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DOE OSTI2024

Identifying Climate Patterns Using Clustering Autoencoder Techniques

Abstract The complexity of growing spatiotemporal resolution of climate simulations produces a variety of climate patterns under different projection scenarios. This paper proposes a new data-driven climate classification workflow via an unsupervised deep learning technique that can dimensionally reduce the vast volume of spatiotemporal numerical climate projection data into a compact representation. We aim to identify distinct zones that capture multiple climate variables as well as their future changes under different climate change scenarios. Our approach leverages convolutional autoencoders combined with k -means clustering (standard autoencoder) and online clustering based on the Sinkhorn–Knopp algorithm (clustering autoencoder) across the conterminous United States (CONUS) to capture unique climate patterns in a data-driven fashion from the Geophysical Fluid Dynamics Laboratory Earth System Model with GOLD component (GFDL-ESM2G). The developed approach compresses 70 years of GFDL-ESM2G simulation at 0.125° spatial resolution across the CONUS under multiple warming scenarios to a lower-dimensional space by a factor of 660 000 and then tested on 150 years of GFDL-ESM2G simulation data. The results show that five climate clusters capture physically reasonable and spatially stable climatological patterns matched to known climate classes defined by human experts. Results also show that using a clustering autoencoder can reduce the computational time for clustering by up to 9.2 times when compared to using a standard autoencoder. Our five unique climate patterns resulting from the deep learning–based clustering of the lower-dimensional space thereby enable us to provide insights on hydrometeorology and its spatial heterogeneity across the conterminous United States immediately without downloading large climate datasets. Significance Statement This paper presents a data-driven climate classification approach using unsupervised deep learning to dimensionally reduce climate model outputs and to identify distinct climate regions for their future changes. Our approach compresses climate information for 70 years of Geophysical Fluid Dynamics Laboratory Earth System Model data across the conterminous United States (CONUS) at 0.125° spatial resolution. The results reveal that five climate clusters capture reasonable and stable climatological patterns matched to known climate patterns. The embedded clustering process in deep learning provides ×9.2 times faster execution than the k -means clustering technique. These results give us insight about climate spatial patterns and heterogeneity of hydrological patterns across the conterminous United States without downloading large climate datasets.

Kurihana, Takuya↗

DOE OSTI2024

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Primer for OTERR Core Reloading Optimization

OTERR (Optimization of Test Reactor Reloading) is a software tool which assists in finding optimal fuel assembly reloading patterns for nuclear reactors. It was created specifically to support the Versatile Test Reactor (VTR) program, but its functionality is general enough to be applied to most fast spectrum reactors which use hexagonal prismatic fuel elements. This document is meant to be a primer for new users of OTERR to walk through example workflows for core reloading optimization cases. Simple cases are followed step-by-step to discuss what needs to be done to complete a reloading optimization sequence. Note that the intent of this document is to provide practical examples for users to follow along with so they can quickly start using OTERR and then make changes to fit their own modeling needs. Detail is limited in terms of addressing additional features not used in these examples and especially lacking in discussion of theory used in the code. To better address these points, users are highly encouraged to refer to the OTERR User Manual and the OTERR Theory Manual.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2021

Singular value decomposition and similarity renormalization group evolution of nuclear interactions

One of the main challenges for ab initio nuclear many-body theory is the growth of computational and storage costs as calculations are extended to heavy, exotic, and structurally complex nuclei. Here, we investigate the factorization of nuclear interactions as a means to address this issue. We perform Singular Value Decompositions of nucleon-nucleon interactions in partial wave representation and study the dependence of the singular value spectrum on interaction characteristics like regularization scheme and resolution scales. We develop and implement the Similarity Renormalization Group (SRG) evolution of the factorized interaction, and demonstrate that this SVD-SRG approach accurately preserves two-nucleon observables. We find that low-resolution interactions allow the truncation of the SVD at low rank, and that a small number of relevant components is sufficient to capture the nuclear interaction and perform an accurate SRG evolution, while the Coulomb interaction requires special consideration. The rank is uniform across all partial waves, and almost independent of the basis choice in the tested cases. This suggests an interpretation of the relevant singular components as mere representations of a small set of abstract operators that can describe the interaction and its SRG flow. Following the traditional workflow for nuclear interactions, we discuss how the transformation between the center-of-mass and laboratory frames creates redundant copies of the partial wave components when implemented in matrix representation, and we discuss strategies for mitigation. Lastly, we test the low-rank approximation to the SRG-evolved interactions in many-body calculations using the In-Medium SRG. By including nuclear radii in our analysis, we verify that the implementation of the SRG using the singular vectors of the interaction does not spoil the evolution of other observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Data Assimilation for Robust UQ Within Agent-Based Simulation on HPC Systems

Agent-based simulation provides a powerful tool for in silico system modeling. However, these simulations do not provide built-in methods for uncertainty quantification (UQ). Within these types of models a typical approach to UQ is to run multiple realizations of the model then compute aggregate statistics. This approach is limited due to the compute time required for a solution. When faced with an emerging biothreat, public health decisions need to be made quickly and solutions for integrating near real-time data with analytic tools are needed. We propose an integrated Bayesian UQ framework for agent-based models based on sequential Monte Carlo sampling. Given streaming or static data about the evolution of an emerging pathogen this Bayesian framework provides a distribution over the parameters governing the spread of a disease through a population. These estimates of the spread of a disease may be provided to public health agencies seeking to abate the spread. By coupling agent-based simulations with Bayesian modeling in a data assimilation, our proposed framework provides a powerful tool for modeling dynamical systems in silico. We propose a method which reduces model error and provides a range of realistic possible outcomes. Moreover, our method addresses two primary limitations of ABMs: the lack of UQ and an inability to assimilate data. Our proposed framework combines the flexibility of an agent-based model with UQ provided by the Bayesian paradigm in a workflow which scales well to HPC systems. We provide algorithmic details and results on a simulated outbreak with both static and streaming data.

Spannaus, Adam [ORNL] (ORCID:0000000225213657)↗

DOE OSTI2024

Introducing NOODLES: Collaborative Visualization in a Flavorful Package

We introduce NOODLES, a lightweight collaborative visualization and analysis protocol. NOODLES was developed to enable new scientific workflows while enhancing existing pipelines. Using a technology-minimal approach to strengthen applicability, this protocol allows researchers to tie disparate software together as well as making domain specific visualizations accessible across various platforms and form factors. In this talk we discuss background, challenges, and gaps in the current tool landscape that lead to the development of the protocol. We then describe the design of the protocol and present several use cases to demonstrate the efficacy of NOODLES in addressing complex visualization challenges and how it co-exists with existing tools. We conclude by outlining in-progress work and potential avenues for future development within the NOODLES framework.

collaborative analysis↗

DOE OSTI2022

Proximity Portability and in Transit , M-to-N Data Partitioning and Movement in SENSEI [Book Chapter]

In high-performance parallel in situ processing, the term in transit processing refers to those configurations where data must move from a producer to a consumer that runs on separate resources. In the context of parallel and distributed computing on an HPC platform one of the central challenges is to determine a mapping of data from producer ranks to consumer ranks. This problem is complicated by the heterogeneity that arises in producer-consumer pairs, such as when producer and consumer codes have different levels of concurrency, different scaling characteristics, or different data models. The resulting mapping and movement of data from M producer to N consumer ranks can have a significant impact on aggregate application performance, particularly when the data consumer requires only a subset of the overall data for its task. This chapter focuses on the design considerations that underlie SENSEI’s implementation to this challenging problem. These design considerations extend the core SENSEI architecture and include ideas like the need to accommodate flexibility in the choice of different partitioning methods, the ability for a data consumer to request and receive only the subset of data needed for its particular operation, and the ability to leverage any of several different data transport tools. The idea of proximity portability, being able to use different data transport methods as part of an in transit workflow, is illustrated through the use of three different transport layers where switching from one transport tool to another is accomplished with only a configuration file change. Here, the chapter also includes a performance analysis summary showing the performance gains that are possible in terms of multiple metrics, such as memory footprint, time to solution, and amount of data moved, when using optimized partitioners in an in transit setting, gains that are made possible by the implementation shaped by specific design considerations.

Bethel, E. Wes↗

DOE OSTI2025

Instantiation of the Damara Tern Platform for Advanced Materials and Manufacturing Technologies (AMMT) Program Collaborative Data Management

This work package focused on deploying an instance of the Damara Tern platform to support AMMT collaborative research activities. The objectives were to provide selected AMMT collaborators with access to a shared environment for capturing operations, trackables, and associated metadata, and to implement data entry functionalities that reflect site-specific procedures. Key activities included creating configurable, schema-driven entry forms and validating the data collection process. The report details the deployment process, the platform infrastructure, and the implemented data entry workflows, providing a reference for end users and establishing a foundation for future production-scale deployments.

36 MATERIALS SCIENCE↗

DOE OSTI2026

What Is the Agent Doing? Visualizing Agentic AI Querying Workflows

We explore how visualizations can help users understand what an AI agent is doing as it builds and runs queries over data. As part of the LinkQ system, a natural language interface for querying knowledge graphs with a large language model (LLM), we designed two complementary views: A State Diagram that shows where the agent is within a larger workflow, and a Live Action Display that gives real-time updates about the agent's current task. In a study with 14 practitioners, we found that these visuals helped participants build stronger mental models of the agent's behavior while also increasing their confidence in the system. However, we also observed that users sometimes trusted incorrect outputs simply because the agent appeared to be doing the "right" thing. Our findings point to both the value and risk of visualizing agent behavior in interactive AI systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Models, data, and scripts associated with “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning”

This data package is associated with the publication “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning’’ submitted to the Journal of Geophysical Research: Machine Learning and Computation (Scheibe et al. 2024). River sediment respiration observations are expensive and labor intensive to obtain and there is no physical model for predicting this quantity. The Worldwide Hydrobiogeochemisty Observation Network for Dynamic River Systems (WHONDRS) observational data set (Goldman et al.; 2020) is used to train machine learning (ML) models to predict respiration rates at unsampled sites. This repository archives training data, ML models, predictions, and model evaluation results for the purposes of reproducibility of the results in the associated manuscript and community reuse of the ML models trained in this project. One of the key challenges in this work was to find an optimum configuration for machine learning models to work with this feature-rich (i.e. 100+ possible input variables) data set. Here, we used a two-tiered approach to managing the analysis of this complex data set: 1) a stacked ensemble of ML models that can automatically optimize hyperparameters to accelerate the process of model selection and tuning and 2) feature permutation importance to iteratively select the most important features (i.e. inputs) to the ML models. The major elements of this ML workflow are modular, portable, open, and cloud-based, thus making this implementation a potential template for other applications. This data package is associated with the GitHub repository found at Please see the file level metadata (flmd; “sl-archive-whondrs_flmd.csv”) for a list of all files contained in this data package and descriptions for each. Please see the data dictionary (dd; “sl-archive-whondrs_dd.csv”) for a list of all column headers contained within comma separated value (csv) files in this data package and descriptions for each. The GitHub repository is organized into five top-level directories: (1) “input_data” holds the training data for the ML models; (2) “ml_models” holds machine learning models trained on the data in “input_data”; (3) “scripts” contains data preprocessing and postprocessing scripts and intermediate results specific to this data set that bookend the ML workflow; (4) “examples” contains the visualization of the results in this repository including plotting scripts for the manuscript (e.g., model evaluation, FPI results) and scripts for running predictions with the ML models (i.e., reusing the trained ML models); (5) “output_data” holds the overall results of the ML model on that branch. Each trained ML model resides on its own branch in the repository; this means that inputs and outputs can be different branch-to-branch. Furthermore, depending on the number of features used to train the ML models, the preprocessing and postprocessing scripts, and their intermediate results, can also be different branch-to-branch. The “main-*” branches are meant to be starting points (i.e. trunks) for each model branch (i.e. sprouts). Please see the Branch Navigation section in the top-level README.md in the GitHub repository for more details. There is also one hidden directory “.github/workflows”. This hidden directory contains information for how to run the ML workflow as an end-to-end automated GitHub Action but it is not needed for reusing the ML models archived here. Please the top-level README.md in the GitHub repository for more details on the automation.

13C↗

DOE OSTI2022

Assembling Multiphysics Nuclear Reactor Simulations Using the MOOSE Framework

The Multiphysics Object Oriented Simulation Environment (MOOSE) [1] is an open-source, parallel finite element framework which provides the foundation for many advanced modeling and simulation tools developed under the Department of Energy (DOE) Nuclear Energy Advanced Modeling and Simulation (NEAMS) Program [2] for the analysis of advanced reactors. The MOOSE framework provides the common foundational capability on which many NEAMS codes for reactor analysis are built. The MOOSE framework also includes several systems to assemble unique workflows and couplingamong MOOSE-based applications. In particular, the MultiApp and Transfer Systems are widely used to assemble different MOOSE-based or MOOSE-wrapped physics applications together to perform loosely or tightly coupled multiphysics simulations. The National Reactor Innovation Center (NRIC) Virtual Test Bed (VTB) [3] hosts publicly available nuclear reactor multiphysics simulation examples which leverage MOOSE’s MultiApp System to meet the modeling needs of different reactor types. The flexibility and robustness of coupling provided by MOOSE permits rapid development of coupled physics models for a wide range of reactor types and events

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2020

Minimally entangled state preparation of localized wave functions on quantum computers

Initializing a single site of a lattice scalar field theory into an arbitrary state with support throughout the quantum register requires $O(2^{nQ})$ entangling gates on a quantum computer with $n_Q$ qubits per site. It is conceivable that instead initializing to functions that are good approximations to states may have utility in reducing the number of required entangling gates. In the case of a single site of a noninteracting scalar field theory, initializing to a symmetric exponential wave function requires $n_Q – 1$ entangling gates, the minimal number necessary to create an entangled state of all $n_Q$ qubits. This is compared with the $2^{nQ – 1} + n_Q – 3 + δ_{nQ, 1}$ required for a symmetric Gaussian wave function. In this work, we explore the initialization of one-site $(n_Q = 4)$, two-site $(n_Q = 3)$, and three-site ( n Q = 3 ) noninteracting scalar field theories with symmetric exponential wave functions using IBM's quantum simulators and quantum devices (Poughkeepsie and Tokyo). With the digitizations attainable with $n_Q = 3,4$, these tensor-product wave functions are found to have large overlap with a Gaussian wave function and provide a suitable low-noise initialization for improvement and Somma inflation. Further, in performing these simulations, we have employed a workflow that interleaves calibrations to mitigate systematic errors in production. The calibrations allow tolerance cuts on gate performance including the fidelity of the symmetrizing Hadamard gate, both in vacuum $(|\textbf{0}\gg^{\bigotimes nQ})$ and in medium ($n_Q –1$ qubits initialized to an exponential function). The results obtained in this work are relevant to systems beyond scalar field theories, such as the deuteron radial wave function, two- and three-dimensional Cartesian-space wave functions, and nonrelativistic multinucleon systems built on a localized eigenbasis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Enhancing dimensionality prediction in hybrid metal halides via feature engineering and class-imbalance mitigation

We present a machine learning (ML) framework for predicting the structural dimensionality of hybrid metal halides (HMHs), including organic-inorganic perovskites, using a combination of chemically-informed feature engineering and advanced class-imbalance handling techniques. This study is motivated by the small and highly imbalanced nature of experimentally available HMH datasets, which limits the applicability and reliability of conventional ML approaches. The dataset, consisting of 494 HMH structures, is highly imbalanced across dimensionality classes (0D, 1D, 2D, 3D), posing significant challenges to predictive modeling. To mitigate this limitation, the dataset was augmented to 1336 samples using the synthetic minority oversampling technique, enabling improved learning of underrepresented dimensionality classes while preserving chemically meaningful feature relationships. We developed interaction-based descriptors designed to capture coupled steric and polarity effects relevant to dimensionality prediction, which are not readily captured by standard single-parameter or composition-only descriptors. These descriptors are integrated into a multi-stage workflow combining feature selection, ensemble stacking, and performance optimization. Our approach significantly improves F1-scores for underrepresented classes, achieving robust cross-validation performance across all dimensionalities. This work demonstrates a generalizable strategy for extracting reliable and interpretable structure–dimensionality relationships from limited experimental data, enabling pre-synthesis screening of organic cations and providing a practical blueprint for small-data ML in hybrid materials systems.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Accelerating Multigrid-based Hierarchical Scientific Data Refactoring on GPUs

Rapid growth in scientific data and a widening gap between computational speed and I/O bandwidth make it increasingly infeasible to store and share all data produced by scientific simulations. Instead, we need methods for reducing data volumes: ideally, methods that can scale data volumes adaptively so as to enable negotiation of performance and fidelity tradeoffs in different situations. Multigrid-based hierarchical data representations hold promise as a solution to this problem, allowing for flexible conversion between different fidelities so that, for example, data can be created at high fidelity and then transferred or stored at lower fidelity via logically simple and mathematically sound operations. However, the effective use of such representations has been hindered until now by the relatively high costs of creating, accessing, reducing, and otherwise operating on such representations. We describe here highly optimized data refactoring kernels for GPU accelerators that enable efficient creation and manipulation of data in multigrid-based hierarchical forms. We demonstrate that our optimized design can achieve up to 250 TB/s aggregated data refactoring throughput—83% of theoretical peak—on 1024 nodes of the Summit supercomputer. We showcase our optimized design by applying it to a large-scale scientific visualization workflow and the MGARD lossy compression software.

Data refactoring↗

DOE OSTI2025

ESMs Latent Space Exploration for Uncertainty Quantification and Spatiotemporal Downscaling

This final report for DOE Award DE-SC0023044 presents advances in two key areas of climate modeling: (1) representative climate model selection and (2) Earth System Model (ESM) downscaling using hybrid AI methods. The first section introduces a reordered, three-stage workflow to select representative GCM runs that more effectively balance historical skill with ensemble spread, validated across Texas, Bihar, and New York. The second section introduces two novel super-resolution frameworks, ViSIR and ViFOR, that integrate Vision Transformers with sinusoidal and Fourier-based implicit neural representations. These models achieve state-of-the-art reconstruction accuracy for ESM variables including surface temperature and heat fluxes. The report includes detailed methodology, benchmarks, and results, demonstrating significant gains in uncertainty quantification, spatial fidelity, and scalability for climate-impact studies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Accelerating Multigrid-based Hierarchical Scientific Data Refactoring on GPUs

Chen, Jieyang↗

DOE OSTI2023

Sequence Design of Random Heteropolymers as Protein Mimics

Random heteropolymers (RHPs) have been computationally designed and experimentally shown to recapitulate protein-like phase behavior and function. However, unlike proteins, RHP sequences are only statistically defined and cannot be sequenced. Recent developments in reversible-deactivation radical polymerization allowed simulated polymer sequences based on the well-established Mayo–Lewis equation to more accurately reflect ground-truth sequences that are experimentally synthesized. This led to opportunities to perform bioinformatics-inspired analysis on simulated sequences to guide the design, synthesis, and interpretation of RHPs. We compared batches on the order of 10000 simulated RHP sequences that vary by synthetically controllable and measurable RHP characteristics such as chemical heterogeneity and average degree of polymerization. Our analysis spans across 3 levels: segments along a single chain, sequences within a batch, and batch-averaged statistics. We discuss simulator fidelity and highlight the importance of robust segment definition. Examples are presented that demonstrate the use of simulated sequence analysis for in-silico iterative design to mimic protein hydrophobic/hydrophilic segment distributions in RHPs and compare RHP and protein sequence segments to explain experimental results of RHPs that mimic protein function. To facilitate the community use of this workflow, the simulator and analysis modules have been made available through an open source toolkit, the RHPapp.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Integrating ytopt and libEnsemble to autotune OpenMC

Ytopt is a Python machine-learning-based autotuning software package developed within the ECP PROTEAS-TUNE project. The ytopt software adopts an asynchronous search framework that consists of sampling a small number of input parameter configurations and progressively fitting a surrogate model over the input-output space until exhausting the user-defined maximum number of evaluations or the wall-clock time. libEnsemble is a Python toolkit for coordinating workflows of asynchronous and dynamic ensembles of calculations across massively parallel resources developed within the ECP PETSc/TAO project. libEnsemble helps users take advantage of massively parallel resources to solve design, decision, and inference problems and expands the class of problems that can benefit from increased parallelism. In this paper we present our methodology and framework to integrate ytopt and libEnsemble to take advantage of massively parallel resources to accelerate the autotuning process. Specifically, we focus on using the proposed framework to autotune the ECP ExaSMR application OpenMC, an open source Monte Carlo particle transport code. OpenMC has seven tunable parameters some of which have large ranges such as the number of particles in-flight, which is in the range of 100,000 to 8 million, with its default setting of 1 million. Setting the proper combination of these parameter values to achieve the best performance is extremely time-consuming. Therefore, we apply the proposed framework to autotune the MPI/OpenMP offload version of OpenMC based on a user-defined metric such as the figure of merit (FoM) (particles/s) or energy efficiency energy-delay product (EDP) on Crusher at Oak Ridge Leadership Computing Facility. In conclusion, the experimental results show that we achieve the improvement up to 29.49% in FoM and up to 30.44% in EDP.

Autotuning↗