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
The paper presents a new retrieval benchmark for the model organism Dictyostelium, created from curator-generated queries linked to PubMed articles and gene annotations. It evaluates three niche retrieval strategies—cross‑encoder reranking, gene‑aware query expansion, and abstract‑only versus full‑text retrieval—finding that reranking and gene‑aware expansion improve results in specific contexts, while full‑text chunks boost recall and top‑rank performance when abstracts lack supporting evidence. The benchmark, data, and code are publicly released on GitHub and Zenodo.
By Yun Wang, Gad Shaulsky, Toma\v{z} Curk, Bla\v{z} Zupan
Lit3R is a system developed by tus-nlp for the LitTraceQA shared task, which focuses on evidence-grounded question answering over scientific literature. The system combines off-the-shelf retrieval, reranking, and large language model components without task-specific training, using an iterative retrieval process that merges BM25-based sparse and dense retrieval, cross-encoder reranking, and LLM verification, along with paper-to-paper expansion. In the official test set, Lit3R achieved a 4th place ranking on the leaderboard.
By Akira Ise, Kotaro Kumagai, Yuta Yamaguchi, Hisanori Ozaki, Yukio Uematsu, Ikuya Yamada
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
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
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