6 papers
Co-Generative De Novo Functional Protein Design
Xinrui Chen, Yizhen Luo, Siqi Fan +1
De novo functional protein design aims to generate protein sequences that realize specified biochemical functions without relying on evolutionary templates, enabling broad applicat…
Structured Scaling of AI Discovery Across Diverse Scientific Domains
Haotian Ye, Haowei Lin, Jingyi Tang +30
Scientific discovery often requires many cycles of proposing, testing, and refining candidate solutions. Language models can increasingly participate in these loops, but simply gen…
Reinforced Reasoning for End-to-End Retrosynthetic Planning
Chenyang Zuo, Siqi Fan, Yizhen Luo +1
Retrosynthetic planning is a fundamental task in organic chemistry, yet remains challenging due to its combinatorial complexity. To address this, conventional approaches typically…
SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics
Suyuan Zhao, Yizhen Luo, Ganbo Yang +3
Spatial Transcriptomics (ST) technologies provide biologists with rich insights into single-cell biology by preserving spatial context of cells. Building foundational models for ST…
PharMolixFM: All-Atom Foundation Models for Molecular Modeling and Generation
Yizhen Luo, Jiashuo Wang, Siqi Fan +1
Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While re…
MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering
Yizhen Luo, Zikun Nie, Massimo Hong +3
Studying protein mutations within amino acid sequences holds tremendous significance in life sciences. Protein language models (PLMs) have demonstrated strong capabilities in broad…