling
Xinyu Yuan, Xixian Liu, Ya Shi Zhang +3
Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput…
OBELiX: A Curated Dataset of Crystal Structures and Experimentally Measured Ionic Conductivities for Lithium Solid-State Electrolytes
Félix Therrien, Jamal Abou Haibeh, Divya Sharma +10
Solid-state electrolyte batteries are expected to replace liquid electrolyte lithium-ion batteries in the near future thanks to their higher theoretical energy density and improved…
Structure Language Models for Protein Conformation Generation
Jiarui Lu, Xiaoyin Chen, Stephen Zhewen Lu +4
Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Tradi…