This work presents SciDataSailor, a framework for synthesizing tool-interactive trajectories by balancing broad exploration with targeted exploitation and presents SciDataSailor, a framework for synthesizing tool-interactive trajectories as Monte Carlo Tree Search (MCTS) with four task-specific mechanisms.
Abstract
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.
SDABench is introduced, a benchmark that reorganizes evaluation around six capabilities (descriptive, exploratory, inferential, inferential, predictive, causal, and mechanistic) across five domains (Biology, Chemistry, Environment, Geography, Physics).
Chuhan Shi, Xiaoquan Ren, Sicheng Song et al.· arXiv.org· 1 citation
Large language model (LLM) agents have been increasingly adopted in scientific research for organizing and invoking specialized computational tools. However, their reliance on predefined tool spaces with static semantics limits their applicability to open-world scientific workflows, where tool requirements, capabilities, and boundaries evolve dynamically. To this end, we propose SciToolAgent-Evo, an ontology-aware self-evolving agent for open-world scientific tool acquisition. Driven by an evolving memory of skills, experiences, and an ontologized tool graph, it distills generalizable knowledge from contrastive trajectories during accumulation, whereas during inference, it formulates active requests and utilizes a LinUCB-based bandit gate to dynamically balance exploration and exploitation. Once a novel tool is acquired, its scientific ontology is completed online for seamless integration into the known graph. Moreover, we introduce OpenSciToolBench, a benchmark containing 900 realistic tasks across four difficulty levels. Extensive evaluations show that SciToolAgent-Evo achieves state-of-the-art performance, validating its robustness and generalization.
Yuqi Tang, Chenyi Zhou, Libin Wang et al.· 0 citations
High-quality biological databases are the bedrock of data-driven scientific discovery. However, the construction of these resources remains a labor-intensive bottleneck, particularly for emerging research frontiers where structured data is non-existent. While LLM-based agents have catalyzed progress in downstream scientific modeling, their potential to automate the critical upstream challenge of database curation remains largely untapped. To bridge this gap, we introduce BioDataLab, a rigorous benchmark comprising 100 tasks meticulously derived from 57 high-impact database publications. BioDataLab evaluates the capability of autonomous agents to transform raw, heterogeneous biological resources into structured, analysis-ready databases. Unlike static evaluations, BioDataLab provides a fully interactive environment encompassing data retrieval, extraction, annotation, and integration, featuring process-oriented curation targets and contamination-control checks. We benchmark 11 state-of-the-art LLMs (including Gemini-3.0, GPT-5.2, and Claude-4.5) under different agent frameworks, revealing a substantial capability gap: the top-performing model achieves only a 40% success rate. Further error analysis identifies significant bottlenecks in multi-step tool orchestration and adherence to complex biological data formats. These findings underscore that while LLMs are proficient in downstream reasoning, autonomous upstream curation remains a formidable frontier. All data and codes are available at GitHub.
Jiaxian Yan, Xi Fang, Jintao Zhu et al.· Proceedings of the 32nd ACM...· 0 citations
Results indicate that SciDSK improves how agents locate and understand scientific datasets, providing a stronger foundation for actionable scientific data use.
Xiaohan Huang, Qingqing Long, Xiaolei Du et al.· 0 citations
SciForge is a multimodal research-native AI workbench that reserves the graphical interface for human judgment while search, parsing, model routing, workflow execution, plotting, writing, and presentation generation run as modular agent-accessible services.
SciForge Team Zhangyang Gao, Minghao Fang, Yifei Liu et al.· arXiv.org· 0 citations
Answering developer questions about a software repository is a critical yet under-explored problem in software engineering. While existing repository understanding methods have advanced the field, they predominantly rely on surface-level code retrieval and lack the ability for deep reasoning over multiple files, complex software architectures, and grounding answers in long-range code dependencies. To address these limitations, we propose DeepRepoQA, a novel question answering (QA) framework for repository-level code understanding. DeepRepoQA builds on an agentic framework where LLM agents find answers through a systematic tree search over the repository structure. A Monte-Carlo Tree Search (MCTS) mechanism is employed to empower agents to dynamically search, navigate, and inspect code, enabling effective multi-hop reasoning over long-range code dependencies. Comprehensive experiments on the SWE-QA benchmark demonstrate substantial performance gains over strong baselines, validating the effectiveness of systematic MCTS-guided exploration for multi-hop repository reasoning.
Wei Peng, Yuling Shi, Yingwei Ma et al.· 0 citations
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