arXiv:2607. 01977v1 Announce Type: new Abstract: Ontology learning (OL) aims to automatically construct structured knowledge models from text, yet progress remains fragmented across methods, domains, and evaluation practices.
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:2609.08174v1 Announce Type: new Abstract: We introduce OntologyBench, a tiered biomedical retrieval benchmark comprising 471,854 training and 125,744 evaluation query-document relevance pairs a...
The pro-team at LLMs4OL 2026 presented a system for ontology learning that tackles both the End-to-End Flagship Task (Task A) and the Ontology Extension Reuse Task (Task B). Their approach uses an offline retrieval‑augmented few‑shot prompting pipeline with Qwen2.5‑14B‑Instruct and MiniLM‑L6‑v2 for retrieval, selecting top‑5 examples for Task A and top‑2 for Task B, and applies a left‑truncated context‑windowing strategy to keep task instructions in long prompts. For Task B, generated triples are filtered deterministically by a vocabulary constraint, keeping triples that involve at least one term from the closed vocabulary and removing duplicates of the initial ontology, achieving high scores in Semantic Graph Similarity, Term‑Typing F1, and Taxonomy Discovery F1, though no non‑taxonomic relations were extracted.
arXiv:2605. 28965v2 Announce Type: replace Abstract: Linking free-text phenotype descriptions to ontology terms, typically referred to as phenotype annotation, is essential for the cross-study integration of comparative morphological data.
arXiv:2606. 26130v1 Announce Type: cross Abstract: Large Language Models (LLMs) are increasingly used to guide research methodology, yet their default methodological tendencies under minimal prompting remain unclear.
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.
arXiv:2607. 16201v1 Announce Type: new Abstract: Ontology engineering remains a critical bottleneck in knowledge-intensive AI systems.
arXiv:2606. 12451v1 Announce Type: new Abstract: Large language models deployed as agents over large tool catalogs face a critical tool-retrieval bottleneck.
arXiv:2604. 08552v2 Announce Type: replace-cross Abstract: Scientific metadata are often incomplete and noncompliant with community standards, limiting dataset findability, interoperability, and reuse.
arXiv:2606. 05693v1 Announce Type: new Abstract: Large language models (LLMs) have shown promise for molecular property prediction, but their ability to reason over chemical structures remains limited, as molecular representations such as SMILES differ substantially from the natural language on which LLMs are primarily trained.