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25 records · Page 2

Plant Bioengineering Atlas: A Knowledge Graph of Genes, DNA Constructs, and Plant Traits.

Plant bioengineering has generated tens of thousands of genotype-to-phenotype relationships, but this knowledge remains fragmented across narrative literature and difficult to use computationally. Inconsistent descriptions of DNA constructs, host species, and traits, including variable species names, omitted regulatory elements, and inconsistent gene symbols, impede data reuse, comparative analysis, and design-build-test-learn cycles. Here, we present the Plant Bioengineering Atlas, a literature-mined, ontology-grounded knowledge base assembled using an artificial intelligence (AI)-aided extraction pipeline. A large language model parsed open-access primary research articles to generate structured, provenance-anchored records of engineered genes, modification types, promoter-gene-terminator constructs, host species, target traits, and reported phenotypes, with every record traceable to its source. The current release contains 14,358 curated records encompassing 6,998 distinct genes across 436 plant species from 6,452 papers published between 2000 and 2026. Corpus analysis reveals that experiments are concentrated in a small group of model and crop species, disease and pathogen resistance is the most frequently engineered trait class, and constitutive regulatory parts (particularly the CaMV 35S promoter and NOS terminator) remain pervasive. Two in five records omit one or both flanking regulatory elements (i.e., promoter and terminator), while only 23.4% describe cassettes in which both elements resolve to named part classes, exposing a systematic reproducibility gap. We organize these data into a knowledge graph linking genes, constructs, species, and traits; provide access through an interactive web portal; and propose an AI-compatible documentation standard for AI-ready reporting. The Plant Bioengineering Atlas provides a foundation for data-driven hypothesis generation and AI-aided plant biodesign.

, Genes, DNA Constructs↗

AI Applications to Physics Experiments at Jefferson Lab

We survey how AI/ML is being deployed across Jefferson Lab's experimental and accelerator programs. In EPSCI, Hydra applies computer vision to automate real-time data-quality monitoring across all four experimental halls, replacing manual inspection of hundreds to thousands of histograms per shift. AIEC (AI Experiment Controls) uses ML to stabilize drift chamber gains and is now part of standard CEBAF production running, while AI Optimized Polarization (AIOP) targets autonomous control of polarized targets and photon beam angular alignment. In CASA, cavity fault classification models identify faulted cavities and trip types from waveform data with ~85% and ~78% agreement to labeled data, respectively, and are deployed in production; a separate effort applies LLMs and hybrid search to make the CEBAF operations logbook AI-ready. QCD-focused work includes transformer- and GAN-based generative models for particle-level event simulation, with distributed GAN training scaling studies on Polaris. Additional efforts span ML-on-FPGA for the EIC and a new Data Science Department coordinating anomaly detection, uncertainty quantification, and HPC-scalable ML lab-wide. Collectively, these projects illustrate AI's growing role in improving efficiency across JLab's nuclear physics mission.

Mei, Xinxin [Thomas Jefferson National Accelerator↗

FAIR Data Meets FAIR Software

Modern scientific research is increasingly defined by the interplay between data, software, and the workflows that connect them. Yet while the FAIR (Findable, Accessible, Interoperable, Reusable) principles have become foundational for scientific data stewardship, the same level of structure and expectation has only recently begun to extend to research software. This talk covers why and how FAIR principles are being applied to data and software to support data reuse. It outlines the gaps in current sharing norms, the growing federal emphasis on persistent identifiers and public access, and the opportunities created when datasets, computational workflows, code, and models are linked through rich, standardized metadata. Practical implementation pathways for the EIC and JLab communities are described, including datacards for structured dataset documentation and provenance-aware workflows. By aligning data lifecycle management with FAIR-aligned software practices, the scientific community can advance toward autonomous knowledge graphs, generative workflows, and high-quality, AI-ready scientific datasets.

McSpadden, Diana [Thomas Jefferson National Accele↗

Considerations for Distributed Edge Data Centers and Use of Building Loads to Support Large Interconnections

The rapid expansion of artificial intelligence (AI) and machine learning is driving unprecedented electricity demand from data centers. It is predicted that by 2030, 90% of AI workloads will be inference-based, requiring interconnection of multiple low-latency edge data centers (<20 MW) sited closer to end users - often on already constrained distribution feeders. Although individually small, these loads can aggregate to large loads per feeder, straining infrastructure, creating multi-year interconnection delays, and driving up customer costs. This paper proposes a data center-focused grid-integration framework that combines feeder hosting capacity analysis with building energy efficiency, building load flexibility, and waste heat reuse to expand effective feeder and substation headroom. Such approaches can reduce interconnection delays, lower costs for ratepayers, and accelerate AI-ready infrastructure deployment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

AI-Ready Control System for the Fermilab Accelerator Complex

Reliable, high-intensity operation of the Fermilab Accelerator Complex is critical to the success of the Long-Baseline Neutrino Facility and Deep Underground Neutrino Experiment. We describe the requirements and infrastructure necessary to support routine use of artificial intelligence and machine learning (AI/ML) in the accelerator control system. Three capabilities are identified: a machine learning operations (MLOps) framework standardizing the lifecycle of AI/ML automation from data management through deployment and monitoring; a data quality framework defining and enforcing standards required to build trustworthy AI/ML applications; and workflow integration with large language models to assist physicists, engineers, and operators with information retrieval, code development, and routine analysis. Use cases spanning beam diagnostics, beam control, and support system automation illustrate the technical requirements across the complex.

43 PARTICLE ACCELERATORS↗

DOE Repository Metadata Profile (DRMP): A Metadata Framework for Advancing Interoperability and AI Readiness Across Scientific Repositories

The Department of Energy (DOE) funds a diverse and distributed ecosystem of repositories that steward scientific data, publications, and software across its research programs, user facilities, and national laboratories. While significant progress has been made in standardizing dataset-level metadata, the metadata describing repositories themselves (their identity, governance, access interfaces, policies, and technical capabilities) remains inconsistent and fragmented across DOE-funded systems. This variability limits discoverability, interoperability, automated validation, and AI-driven analysis, all of which are increasingly essential for modern scientific workflows. To address this gap, the DOE Data Curation Working Group (DCWG) developed the DOE Repository Metadata Profile (DRMP). The DRMP is a practical, community-driven framework that defines how repositories can describe themselves in a consistent, machine-actionable, and scalable manner. The DRMP is not a new metadata schema. Instead, it is a mapping profile and structured element set capturing the essential characteristics of DOE repositories. It harmonizes repository-level metadata across six widely adopted community schemas: RE3Data; DCAT-US v3; Schema.org; Dublin Core; DataCite 4.6; and PREMIS 3.0. This harmonization eliminates reinvention and enables interoperability within DOE and across the broader scientific ecosystem. A core objective of the DRMP is to reduce burden on repositories by allowing them to reuse their existing metadata through a Rosetta-style crosswalk rather than redesigning local implementations. The profile introduces a three-level conformance model that supports incremental adoption: • Level 1 – Minimum Viable Record (MVR): foundational identification elements required for workflows, project registration, and basic repository presence. • Level 2 – Interoperable: structured metadata enabling alignment with national and international discovery systems. • Level 3 – AI-Ready: enhanced provenance, policy transparency, fixity, semantic context, and capabilities that support automated reasoning, model training governance, and machine-assisted curation. To support implementation, the DRMP includes JSON Schema definitions, OpenAPI patterns, and MCP templates that allow repositories to publish machine-readable metadata directly within existing platforms. These resources are modular and lightweight, enabling adoption without major architectural change. Adopting the DRMP enables repositories to: • Enhance discoverability and interoperability by aligning identifiers, classifications, and descriptive elements across widely used schema standards. • Support federated discovery and cross-registration across DOE systems, Data.gov, and international catalogs. • Enable AI agents and workflow orchestration systems to interpret repository-level metadata within the American Science Cloud (AmSC) through Model Context Protocol (MCP)-based context publication. • Demonstrate alignment with DOE’s open science, stewardship, and FAIR data priorities. This guidance represents a community-driven step forward. Through voluntary adoption and continued feedback, the DRMP advances a cohesive, machine-actionable description of DOE repositories that supports FAIR data practices, preparing the infrastructure for AI-enabled research, and strengthening the discoverability and reuse of DOE’s scientific outputs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Dual Context: Leveraging Structured Application Context for Code Generation and Runtime Feature Activation via Chat Interfaces

Integrating artificial intelligence (AI) capabilities into software applications typically involves two common paths. For developers, AI assists in generating and documenting source code and other related software engineering efforts. For users, AI assists them through question-and-answer exchanges via chatbots. Both approaches have their value, but neither effectively leverages the modularity of component-based architectures that modern web application frameworks offer. We implement a proof of concept within a centralized suite of applications used for the Atmospheric Radiation Measurement (ARM) Data Center Operational Tools, where we introduce a third integration path through the ARM Context Engine (ACE). ACE is a context driven system that uses structured contextual specifications to enable Large Language Models (LLMs) to render interactive and feature-rich user interface (UI) components directly within chat responses, alongside or in place of conventional text outputs. These specifications serve two important purposes across what we call code context and UI context. Code context provides AI-assisted development tools with structured application knowledge beyond raw code, including component relationships, architectural patterns and schematic information, enabling the generation of consistent, well-structured code. UI context defines the rules for enabling and rendering component features at runtime based on the user's natural language input, allowing end users to activate capabilities such as data export, filtering, and pagination within chat responses, without requiring code changes or redeployment. We demonstrate, through a comparative evaluation against general-purpose AI chatbots, that context-driven component rendering provides interactive capabilities that text-based responses cannot replicate, including deterministic component behavior, application-consistent design language, and on-demand feature activation. A development effort comparison further shows that features that traditionally require multi-step development cycles can be activated with a single naturallanguage request. In this ongoing work, we present ACE as an emerging approach to AI integration that positions modular, well-documented software architecture as the foundation for AI-ready applications. ACE treats context as a shared resource across both development and user-facing AI, bringing cohesion to conventionally disconnected efforts, bridging developer tooling and end-user capabilities within a single framework.

Tadimeti, Vijay [ORNL]↗