Yi Luo

Yi Luo, Linghang Shi, Yihao Li et al.

Conventional biomedical research is increasingly labor-intensive due to the exponential growth of scientific literature and datasets. Artificial intelligence (AI), particularly Large Language Models (LLMs), has the potential to revolutionize this process by automating various steps. Still, significant challenges remain, including the need for multidisciplinary expertise, logicality of experimental design, and performance measurements. This paper introduces BioResearcher, the first end-to-end automated system designed to streamline the entire biomedical research process involving dry lab experiments. BioResearcher employs a modular multi-agent architecture, integrating specialized agents for search, literature processing, experimental design, and programming. By decomposing complex tasks into logically related sub-tasks and utilizing a hierarchical learning approach, BioResearcher effectively addresses the challenges of multidisciplinary requirements and logical complexity. Furthermore, BioResearcher incorporates an LLM-based reviewer for in-process quality control and introduces novel evaluation metrics to assess the quality and automation of experimental protocols. BioResearcher successfully achieves an average execution success rate of 63.07% across eight previously unmet research objectives. The generated protocols, on average, outperform typical agent systems by 22.0% on five quality metrics. The system demonstrates significant potential to reduce researchers' workloads and accelerate biomedical discoveries, paving the way for future innovations in automated research systems.

Yi Luo, Qiwen Wang, Junqi Yang et al.

Generalized Category Discovery (GCD) aims to classify both known and novel categories using partially labeled data that contains only known classes. Despite achieving strong performance on existing benchmarks, current textual GCD methods lack sufficient validation in realistic settings. We introduce Event-Centric GCD (EC-GCD), characterized by long, complex narratives and highly imbalanced class distributions, posing two main challenges: (1) divergent clustering versus classification groupings caused by subjective criteria, and (2) Unfair alignment for minority classes. To tackle these, we propose PaMA, a framework leveraging LLMs to extract and refine event patterns for improved cluster-class alignment. Additionally, a ranking-filtering-mining pipeline ensures balanced representation of prototypes across imbalanced categories. Evaluations on two EC-GCD benchmarks, including a newly constructed Scam Report dataset, demonstrate that PaMA outperforms prior methods with up to 12.58% H-score gains, while maintaining strong generalization on base GCD datasets.