An LLM agent for end-to-end computational materials discovery

The coordination of multi-scale tasks is an effective strategy for computational materials discovery, yet the repeated application of diverse algorithms and tools renders it challenging. We report MAESTRO, a large language model (LLM) agent system capable of executing the entire screening pipeline for metal-organic frameworks (MOFs). It processes a large body of MOF literature, links relevant publications to their crystal structures, and curates the results into a computation-ready database, which is then screened through a strategy of progressively increasing computational cost. The promising candidates identified for separation under wet flue gas conditions all originate from unrelated studies. By connecting the heterogeneous stages of computational materials discovery, the LLM-based agents of MAESTRO can operate across application domains and uncover high-performance materials that conventional screening approaches would be unlikely to consider.

Neural Circuit Function Inference with LLMs

The success of connectome mapping now shifts the challenge of understanding the nervous system to the interpretation of neural circuits. Here, we devise a new automated method, LLantia (LLM automated neural circuit inference and analysis), to systematically infer neural circuit function and the role of its component neural cell types. Our approach distills descriptions of cell type function from the literature and, in combination with the connectome, then infers the function for all other cell types, which serves as a basis for subsequent neural circuit function inference. Results are structured hierarchically, with different possible circuit functions organised under multiple possible behavioural and physiological contexts, and each circuit function composed of subcircuit descriptions alongside relevant cell types to facilitate both backtracking to known, published information and support further experimental research. We illustrate our method by inferring cell type function for all cell types of the adult fruit fly brain and for select broader circuits within, and validate our findings, including by cross-checking with literature published after the release date of our analysis.

Harnessing X-ray Absorption Spectroscopy Data through Multimodal Mining of Battery Literature

X-ray absorption spectroscopy (XAS) is central to understanding the local electronic and atomic structure of materials, yet most published spectra remain inaccessible to data-driven analysis because they are embedded in figures and described through fragmented textual context in the literature. Here, we use multimodal (image and text) literature mining to transform this dispersed knowledge into an AI-ready experimental data resource. We developed a scalable spectroscopy data digitization pipeline that identifies XAS figures in full-text articles, digitizes spectral curves, and links each spectrum to accompanying metadata on the measured edge and material. Applying this pipeline to the battery literature produced an open dataset of 13,740 XAS spectra, spanning 66 absorbing elements and diverse battery chemistries, with expert validation confirming accurate extraction of spectral and metadata information. By converting literature-embedded spectra into structured numerical data, this dataset provides a foundation for large-scale XAS analysis, cross-laboratory comparison, high-throughput characterization, and autonomous discovery of advanced materials.

An Autonomous Scientific Knowledge Generation Framework for AI-Driven Scientific Discovery

Artificial intelligence (AI) is transforming scientific discovery, but its effectiveness is fundamentally limited by the availability of structured scientific knowledge. Although existing databases have accelerated data-driven materials research, much of the knowledge needed for predictive modeling and inverse design remains embedded in unstructured scientific literature. We present an Autonomous Scientific Knowledge Generation Framework that transforms scientific publications into a Unified AI-Ready Scientific Knowledge Base. The framework integrates ontology-guided literature acquisition, hybrid scientific knowledge extraction, semantic harmonization, knowledge fusion, and validation within a unified workflow. Rather than treating literature retrieval, information extraction, and database construction as separate tasks, the framework progressively converts scientific publications into structured, semantically consistent, and provenance-preserving knowledge suitable for AI-driven reasoning. As a proof of concept, the framework was applied to electro-optic materials. Autonomous literature acquisition retrieved and validated about 1,000 publications from multiple scholarly repositories. A representative subset of eight publications was processed through the complete workflow, generating 29 structured scientific records that were harmonized into 7 canonical scientific records. The results demonstrate the complete transformation from scientific literature to an AI-ready scientific knowledge base while preserving quantitative measurements, operating conditions, provenance, and scientific context. The proposed framework provides a scalable, domain-independent foundation for predictive AI, generative AI, and closed-loop AI-driven scientific discovery.

Automatic bioinformatic software named entity recognition from literature

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. The lack of a comprehensive and up-to-date catalog of bioinformatics resources hinders efforts toward automated biomedical knowledge extraction and streamlined data analysis. Here we present SNAIL, a hybrid named entity recognition framework designed to automatically identify bioinformatics software and database (SW/DB) names from biomedical texts. SNAIL integrates complementary lexical and semantic modeling strategies. The lexical component captures orthographic patterns and contextual cues characteristic of SW/DB names, while the semantic component leverages contextual embeddings generated by transformer-based language models such as SciBERT, combined with an explicit token-masking strategy to enhance entity-focused representations. A large training corpus was constructed automatically through a hybrid pipeline that integrates citation-hinted extraction with large language model-assisted distillation. Evaluation on two independent benchmark datasets and real-world research articles demonstrates that SNAIL substantially outperforms existing approaches, including domain-specific methods such as bioNerDS2 and general-purpose large language models such as ChatGPT, Gemini, Grok and Claude. Applying SNAIL to large-scale literature analysis further reveals distinct journal-level preferences across bioinformatics subfields. These results demonstrate that SNAIL provides an accurate and scalable solution for identifying bioinformatics resources in scientific texts and enables systematic meta-analysis of tool usage and research trends.

From Experimental Limits to Physical Insight: A Retrieval-Augmented Multi-Agent Framework for Interpreting Searches Beyond the Standard Model

Modern searches for physics beyond the Standard Model produce rapidly expanding literature containing heterogeneous information, including textual analyses, numerical datasets, and graphical exclusion limits. Integrating these distributed sources remains a time-consuming and manual process for physicists. We present HEP-CoPilot, a retrieval-augmented multi-agent AI framework for the exploration and interpretation of high-energy physics literature. The system unifies textual information from publications, structured experimental data from HEPData, and reconstructed physics plots within a multimodal retrieval and reasoning architecture. By combining retrieval-augmented language models with coordinated agent workflows, it enables evidence-grounded reasoning over experimental analyses and structured interpretation of collider results. We evaluate the framework on recent CMS searches for physics beyond the Standard Model. Case studies show that HEP-CoPilot can retrieve relevant measurements, reconstruct exclusion limits directly from HEPData records, and perform cross-paper comparisons of experimental constraints. This enables consistent, physics-aware comparison across analyses without manual data integration. These results demonstrate that retrieval-augmented AI systems can function as scientific co-pilots for particle physics, facilitating navigation of complex literature, structuring heterogeneous evidence, and accelerating the interpretation pipeline for new physics searches.