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DOE OSTI2020

Updates to Relevance Vector Machine: Multiclass Classification, Variable Selection, and Proof-of-Concept Application to Safeguards Fresh Fuel Verification using List-Mode Neutron Collar Data

To expand the capabilities of safeguards authorities to verify the integrity of fresh fuel assemblies, Oak Ridge National Laboratory has retrofit the existing electronics of the JCC-71 uranium neutron coincidence collar, which contains 18 3 He neutron detectors and an external 241 AmLi(α, n) neutron interrogation source arranged to surround a fresh nuclear fuel assembly. The new electronics system allows analysts to record list-mode neutron multiplicity data in addition to the singles and doubles rates that are currently measured. Based on previous proof-of-concept research, analysis of these new data will identify off-normal fuel configurations in an assembly and characterize or localize the specific partial fuel defects. The purpose of this report it to document the analysis algorithm development and then to demonstrate its capability for the safeguards verification of fresh fuel assemblies using list mode neutron collar data. To analyze the complex list-mode data collected with the upgraded uranium neutron collar, multivariate classification algorithms are being developed using a novel classification method, the relevance vector machine. This approach may be applied to multiclass problems to estimate the probability that test data belongs to one of many possible classes of data. In addition, our method identifies the most useful variables/channels for making predictions, which illuminates the basis for the model’s predictions, and this interpretability is largely unique among data analytics methods. Variable selection occurs during model training and parameter tuning and does not need any external hyperparameter tuning routines. Finally, we apply the modified relevance vector machine to a simulated dataset of list-mode neutron collar data generated with the radiation transport code MCNP. The method can correctly identify off-normal fuel configurations, categorize the data according to four fuel defect scenarios, and rank the channels in the data according to prediction utility. For nuclear safeguards applications, it is concluded that this method has the potential to increase the sensitivity and reliability to detect missing fuel rods from a standard 17 x 17 Pressurized Water Reactor (PWR) fresh fuel assembly. Within this analysis, “off-normal” (i.e., missing fuel rods) were correctly classified in 17 simulated test scenarios with one quarter (25%) of the fresh fuel rods missing using a training data set of 58 simulated measurements.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2018

ISAP-MATLAB Package for Sensitivity Analysis of High-Dimensional Stochastic Chemical Networks

Stochastic simulation and modeling play an important role to elucidate the fundamental mechanisms in complex biochemical networks. The parametric sensitivity analysis of reaction networks becomes a powerful mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. However, due to overwhelming computational cost, parametric sensitivity analysis is a extremely challenging problem for stochastic models with a high-dimensional parameter space and for which existing approaches are very slow. Here we present an information-theoretic sensitivity analysis in path-space (ISAP) MATLAB package that simulates stochastic processes with various algorithms and most importantly implements a gradient-free approach to quantify the parameter sensitivities of stochastic chemical reaction network dynamics using the pathwise Fisher information matrix (PFIM; Pantazis, Katsoulakis, and Vlachos 2013). The sparse, block-diagonal structure of the PFIM makes its computational complexity scale linearly with the number of model parameters. As a result of the gradientfree and the sparse nature of the PFIM, it is highly suitable for the sensitivity analysis of stochastic reaction networks with a very large number of model parameters, which are typical in the modeling and simulation of complex biochemical phenomena. Finally, the PFIM provides a fast sensitivity screening method (Arampatzis, Katsoulakis, and Pantazis 2015) which allows it to be combined with any existing sensitivity analysis software.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Correlations Between Panoramic Imagery and Gamma-Ray Background in an Urban Area

When searching for radiological sources in an urban area, a vehicle-borne detector system will often measure complex, varying backgrounds primarily from natural gamma-ray sources. Much work has been focused on developing spectral algorithms that retain sensitivity and minimize the false-positive rate even in the presence of such spectral and temporal variability. However, information about the environment surrounding the detector system might also provide useful clues about the expected background, which if incorporated into an algorithm, could improve performance. Recent work has focused on extensive measuring and modeling of urban areas with the goal of understanding how these complex backgrounds arise. This work presents an analysis of panoramic video images and gamma-ray background data collected in Oakland, California, by the radiological multisensor analysis platform (RadMAP) vehicle. Features were extracted from the panoramic images by semantically labeling the images and then convolving the labeled regions with the detector response. A linear model was used to relate the image-derived features to gamma-ray spectral features obtained using nonnegative matrix factorization (NMF) under different regularizations. Here we find some gamma-ray background features correlate strongly with image-derived features that measure the response-adjusted solid angle subtended by sky and buildings, and we discuss the implications for the development of future, contextually aware detection algorithms.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2019

Mapping Lipid Fragmentation for Tailored Mass Spectral Libraries

Libraries of simulated lipid fragmentation spectra enable the identification of hundreds of unique lipids from complex lipid extracts, even when the corresponding lipid reference standards do not exist. Often, these in silico libraries are generated through expert annotation of spectra to extract and model fragmentation rules common to a given lipid class. Although useful for a given sample source or instrumental platform, the time-consuming nature of this approach renders it impractical for the growing array of dissociation techniques and instrument platforms. Here, we introduce Library Forge, a unique algorithm capable of deriving lipid fragment mass-to-charge (m/z) and intensity patterns directly from high-resolution experimental spectra with minimal user input. Library Forge exploits the modular construction of lipids to generate m/z transformed spectra in silico which reveal the underlying fragmentation pathways common to a given lipid class. By learning these fragmentation patterns directly from observed spectra, the algorithm increases lipid spectral matching confidence while reducing spectral library development time from days to minutes. We embed the algorithm within the preexisting lipid analysis architecture of LipiDex to integrate automated and robust library generation within a comprehensive LC-MS/MS lipidomics workflow. .

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

AI-Batt (Autonomous Identification of Battery Life Models) [SWR 21-36]

Autonomous Identification of Battery Life Models (AI-Batt) AI-Batt is a MATLAB code base for developing lifetime models for batteries from accelerated aging data. The code base provides many functions for processing, visualizing, and modeling battery aging data, making the data processing, exploration, and modeling workflow substantially faster. These tools are tailored for working with battery aging data sets, which usually consist of many separate time-series for each cell, with many test conditions and possible replicates at each condition, which makes it difficult to simply process or visualize the data set. Complex modeling tasks, such as cross-validation, sensitivity analysis, and uncertainty quantification have been implemented to enable thorough statistical investigation of model predictions. Additionally, several machine-learning algorithms are implemented to autonomously identify suitable models via symbolic regression. Data processing functions automatically cast data from the struct data type, which is commonly used to store experimental data, but is not an acceptable input for most algorithms, to the table data type, which can be easily used as input to any optimization algorithm. Also, the data can be separated into time-invariant and time-variant data tables, which is helpful for exploring the data set as well as developing separate models for time-variant and time-invariant aging mechanisms. For example, in aging tests with constant temperature, temperature is a time-invariant experimental condition. Visualization tools enable plotting of data, model fits, and model simulations possible with single-line function calls, empowering data exploration of complex data sets with both time-varying and time-invariant trends. Plots can be automatically generated for the whole data set, or separated by data group (groups of test replicates) or individual data series. Data points or data series can be automatically colored by the value of a variable with a variety of color maps, and model predictions can also be colored by the value of a fit statistic. Comparisons between data sets and the predictions/simulations of different models on the same data set can be easily plotted as well. Distributions of parameter values from bootstrap resampling can be plotted to visualize the reliability of parameter estimation, or determine any correlations between parameters. Modeling tools handle the complex task of creating and parsing symbolic equations for modeling battery lifetime. Equations are parsed to grab relevant data variables, parameter values, or specified sub-models for input into optimization, evaluation, or simulation functions. Models can be optimized locally (one set of parameters for each data series), bi-level (some parameters shared across the data set), or globally (single set of parameters for all data). Functions implementing symbolic regression algorithms help users to discover effective model equations, even in poorly sampled, high-dimensional data.

Smith, Kandler↗

DOE OSTI2024

An Assessment of Receiver Algorithms for Distributed Massive MIMO Systems: Investigating Design Solutions and Performance

This study investigates receiver design solutions for distributed Massive Multiple Input Multiple Output (D-m MIMO) systems, taking into account parameters such as number of access points as well as concerns related to channel estimates that use single-carrier frequency-domain equalization (SC-FDE). A significant contribution of this research is the integration of Low-Density Parity-Check (LDPC) codes to simplify coding complexity and enhance communication efficiency. The research examines different receiver designs, such as spatial antenna correlation and sophisticated channel estimation methods. The authors propose integrating LDPC codes into the receiver architecture to simplify computations and enhance error correction and decoding. Moreover, the paper examines performance evaluation measures and approaches, highlighting the trade-offs among complexity, spectral efficiency, and error performance. The comparative analysis indicates the benefits, in terms of performance, of incorporating LDPC codes and improving system throughput and dependability. We examine four distinct receiver algorithms: zero-forcing (ZF), minimum mean square error (MMSE), maximum ratio combining (MRC), and equal gain combining (EGC). The study shows that MRC and EGC receivers work well in D-m MIMO because they make the receiver system less computationally demanding.

Gashtasbi, Ali↗

DOE OSTI2022

Construction of Women’s All-Around Speed Skating Event Performance Prediction Model and Competition Strategy Analysis Based on Machine Learning Algorithms

Introduction Accurately predicting the competitive performance of elite athletes is an essential prerequisite for formulating competitive strategies. Women’s all-around speed skating event consists of four individual subevents, and the competition system is complex and challenging to make accurate predictions on their performance. Objective The present study aims to explore the feasibility and effectiveness of machine learning algorithms for predicting the performance of women’s all-around speed skating event and provide effective training and competition strategies. Methods The data, consisting of 16 seasons of world-class women’s all-around speed skating competition results, used in the present study came from the International Skating Union (ISU). According to the competition rules, distinct features are filtered using lasso regression, and a 5,000 m race model and a medal model are built using a fivefold cross-validation method. Results The results showed that the support vector machine model was the most stable among the 5,000 m race and the medal models, with the highest AUC (0.86, 0.81, respectively). Furthermore, 3,000 m points are the main characteristic factors that decide whether an athlete can qualify for the final. The 11th lap of the 5,000 m, the second lap of the 500 m, and the fourth lap of the 1,500 m are the main characteristic factors that affect the athlete’s ability to win medals. Conclusion Compared with logistic regression, random forest, K-nearest neighbor, naive Bayes, neural network, support vector machine is a more viable algorithm to establish the performance prediction model of women’s all-around speed skating event; excellent performance in the 3,000 m event can facilitate athletes to advance to the final, and athletes with outstanding performance in the 500 m event are more likely competitive for medals.

Liu, Meng↗

DOE OSTI2023

Seven open problems in applied combinatorics

We present and discuss seven different open problems in applied combinatorics. Additionally, the application areas relevant to this compilation include quantum computing, algorithmic differentiation, topological data analysis, iterative methods, hypergraph cut algorithms, and power systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Scalable Graph Analytics and HPC Operational Enhancement: Parallel Computing and ML/DL Innovations

Parallel computing plays a pivotal role in the efficient processing of large-scale graphs. Complex network analysis stands as a capti- vating research frontier, holding promise across diverse scientific domains such as sociology, biology, online media, and recommenda- tion systems. In this era, Machine Learning (ML) and Deep Learning (DL) have emerged as indispensable tools, underpinning remarkable technological achievements. Within this dynamic landscape, my research revolves around advancing parallel algorithms tailored for large-scale graph operations. To achieve this, I harness the power of cutting-edge technologies including OpenMP, MPI, HIP, and CUDA, on the High-Performance Computing (HPC) platforms to unlock optimal performance. I also apply ML/DL techniques to HPC operational data, to streamline the monitoring and maintenance of supercomputers, alleviating the complexities associated with their upkeep and enhancing user support. My research echoes the syn- ergy between parallel computing, large-scale graph analysis, and ML/DL, improving computational efficiency and user experience.

Sattar, Naw Safrin↗

DOE OSTI2022

A Mountaintop View Requires Minimal Sorting: A Faster Contour Tree Algorithm

Consider a scalar field f : M → R, where M is a triangulated simplicial mesh in R d . A level set, or contour, at value v is a connected component of f –1 (v). As v is changed, these contours change topology, merge into each other, or split. Contour trees are concise representations of f that track this contour behavior. The vertices of these trees are the critical points of f, where the gradient is zero. The edges represent changes in the topology of contours. It is a fundamental data structure in data analysis and visualization, and there is significant previous work (both theoretical and practical) on algorithms for constructing contour trees. Suppose M has n vertices, N facets, and t critical points. A classic result of Carr, Snoeyink, and Axen (2000) gives an algorithm that takes O(n log n+Nα(N)) time (where α(·) is the inverse Ackermann function). A further improvement to O(t log t + N) time was given by Chiang et al. All these algorithms involve a global sort of the critical points, a significant computational bottleneck. Unfortunately, lower bounds of Ω(t log t) also exist. We present the first algorithm that can avoid the global sort and has a refined time complexity that depends on the contour tree structure. Intuitively, if the tree is short and fat, we get significant improvements in running time. For a partition of the contour tree into a set of descending paths, P, our algorithm runs in O($\Sigma$ pϵP |p| log |p| + tα(t) + N). This is at most O(t log D + N), where D is the diameter of the contour tree. Moreover, it is O(tα(t) + N) for balanced trees, a significant improvement over the previous complexity. Our algorithm requires numerous ideas: partitioning the contour tree into join and split trees, a local growing procedure to iteratively build contour trees, and the use of heavy path decompositions for the time complexity analysis. There is a crucial use of a family of binomial heaps to maintain priorities, ensuring that any comparison made is between comparable nodes of the contour tree. We also prove lower bounds showing that the $\Sigma$ pϵP |p| log |p| complexity is inherent to computing contour trees.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Reliable and Efficient Machine Learning (Final Technical Report)

Modern scientific experiments generate massive amounts of data at a pace much faster than humans can manually analyze. While machine learning has revolutionized commercial data analysis (such as recommending movies or recognizing faces), applying these tools to complex scientific discovery is challenging because scientific answers must be precise, interpretable, and adhere to physical laws. The research under this project aims to develop new mathematical tools and computer algorithms specifically designed for scientific applications. Major progress has been made in automatically cleaning and deconstructing messy experimental data, analyzing the visual information of physical phenomena, determining the underlying physical variables, and providing rig orous mathematical analysis of interesting algorithms and concepts widely used in machine learning. This project addressed the critical gap between our ability to generate massive scientific data and our ability to extract interpretable information from it. We established mathematical foundations for Scientific Machine Learning (SciML) aimed at effective data analytics and automated discovery. Our work focused on three core objectives: (1) developing reliable feature extraction methods for dynamic high-dimensional data, (2) establishing mathematical foundations for discovering dynamics via neural networks, and (3) creating rigorous optimization techniques for these models. Key outcomes come from two fronts. On the practical side, they include the development of algorithms that significantly enhance the extraction of signals from field data, as well as the capability to handle situations that exhibit smooth variations or physical stretching due to temperature changes. They also include the creation of an automated framework for discovering fundamental state variables from raw experimental data, demonstrating the ability to identify intrinsic physical dimensions without prior knowledge of the governing laws. On the theoretical front, the research results in theoretical advances in Optimal Transport, a widely used notion in SciML, specifically regarding functions with fixed-size nodal sets, provide sharp bounds relevant to uncertainty quantification. Meanwhile, the outcomes also include the establishment of convergence theories for nonlocal gradient descent methods, enabling robust optimization with noisy data in high-dimensional settings commonly encountered in scientific modeling. The project also helps creating opportunities to train the next generation of researchers, equipping them with the necessary technical skills for today’s workplace and preparing them for future advances.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

Biochemistry & Molecular Biology↗

DOE OSTI2019

Computing the small-scale galaxy power spectrum and bispectrum in configuration space

ABSTRACT We present a new class of estimators for computing small-scale power spectra and bispectra in configuration space via weighted pair and triple counts, with no explicit use of Fourier transforms. Particle counts are truncated at $R_0\sim 100\, h^{-1}\, \mathrm{Mpc}$ via a continuous window function, which has negligible effect on the measured power spectrum multipoles at small scales. This gives a power spectrum algorithm with complexity $\mathcal {O}(NnR_0^3)$ (or $\mathcal {O}(Nn^2R_0^6)$ for the bispectrum), measuring N galaxies with number density n. Our estimators are corrected for the survey geometry and have neither self-count contributions nor discretization artefacts, making them ideal for high-k analysis. Unlike conventional Fourier-transform-based approaches, our algorithm becomes more efficient on small scales (since a smaller R0 may be used), thus we may efficiently estimate spectra across k-space by coupling this method with standard techniques. We demonstrate the utility of the publicly available power spectrum algorithm by applying it to BOSS DR12 simulations to compute the high-k power spectrum and its covariance. In addition, we derive a theoretical rescaled-Gaussian covariance matrix, which incorporates the survey geometry and is found to be in good agreement with that from mocks. Computing configuration- and Fourier-space statistics in the same manner allows us to consider joint analyses, which can place stronger bounds on cosmological parameters; to this end we also discuss the cross-covariance between the two-point correlation function and the small-scale power spectrum.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Large Scale Tensor Factorization via Parallel Sketches

Tensor factorization methods have recently gained increased popularity. A key feature that renders tensors attractive is the ability to directly model multi-relational data. In this work, we propose ParaSketch, a parallel tensor factorization algorithm that enables massive parallelism, to deal with large tensors. The idea is to compress the large tensor into multiple small tensors, decompose each small tensor in parallel, and combine the results to reconstruct the desired latent factors. Prior art in this direction entails potentially very high complexity in the (Gaussian) compression and final combining stages. Adopting sketching matrices for compression, the proposed method enjoys a dramatic reduction in compression complexity, and features a much lighter combining step. Moreover, theoretical analysis shows that the compressed tensors inherit latent identifiability under mild conditions, hence establishing correctness of the overall approach. Numerical experiments corroborate the theory and demonstrate the effectiveness of the proposed algorithm.

block term decomposition↗

DOE OSTI2021

Reaction paths of methane activation and oxidation of surface intermediates over NiO on Ceria-Zirconia catalysts studied by In-situ FTIR spectroscopy

Methane activation over NiO/Ce 0.82 Zr 0.18 O 2 catalysts synthesized by combustion synthesis is studied by in-situ IR spectroscopy and correlated to the properties and oxygen speciation of the catalyst. Through XRD, H 2 -TPR, and pyridine adsorption followed by FTIR spectroscopy, the reducibility and Lewis acidity of the catalysts are assessed. In-situ FTIR spectroscopy is used to monitor the methane activation on catalyst surfaces. Complex IR features of methane-derived surface species are observed and are attributed to the formation of surface alkyl/alkoxy, aldehyde, formate/carbonate, and aromatic species. A data analysis algorithm is developed to evaluate the evolution of different surface species over time. The formation of formate and carbonate species is driven by adsorbed surface oxygen, while less reactive oxygen species associated with NiO allow for the production of aromatics and alkoxy intermediates. Finally, by tuning the reducibility and Lewis acidity of the catalyst, the selectivity to alkoxy intermediates can be improved.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Theoretical simulation of a signal for a scheme of an atomic spin gyroscope with optical detection

An operation scheme of an atomic spin gyroscope with optical detection is described, in which two noble gas isotopes, {sup 129} Xe and {sup 131} Xe, are used as carriers of the spin of an atomic nucleus. Based on this scheme, we construct a theoretical model of the dynamics of the spin polarisation of an alkali metal and the magnetisation of a noble gas under conditions of spin-exchange interaction and optical pumping. This model allows one to simulate the pumping and signal readout in the gyroscope scheme. The time dependences of this signal are plotted, the analysis of which shows that the signal has a sophisticated complex structure. Thus, the problem arises of demodulating this signal based on the improvement of demodulation methods and algorithms. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Three-dimensional imaging of grain boundaries via quantitative fluorescence X-ray tomography analysis

Abstract Three-dimensional visualization of material composition within multiple grains and across complex networks of grain boundaries at nanoscales can provide new insight into the structure evolution and emerging functional properties of the material for diverse applications. Here, using nanoscale scanning X-ray fluorescence tomography, coupled with an advanced self-absorption correction algorithm developed in this work, we analyze the three-dimensional gain distributions and compositions in a Ce 0.8 Gd 0.2 O 2-δ -CoFe 2 O 4 mixed ionic-electronic conductor system with high accuracy and statistical significance. Our systematic investigation reveals an additional emergent phase and uncovers highly intriguing composition stability ranges for the multiple material phases within this system. The presented visualization of composition variations across complex interfaces, supported by our quantitative composition analysis, discloses mechanistic pathways of the diverse phase transformations occurring in the material synthesis, providing insights for the optimization of transport properties in the mixed ionic-electronic conductor system.

36 MATERIALS SCIENCE↗