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.
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.
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...
arXiv:2606. 15412v1 Announce Type: cross Abstract: Biomedical relation extraction (BioRE) is a key step in transforming biomedical literature into structured knowledge.
arXiv:2606. 24200v1 Announce Type: cross Abstract: Retrieval-augmented generation (RAG) in clinical settings increasingly requires multilingual retrieval against predominantly English evidence corpora.
arXiv:2608. 00065v1 Announce Type: cross Abstract: Terminology-intensive retrieval, especially in medical settings, depends on preserving multi-word entities, abbreviations, numerical constraints, and compositional concepts.
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.
The paper investigates modular entity disambiguation by separating candidate retrieval from entity selection. It compares sparse retrieval (BM25), Web KB search, and a dense retriever, all paired with large language model selectors. Results show that a training‑free BM25 retriever combined with an LLM selector achieves state‑of‑the‑art performance on the ZELDA benchmark, and the modular approach enables abstention when retrieval fails.
arXiv:2609.00998v1 Announce Type: cross Abstract: Word Sense Disambiguation has advanced rapidly for English and a handful of well-resourced modern languages, but it continues to assume the existence...
arXiv:2607. 08803v1 Announce Type: cross Abstract: The push toward large language models for biology (BioLM) has created a need for training corpora that can endow models with a genuine understanding of biology.
arXiv:2607. 08490v1 Announce Type: new Abstract: Biomedical language evolves rapidly as new discoveries emerge, causing traditional text models to lose semantic fidelity over time.
arXiv:2602. 09616v2 Announce Type: replace-cross Abstract: Reliable retrieval-augmented generation (RAG) systems depend fundamentally on the retriever's ability to find relevant information.
The paper introduces GPTKB 2.0, a method for building disambiguated knowledge bases directly from large language models. It addresses the lack of native entity representation in LLMs by performing on‑the‑fly disambiguation of entities, relations, and classes, achieving a million‑scale KB with over 1 million disambiguated entities and 38.4 million triples. The authors analyze trade‑offs among accuracy, scale, and cost, and release the system at https://gptkb.org/.