Organizations: Shanghai Artificial Intelligence Laboratory · Tongji University
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.
Large language model agents have shown promising capabilities in data-driven scientific discovery tasks, where an agent interacts with an execution environment and produces a statistical claim. Long-horizon scientific analysis remains constrained by the lack of process supervised environments over real-world scientific data. This paper introduces SciDisco, a scalable framework for training Scientific Discovery agents in process-verifiable environments. SciThèque compiles hypotheses, datasets, hidden evidence graphs, and verifiers into task environments where analytical progress can be checked during interaction. DAG-grounded trajectory synthesis uses these environments to construct verifier-filtered multi-turn demonstrations. DiscoPO then uses the environment as the source of training signal, assigning turn-level credit to actions that produce verifiable analytical evidence. Experiments show that SciDisco-14B reaches state-of-the-art on hypothesis-driven scientific data analysis benchmarks.
Scientific research involves complex information-seeking and reasoning workflows across heterogeneous sources. However, existing benchmarks primarily emphasize general-domain retrieval or static scientific question answering, and therefore fail to assess key capabilities required in realistic scientific research workflows. We introduce SciExplore, a benchmark designed to evaluate scientific information-seeking and reasoning capabilities of LLMs and agents. SciExplore comprises four task types covering 103 expert-curated tasks across more than ten scientific disciplines: scientific database navigation, ambiguous literature retrieval, missing reference completion, and cross-source structured knowledge synthesis, which probe progressively higher-level abilities from entity-level reasoning and document-level identification to evidence-level grounding and domain-level synthesis. We evaluate over ten state-of-the-art LLMs and autonomous agents on SciExplore, revealing substantial performance gaps with performance degrading sharply as task complexity increases and extremely low accuracy on the most challenging structured synthesis tasks. These results highlight significant limitations of current models and agents in realistic scientific information-seeking scenarios.
Despite recent progress in language models and agents for scientific data-driven discovery, advancing their capabilities is held back by the absence of verifiable environments representing real-world scientific tasks. To fill this gap, we introduce D3-Gym, the first automatically constructed dataset with verifiable environments for scientific Data-Driven Discovery. D3-Gym comprises 565 tasks from 239 real scientific repositories across four disciplines, each with a natural language instruction, an executable environment with pre-installed dependencies, dataset previews, a reference solution, and an automatically synthesized evaluation script. Our evaluation scripts achieve 87.5% agreement with human-annotated gold standards and strong alignment in domain-specific evaluation logic. Training on trajectories sampled from D3-Gym yields consistent gains across Qwen3 models on ScienceAgentBench, boosting Qwen3-32B by 7.8 absolute points and shrinking the gap with strong proprietary models. We further illustrate, through case studies, how D3-Gym environments can serve as a testbed for studying agentic optimization loops such as Autoresearch on real scientific workflows. We open-source D3-Gym, its creation workflow, sampled trajectories, and training scripts at https://github.com/OSU-NLP-Group/D3-Gym.