6 papers
The Latent Space: Foundation, Evolution, Mechanism, Ability, and Outlook
Xinlei Yu, Zhangquan Chen, Yongbo He +36
Latent space is rapidly emerging as a native substrate for language-based models. While modern systems are still commonly understood through explicit token-level generation, an inc…
CA-DEL: An Open Multi-Target, Multi-Modal Benchmark for Learning from DNA-Encoded Library Screens
Mutian He, Hanqun Cao, Cheng Tan +4
The success of machine learning in drug discovery hinges on learning the relationship between a chemical structure and its biological activity. While DNA-Encoded Library (DEL) tech…
RiboSphere: Learning Unified and Efficient Representations of RNA Structures
Zhou Zhang, Hanqun Cao, Cheng Tan +3
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures a…
Co-Diffusion: An Affinity-Aware Two-Stage Latent Diffusion Framework for Generalizable Drug-Target Affinity Prediction
Yining Qian, Pengjie Wang, Yixiao Li +4
Predicting drug-target affinity is fundamental to virtual screening and lead optimization. However, existing deep models often suffer from representation collapse in stringent cold…
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…
Learning the PTM Code through a Coarse-to-Fine, Mechanism-Aware Framework
Jingjie Zhang, Hanqun Cao, Zijun Gao +8
Post-translational modifications (PTMs) form a combinatorial "code" that regulates protein function, yet deciphering this code - linking modified sites to their catalytic enzymes -…