The paper introduces a configurable semantic chunking framework for biomedical information extraction in retrieval‑augmented generation systems. It replaces the fixed‑size chunking stage of BioMedRAG with entity‑preserving windows, trigger‑centered chunking, proposition‑first extraction, tiered trigger prioritization, and hierarchical relation resolution, while keeping the rest of the pipeline unchanged. Experiments on relation extraction benchmarks (GM‑CIHT, DDI, ChemProt) and adverse event classification (ADE) show that the hybrid configuration boosts performance on datasets with explicit relation cues, achieving 82.6% F1 on GM‑CIHT compared to 74.2% with the baseline.
arXiv:2606. 15412v1 Announce Type: cross Abstract: Biomedical relation extraction (BioRE) is a key step in transforming biomedical literature into structured knowledge.
arXiv:2609.00073v1 Announce Type: new Abstract: Malaria remains a significant global health burden, necessitating continuous research efforts to understand its complex molecular mechanisms, epidemiol...
arXiv:2601. 04524v2 Announce Type: replace Abstract: Understanding biomedical experiments provides a foundation for downstream tasks, e.
arXiv:2608.28974v1 Announce Type: new Abstract: Clinically relevant oncology information is distributed across heterogeneous, longitudinal documentation, creating substantial abstraction burden and r...
The paper introduces a scalable cross‑domain event extraction system built on a unified generative sequence‑to‑sequence framework. It jointly handles event detection and argument extraction, allowing both pipeline and end‑to‑end configurations. By fine‑tuning pretrained language models on multiple event datasets from diverse domains, the system retains domain‑specific semantics while generalizing across large, evolving label spaces, and offers a web‑based application for researchers to upload documents, extract events, visualize triggers and arguments, and compare configurations.
arXiv:2606. 19852v1 Announce Type: cross Abstract: Information extraction from pathology reports is essential for cancer staging, tumor registry population.
arXiv:2606. 12569v1 Announce Type: cross Abstract: We present EDEN (Emergency Department Electronic Notes), a new and unique large-scale corpus of clinical notes produced in Emergency Departments of Italian hospitals.
MedRAGChecker is a claim-level verification framework designed for biomedical retrieval‑augmented generation (RAG). It decomposes generated answers into atomic claims and assesses each claim’s support by combining evidence‑grounded natural language inference with biomedical knowledge‑graph consistency signals. The aggregated claim decisions provide diagnostics that distinguish retrieval and generation failures, such as faithfulness, under‑evidence, contradiction, and safety‑critical errors, and the system is distilled into compact models for scalable evaluation.
arXiv:2607. 22592v1 Announce Type: new Abstract: Graph-based retrieval-augmented generation (GraphRAG) grounds answers in structured knowledge, but current systems extract entities and relationships exhaustively, producing graphs whose size and construction cost scale with corpus length rather than with the reasoning a query requires.
arXiv:2608. 03148v1 Announce Type: cross Abstract: RAG improves the factual grounding of LLM by incorporating external knowledge, but deploying RAG on mobile and edge devices remains challenging because retrieved context increases computation and memory.
arXiv:2608. 04144v1 Announce Type: cross Abstract: Biomedical entity linking grounds mentions in clinical and scientific text to entities in a curated knowledge base (KB) with ontological structure, which supports downstream applications such as literature-scale information extraction and patient-record normalization.
arXiv:2607. 00008v1 Announce Type: cross Abstract: Extracting structured data from unstructured text using large language models (LLMs) becomes challenging when target schemas are large and complex.