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
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. 30120v3 Announce Type: replace-cross Abstract: Multi-vector retrieval (MVR) models, exemplified by ColBERT, have established new benchmarks in retrieval accuracy by preserving fine-grained token-level interactions.
By Lixuan Guo, Yifei Wang, Tiansheng Wen, Aosong Feng, Stefanie Jegelka, Chenyu You
arXiv:2606.16661v2 Announce Type: replace-cross
Abstract: Fixed-length chunking in Retrieval-Augmented Generation (RAG) often leads to boundary fragmentation, where critical evidence is split across...
By Nathana\"el Langlois
The paper introduces DEPT, a method that trains a single decoder-only large language model to both expand queries and encode documents for retrieval. By preserving document embeddings close to their initial cached values while allowing gradients to flow through the generator, DEPT stabilizes retrieval targets and enables efficient index reuse and online hard‑negative mining. Experiments on the BEIR benchmark with Qwen3‑4B‑Instruct‑2507 and LLaMA‑3.2‑3B‑Instruct show that DEPT outperforms training‑free, independently trained, and staged unified baselines, with ablations confirming the benefits of preservation, whitening, end‑to‑end expansion training, and online negatives.
By Jingyuan Wang, Richong Zhang, Zhijie Nie, Mingxin Li, Yanzhao Zhang
The study investigates how document segmentation and chunk representation affect retrieval-augmented generation (RAG) for chemistry texts. Using the ChemQuests corpus, the authors benchmark 41 embedding models and evaluate them across five chunking strategies, seven chunk sizes, and various overlap settings. They find that embedding choice has the largest impact, with models like E5, BGE, and Nomic performing best, and recommend medium-to-large chunks with fixed-token, recursive-token, or hierarchical-section chunking and low overlap for effective chemistry-aware RAG.
By Mahmoud Amiri, Thomas Bocklitz