13 papers
Contextualizing Biological Language Models across Modalities via Logit-Space Contrastive Alignment
Yanjun Shao, Yundi Chen, Yashvi Patel +2
Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, var…
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…
FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization
Qingchuan Zhang, He Cao, Hao Li +6
Molecular optimization seeks to improve a molecule through small structural edits while preserving similarity to the starting compound. Recent language-model approaches typically t…
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…
Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations
Hao Li, He Cao, Bin Feng +6
While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding…
On Eigenvector Computation and Eigenvalue Reordering for the Non-Hermitian Quaternion Eigenvalue Problem
Zhigang Jia, Meiyue Shao, Yanjun Shao
In this paper we present several additions to the quaternion QR algorithm, including algorithms for eigenvector computation and eigenvalue reordering. A key outcome of the eigenval…