FlyAOC is a benchmark that tests AI agents on end‑to‑end ontology curation of Drosophila scientific literature. Given a gene symbol, a brief description, a large paper corpus, and ontology resources, agents must search for evidence and produce structured annotations such as function terms, expression patterns, and historical synonyms. The benchmark contains 7,397 expert‑curated annotations across 100 genes and evaluates different agent harnesses, revealing system‑level failure modes that single‑task evaluations miss.
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:2607. 28229v1 Announce Type: cross Abstract: The web is increasingly accessed by AI agents rather than humans.
arXiv:2603. 03322v2 Announce Type: replace-cross Abstract: Recent advancements in Large Language Model (LLM) agents have demonstrated remarkable potential in automatic knowledge discovery.
arXiv:2608. 19201v1 Announce Type: cross Abstract: Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale.
arXiv:2510. 17064v4 Announce Type: replace Abstract: Single-cell RNA sequencing has transformed our ability to identify diverse cell types and their transcriptomic signatures.
arXiv:2606. 13669v1 Announce Type: new Abstract: Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration.
arXiv:2607. 20926v1 Announce Type: new Abstract: Scientific research involves complex information-seeking and reasoning workflows across heterogeneous sources.
Modelpedia is an automated, LLM-assisted framework that extracts and organizes findings about AI models from published papers into a searchable public catalog. It links each finding to the relevant model, dataset, method, and concept, and has already extracted over a thousand findings from ICLR 2024 and 2025 papers. The authors invite the community to explore, contribute to, and build on this open catalog, positioning model findings as a shared foundation for the meta‑science of AI.
arXiv:2608. 14228v1 Announce Type: new Abstract: Life science knowledge graphs make large collections of structured data available through SPARQL, but each resource uses its own schema, identifiers, and links.
The paper introduces a modular agentic-AI platform that transforms heterogeneous CMC process-development documents into a dual-layer knowledge graph. The base layer creates a lexical Document‑Section‑Chunk hierarchy, while the intelligence layer extracts ontology‑aligned entities and links cross‑document concepts, all anchored by provenance. LLM agents navigate these layers to answer queries, and a novel three‑tier evaluation protocol demonstrates high retrieval‑augmented generation performance on proprietary data from a Sanofi program.
arXiv:2607. 28692v1 Announce Type: new Abstract: Large language model (LLM) agents have been increasingly adopted in scientific research for organizing and invoking specialized computational tools.
The paper introduces an ontology‑guided multi‑agent framework for extracting evaluation objects from academic review texts, addressing challenges such as abstractness, context‑dependency, and ambiguous type boundaries. The system combines candidate discovery, ontology‑constrained classification, and domain review, achieving high precision (90.33%) and recall (84.55%) and outperforming rule‑based and zero‑shot baselines. Ablation studies show that the multi‑agent workflow boosts recall and stability, while ontology‑based constraints improve fine‑grained classification and reduce category confusion.