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cs.LG2026
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…
cs.LG2026
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…
cs.LG2025
Learning 3D Anisotropic Noise Distributions Improves Molecular Force Field Modeling
Xixian Liu, Rui Jiao, Zhiyuan Liu +6
Coordinate denoising has emerged as a promising method for 3D molecular pretraining due to its theoretical connection to learning molecular force field. However, existing denoising…