Compass: Navigating Global Marine Lead Data Integration through Expert-Guided LLM Agent
Authors: Yiming Liu, Bin Lu, Meng Jin, Ziyuan Sang, Shuo Jiang, Lei Zhou, Xinbing Wang, Chenghu Zhou, +1 more
Abstract
Marine lead (Pb) and its isotopes are critical tracers for ocean circulation and anthropogenic pollution, yet in-situ observations remain costly and sparse. While vast historical records exist, they lie buried within the unstructured content of academic papers, creating "data silos" inaccessible to comprehensive analysis. Manual extraction is unscalable, while general-purpose Large Language Models (LLMs) lack the necessary domain-specific knowledge, leading to hallucinations and scientifically invalid outputs. To address this, we introduce an expert-guided adaptation approach that enables LLMs to perform rigorous scientific data extraction without fine-tuning. We operationalize this approach through Compass, an LLM agent framework enhanced by a Knowledge Tree co-designed with marine scientists, which decomposes complex tasks into verifiable steps, guiding the agent's reasoning to ensure scientific validity. Deploying Compass across a corpus of over 230,000 relevant open-access papers, we successfully extract 3,751 previously unincorporated Pb records. This effort establishes the largest integrated marine Pb database to date. Beyond standard metrics, Compass demonstrates superior reliability through multi-layered validation, achieving 92% accuracy as confirmed through expert manual verification. The newly integrated data expand coverage in previously under-sampled regions such as the East China Sea and the Southern Ocean, providing an enriched data foundation for future scientific discoveries. We release an interactive visualization platform to facilitate open scientific access. Our work demonstrates that expert-guided agents can effectively bridge the gap between general-purpose LLMs and high-stakes scientific domains, enabling scalable data discovery in geosciences.
Scientific datasets are commonly organized as hierarchical repositories containing heterogeneous and interdependent files, making their inspection, integration, and analysis labor-intensive and reliant on domain expertise. Although large language model (LLM) agents have advanced substantially in planning, reasoning, and tool use, existing research has largely overlooked their ability to interact with real scientific data assets through executable environments. We introduce Deep Scientific Data Exploration, an agentic task paradigm in which agents navigate repositories, interpret heterogeneous files and schemas, execute analyses, integrate cross-file evidence, and produce conclusions grounded in executed observations. To operationalize this paradigm, we present SciDataSailor, a framework for synthesizing tool-interactive trajectories by balancing broad exploration with targeted exploitation. SciDataSailor instantiates trajectory synthesis as Monte Carlo Tree Search (MCTS) with four task-specific mechanisms: difficulty-stratified exploration seeds, dual-feedback first-play urgency, hierarchical strategy-to-tool action generation, and entropy-guided branching. Using this framework, we construct SciDataSailor-SFT-2K for supervised fine-tuning and SciDataSailor-Bench for evaluation, with the latter comprising 627 meta-information summarization tasks and 586 scientific question-answering tasks across 27 datasets spanning the life, earth, and physical sciences.
NASA and its data centers hold thousands of geoscience datasets and tools like Worldview, Giovanni, the Science Discovery Engine, and Harmony. Finding the right one is hard even for domain experts. We present an agentic search system, deployed as a public service for the geoscience community, that takes a natural-language research query and returns the matching datasets and tools. We demonstrate that, in the era of large language models, the latent value of knowledge graphs (KGs) can be substantially amplified through agentic search. From the NASA Earth Observation Knowledge Graph (NASA EO-KG) we derive NASA-EO-Bench, an open benchmark of 47k query-dataset pairs (21k task-based queries). A neural scorer fine-tuned on NASA-EO-Bench beats cosine and BM25 baselines. Further combining it with BM25 via score fusion raises both Recall@10 (R@10) and MRR by over 5x. On top of this supervised pipeline, we add a zero-shot agentic reranking stage that, without any additional training, lifts MRR by 28% on a stratified N=200 subset, showing that LLM reasoning is complementary to supervised retrieval.
The promise of data-driven materials discovery remains constrained by the scarcity of large, high-quality, and accessible experimental datasets. Here, we introduce a generalizable large language model (LLM)-powered pipeline for automated extraction and structuring of materials data from unstructured scientific literature, using concrete materials as a representative and particularly challenging example. The pipeline exhibits robust performance across a broad range of LLMs and achieves an F1 score of up to 0.98 for diverse composition--process--property attributes. Within one hour, it extracts nearly 9,000 high-quality records with over 100 attributes from a corpus screened from more than 27,000 publications, enabling the construction of the largest open laboratory database for blended cement concrete. Machine learning analyses underscore the importance of large, diverse, and information-rich datasets for enhancing both in-distribution accuracy and out-of-distribution generalization to unseen materials. The proposed pipeline is readily adaptable to other materials domains and accelerates the development of scalable data infrastructures for materials informatics.