6 papers
SciForge: An AI-Native, Multimodal Workbench for Scientific Discovery
SciForge Team, Zhangyang Gao, Minghao Fang +10
Scientific work increasingly spans heterogeneous artifacts -- papers, code, datasets, scientific file formats, model outputs, figures, manuscripts, and team decisions -- yet genera…
AblateCell: A Reproduce-then-Ablate Agent for Virtual Cell Repositories
Xue Xia, Chengkai Yao, Mingyu Tsoi +10
Systematic ablations are essential to attribute performance gains in AI Virtual Cells, yet they are rarely performed because biological repositories are under-standardized and tigh…
Lost in Tokenization: Context as the Key to Unlocking Biomolecular Understanding in Scientific LLMs
Kai Zhuang, Jiawei Zhang, Yumou Liu +10
Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when proc…
PFMBench: Protein Foundation Model Benchmark
Zhangyang Gao, Hao Wang, Cheng Tan +6
This study investigates the current landscape and future directions of protein foundation model research. While recent advancements have transformed protein science and engineering…
ProtInvTree: Deliberate Protein Inverse Folding with Reward-guided Tree Search
Mengdi Liu, Xiaoxue Cheng, Zhangyang Gao +4
Designing protein sequences that fold into a target 3D structure, known as protein inverse folding, is a fundamental challenge in protein engineering. While recent deep learning me…
G2PDiffusion: Cross-Species Genotype-to-Phenotype Prediction via Evolutionary Diffusion
Mengdi Liu, Zhangyang Gao, Hong Chang +3
Understanding how genes influence phenotype across species is a fundamental challenge in genetic engineering, which will facilitate advances in various fields such as crop breeding…