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: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
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 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
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
The paper introduces MITE, a method that transforms biomedical named entity recognition (BioNER) into a structure‑to‑structure generation task by encoding instructions and outputs in multiple programming languages (Python, C++, Java). This approach provides structurally diverse supervision without extra biomedical knowledge, and during inference it aggregates predictions via entity‑level voting to reduce language‑specific variance. Experiments on six BioNER datasets show that MITE outperforms BERT‑based and LLM‑based baselines and generalizes well across datasets.
By Songtao Li, Yijia Zhang, Jianyuan Yuan, Shidi Zhang, Fengyu Zhang, Hongfei Lin