9 papers
MedicalAgentsBench for Complex Medical Reasoning: Comparing Internalized Reasoning Models versus Externalized Agent-based Frameworks
Yanjun Shao, Xiangru Tang, Jiwoong Sohn +10
Complex medical reasoning requires integrating heterogeneous clinical evidence across multiple inference steps. Large language models (LLMs) now approach this through two routes: i…
SurfDesign: Effective Protein Design on Molecular Surfaces
Fang Wu, Shuting Jin, Xiangru Tang +5
Protein function is largely determined by molecular surface geometry and physicochemical complementarity, yet most protein design methods condition only on backbone structure. We i…
Dispersion Loss Counteracts Embedding Condensation and Improves Generalization in Small Language Models
Chen Liu, Xingzhi Sun, Xi Xiao +8
Large language models (LLMs) achieve remarkable performance through ever-increasing parameter counts, but scaling incurs steep computational costs. To better understand LLM scaling…
D-Flow: Multi-modality Flow Matching for D-peptide Design
Fang Wu, Shuting Jin, Xiangru Tang +3
Among these, D-peptides are resistant to proteolysis, exhibit greater in vivo stability, and are easier to synthesize. Despite advances in deep learning for peptide discovery, the…
Advancing AI Research Assistants with Expert-Involved Learning
Tianyu Liu, Simeng Han, Hanchen Wang +27
Large language models (LLMs) and large multimodal models (LMMs) promise to accelerate biomedical discovery, yet their reliability remains unclear. We introduce ARIEL (AI Research A…
CellForge: Agentic Design of Virtual Cell Models
Xiangru Tang, Zhuoyun Yu, Jiapeng Chen +12
Virtual cell modeling aims to predict cellular responses to diverse perturbations but faces challenges from biological complexity, multimodal data heterogeneity, and the need for i…