arXiv subjects

John Lagergren

Publications and source records attributed to John Lagergren.

6 recordsLinked to original sources

arXiv2026

Exploring the Genesis Platform Capabilities to Accelerate Scientific Discovery in OPAL

Autonomous, cross-facility science requires capabilities that no individual project should have to build for itself: managed execution for long-lived services, versioned distribution of models to remote compute systems, governed access to large language models, a shared substrate for experimental data, and end-to-end provenance. The U.S. Department of Energy Genesis Mission platform, delivered through the American Science Cloud, provides these as reusable services. This paper reports how the Genesis platform enables cross-facility experiments and accelerates scientific discovery. We explore the plant phenotyping workflow of the Orchestrated Platform for Autonomous Laboratories as the exemplar: it couples Oak Ridge National Laboratory's Advanced Plant Phenotyping Laboratory with the Frontier supercomputer. In a 40-day nickel-treatment campaign, the resulting workflow replaced roughly twelve hours of manual analysis with interactive queries returning in seconds to minutes.

cs.DC↗

arXiv2026

An Agentic AI Framework to Accelerate Scientific Discovery in Plant Phenotyping

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.

cs.AI↗

arXiv2025

FOCUS: Fused Observation of Channels for Unveiling Spectra

Hyperspectral imaging (HSI) captures hundreds of narrow, contiguous wavelength bands, making it a powerful tool in biology, agriculture, and environmental monitoring. However, interpreting Vision Transformers (ViTs) in this setting remains largely unexplored due to two key challenges: (1) existing saliency methods struggle to capture meaningful spectral cues, often collapsing attention onto the class token, and (2) full-spectrum ViTs are computationally prohibitive for interpretability, given the high-dimensional nature of HSI data. We present FOCUS, the first framework that enables reliable and efficient spatial-spectral interpretability for frozen ViTs. FOCUS introduces two core components: class-specific spectral prompts that guide attention toward semantically meaningful wavelength groups, and a learnable [SINK] token trained with an attraction loss to absorb noisy or redundant attention. Together, these designs make it possible to generate stable and interpretable 3D saliency maps and spectral importance curves in a single forward pass, without any gradient backpropagation or backbone modification. FOCUS improves band-level IoU by 15 percent, reduces attention collapse by over 40 percent, and produces saliency results that align closely with expert annotations. With less than 1 percent parameter overhead, our method makes high-resolution ViT interpretability practical for real-world hyperspectral applications, bridging a long-standing gap between black-box modeling and trustworthy HSI decision-making.

cs.CV↗

arXiv2023

Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa

Plant phenotyping is typically a time-consuming and expensive endeavor, requiring large groups of researchers to meticulously measure biologically relevant plant traits, and is the main bottleneck in understanding plant adaptation and the genetic architecture underlying complex traits at population scale. In this work, we address these challenges by leveraging few-shot learning with convolutional neural networks (CNNs) to segment the leaf body and visible venation of 2,906 P. trichocarpa leaf images obtained in the field. In contrast to previous methods, our approach (i) does not require experimental or image pre-processing, (ii) uses the raw RGB images at full resolution, and (iii) requires very few samples for training (e.g., just eight images for vein segmentation). Traits relating to leaf morphology and vein topology are extracted from the resulting segmentations using traditional open-source image-processing tools, validated using real-world physical measurements, and used to conduct a genome-wide association study to identify genes controlling the traits. In this way, the current work is designed to provide the plant phenotyping community with (i) methods for fast and accurate image-based feature extraction that require minimal training data, and (ii) a new population-scale data set, including 68 different leaf phenotypes, for domain scientists and machine learning researchers. All of the few-shot learning code, data, and results are made publicly available.

cs.CV↗

arXiv2020

Region Growing with Convolutional Neural Networks for Biomedical Image Segmentation

In this paper we present a methodology that uses convolutional neural networks (CNNs) for segmentation by iteratively growing predicted mask regions in each coordinate direction. The CNN is used to predict class probability scores in a small neighborhood of the center pixel in a tile of an image. We use a threshold on the CNN probability scores to determine whether pixels are added to the region and the iteration continues until no new pixels are added to the region. Our method is able to achieve high segmentation accuracy and preserve biologically realistic morphological features while leveraging small amounts of training data and maintaining computational efficiency. Using retinal blood vessel images from the DRIVE database we found that our method is more accurate than a fully convolutional semantic segmentation CNN for several evaluation metrics.

eess.IV↗

arXiv2019

Learning partial differential equations for biological transport models from noisy spatiotemporal data

We investigate methods for learning partial differential equation (PDE) models from spatiotemporal data under biologically realistic levels and forms of noise. Recent progress in learning PDEs from data have used sparse regression to select candidate terms from a denoised set of data, including approximated partial derivatives. We analyze the performance in utilizing previous methods to denoise data for the task of discovering the governing system of partial differential equations (PDEs). We also develop a novel methodology that uses artificial neural networks (ANNs) to denoise data and approximate partial derivatives. We test the methodology on three PDE models for biological transport, i.e., the advection-diffusion, classical Fisher-KPP, and nonlinear Fisher-KPP equations. We show that the ANN methodology outperforms previous denoising methods, including finite differences and polynomial regression splines, in the ability to accurately approximate partial derivatives and learn the correct PDE model.

math.DS↗