Fuyi Yang

Fuyi Yang, Chenchen Ye, Mingyu Derek Ma et al.

Hypothesis generation in biomedical research has traditionally centered on uncovering hidden relationships within vast scientific literature, often using methods like Literature-Based Discovery (LBD). Despite progress, current approaches typically depend on single data types or predefined extraction patterns, which restricts the discovery of novel and complex connections. Recent advances in Large Language Model (LLM) agents show significant potential, with capabilities in information retrieval, reasoning, and generation. However, their application to biomedical hypothesis generation has been limited by the absence of standardized datasets and execution environments. To address this, we introduce BioVerge, a comprehensive benchmark, and BioVerge Agent, an LLM-based agent framework, to create a standardized environment for exploring biomedical hypothesis generation at the frontier of existing scientific knowledge. Our dataset includes structured and textual data derived from historical biomedical hypotheses and PubMed literature, organized to support exploration by LLM agents. BioVerge Agent utilizes a ReAct-based approach with distinct Generation and Evaluation modules that iteratively produce and self-assess hypothesis proposals. Through extensive experimentation, we uncover key insights: 1) different architectures of BioVerge Agent influence exploration diversity and reasoning strategies; 2) structured and textual information sources each provide unique, critical contexts that enhance hypothesis generation; and 3) self-evaluation significantly improves the novelty and relevance of proposed hypotheses.

Fuyi Yang, Jiazuo Mu, Yanshun Zhang et al.

We introduce CADSpotting, an effective method for panoptic symbol spotting in large-scale architectural CAD drawings. Existing approaches often struggle with symbol diversity, scale variations, and overlapping elements in CAD designs, and typically rely on additional features (e.g., primitive types or graphical layers) to improve performance. CADSpotting overcomes these challenges by representing primitives through densely sampled points with only coordinate attributes, using a unified 3D point cloud model for robust feature learning. To enable accurate segmentation in large drawings, we further propose a novel Sliding Window Aggregation (SWA) technique that combines weighted voting and Non-Maximum Suppression (NMS). Moreover, we introduce LS-CAD, a new large-scale dataset comprising 45 finely annotated floorplans, each covering approximately 1,000 $m^2$, significantly larger than prior benchmarks. LS-CAD will be publicly released to support future research. Experiments on FloorPlanCAD and LS-CAD demonstrate that CADSpotting significantly outperforms existing methods. We also showcase its practical value by enabling automated parametric 3D interior reconstruction directly from raw CAD inputs.