9 papers
Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Coupling
Keyue Qiu, Xintong Wang, Zhilong Zhang +2
Biomolecules such as proteins and small-molecule ligands play a central role in biological systems, arising from the tight interplay between sequence and three-dimensional structur…
Enhancing LLM Metacognition via Cognitive Pairwise Training
Weitao Li, Hao Zhou, Xuanyu Lei +11
Reinforcement learning with verifiable rewards (RLVR) has become central to LLM reasoning, but its outcome-level rewards can make models more willing to give confident answers when…
AMix-2: Establishing Protein as a Native Modality in Large Language Models
Keyue Qiu, Yixin Wu, Lihao Wang +19
We present AMix-2, a protein-text foundation model that establishes protein as a native modality in large language models (LLMs), unifying protein understanding and sequence design…
ShortListing Model: A Streamlined SimplexDiffusion for Discrete Variable Generation
Yuxuan Song, Zhe Zhang, Yu Pei +7
Generative modeling of discrete variables is challenging yet crucial for applications in natural language processing and biological sequence design. We introduce the Shortlisting M…
RetroDiff: Retrosynthesis as Multi-stage Distribution Interpolation
Yiming Wang, Yuxuan Song, Yiqun Wang +4
Retrosynthesis poses a key challenge in biopharmaceuticals, aiding chemists in finding appropriate reactant molecules for given product molecules. With reactants and products repre…
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule
Keyue Qiu, Yuxuan Song, Zhehuan Fan +5
Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major…