BioVerge: A Comprehensive Benchmark and Study of Self-Evaluating Agents for Biomedical Hypothesis Generation

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.

CADSpotting: Robust Panoptic Symbol Spotting on Large-Scale CAD Drawings

We introduce CADSpotting, an efficient method for panoptic symbol spotting in large-scale architectural CAD drawings. Existing approaches struggle with the diversity of symbols, scale variations, and overlapping elements in CAD designs. CADSpotting overcomes these challenges by representing each primitive with dense points instead of a single primitive point, described by essential attributes like coordinates and color. Building upon a unified 3D point cloud model for joint semantic, instance, and panoptic segmentation, CADSpotting learns robust feature representations. To enable accurate segmentation in large, complex drawings, we further propose a novel Sliding Window Aggregation (SWA) technique, combining weighted voting and Non-Maximum Suppression (NMS). Moreover, we introduce a large-scale CAD dataset named LS-CAD to support our experiments. Each floorplan in LS-CAD has an average coverage of 1,000 square meter(versus 100 square meter in the existing dataset), providing a valuable benchmark for symbol spotting research. Experimental results on FloorPlanCAD and LS-CAD datasets demonstrate that CADSpotting outperforms existing methods, showcasing its robustness and scalability for real-world CAD applications.