10 citations · 35 across the 39 of their papers we have counts for
42 papers
CODesign: Consistency from Data to Trajectory in All-Atom Protein Binder Co-Design
Yuanle Mo, Bo Qiang, Haitao Lin +4
The central challenge in de novo protein design is generating plausible, mutually compatible structures and sequences, such that each designed sequence folds into its intended stru…
An immune world model for multiscale forecasting and therapeutic hypothesis generation
Taoyong Cui, Xi Wang, Zonghang Li +11
Immune therapies act across cell-intrinsic programs, tissue ecosystems, and patient-specific immune states, yet most predictors address these scales separately. We used a governed…
Exploring the Alignment of Generation and Understanding in Protein Structure Modeling
Junde Xu, Yuansheng Huang, Zijun Gao +5
Understanding and generation are often treated as two separate paradigms in training deep neural networks, despite the fact that both are trained with closely related objectives su…
SF-Cluster: Frustration-Guided MSA Subsampling for Alternative Protein Conformation Recovery
Hanqun Cao, Zijun Gao, Chunbin Gu +3
Deep-learning structure predictors are sensitive to their multiple sequence alignment (MSA) input, making MSA subsampling a practical route to recovering alternative conformations.…
Struct-Searcher: Agentic Structural Thinking Advances Multimodal Deep Information Seeking
Fan Zhang, Vireo Zhang, Shengju Qian +7
Deep research agents have attracted increasing attention for their ability to collect large-scale online information to acquire target knowledge, with recent efforts shifting from…
AlloGen: Conformation-Selective Binder Generation with Differential State Scoring
Hanqun Cao, Zachary Quinn, Aastha Pal +4
Protein binder design has largely optimized for affinity alone, leaving conformational selectivity unaddressed: for allosteric targets such as kinases, nuclear receptors, and GPCRs…
GeoCycler: Reward-Aligned 3D Diffusion for Constraint-Conditioned Cyclic Peptide Design
Jingjie Zhang, Hanqun Cao, Haosen Shi +10
Cyclic peptides are attractive therapeutic modalities because their closed-ring topology can improve stability and target specificity. However, de novo cyclic peptide design remain…
SurgLQA: Scalable Long-Horizon Surgical Video Question Answering
Diandian Guo, Xikai Yang, Ruiyang Li +2
Surgical Video Question Answering (VideoQA) provides a promising paradigm for dynamic intraoperative interpretation, enabling real-time decision support and context-aware retrieval…
TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation
Hanqun Cao, Aastha Pal, Sophia Tang +4
Protein function is often controlled by ligands that bias the direction of state transitions, such as agonists and antagonists, rather than stabilizing a single conformation. This…
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…
Proteo-R1: Reasoning Foundation Models for De Novo Protein Design
Fang Wu, Weihao Xuan, Heli Qi +26
Deep learning in de novo protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries…
PARM: Pipeline-Adapted Reward Model
Xingyu Fan, Wei Shao, Jiacheng Liu +2
Reward models (RMs) are central to aligning large language models (LLMs) with human preferences, powering RLHF and advanced decoding strategies. While most prior work focuses on si…
An SO(3)-equivariant reciprocal-space neural potential for long-range interactions
Lingfeng Zhang, Taoyong Cui, Dongzhan Zhou +6
Long-range electrostatic and polarization interactions play a central role in molecular and condensed-phase systems, yet remain fundamentally incompatible with locality-based machi…
Med-Evo: Test-time Self-evolution for Medical Multimodal Large Language Models
Dunyuan Xu, Xikai Yang, Juzheng Miao +3
Medical Multimodal Large Language Models (MLLMs) have demonstrated remarkable capabilities across diverse healthcare tasks. However, current post-training strategies, such as super…
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…
CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design
Zijun Gao, Mutian He, Shijia Sun +8
Reliable evaluation of protein structure predictions remains challenging, as metrics like pLDDT capture energetic stability but often miss subtle errors such as atomic clashes or c…
Boosting In-Silicon Directed Evolution with Fine-Tuned Protein Language Model and Tree Search
Yaodong Yang, Yang Wang, Jinpeng Li +4
Protein evolution through amino acid mutations is a cornerstone of life sciences. Recent advances in protein language models have shown rich evolutionary patterns, offering unprece…
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…
ODesign: A World Model for Biomolecular Interaction Design
Odin Zhang, Xujun Zhang, Haitao Lin +34
Biomolecular interactions underpin almost all biological processes, and their rational design is central to programming new biological functions. Generative AI models have emerged…
RiboPO: Preference Optimization for Structure- and Stability-Aware RNA Design
Minghao Sun, Hanqun Cao, Zhou Zhang +10
Designing RNA sequences that reliably adopt specified three-dimensional structures while maintaining thermodynamic stability remains challenging for synthetic biology and therapeut…
REAR: Rethinking Visual Autoregressive Models via Generator-Tokenizer Consistency Regularization
Qiyuan He, Yicong Li, Haotian Ye +6
Visual autoregressive (AR) generation offers a promising path toward unifying vision and language models, yet its performance remains suboptimal against diffusion models. Prior wor…
InstructPLM-mu: 1-Hour Fine-Tuning of ESM2 Beats ESM3 in Protein Mutation Predictions
Junde Xu, Yapin Shi, Lijun Lang +5
Multimodal protein language models deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In t…
KnowGuard: Knowledge-Driven Abstention for Multi-Round Clinical Reasoning
Xilin Dang, Kexin Chen, Xiaorui Su +7
In clinical practice, physicians refrain from making decisions when patient information is insufficient. This behavior, known as abstention, is a critical safety mechanism preventi…
A deep reinforcement learning platform for antibiotic discovery
Hanqun Cao, Marcelo D. T. Torres, Jingjie Zhang +8
Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here we present ApexAmphion, a deep…