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DOE OSTI2026

NeuDiff Agent: a governed AI workflow for single-crystal neutron crystallography

Large-scale facilities increasingly face analysis and reporting latency as a limiting step in scientific throughput, particularly for structural studies that require iterative reduction, integration, refinement and validation. To improve the time to result and analysis efficiency, NeuDiff Agent is introduced as a governed, tool-using AI workflow for TOPAZ at the Spallation Neutron Source. NeuDiff Agent takes instrument data through reduction, integration, refinement and validation to a validated crystal structure and a publication-ready CIF. NeuDiff Agent coordinates established crystallographic tools under explicit governance by restricting actions to allowlisted tools, enforcing fail-closed verification gates at key workflow boundaries, and capturing complete provenance for inspection, auditing and controlled replay. The present benchmark is limited to structural crystallography for periodic structures; magnetic structure analysis and incommensurate or superspace refinement are outside the scope of the current workflow. Performance is assessed using a fixed prompt protocol and repeated end-to-end runs with two large language model backends, with user and machine time partitioned and intervention burden and recovery behaviors quantified under gating. In a reference-case benchmark, NeuDiff Agent reduces wall time from 435 min (manual) to 86.5 ± 4.7 to 94.4 ± 3.5 min (4.6–5.0× faster) while producing a validated CIF with no checkCIF level A or B alerts. These results establish a practical route to deploy agentic AI in facility crystallography while preserving traceability and publication-facing validation requirements.

Xiao, Zhongcan [ORNL] (ORCID:0000000220761961)↗

DOE OSTI2024

DaYu: Optimizing Distributed Scientific Workflows by Decoding Dataflow Semantics and Dynamics

The combination of ever-growing scientific datasets and distributed workflow complexity creates I/O performance bottlenecks due to data volume, velocity, and variety. Although the increasing use of descriptive data formats (e.g., HDF5, netCDF) helps organize these datasets, it also creates obscure bottlenecks due to the need to translate high level operations into file addresses and then into low-level I/O operations. To address this challenge, we introduce DaYu, a method and toolset for analyzing (a) semantic relationships between logical datasets and file addresses, (b) how dataset operations translate into I/O, and (c) the combination across entire workflows. DaYu's analysis and visualization enables identification of critical bottlenecks and reasoning about remediation. We describe our methodology and propose optimization guidelines. Evaluation on scientific workflows demonstrates up to 3.7x performance improvements in I/O time for obscure bottlenecks. The time and storage overhead for DaYu's time-ordered data is typically under 0.2% of runtime and 0.25% of data volume, respectively.

Tang, Meng↗

DOE OSTI2023

Building the I (Interoperability) of FAIR for performance reproducibility of large-scale composable workflows in RECUP

Abstract-Scientific computing communities increasingly run their experiments using complex data- and compute-intensive workflows that utilize distributed and heterogeneous architectures targeting numerical simulations and machine learning, often executed on the Department of Energy Leadership Computing Facilities (LCFs). We argue that a principled, systematic approach to implementing FAIR principles at scale, including fine-grained metadata extraction and organization, can help with the numerous challenges to performance reproducibility posed by such workflows. We extract workflow patterns, propose a set of tools to manage the entire life cycle of performance metadata, and aggregate them in an HPC-ready framework for reproducibility (RECUP). We describe the challenges in making these tools interoperable, preliminary work, and lessons learned from this experiment.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Diaspora: Resilience-Enabling Services for Real-Time Distributed Workflows

The need for real-time processing to enable automated decision making and experimental steering has driven a shift from high-performance computing workflows on a centralized system to a distributed approach that integrates remote data sources, edge devices, and diverse compute facilities. Under this paradigm, data can be processed close to the source where it is generated, thus reducing latency and bandwidth usage. System resilience is thus a key challenge, requiring distributed workflows to survive component failures and to meet stringent quality-of-service requirements, which results in the need to mitigate anomalies such as congestion and low availability of resources. To address these challenges, we propose Diaspora, a unified resilience framework that is inspired by event-driven communication patterns used in public clouds. Specifically, we propose an event fabric that extends across sites, facilities, and computations to provide timely, reliable, and accurate information about data, application, and resource status. On top of the event fabric, we build resilience-enabling services that combine QoS-aware data streaming, resilient data views, resilient compute and data resources, and anomaly detection and prediction, all of which collectively enhance workflow resilience for these scientific cases.

Rao, Nageswara↗

DOE OSTI2023

A Parallel Machine Learning Workflow for Neutron Scattering Data Analysis

As part of a larger effort, this work-in-progress reports the possible advantages of modifying conventional workflows used to generate labelled training samples and train machine learning (ML) models on them. We compare results from three different workflows using neutron scattering data analysis as the motivating application and report about 20% improvement in speedup, with no appreciable loss of model accuracy, over a baseline workflow.

Wang, Tianle↗

DOE OSTI2025

End-to-End Workflow for Machine-Learning-Based Qubit Readout With QICK and hls4ml

In this article, we present an end-to-end workflow for superconducting qubit readout that embeds codesigned neural networks into the quantum instrumentation control kit (QICK). Capitalizing on the custom firmware and software of the QICK platform, which is built on Xilinx radiofrequency system-on-chip field-programmable gate arrays (FPGAs), we aim to leverage machine learning (ML) to address critical challenges in qubit readout accuracy and scalability. The workflow utilizes the hls4ml package and employs quantization-aware training to translate ML models into hardware-efficient FPGA implementations via user-friendly Python application programming interfaces. We experimentally demonstrate the design, optimization, and integration of an ML algorithm for single transmon qubit readout, achieving 96% single-shot fidelity with a latency of 32.25 ns and less than 16% FPGA lookup table resource utilization. Our results offer the community an accessible workflow to advance ML-driven readout and adaptive control in quantum information processing applications.

42 ENGINEERING↗

DOE OSTI2026

JANUS: Resilient and Adaptive Data Transmission for Enabling Timely and Efficient Cross-Facility Scientific Workflows

In modern science, the growing complexity of large-scale scientific projects has led to an increasing reliance on cross-facility scientific workflows, where resources and expertise from multiple institutions and geographic locations are leveraged to accelerate scientific discovery. These workflows often require transmitting huge amounts of scientific data through wide-area networks. Although high-speed networks like ESnet and transfer services such as Globus have improved data mobility, several challenges remain. The sheer volume of data can overwhelm network bandwidth, widely used transport protocols such as TCP suffer from inefficiencies due to retransmissions triggered by packet loss, and existing fault-tolerance mechanisms like erasure coding introduce substantial overhead. In this paper, we propose Janus, a resilient and adaptable data transmission approach designed for cross-facility scientific workflows. Unlike traditional TCP-based methods, Janus leverages UDP, integrates erasure coding for fault tolerance, and combines it with error-bounded lossy compression to reduce overhead. This novel design allows users to balance data transmission time and accuracy, optimizing transfer performance based on specific scientific requirements. Additionally, Janus dynamically adjusts erasure coding parameters in response to real-time network conditions, ensuring efficient data transfers even in fluctuating environments. We develop optimization models for determining ideal configurations and implement adaptive data transfer protocols to enhance reliability. Through extensive simulations and real-network experiments, we demonstrate that Janus significantly improves transfer efficiency while maintaining data fidelity.

Esaulov, Vladislav [Georgia State University, Atla↗

DOE OSTI2026

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗

DOE OSTI2020

An automated workflow to screen alkene reductases using high-throughput thin layer chromatography

Background: Synthetic biology efforts often require high-throughput screening tools for enzyme engineering campaigns. While innovations in chromatographic and mass spectrometry-based techniques provide relevant structural information associated with enzyme activity, these approaches can require cost-intensive instrumentation and technical expertise not broadly available. Moreover, complex workflows and analysis time can significantly impact throughput. To this end, we develop an automated, 96-well screening platform based on thin layer chromatography (TLC) and use it to monitor in vitro activity of a geranylgeranyl reductase isolated from Sulfolobus acidocaldarius (SaGGR). Results: Unreduced SaGGR products are oxidized to their corresponding epoxide and applied to thin layer silica plates by acoustic printing. These derivatives are chromatographically separated based on the extent of epoxidation and are covalently ligated to a chromophore, allowing detection of enzyme variants with unique product distributions or enhanced reductase activity. Herein, we employ this workflow to examine farnesol reduction using a codon-saturation mutagenesis library at the Leu377 site of SaGGR. We show this TLC-based screen can distinguish between fourfold differences in enzyme activity for select mutants and validated those results by GC–MS. Conclusions: With appropriate quantitation methods, this workflow can be used to screen polyprenyl reductase activity and can be readily adapted to analyze broader catalyst libraries whose products are amenable to TLC analysis.

09 BIOMASS FUELS↗

DOE OSTI2026

Constructing a High‐Resolution Aftershock Catalog for the 2017 Mw 8.2 Tehuantepec Earthquake Sequence Using a Machine Learning–Based Workflow

The 8 September 2017 Mw 8.2 Tehuantepec earthquake was the largest instrumentally recorded normal‐faulting earthquake in Mexico. The mainshock occurred offshore within the Tehuantepec seismic gap, generating >30,000 aftershocks in the following year. We applied an open‐source, machine learning (ML)–assisted workflow to construct a high‐resolution aftershock catalog using data from temporary and permanent seismic networks in southern Mexico. The workflow integrates PhaseNet for phase detection; GaMMA for phase association; and VELEST, HypoInverse, and HypoDD for velocity modeling and relocation. We processed seven months of continuous waveform data from 29 broadband stations, including a temporary rapid‐response deployment that improved station coverage of the offshore rupture zone. To evaluate performance, we compared our results against analyst‐reviewed picks and event locations from the Servicio Sismológico Nacional catalog. The resulting catalog contains 11,374 relocated earthquakes and represents the most comprehensive published dataset for this sequence, incorporating the first full use of the temporary network. Relocated hypocenters show improved depth control and align well with the Slab2.0 subduction geometry, revealing clearer separation between offshore slab events and onshore crustal seismicity. This study demonstrates that combining ML‐based detection with established methods provides a scalable and reproducible approach for constructing high‐quality earthquake catalogs in tectonically complex environments and offers practical guidance for adapting similar workflows to other earthquake sequences.

Garcia, Marc [The University of Texas at El Paso, ↗

DOE OSTI2020

Toward Resilient Heterogeneous Computing Workflow through Kokkos-DataSpaces Integration

With the growing number of applications designed for heterogeneous HPC devices, application programmers and users are finding it challenging to compose scalable workflows as ensembles of these applications, that are portable, performant and resilient. The Kokkos C++ library has been designed to simplify this cumbersome procedure by providing an intra-application uniform programming model and portable performance. However, assembling multiple Kokkos-enabled applications into a complex workflow is still a challenge. Although Kokkos enables a uniform programming model, the inter-application data exchange still remains a challenge from both performance and software development cost perspectives. In order to address this issue, we propose a Kokkos-DataSpaces Integration, with the goal of providing a virtual shared-space abstraction that can be accessed concurrently by all applications in an Kokkos workflow, thus extending Kokkos to support inter-application data exchange.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

NEAMS Workbench Workflows

Modeling and simulation efforts frequently involve loosely coupled workflows. Automation of workflows, data exchanges, and simulation software execution is a productive and often desired feature or improvement for enhancing consistency of results and productivity of the analyst. It facilitates cross-collaboration of different analysts of multidisciplinary simulation by streamlining data exchange processes across local and high performance computing resources. This report proposes a high-level, extensible workflow module to enable consistent and efficient use of tools integrated into the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench with as little user intervention as possible.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Scaling the SciDAC QuantOm Workflow

As part of the Scientific Discovery through Advanced Computing (SciDAC) program, the Quantum Chromodynamics Nuclear Tomography (QuantOM) project aims to analyze data from Deep Inelastic Scattering (DIS) experiments conducted at Jefferson Lab and the upcoming Electron Ion Collider. The DIS data analysis is performed on an event-level by combining the input from theoretical and experimental nuclear physics into a single, composable workflow. The optimization itself (I.e. fitting the experimental data with theoretical predictions) is carried out by a machine / deep learning algorithm. The size of the acquired DIS data as well as the complexity of the workflow itself require that the analysis is performed across multiple GPUs on high performance computing systems, such as Polaris at Argonne National Laboratory. This presentation discusses the novelties and challenges that came along with parallelizing this workflow. Recent results are compared to common distributed training techniques.

Lersch, Daniel↗

DOE OSTI2025

Replace Human Intelligence with Fast and Smart Geometric Reasoning and Graph Neural Network to Accelerate Next Gen ModSim Workflows

We present an agent-guided approach to CAD geometry decomposition that automates hex/hybrid meshing with graph neural networks (GNNs) to accelerate next-generation ModSim workflows. Our end-to-end pipeline (i) reduces 3D boundary-representation (B-Rep) models to a 2D chordal axis skeleton (CAT) and then to a 1D bipartite graph of surface and curve nodes, (ii) assigns per node labels as Cubit® WebCut actions, (iii) trains a multi-action GNN under supervised learning, and (iv) predicts five surface-node and three curve-node actions on out-of-distribution test geometries. Each graph node carries geometric, topological, and meshing attributes drawn from the B-Rep “skin” and CAT “skeleton,” with two-way mappings across 3D↔2D↔1D representations to maintain traceability back to 3D CAD. The supervised learning model exhibits stable convergence of the binary cross-entropy loss and achieves 98.7% accuracy on unseen lattice models. To operationalize decision-making, we rank predicted commands by geometric significance and prototyped the agent-guided workflow through the Cubit® Meshing PowerTool GUI. As a stretch goal, we explore reinforcement learning (RL) to reduce or remove label requirements and to learn policies for action sequences that maximize total reward (e.g., size of hex-meshable regions and resulting hex mesh quality). When all-hex meshing is not feasible, the agent assists in producing hybrid meshes—prioritizing hex in critical regions and transitioning to tetrahedral elements (tets) elsewhere—maintaining fidelity while ensuring robustness. The overarching objective is to replace manual, heuristics-based decomposition with data-driven, reproducible automation, cutting meshing turnaround time by orders of magnitude. We anticipate direct impact on simulation workflows through intelligent, scalable decomposition of complex CAD models into hex-meshable subdomains.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Scalable workflow for evaluating and optimizing large language models

This work describes the improved workflow for evaluating open-source large language models (LLMs) for trustworthiness. The workflow facilitates the acquisition of LLMs, the generation of LLM responses, and the evaluation of the responses for their trustworthiness. As a use case, the workflow is employed to evaluate dense, quantized, and pruned Meta Llama3.1 LLMs for their truthfulness. The outcome of the project could set the stage for understanding and developing trustworthy models in the future projects.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Workflow for Process Automation of Soil Gas Results from an Automated Soil Gas-Sampling System for Application in Carbon Storage Projects

Conference presentation at Geoconvention, Calgary, Alberta, Canada, May 12–14, 2025. The Energy & Environmental Research Center (EERC) developed an automated workflow for processing soil gas measurements collected from the automated soil gas-sampling systems deployed across the project site. Raw soil gas measurements are collected from each station every 4 hours and automatically uploaded to a cloud database. The workflow begins by writing code to download the data to a workstation automatically, then the data are published to an online dashboard that visualizes the measurements in time-series plots and a process-based decision-making framework. This automated workflow accelerates the time from data acquisition to decision-making. It supports carbon storage project operators by preparing and delivering a live, standardized dataset for quick analysis and source attribution to provide assurance of containment and overall permit compliance.

02 PETROLEUM↗

DOE OSTI2021

Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes

Motivation: Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As `omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results: We propose a workflow (`Omics to Reactive Transport – ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBASE and PFLOTRAN. Live, interactive models, which incorporate the results from this narrative into a PFLOTRAN simulation, are available (without login) at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/.

Rubinstein, Rebecca L↗

DOE OSTI2021

Risk Assessment and Management Workflow—An Example of the Southwest Regional Partnership

This paper summarizes the risk assessment and management workflow developed and applied to the Southwest Regional Partnership on Carbon Sequestration (SWP) Phase III Demonstration Project. The risk assessment and management workflow consists of six primary tasks, including management planning, identification, qualitative analysis, quantitative analysis, response planning, and monitoring. Within the workflow, the SWP assembled and iteratively updated a risk registry that identifies risks for all major activities of the project. Risk elements were ranked with respect to the potential impact to the project and the likelihood of occurrence. Both qualitative and quantitative risk analyses were performed. To graphically depict the interactions among risk elements and help building risk scenarios, process influence diagrams were used to represent the interactions. The SWP employed quantitative methods of risk analysis including Response Surface Method (RSM), Polynomial Chaos Expansion (PCE), and the National Risk Assessment Partnership (NRAP) toolset. The SWP also developed risk response planning and performed risk control and monitoring to prevent the risks from affecting the project and ensure the effectiveness of risk management. As part of risk control and monitoring, existing and new risks have been tracked and the response plan was subsequently evaluated. Findings and lessons learned from the SWP’s risk assessment and management efforts will provide valuable information for other commercial geological CO2 storage projects.

Lee, Si-Yong↗