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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2016

Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks

Spatial gene expression patterns enable the detection of local covariability and are extremely useful for identifying local gene interactions during normal development. The abundance of spatial expression data in recent years has led to the modeling and analysis of regulatory networks. The inherent complexity of such data makes it a challenge to extract biological information. We developed staNMF, a method that combines a scalable implementation of nonnegative matrix factorization (NMF) with a new stability-driven model selection criterion. When applied to a set of Drosophila early embryonic spatial gene expression images, one of the largest datasets of its kind, staNMF identified 21 principal patterns (PP). Providing a compact yet biologically interpretable representation of Drosophila expression patterns, PP are comparable to a fate map generated experimentally by laser ablation and show exceptional promise as a data-driven alternative to manual annotations. Our analysis mapped genes to cell-fate programs and assigned putative biological roles to uncharacterized genes. Finally, we used the PP to generate local transcription factor regulatory networks. Spatially local correlation networks were constructed for six PP that span along the embryonic anterior-posterior axis. Using a two-tail 5% cutoff on correlation, we reproduced 10 of the 11 links in the well-studied gap gene network. In conclusion, the performance of PP with the Drosophila data suggests that staNMF provides informative decompositions and constitutes a useful computational lens through which to extract biological insight from complex and often noisy gene expression data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Criticality analysis of nuclear binding energy neural networks

Machine learning methods, in particular deep learning methods such as artificial neural networks (ANNs) with many layers, have become widespread and useful tools in nuclear physics. However, these ANNs are typically treated as ‘black boxes’, with their architecture (width, depth, and weight/bias initialization) and the training algorithm and parameters chosen empirically by optimizing learning based on limited exploration. We test a non-empirical approach to understanding and optimizing nuclear physics ANNs by adapting a criticality analysis based on renormalization group flows in terms of the hyperparameters for weight/bias initialization, training rates, and the ratio of depth to width. This treatment utilizes the statistical properties of neural network initialization to find a generating functional for network outputs at any layer, allowing for a path integral formulation of the ANN outputs as a Euclidean statistical field theory. We use a prototypical example to test the applicability of this approach: a simple ANN for nuclear binding energies. We find that with training using a stochastic gradient descent optimizer, the predicted criticality behavior is realized, and optimal performance is found with critical tuning. However, the use of an adaptive learning algorithm leads to somewhat superior results without concern for tuning and thus obscures the analysis. Nevertheless, the criticality analysis offers a way to look within the black box of ANNs, which is a first step towards potential improvements in network performance beyond using adaptive optimizers.

artificial neural network↗

DOE OSTI2017

Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Results: Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Simultaneous global and local clustering in multiplex networks with covariate information

Understanding both global and layer-specific group structures is useful for uncovering complex patterns in networks with multiple interaction types. In this work, we introduce a new model, the hierarchical multiplex stochastic blockmodel, which simultaneously detects communities within individual layers of a multiplex network while inferring a global node clustering across the layers. A stochastic blockmodel is assumed in each layer, with probabilities of layer-level group memberships determined by a node’s global group assignment. Our model uses a Bayesian framework, employing a probit stick-breaking process to construct node-specific mixing proportions over a set of shared Griffiths–Engen–McCloseky distributions. These proportions determine layer-level community assignment, allowing for an unknown and varying number of groups across layers, while incorporating nodal covariate information to inform the global clustering. We propose a scalable variational inference procedure with parallelisable updates for application to large networks. Extensive simulation studies demonstrate our model’s ability to accurately recover both global and layer-level clusters in complicated settings, and applications to real data showcase the model’s effectiveness in uncovering interesting latent network structure.

community detection↗

DOE OSTI2018

Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils

Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ ρ ≥ 0.80, adjusted P <0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H + +Al 3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Sample-Efficient Adaptive Calibration of Quantum Networks Using Bayesian Optimization

All physical systems employed for quantum information tasks must act as unbiased carriers of encoded quantum states. Ensuring such indistinguishability of information carriers is a major challenge in many quantum information applications, including advanced quantum communication protocols. For photons, the workhorses of quantum communication networks, it is difficult to obtain and maintain their indistinguishability because of environment-induced transformations and loss imparted by communication channels, especially in noisy scenarios. Conventional strategies to mitigate these transformations often require hardware or software overhead that is restrictive (e.g., adding noise), infeasible (e.g., on a satellite), or time-consuming for deployed networks. In this work we propose and develop resource-efficient Bayesian optimization techniques to rapidly and adaptively calibrate the indistinguishability of individual photons for quantum networks using only information derived from their measurement. To experimentally validate our approach, we demonstrate the optimization of Hong-Ou-Mandel interference between two photons-a central task in quantum networking- finding rapid, efficient, and reliable convergence towards maximal photon indistinguishability in the presence of high loss and shot noise. We expect our resource-optimized and experimentally friendly methodology will allow fast and reliable calibration of indistinguishable quanta, a necessary task in distributed quantum computing, communications, and sensing, as well as for fundamental investigations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Entanglement phase transitions in random stabilizer tensor networks

Here we explore a class of random tensor network models with “stabilizer” local tensors which we name random stabilizer tensor networks (RSTNs). For RSTNs defined on a two-dimensional square lattice, we perform extensive numerical studies of entanglement phase transitions between volume-law and area-law entangled phases of the one-dimensional boundary states. These transitions occur when either (a) the bond dimension D of the constituent tensors is varied or (b) the tensor network is subject to random breaking of bulk bonds, implemented by forced measurements. In the absence of broken bonds, we find that the RSTN supports a volume-law entangled boundary state with bond dimension D ≥ 3 where D is a prime number, and an area-law entangled boundary state for D = 2. Upon breaking bonds at random in the bulk with probability p, there exists a critical measurement rate p c for each D ≥ 3 above which the boundary state becomes area-law entangled. To explore the conformal invariance at these entanglement transitions for different prime D, we consider tensor networks on a finite rectangular geometry with a variety of boundary conditions, and extract universal operator scaling dimensions via extensive numerical calculations of the entanglement entropy, mutual information, and mutual negativity at their respective critical points. Our results at large D approach known universal data of percolation conformal field theory, while showing clear discrepancies at smaller D, suggesting a distinct entanglement transition universality class for each prime D. We further study universal entanglement properties in the volume-law phase and demonstrate quantitative agreement with the recently proposed description in terms of a directed polymer in a random environment.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Real-time evolution of Anderson impurity models via tensor network influence functionals

In this work, we present and analyze two tensor network-based influence functional approaches for simulating the real-time dynamics of quantum impurity models such as the Anderson model. Via comparison with recent numerically exact simulations, we show that such methods accurately capture the long-time nonequilibrium quench dynamics. The two parameters that must be controlled in these tensor network influence functional approaches are a time discretization (Trotter) error and a bond dimension (tensor network truncation) error. We show that the actual numerical uncertainties are controlled by an intricate interplay of these two approximations, which we demonstrate in different regimes. Our work opens the door to using these tensor network influence functional methods as general impurity solvers.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Data-driven analysis of dipole strength functions using artificial neural networks

Here, we present a data-driven analysis of dipole strength functions across the nuclear chart, employing an artificial neural network to model nuclear dipole responses. We train the network on a dataset of experimentally measured dipole strength functions for 216 different nuclei. To assess its predictive capability, we test the trained model on an additional set of 10 new nuclei, where experimental data exist. We demonstrate that the artificial neural network not only accurately reproduces known data but also identifies potential inconsistencies in experimental datasets, indicating which results may warrant further review or possible rejection. For nuclei where experimental data are sparse or unavailable, the network confirms theoretical calculations, reinforcing its utility as a predictive tool in nuclear physics. Finally, utilizing the predicted electric dipole polarizability, we extract the value of the symmetry energy at saturation density and find it consistent with results from the literature.

artificial neural networks↗

DOE OSTI2021

Semantic segmentation with a sparse convolutional neural network for event reconstruction in MicroBooNE

We present the performance of a semantic segmentation network, SparseSSNet, that provides pixel-level classification of MicroBooNE data. The MicroBooNE experiment employs a liquid argon time projection chamber for the study of neutrino properties and interactions. SparseSSNet is a submanifold sparse convolutional neural network, which provides the initial machine learning based algorithm utilized in one of MicroBooNE's ν e -appearance oscillation analyses. The network is trained to categorize pixels into five classes, which are re-classified into two classes more relevant to the current analysis. The output of SparseSSNet is a key input in further analysis steps. This technique, used for the first time in liquid argon time projection chambers data and is an improvement compared to a previously used convolutional neural network, both in accuracy and computing resource utilization. Here, the accuracy achieved on the test sample is ≥ 99%. For full neutrino interaction simulations, the time for processing one image is ≈ 0.5 sec, the memory usage is at 1 GB level, which allows utilization of most typical CPU worker machine.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

Predictions of first passage times in sparse discrete fracture networks using graph-based reductions

Here, we present a graph-based methodology to reduce the computational cost of obtaining first passage times through sparse fracture networks. We also derive graph representations of generic three-dimensional discrete fracture networks (DFNs) using the DFN topology and flow boundary conditions. Subgraphs corresponding to the union of the k shortest paths between the inflow and outflow boundaries are identified and transport on their equivalent subnetworks is compared to transport through the full network. The number of paths included in the subgraphs is based on the scaling behavior of the number of edges in the graph with the number of shortest paths. First passage times through the subnetworks are in good agreement with those obtained in the full network, both for individual realizations and in distribution. We obtain accurate estimates of first passage times with an order of magnitude reduction of CPU time and mesh size using the proposed method.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Using limited neural networks to assess relative mechanistic influence on shock heating in granular solids

The rapid compaction of granular media results in localized heating that can induce chemical reactions, phase transformations, and melting. However, there are numerous mechanisms in play that can be dependent on a variety of microstructural features. Machine learning techniques such as neural networks offer a ubiquitous method to develop models for physical processes. Limiting what kind of microstructural information is used as an input and assessing normalized changes in network error, the relative importance of different mechanisms can be inferred. Here we utilize binned, initial density information as network inputs to predict local shock heating in a granular high explosive trained from large-scale molecular dynamics simulations. In this study, the spatial extent of the density field used in the network is altered to assess the importance and relevant length scales of the physical mechanisms in play, where different microstructural features result in different predictive capabilities.

36 MATERIALS SCIENCE↗

DOE OSTI2019

BraggNet: integrating Bragg peaks using neural networks

Neutron crystallography offers enormous potential to complement structures from X-ray crystallography by clarifying the positions of low-Z elements, namely hydrogen. Macromolecular neutron crystallography, however, remains limited, in part owing to the challenge of integrating peak shapes from pulsed-source experiments. To advance existing software, this article demonstrates the use of machine learning to refine peak locations, predict peak shapes and yield more accurate integrated intensities when applied to whole data sets from a protein crystal. The artificial neural network, based on the U-Net architecture commonly used for image segmentation, is trained using about 100 000 simulated training peaks derived from strong peaks. After 100 training epochs (a round of training over the whole data set broken into smaller batches), training converges and achieves a Dice coefficient of around 65%, in contrast to just 15% for negative control data sets. Integrating whole peak sets using the neural network yields improved intensity statistics compared with other integration methods, including k-nearest neighbours. These results demonstrate, for the first time, that neural networks can learn peak shapes and be used to integrate Bragg peaks. In conclusion, it is expected that integration using neural networks can be further developed to increase the quality of neutron, electron and X-ray crystallography data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Optimal Network Topology for Node-Breaker Representations With AC Power Flow Constraints

It has been demonstrated that network topology optimization (NTO) may change the topology of power system networks, and consequently, provide additional flexibility to reduce network congestion and violations. Most NTO problems are formulated based on the bus-branch model in which it is challenging to represent a realistic picture of all substation configurations. In this paper, we explore advantages of substation reconfiguration modeling based on node-breaker representations for NTO problem with full nonlinear alternating current power flow. It also proposes a tailored solution algorithm to solve this nonconvex mixed-integer nonlinear programming through the outer approximation method. The proposed solution approach iterates between a mixed-integer linear programming and a nonlinear subproblem. Additional enhancements to further accelerate the iteration process are illustrated. Numerical case studies demonstrate the relative economic and operational impact of optimal network topology with node-breaker representations.

42 ENGINEERING↗

DOE OSTI2025

Machine Learning-Assisted Distribution System Network Reconfiguration Problem

High penetration from volatile renewable energy resources in the grid and the varying nature of loads raise the need for frequent line switching to ensure the efficient operation of electrical distribution networks. Operators must ensure maximum load delivery, reduced losses, and the operation between voltage limits. However, computations to decide the optimal feeder configuration are often computationally expensive and intractable, making it unfavorable for real-time operations. This is mainly due to the existence of binary variables in the network reconfiguration optimization problem. To tackle this issue, we have devised an approach that leverages machine learning techniques to reshape distribution networks featuring multiple substations. This involves predicting the substation responsible for serving each part of the network. Hence, it leaves simple and more tractable Optimal Power Flow problems to be solved. This method can produce accurate results in a significantly faster time, as demonstrated using the IEEE 37-bus distribution feeder. Compared to the traditional optimization-based approaches, a feasible solution is achieved approximately ten times faster for all the tested scenarios.

deep neural networks↗

DOE OSTI2018

Building Extraction at Scale Using Convolutional Neural Network: Mapping of the United States

Establishing up-to-date large scale building maps is essential to understand the urban dynamics, such as estimating population, urban planning, and many other applications. Although many computer vision tasks have been successfully carried out with deep convolutional neural networks, there is a growing need to understand their large scale impact on building mapping with remote sensing imagery. In this paper, taking advantage of the scalability of convolutional neural networks (CNNs) and using only few areas with the abundance of building footprints, for the first time we conduct a comparative analysis of four state-of-the-art CNNs for extracting building footprints across the entire continental United States. The four CNN architectures namely: Branch-out CNN, fully convolutional network (FCN), conditional random field as recurrent neural network (CRFasRNN), and SegNet, support semantic pixelwise labeling and focus on capturing textural information at multiscale. We use 1-meter resolution aerial images from National Agriculture Imagery Program as the test-bed, and compare the extraction results across the four methods. In addition, we propose to combine signed-distance labels with SegNet, the preferred CNN architecture identified by our extensive evaluations, to advance building extraction results to instance level. We further demonstrate the usefulness of fusing additional near IR information into the building extraction framework. Large scale experimental evaluations are conducted and reported using metrics that include: Precision, recall rate, intersection over union, and the number of buildings extracted. With the improved CNN model and no requirement of further postprocessing, we have generated building maps for the United States with an average processing time less than one minute for an area of size ∼ 56 km 2 . Finally, the quality of extracted buildings and processing time demonstrated that the proposed CNN based framework fits the need of building extraction at scale.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

A Trilevel Model for Segmentation of the Power Transmission Grid Cyber Network

Network segmentation of a power grid's communication system can make the grid more resilient to cyberattacks. Here we develop a novel trilevel programming model to optimally segment a grid communication system, taking into account the actions of an information technology (IT) administrator, attacker, and grid operator. The IT administrator is allowed to segment existing networks, and the attacker is given a budget to inflict damage on the grid by attacking the segmented communication system. Finally, the grid operator can redispatch the grid after the attack to minimize damage. The resulting problem is a trilevel interdiction problem that we solve using a branch and bound algorithm for bilevel problems. We demonstrate the benefits of optimal network segmentation through case studies on the 9-bus Western System Coordinating Council (WSCC) system and the 30-bus IEEE system. These examples illustrate that network segmentation can significantly reduce the threat posed by a cyberattacker.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Joint Expansion Planning of Power and Water Distribution Networks

This research considers the joint expansion planning of power and water distribution networks, which are interdependent at various levels. We consider the dependency arising through the power consumption of pumps and develop models for integrating new components into existing networks. Then, we formulate the joint expansion planning as a Mixed Integer Nonlinear Program (MINLP). Applying this MINLP to a small-scale test network, we illustrate the advantages offered by joint expansion planning, such as increased flexibility and reduced costs and redundancy, over independently expanding power and water distribution networks.

expansion planning↗