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.
By Decheng Duan, Yingyi Zhang, Jitong Peng, Chengzhi Zhang
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.
By Riya Ahuja (Institute of Data Science in Biomedicine, TU Braunschweig, Braunschweig, Germany, Braunschweig Integrated Centre of Systems Biology, TU Braunschweig, Braunschweig, Germany), Tim Kacprowski (Institute of Data Science in Biomedicine, TU Braunschweig, Braunschweig, Germany, Braunschweig Integrated Centre of Systems Biology, TU Braunschweig, Braunschweig, Germany), Roya Shiasi Sardoabi (Institute of Data Science in Biomedicine, TU Braunschweig, Braunschweig, Germany, Braunschweig Integrated Centre of Systems Biology, TU Braunschweig, Braunschweig, Germany)
The paper introduces a second-pass method for uncovering hidden relationships in knowledge graphs extracted from text, without altering the original facts. By chunking documents and embedding each chunk once, the approach uses top‑k nearest‑neighbor queries and Shepard inverse‑distance weighting to score candidate node pairs, avoiding threshold issues inherent in cosine scoring. The technique is order‑independent, scalable, and has been implemented across multiple graph databases, demonstrating high edge fidelity with lower‑dimensional embeddings and a 25× speedup in top‑k computation.
By Bilge Kaan Karamete, Hunter Casten
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.
By Samuele Garda, Ulf Leser
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.
By Yicheng Tao, Jie Liu
arXiv:2606. 15412v1 Announce Type: cross Abstract: Biomedical relation extraction (BioRE) is a key step in transforming biomedical literature into structured knowledge.
By Jakob Mraz, Toma\v{z} Curk, Bla\v{z} Zupan
arXiv:2608. 19201v1 Announce Type: cross Abstract: Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale.
By Hao Xuan, Rithvij Pasupuleti, Ben Liu, Haishuo Sun, Jun Zhang, Zijun Yao, Cuncong Zhong
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.
By Jiaxin Duan, Fengyu Lu, Junfei Liu
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.
By Chang Zong, Jinyu Chen, Sicheng Lv, Si-tu Xue, Huilin Zheng, Jian Wan, Lei Zhang
arXiv:2608. 08636v1 Announce Type: cross Abstract: Scientific named entity recognition (SciNER) plays a crucial role in information extraction and knowledge discovery from scientific texts.
By Tong Bao, Yi Zhao, Heng Zhang, Chengzhi Zhang
arXiv:2609.39975v1 Announce Type: cross
Abstract: This paper presents an overview of the fourteenth edition of the BioASQ challenge, organized in the context of the Conference and Labs of the Evaluat...
By Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Martin Krallinger, Miguel Rodr\'iguez-Ortega, Eduard Rodriguez-L\'opez, Natalia Loukachevitch, Igor Rozhkov, Elena Tutubalina, Dimitris Dimitriadis, Vasiliki Patsiou, Grigorios Tsoumakas, George Giannakoulas, Alexandra Bekiaridou, Athanasios Samaras, Giorgio Maria Di Nunzio, Nicola Ferro, Stefano Marchesin, Marco Martinelli, Gianmaria Silvello, Georgios Paliouras
arXiv:2606. 19852v1 Announce Type: cross Abstract: Information extraction from pathology reports is essential for cancer staging, tumor registry population.
By Aman Pathak, Cheng Peng, Mengxian Lyu, Ziyi Chen, Reema Solan, Sankalp Talankar, Yasir Khan, Hiren Mehta, Aokun Chen, Yi Guo, Yonghui Wu