5 papers
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…
Protein Structure Tokenization: Benchmarking and New Recipe
Xinyu Yuan, Zichen Wang, Marcus Collins +1
Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. St…
Cell-ontology guided transcriptome foundation model
Xinyu Yuan, Zhihao Zhan, Zuobai Zhang +5
Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale s…