Asking the Right Questions: Ontology-Grounded Interpretable Embeddings for Biomedical Text
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arXiv:2607. 11891v1 Announce Type: cross Abstract: The deployment of large language models (LLMs) in specialized domains like medical diagnostics and financial advisory necessitates evaluating capabilities beyond general knowledge.
arXiv:2607. 06452v1 Announce Type: cross Abstract: Biomedical question answering requires not only accurate extraction of information from scientific literature but also reliable integration of evidence across multiple documents.
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:2605.28740v2 Announce Type: replace-cross Abstract: As large language models are increasingly deployed for clinical text, ensuring they can reliably signal their own uncertainty becomes critica...
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:2604. 15591v2 Announce Type: replace-cross Abstract: Effective biomedical information retrieval requires modeling domain semantics and hierarchical relationships among biomedical texts.