AskChem is a new retrieval infrastructure that reframes chemistry literature search around atomic, provenance-carrying claims rather than document rankings, indexing 2.4M claims from 147K papers. Each claim is grounded with a source DOI and verbatim quote, and the system exposes a faceted taxonomy, evidence graph, and living taxonomy for synthesis. The system provides REST, SDK, and MCP access for AI agents, and benchmarking shows that grounding GPT-5.5 in AskChem yields 100% resolvable DOIs versus 88.3% without retrieval. The work is relevant both as a domain-specific RAG infrastructure paper and as an example of MCP-native scientific tooling for AI agents.
Researchers introduce ProvenanceGuard, a verifier that checks factual claims in MCP-grounded LLM agent answers against their specific source provenance rather than pooled evidence. The system decomposes answers into atomic claims, routes each to its attributed source via MCP trace metadata, and applies NLI plus token-alignment checks to detect 'cross-source conflation' — where a claim is supported somewhere but attributed to the wrong source. Evaluated on 281 medical-domain MCP-agent traces, it achieves block F1 of 0.802 and source accuracy of 0.858 on held-out data, and detects all injected attribution swaps in 50 controlled clinical probes. The work establishes source attribution as an independent factuality axis distinct from standard grounding checks.
Researchers present a fully automated pipeline using a multi-agent LLM framework to classify chemical reactions and generate verifiable reaction rules across 665,901 US patent reactions. The system expands a standard taxonomy from 68 to 14,073 classes without human curation, using a verification loop that tests each generated rule against the corpus. A lightweight fingerprint classifier trained on the output achieves 97.7% accuracy on unseen reactions, matching leading proprietary classifiers while extending to novel chemistries. The work demonstrates a general approach for converting generative LLMs into self-expanding symbolic rule systems.
Researchers introduce SciReasoner, a multimodal scientific foundation model that discretizes molecular coordinates, topologies, and periodic connectivities into a unified structure-aware vocabulary for reasoning over proteins, small molecules, and inorganic crystals. The model achieves state-of-the-art performance on 67 of 86 benchmarks, with notable gains in Gene Ontology prediction (F_max 0.42→0.55), retrosynthesis accuracy (0.63→0.72), and materials phase separation. Expert evaluators rated its reasoning traces as preferred or comparable to a frontier LLM in 98% of cases, suggesting meaningful interpretability alongside accuracy gains.
A preprint analyzes web analytics from August 2023 to October 2025 to quantify AI-mediated referral traffic to an academic library's institutional repository. ChatGPT, Perplexity, and Gemini are identified as the primary platforms driving this traffic, with open-access theses and dissertations being the most commonly surfaced resources. The study finds that structured metadata and stable permalinks correlate with higher AI retrieval rates, suggesting that resource discoverability in AI ecosystems depends on metadata quality and open-access status.
This paper evaluates whether LLM-based agents still need structured semantic metadata (e.g., schema.org) for data retrieval, comparing a Baseline Agent searching open-web documents against a Semantic Agent leveraging 90 million schema.org-annotated datasets. Using an LLM-as-a-judge pipeline aligned to FAIR principles, the Semantic Agent achieves 65.7% higher overall precision in retrieving FAIR-compliant datasets, while the Baseline Agent answers 40% more questions but frequently returns prose-heavy or portal landing pages instead of actionable data. The study concludes that structured semantic ecosystems remain essential for reliable, execution-oriented agentic workflows despite LLMs' broad unstructured retrieval capabilities.
The paper introduces ACL-Verbatim, an extractive question answering system built on VerbatimRAG that maps user queries directly to verbatim text spans in ACL Anthology papers, eliminating hallucination by design. The authors contribute a new ground-truth benchmark dataset created via human NLP-researcher annotation over synthetic queries generated using a ScIRGen-based pipeline. A 150M-parameter ModernBERT token classifier trained on silver supervision achieves the best word-level F1 of 53.6, outperforming the strongest LLM-based extractor at 48.7. The work demonstrates that smaller extractive models can outperform large generative LLMs on precision-critical retrieval tasks.
Researchers introduce SupraBench, the first benchmark designed to systematically evaluate LLMs on supramolecular chemistry tasks including binding affinity prediction, top-binder selection, solvent identification, and host-guest description. The work also releases SupraPMC, a 16M-token corpus of supramolecular chemistry articles from Europe PMC to support domain adaptation. Evaluation of broad open and proprietary LLMs reveals substantial headroom across all tasks, with domain pretraining improving in-distribution regression but creating format compliance tradeoffs. The benchmark targets a narrow but practically important scientific domain where LLM acceleration could reduce days-long dry-lab verification cycles.
Researchers present APS-RAG, a deployed retrieval-augmented generation platform for the Advanced Photon Source (APS) scientific facility that fuses dense, sparse, and knowledge-graph retrieval channels with a corrective agentic loop and a ReAct executor over an MCP tooling layer. The system is evaluated on APS-Bench, a new 50-question QA dataset with auditable gold answers, where the full corrective Agentic GraphRAG achieves 70.3% strict vital-nugget recall versus 63.8% for a BM25 baseline. The cross-encoder reranker is identified as the most impactful component, with its removal causing a 32.8% drop in recall. The codebase, evaluation harness, and benchmark construction methodology are released to support adoption at other scientific facilities.