An Agentic AI Framework to Accelerate Scientific Discovery in Plant Phenotyping
Authors: Renan Souza, Daniel Rosendo, Kelsey Carter, John Lagergren, Frédéric Suter, Shelaine L. Curd, Gerald A. Tuskan, Rafael Ferreira da Silva, +1 more
Organizations: Oak Ridge National Laboratory, Oak Ridge, TN, USA
Abstract
High-throughput plant phenotyping now generates image derived datasets far faster than scientists can analyze them. At Oak Ridge National Laboratory's Advanced Plant Phenotyping Laboratory (APPL), automated stations image hundreds of plants daily across multiple remote sensing modalities; yet, trait extraction and interpretation remain manual, expert-bound, and strictly post-hoc, making analysis, not acquisition, the binding constraint on discovery. We present an end-to-end agentic AI framework that turns the facility from a data factory into an interactive autonomous, discovery platform, where scientists partner with AI agents to accelerate time to insight. A conversational Co-Scientist Agent translates a scientist's natural-language question into a structured analysis plan, and a headless Compute Agent dispatches Vision Transformer segmentation and trait extraction on the Frontier exascale supercomputer. The two agents run in separate security and resource domains and communicate over a secure, token-authenticated streaming channel, a design that accounts for the federation, data-movement, and provenance realities cloud-native agentic frameworks ignore, ensuring end-to-end provenance is captured for every interaction. The framework turns a days- to weeks-long analysis process into an interactive loop where agents reason over results, recommend next analyses, and respond to follow-up questions in seconds.
This paper details two novel frameworks for developing autonomous, agentic AI in scientific workflows. Both systems leverage a hybrid Local Body, Remote Brain architecture via Google Colab, utilizing Python-based local orchestrators to invoke large language model (LLM) cloud backends. The first agent, DeepTS/DeepCollector, automates the large-scale curation, extraction, and deduplication of time-series datasets. The second, DeepScribe, is an autonomous presentation analyzer that converts visually dense, mathematically complex physics lectures into structured scientific reports. Through practical systems engineering-such as granular attribute extraction (Cellular RAG), remote data inspection, and distributed concurrency controls-we demonstrate how agentic AI can overcome the context and reasoning limitations of current state-of-the-art systems to rigorously support scientific workflows. Finally, we outline a generalization of DeepTS to support deep knowledge graphs and discuss the application of this conceptual approach to high-energy physics (DeepQCD).
The ability to inspect, interpret, and communicate complex data is crucial for virtually any scientific endeavor, but often requires significant expertise outside the core domain ranging from data management and analysis to visualization design and implementation. We present an end-to-end agentic harness that, based on only the data and a high level description of the tasks, independently designs custom visual analysis applications (VIS apps). This represents an important step towards a general AI co-scientist envisioned by many as an autonomous system that can autonomously execute long horizon tasks based on high-level directions. Our proposed VIS co-scientist is an essential component of this broader AI co-scientist vision: a harness that can autonomously analyze data and design visualization solutions using a collection of agents and specialized skills that coordinate exploratory analysis, plan, configure the environment, implement, validate the interface, and most importantly evaluate the overall task completion. Each stage produces document and instruction artifacts that guide downstream work and enable iterative refinement. We validate this approach on IEEE SciVis Contests spanning multiple science and engineering fields. These contests serve as ideal proving grounds because they encode real-world complexity: ambiguous requirements, diverse data modalities, design trade-offs, and task-driven validation. Given only the data and target tasks, our system autonomously produces functional single-page VIS Apps with verified linked-view behavior, highly customized to domain experts' specified tasks and needs.
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.