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
ResearchHub is an interactive system designed for personalized discovery of biomedical preprints. It uses a bi‑encoder retriever called prism, which leverages GPT‑4o‑generated queries and a hybrid ranking objective, to retrieve relevant papers from a MedRxiv corpus. The system enhances recommendation quality through novelty, diversity, curriculum ordering, and provides frontier retrieval, DPP‑based re‑ranking, and lightweight attribution cards, all operating with low latency.
By Viswonathan Manoranjan, Taeyoon Kim, Nicholas Do, Sang Woo Kim, Dawei Li, Zhen Tan, Tianlong Chen, Yunmei Liu
arXiv:2411. 06024v1 Announce Type: cross Abstract: The exponential growth in protein-related databases and scientific literature, combined with increasing demands for efficient biological information retrieval, has created an urgent need for unified and accessible search methods in protein engineering research.
By Yungeng Liu, Zan Chen, Yu Guang Wang, Yiqing Shen
arXiv:2609.08174v1 Announce Type: new
Abstract: We introduce OntologyBench, a tiered biomedical retrieval benchmark comprising 471,854 training and 125,744 evaluation query-document relevance pairs a...
By Xiao Yu Cindy Zhang, Wyeth Wasserman, Jian Zhu
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
arXiv:2605. 06647v2 Announce Type: replace-cross Abstract: Retrieval-augmented agents are increasingly the interface to large knowledge bases, yet most treat retrieval as a black box: they issue exploratory queries, inspect snippets, and reformulate until evidence emerges.
By Zeyu Yang, Qi Ma, Jason Chen, Anshumali Shrivastava