5 papers
Autonomous Science Bench: Evaluating AI Agents for Autonomous Scientific Discovery
Yibo Wen, Han Liu
AI agents for autonomous scientific discovery must decide which experiments to run under a limited budget. Most benchmarks for science agents provide fixed datasets, while others t…
DiMOS: Doob-Guided Inference-Time Multi-Objective Search for Scientific Design
Ziqing Wang, Qijie Zhu, Weimin Wu +4
Scientific design often requires jointly satisfying multiple objectives and constraints. Pretrained masked diffusion models provide a generative foundation for this task, but fine-…
TIGER: Text-Informed Generalized Enzyme-Reaction Retrieval
Yuhang Zhang, Keyan Ding, Peilin Chen +5
Enzyme-reaction retrieval is a fundamental problem in computational biology, underpinning enzyme characterization, reaction mechanism elucidation, and the rational design of metabo…
Cell-JEPA: Latent Representation Learning for Single-Cell Transcriptomics
Ali ElSheikh, Rui-Xi Wang, Weimin Wu +9
Single-cell foundation models learn by reconstructing masked gene expression, implicitly treating technical noise as signal. With dropout rates exceeding 90%, reconstruction object…
Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models
Weimin Wu, Xuefeng Song, Yibo Wen +5
We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify t…