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
arXiv:2609.00228v1 Announce Type: new
Abstract: Scientific domain entity linking (EL) differs from general domain EL because mentions and entity names often lack lexical overlap. Another challenge is...
By Md Rasel Khondokar, Qiao Qiao, Farjana Sultana Samia, Nhat Le, Yuepei Li, Qi Li
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
The paper introduces a multilingual, multi-functional framework for disambiguating funder names in scientific publications, using a training dataset that merges the Research Organization Registry with Web of Science and Crossref Open Funder Registry data. By applying multi-task learning with contrastive and multiple negatives ranking losses, the authors fine‑tune open‑weight embedding models from the Sentence Transformer, Gemma, and Qwen3 families, achieving over 90% accuracy in matching Web of Science funder names to ROR identifiers and surpassing general‑purpose LLMs by more than 0.1. For funders not present in ROR, a similarity network is constructed to identify clusters, and the study discusses challenges related to smaller and non‑English‑speaking funders.
By Kanyao Han, Zhiwen You, Jinseok Kim, Jana Diesner
This thesis explores how to select and adapt NLP models for global health literature when annotated data and computational resources are scarce. It compares skip‑gram word2vec models trained on increasingly large specialized corpora with BioWordVec for semantic tag discovery, finding that larger coverage does not always yield more useful domain associations. The study also evaluates convolutional spaCy models versus a RoBERTa transformer for named entity recognition, noting a trade‑off between higher F1 scores and longer inference time, and investigates MiniLM few‑shot versus BART‑MNLI zero‑shot classification for multi‑label topic classification, highlighting practical constraints of inference cost.
"whyItMatters":"The work provides empirical guidance on balancing model accuracy and resource demands for building knowledge systems in low‑resource global health settings."
By Genis Skura, Antoine Geissb\"uhler, Jean-Luc Falcone
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:2607. 20926v1 Announce Type: new Abstract: Scientific research involves complex information-seeking and reasoning workflows across heterogeneous sources.
By Yinhao Tang, Youqing Fang, Yanan Sun, Wenran Liu, Weiming Zhang, Bin Liu, Kuikun Liu, Wenwei Zhang, Kai Chen
BioELX is a retrieve‑rerank framework for cross‑lingual biomedical entity linking that tackles two key problems: the English‑biased UMLS alias training data and the degradation caused by naïvely adding context. It fine‑tunes SapBERT_multi with Wikidata‑derived cross‑lingual alias supervision to create shared concept neighborhoods, and then reranks candidates using pretrained LLMs with mention‑anchored prompting to focus on the target mention. Experiments demonstrate state‑of‑the‑art performance on four benchmarks, improving Recall@1 by 4.8–18.2 percentage points without task‑specific annotations.
By Yi Wang, Corina Dima, Liangyu Zhong, Steffen Staab
The paper introduces WaterBERT, a domain‑adapted encoder model trained on a 2.97‑billion‑token water treatment corpus to capture domain‑specific semantics for literature mining. Fine‑tuned versions of WaterBERT outperform general‑purpose and other domain BERT models on tasks such as treatment process classification, named entity recognition, and relation extraction. The authors also demonstrate WaterBERT’s utility in large‑scale processing, generating coherent research topics, building a structured knowledge graph from 693,211 abstracts, and creating a Water Knowledge‑Enhanced Retrieval System that surpasses text‑based baselines.
By Mudi Zhai (UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia), Ruihong Qiu (School of Electrical Engineering and Computer Science, The University of Queensland, Brisbane, QLD 4072, Australia), Qingyun Zeng (Microsoft Copilot Studio AI, Redmond, WA 98052, United States, Departments of Mathematics & Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, United States), T. David Waite (UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia), Bing-Jie Ni (UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia), Haoran Duan (UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China)
arXiv:2606. 10716v1 Announce Type: cross Abstract: Pre-trained language models (PLMs) have achieved strong performance in keyphrase extraction (KPE), largely due to their ability to generate rich contextualized representations.
By Roberto Mart\'inez-Cruz, Alvaro J. L\'opez-L\'opez, Jos\'e Portela
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.
By V. S. Anoop, Devika N
The paper investigates cross‑lingual transfer for sequential sentence classification (SSC) in research papers, focusing on 13 non‑English languages. Experiments show that linguistic proximity does not reliably predict transfer success, whereas structural similarity in rhetorical organization—particularly label distribution similarity—correlates positively with performance. The authors introduce three generative‑model methods that exploit structural cues, achieving parity with strong encoder baselines on‑domain and outperforming them when transferring to unseen languages.
By Kazuhiro Yamauchi, Marie Katsurai