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
arXiv:2601. 00567v2 Announce Type: replace-cross Abstract: Adapting general-domain retrievers to scientific domains is challenging due to the scarcity of large-scale domain-specific relevance annotations and the substantial mismatch in vocabulary and information needs.
By Jeyun Lee, Junhyoung Lee, Wonbin Kweon, Bowen Jin, Yu Zhang, Susik Yoon, Dongha Lee, Hwanjo Yu, Jiawei Han, Seongku Kang
arXiv:2606. 28367v1 Announce Type: cross Abstract: Retrieval-augmented generation (RAG) is routinely extended with methods meant to improve retrieval: query expansion, hierarchical and cross-document summarization, graph-based expansion, per-query routing, rank fusion, and corrective re-retrieval.
By Sadanand Singh, Allam Reddy, Manan Chopra
arXiv:2608. 03860v1 Announce Type: cross Abstract: We introduce SciRet, a compute-aware empirical study of retrieval-augmented generation for scientific question answering over CORD-19.
By Kaysarul Anas Apurba, Md. Hasibul Hasan, Rofiqul Alam Shehab, Asab Azad
arXiv:2607. 24799v1 Announce Type: cross Abstract: Large Language Models tend to hallucinate when answering domain-specific ques tions from scientific documents without prior fine-tuning.
By Alexandru-Andrei Sauc\u{a}, Ana-Luiza Rusnac
The paper presents a controlled comparison of six retrieval-augmented generation (RAG) strategies for scientific question answering on a large arXiv corpus. All pipelines use the same LLM generator and evaluation protocol, differing only in retrieval design—ranging from classic dense retrieval to late‑interaction methods like ColBERTv2. The authors also release a synthetic question dataset and code to enable reproducible, large‑scale evaluation of RAG trade‑offs.
By Bhagyesh Rathi, Eshan Chawla, William B. Andreopoulos
The study introduces an evidence-aware evaluation protocol for a retrieval‑augmented generation system focused on breast lesion management literature. Using an 18‑document corpus and 18 queries, the authors compared dense embeddings, BM25, and cross‑encoder reranking across various chunk sizes and overlaps, finding that a hybrid retriever with 384‑token chunks and 20% overlap achieved top‑three retrieval success for 17 of 18 queries and high recall and precision metrics. Expanding ground‑truth relevance annotations increased recognized evidence spans and accepted chunk targets, though retrieval rankings remained unchanged, underscoring the sensitivity of evaluation to annotation coverage.
By Miguel Mochizuki Silva, Samuel Ismael, Mateus C. Dias, Tha\'is Gaud\^encio, Yuri Malheiros, Barufaldi