From Intent to AI Pipelines: A Controlled Agentic Framework for Non-AI Expert Scientists

Agentic AI tools offer a promising path to automating software development bottlenecks in scientific research pipelines, particularly for stages that take domain experts days to months to build, where scientists care about correctness and robustness, not implementation details. We present an empirical study of general-purpose coding agents on a fly optogenetics data-to-discovery pipeline. We assess agents on tasks substantially larger than existing benchmarks, datasets orders of magnitude bigger, and evaluation criteria grounded in domain expert standards. We show that agents can solve several individual pipeline stages, suggesting stage-level automation is tractable. By analyzing agents' code iterations, we show that they struggle most when there is not a pre-defined criterion to iterate on, and they must instead use their scientific judgment to assess their current solution, a key open challenge. Mirroring scientific practice, they sometimes attempt visual inspection of intermediate outputs for self-evaluation, but largely fail to interpret what they see or act on it appropriately. Solving the end-to-end pipeline correctly requires stringing together successes across all pipeline stages, and this is beyond agents' current abilities. We identify challenges largely absent from existing benchmarks, including computational resource management and generalization to large held-out data collections. Finally, we distill principles for constructing scientific tasks and rigorous evaluation criteria for open-ended problems.

Recent advances in agentic AI have enabled increasingly autonomous workflows, but existing systems still face substantial challenges in achieving reliable deployment in real-world scientific research. In this work, we present a safe, lightweight, and user-friendly agentic framework for the autonomous execution of well-defined scientific tasks. The framework combines an isolated execution environment, a three-layer agent loop, and a self-assessing do-until mechanism to ensure safe and reliable operation while effectively leveraging large language models of varying capability levels. By focusing on structured tasks with clearly defined context and stopping criteria, the framework supports end-to-end automation with minimal human intervention, enabling researchers to offload routine workloads and devote more effort to creative activities and open-ended scientific inquiry.

AI models underpin data-centric applications from image and text processing to scientific discovery in biology, physics, and chemistry. Yet developing them remains heavily manual, requiring practitioners to design architectures, build training pipelines, and iteratively refine solutions, making it challenging for natural scientists without specialized AI engineering expertise to build the high-performing models their research demands. To reduce this burden and broaden access to AI for scientific discovery, agents that automatically build AI models have been proposed. However, the performance of these agents is largely limited by the parametric knowledge of their underlying large language models, which is static, often outdated, and sparse on practical AI model engineering know-how. To address this limitation, we introduce AIBuildAI-2, a knowledge-enhanced agent with an external, evolving knowledge system for automatically building AI models. The knowledge system of AIBuildAI-2 is hierarchical, organizing curated AI development knowledge into high-level knowledge instructions over topical categories and low-level knowledge documents under each category, from which the agent dynamically loads only the context relevant to its current state and the AI task being solved, grounding each design and implementation decision in concrete, externally verifiable expertise. The system is initialized by collecting and cleaning AI-development-related documents from the web and organizing them into the corresponding categories, and continually evolves from the agent's own experience by distilling each completed run on an AI task into structured takeaways that are written back into the knowledge system. AIBuildAI-2 achieves state-of-the-art results, ranking first on MLE-Bench with a 70.7% medal rate and placing in the top 6.6% among 4,370 human-expert teams in a heart disease prediction competition.