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.
EvidenceNet is a disease‑specific dataset that transforms full‑text biomedical literature into structured evidence records and graph representations, preserving study design, provenance, and quantitative support. Using an LLM‑assisted pipeline, it extracts experimentally grounded findings, normalizes entities, scores evidence quality, and links related records via typed semantic relations. The released subsets—EvidenceNet‑HCC and EvidenceNet‑CRC—contain thousands of evidence records and richly connected graphs, with high extraction and relation‑type accuracy, enabling retrieval‑augmented question answering and graph‑based tasks such as link prediction and target prioritization.
PiPMRE is a new pipeline for medical relation extraction that uses language models instead of traditional tagging schemes. The framework includes a relation generator that produces multiple relational triplets from a text and a relation filter that scores and selects the most reliable triplets. Experiments on two public datasets show that PiPMRE outperforms previous state‑of‑the‑art methods, improving recall by 5.6 points and accuracy by 4.4 points, and it also performs well in few‑shot scenarios.
BELXTR is a new biomedical entity linking model that uses a multi‑vector (late interaction) architecture to preserve token‑level matching information, unlike traditional embedding‑based approaches that compress mentions into a single vector. By extending the XTR model with a task‑specific training objective and active query expansion, BELXTR achieves state‑of‑the‑art performance on half of ten evaluated corpora, with an average 5‑percentage‑point gain in recall@1. The model shows especially strong results on cross‑species gene disambiguation, outperforming an LLM‑powered retrieve‑and‑rerank pipeline and approaching a specialized rule‑based system.
arXiv:2608.03154v2 Announce Type: replace Abstract: Biomedical relation extraction (BioRE) supports knowledge graph construction and hypothesis generation. In real-world settings, most candidate enti...
The paper introduces MiNER, a fine‑tuned biomedical NLP system that uses BioBERT to extract malaria‑related named entities from scientific literature. It builds a large, annotated corpus of malaria articles, preprocesses the text, and applies supervised learning to improve extraction performance. Experiments show that MiNER outperforms other encoding and machine‑learning methods in precision, recall, and accuracy, and the authors release the human‑labeled dataset for further research.
arXiv:2601. 04524v2 Announce Type: replace Abstract: Understanding biomedical experiments provides a foundation for downstream tasks, e.
arXiv:2610.17113v1 Announce Type: cross Abstract: Information extraction models often perform well on the datasets they are trained on, but transferring to new domains and annotation guidelines remai...
SciNLP is a new benchmark dataset for full‑text entity and relation extraction in the NLP domain, comprising 60 manually annotated papers with 6,429 entities and 1,649 relations. It is the first dataset to provide full‑text annotations of entities and their relationships specifically for NLP literature. Experiments show that models trained on SciNLP outperform baselines on certain tasks, and the dataset enabled the automatic construction of a fine‑grained knowledge graph with an average node degree of 3.3.
arXiv:2608.28974v1 Announce Type: new Abstract: Clinically relevant oncology information is distributed across heterogeneous, longitudinal documentation, creating substantial abstraction burden and r...
arXiv:2603.08166v2 Announce Type: replace Abstract: Automated Drug Combination Extraction (DCE) from large-scale biomedical literature is crucial for advancing precision medicine and pharmacological...
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.