arXiv:2609.10055v1 Announce Type: cross Abstract: Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical dat...
Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical va...
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.
The paper proposes a behavior-based fusion model that combines large language models (LLMs) with ontology rankers to improve rare-disease diagnosis. By examining ranked lists, agreement, and ontology support, the model learns how much to rely on each system per case, achieving significant recall gains on Phenopacket Store and RAMEDIS benchmarks. Importantly, the fused diagnoses retain candidate-level ontology evidence for inspection.
EvidenceNet is a disease‑specific dataset that transforms full‑text biomedical literature into structured evidence records and graph representations, preserving study design, provenance, and quantitative support. Using an LLM‑assisted pipeline, it extracts experimentally grounded findings, normalizes entities, scores evidence quality, and links related records via typed semantic relations. The released subsets—EvidenceNet‑HCC and EvidenceNet‑CRC—contain thousands of evidence records and richly connected graphs, with high extraction and relation‑type accuracy, enabling retrieval‑augmented question answering and graph‑based tasks such as link prediction and target prioritization.
arXiv:2608.31118v1 Announce Type: new Abstract: The effect of Large Language Model (LLM) scale on ontology learning (OL) performance remains insufficiently characterized. We present a controlled eval...
arXiv:2604. 25605v2 Announce Type: replace-cross Abstract: Introduction: Semantic search, which retrieves documents based on conceptual similarity rather than keywords, offers advantages for retrieval of clinical information.
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:2607. 00147v1 Announce Type: new Abstract: Rare disease differential diagnosis is a critical yet arduous clinical task, requiring physicians to identify precise phenotypes from complex, unstructured patient symptoms and execute intricate reasoning within a vast search space.
arXiv:2606.22419v3 Announce Type: replace Abstract: A recent Nature Medicine study reports that general-purpose frontier LLMs outperform specialized retrieval-augmented clinical tools on medical benc...
The paper introduces a benchmark for recommending SNOMED CT concepts from masked clinical contexts, using data from the SNOMED CT Entity Linking Challenge v1.2.1 derived from MIMIC-IV-Note. It evaluates several methods—including a popularity baseline, sparse TF‑IDF prototypes, dense embeddings, and retrieval‑augmented hybrids—finding that sparse TF‑IDF achieves the best performance with Recall@1 of 14.81% and Recall@10 of 33.43%. The study highlights that concept frequency and lexical context strongly influence recommendation quality, with many test pairs involving concepts unseen during training.
arXiv:2605. 30237v2 Announce Type: replace-cross Abstract: Semi-structured knowledge bases (SKBs) embed textual documents in a typed graph of entities and relations, and underpin applications such as product search, academic paper search, and precision-medicine inquiries.