arXiv:2411. 06024v1 Announce Type: cross Abstract: The exponential growth in protein-related databases and scientific literature, combined with increasing demands for efficient biological information retrieval, has created an urgent need for unified and accessible search methods in protein engineering research.
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:2607. 28229v1 Announce Type: cross Abstract: The web is increasingly accessed by AI agents rather than humans.
arXiv:2607. 26070v1 Announce Type: cross Abstract: Large language model (LLM)-based agentic search systems are often evaluated as if the underlying LLM were the only component that matters, yet their measured performance also depends on the surrounding search environment: the Wikipedia snapshot, preprocessing pipeline, chunking policy, retrieval backend, tool schema, observation format, and answer submission rule.
arXiv:2411. 04440v1 Announce Type: cross Abstract: Protein engineering is important for biomedical applications, but conventional approaches are often inefficient and resource-intensive.
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: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:2606. 13669v1 Announce Type: new Abstract: Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration.
arXiv:2606. 20235v1 Announce Type: cross Abstract: Academic paper search is a core step in scientific research, and LLM-based search agents are emerging as a promising paradigm for iterative, intent-driven literature exploration.
arXiv:2607. 20498v1 Announce Type: new Abstract: Large language models (LLMs) augmented with tools are emerging as autonomous agents capable of using Web engine, APIs, and code to solve complex, long-horizon tasks.
arXiv:2609.05818v1 Announce Type: new Abstract: We introduce ABLE, a benchmark for evaluating LLM agents' ability to use biological AI models (BAIMs), such as ProteinMPNN and AlphaFold3, in dual-use...
ClinAgent is a conversational system that uses a ReAct-based LLM agent to retrieve and synthesize clinical trial information from multiple sources such as ClinicalTrials.gov, PubMed, and a local dataset. The agent iteratively reasons over user queries, selects appropriate tools, and refines its actions to provide grounded, up-to-date responses in natural language across multi-turn interactions. Evaluation across three phases shows that DeepSeek (thinking mode) excels in planning quality while Gemini 3.0 Flash delivers the highest overall performance and expert ratings, demonstrating the promise of agentic AI for improving clinical trial data access.
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.