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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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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

A learning-based measurement framework for traffic matrix inference in software defined networks

Here, we propose an intelligent framework for Traffic Matrix (TM) inference in Software Defined Networks (SDN) where the Ternary Content Addressable Memory (TCAM) entries of switches are partitioned into two parts to: (1) effectively aggregate part of incoming flows for aggregate measurements, and (2) de-aggregate and directly measure the most informative flows for per-flow measurements. These measurements are then processed to effectively estimate the size of network flows. Under hard resource constraints of limited TCAM sizes, we show how to design the optimal and efficient-compressed flow aggregation matrices. We propose an optimal Multi-Armed Bandit (MAB) based algorithm to adaptively measure the most rewarding flows. We evaluate the performance of our framework using real traffic traces from different network environments and by considering two main applications: TM estimation and Heavy Hitter (HH) detection. Moreover, we have implemented a prototype of our framework in Mininet to demonstrate its effectiveness.

42 ENGINEERING↗
DOE OSTI2019

Topology Inference of Unknown Networks Based on Robust Virtual Coordinate Systems

Learning and exploring the connectivity of unknown networks represent an important problem in practical applications of communication networks and social-media networks. Modeling large-scale networks as connected graphs is highly desirable to extract their connectivity information among nodes to visualize network topology, disseminate data, and improve routing efficiency. This paper investigates a simple measurement model in which a small subset of source nodes collect hop distance information from networked nodes in order to generate a virtual coordinate system (VCS) for networks of unknown topology. We establish the VCS to define logical distance among nodes based on principal component analysis and to determine connectivity relationship and effective routing methods. More importantly, we present a robust analytical algorithm to derive the VCS against practical issues of missing and corrupted measurements. We also develop a connectivity inference method which classifies nodes into layers based on the hop distances and derives partial information on network connectivity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Statistical data analysis of x-ray spectroscopy data enabled by neural network accelerated Bayesian inference

Bayesian inference applied to x-ray spectroscopy data analysis enables uncertainty quantification necessary to rigorously test theoretical models. However, when comparing to data, detailed atomic physics and radiation transfer calculations of x-ray emission from non-uniform plasma conditions are typically too slow to be performed in line with statistical sampling methods, such as Markov Chain Monte Carlo sampling. Furthermore, differences in transition energies and x-ray opacities often make direct comparisons between simulated and measured spectra unreliable. Here, we present a spectral decomposition method that allows for corrections to line positions and bound–bound opacities to best fit experimental data, with the goal of providing quantitative feedback to improve the underlying theoretical models and guide future experiments. In this work, we use a neural network (NN) surrogate model to replace spectral calculations of isobaric hot-spots created in Kr-doped implosions at the National Ignition Facility. The NN was trained on calculations of x-ray spectra using an isobaric hot-spot model post-processed with Cretin, a multi-species atomic kinetics and radiation code. The speedup provided by the NN model to generate x-ray emission spectra enables statistical analysis of parameterized models with sufficient detail to accurately represent the physical system and extract the plasma parameters of interest.

47 OTHER INSTRUMENTATION↗
NASA NTRS2016

A Neural Network Approach to Infer Optical Depth of Thick Ice Clouds at Night

One of the roadblocks to continuously monitoring cloud properties is the tendency of clouds to become optically black at cloud optical depths (COD) of 6 or less. This constraint dramatically reduces the quantitative information content at night. A recent study found that because of their diffuse nature, ice clouds remain optically gray, to some extent, up to COD of 100 at certain wavelengths. Taking advantage of this weak dependency and the availability of COD retrievals from CloudSat, an artificial neural network algorithm was developed to estimate COD values up to 70 from common satellite imager infrared channels. The method was trained using matched 2007 CloudSat and Aqua MODIS data and is tested using similar data from 2008. The results show a significant improvement over the use of default values at night with high correlation. This paper summarizes the results and suggests paths for future improvement.

Minnis, P.↗
DOE OSTI2013

Network portal: a database for storage, analysis and visualization of biological networks

The ease of generating high-throughput data has enabled investigations into organismal complexity at the systems level through the inference of networks of interactions among the various cellular components (genes, RNAs, proteins and metabolites). The wider scientific community, however, currently has limited access to tools for network inference, visualization and analysis because these tasks often require advanced computational knowledge and expensive computing resources. We have designed the network portal (http://networks.systemsbiology.net) to serve as a modular database for the integration of user uploaded and public data, with inference algorithms and tools for the storage, visualization and analysis of biological networks. The portal is fully integrated into the Gaggle framework to seamlessly exchange data with desktop and web applications and to allow the user to create, save and modify workspaces, and it includes social networking capabilities for collaborative projects. While the current release of the database contains networks for 13 prokaryotic organisms from diverse phylogenetic clades (4678 co-regulated gene modules, 3466 regulators and 9291 cis-regulatory motifs), it will be rapidly populated with prokaryotic and eukaryotic organisms as relevant data become available in public repositories and through user input. The modular architecture, simple data formats and open API support community development of the portal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Image feature based GPS trace filtering for road network generation and road segmentation

We propose a new method to infer road networks from GPS trace data and accurately segment road regions in high-resolution aerial images. Unlike previous efforts that rely on GPS traces alone, we exploit image features to infer road networks from noisy trace data. The inferred road network is used to guide road segmentation. We show that the number of image segments spanned by the traces and the trace orientation validated with image features are important attributes for identifying GPS traces on road regions. Based on filtered traces , we construct road networks and integrate them with image features to segment road regions. Lastly, our experiments show that the proposed method produces more accurate road networks than the leading method that uses GPS traces alone, and also achieves high accuracy in segmenting road regions even with very noisy GPS data.

58 GEOSCIENCES↗
DOE OSTI2019

Inferring Convolutional Neural Networks' Accuracies from Their Architectural Characterizations

The challenge of choosing an appropriate convolutional neural network (CNN) architecture for specific applications and different data sets is still poorly understood in the literature. This is problematic, since CNNs have shown strong promise for analyzing scientific data from many domains including particle imaging detectors. In this paper, we proposed a systematic language that is useful for comparison between different CNN's architectures before training time. This helps us predict whether a network can perform better than a certain threshold accuracy before training up to 70% accuracy using simple machine learning models. Additionally, we found a coefficient of determination of 0.966 for an Ordinary Least Squares model in a regression task to predict accuracy of a large population of networks.

Hoang, Duc↗
DOE OSTI2015

On the data-driven inference of modulatory networks in climate science: An application to West African rainfall

Decades of hypothesis-driven and/or first-principles research have been applied towards the discovery and explanation of the mechanisms that drive climate phenomena, such as western African Sahel summer rainfall~variability. Although connections between various climate factors have been theorized, not all of the key relationships are fully understood. We propose a data-driven approach to identify candidate players in this climate system, which can help explain underlying mechanisms and/or even suggest new relationships, to facilitate building a more comprehensive and predictive model of the modulatory relationships influencing a climate phenomenon of interest. We applied coupled heterogeneous association rule mining (CHARM), Lasso multivariate regression, and dynamic Bayesian networks to find relationships within a complex system, and explored means with which to obtain a consensus result from the application of such varied methodologies. Using this fusion of approaches, we identified relationships among climate factors that modulate Sahel rainfall. As a result, these relationships fall into two categories: well-known associations from prior climate knowledge, such as the relationship with the El Niño–Southern Oscillation (ENSO) and putative links, such as North Atlantic Oscillation, that invite further research.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

pyFLANK, a graph neural network based null distribution inference model for F ST outlier detection

Detecting genomic regions under selection is essential for understanding how populations adapt to different environments, yet it remains challenging due to the confounding effects of demographic history and linkage disequilibrium (LD). Fixation index (F ST ) is a widely used statistic to identify genomic regions under adaptation. However, identifying genes under selection by defining F ST outliers often remains challenging, owing to confounding effects of underlying demographic history. Traditional methods assume independence among loci and rely on simple demographic models, while newer models perform much better but are computationally expensive and not easily scalable. Here, we present pyFLANK, an open-source and automated Python implementation which detects F ST outliers using a null distribution inferred from quasi-independent loci. Our tool integrates three approaches to identify loci obeying a null distribution: graph neural network (GNN) inference, linkage disequilibrium (LD)-based inference, and user-defined input. Because pyFLANK uses GNN-based inference of quasi-independent loci, it yields a more accurate null model with less need for user parameter input. In simulation experiments, pyFLANK achieved lower false positive rates than current methods while maintaining comparable detection power, indicating that its refined null model better distinguishes true adaptive loci from background variation. The GNN-based model, in particular, detected additional loci associated with phenotypic variance that were not identified by existing methods. Assessments of simulation and real data from different species demonstrate that pyFLANK achieves lower false positive rates compared with other commonly used F ST outlier detectors, while maintaining comparable detection power and excellent computational performance, providing a robust and user-friendly tool for identifying loci under divergent selection. It extends existing F ST outlier frameworks by incorporating explicit LD-aware strategies for null model calibration. The method is intended as a practical and scalable complement to existing genome scan approaches.

FST↗
DOE OSTI2014

Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

The primary focus in the network-centric analysis of cellular metabolism by systems biology approaches is to identify the active metabolic network for the condition of interest. Two major approaches are available for the discovery of the condition-specific metabolic networks. One approach starts from genome-scale metabolic networks, which cover all possible reactions known to occur in the related organism in a condition-independent manner, and applies methods such as the optimization-based Flux-Balance Analysis to elucidate the active network. The other approach starts from the condition-specific metabolome data, and processes the data with statistical or optimization-based methods to extract information content of the data such that the active network is inferred. These approaches, termed bottom-up and top-down, respectively, are currently employed independently. However, considering that both approaches have the same goal, they can both benefit from each other paving the way for the novel integrative analysis methods of metabolome data- and flux-analysis approaches in the post-genomic era. This study reviews the strengths of constraint-based analysis and network inference methods reported in the metabolic systems biology field; then elaborates on the potential paths to reconcile the two approaches to shed better light on how the metabolism functions.

60 APPLIED LIFE SCIENCES↗
NASA NTRSDate not supplied

Use of Design of Experiments and Rule-Based Inference in Determining Neural Network Architectures for Loss of Control Detection

In this work, we describe methods for selecting the neural network architectures and input spaces to implement belief state inference on generic commercial transport aircraft. First, we highlight a case study on the planning, execution, and analysis of a set of experiments to determine the configurations of a conditional variational autoencoder (CVAE). We present a structured method that can be used in a number of aerospace applications, to optimize the structure and training parameters of the CVAE for belief state inference, using Design of Experiments (DOE) statistical methodologies. The motivation for this specific DOE was to identify the appropriate hyperparameters for measuring the CVAE reconstruction probability and latent space, such that the measurements can be used to infer qualitative state changes for the aircraft. We demonstrate that this process yields information about a trained neural network’s utility for this specific application, along with a quantifiable range of certainty. We execute 84 experiments using loss-of-control flight maneuver data from a NASA T-2 aircraft, demonstrating that this empirical process allows us to construct cheap and simple models with specific attributes amenable to belief state inference in aerospace applications. While theoretically, we could create a single CVAE with an input space the size of all measurable flight variables and environmental dynamics, it becomes intractable to use such a neural network in an in-situ intelligent multi-agent system. Using the recommendations from our case study, we introduce a technical approach for feasibly describing the belief space by (1) identifying significant statistical relationships among flight variables using rule induction, (2) using a set of rules that cover all features to define the input space of multiple CVAEs, and (3) forming a belief space based on the joint probability density of their collective latent spaces. This results in a series of relatively small matrix multiplications that can be performed in real time, as opposed to large matrix computations in a single CVAE. We demonstrate the application of this approach on the T-2 flight loss-of control experiments, using the architecture and hyperparameter recommendations from the case study. We compare the utilities of an individual CVAE trained on all flight variables and multiple CVAEs defined on subsets of flight variables for detecting qualitative changes in flight. We demonstrate that the use of multiple CVAEs with smaller input spaces permits the CVAE to capture more granular relationships in the latent space, permitting better state space characterization and loss-of-control detection.

Design of experiments↗
DOE OSTI2023

Bayesian Inference with Latent Hamiltonian Neural Networks (L-HNNs)

When sampling for Bayesian inference, one popular approach is to use Hamiltonian Monte Carlo (HMC) and the No-U-Turn Sampler (NUTS). However, HMC and NUTS can require numerous numerical gradients of the target density and can prove slow in practice. We propose Hamiltonian neural networks (HNNs) with HMC and NUTS for solving Bayesian inference problems [1, 2]. Once trained, HNNs do not require gradients of the target density while sampling. Moreover, they satisfy important properties such as perfect time reversibility and Hamiltonian conservation, making them well suited for use within HMC and NUTS because stationarity can be shown. We also propose an HNN extension called latent HNNs (L-HNNs), which predict latent variable outputs. Compared to HNNs, L-HNNs offer improved expressivity and a reduction in integration errors. Finally, we propose employing L-HNNs in NUTS with an online error monitoring scheme to prevent degeneracy of the sampling in regions of low probability density. We demonstrate L-HNNs in NUTS with online error monitoring by using several example cases involving complex, heavy-tailed, and high local curvature probability densities. Overall, L-HNNs in NUTS with online error monitoring satisfactorily inferred these probability densities. Compared to traditional NUTS, L-HNNs in NUTS with online error monitoring improved the effective sample size (ESS) per gradient by an order of magnitude.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Inference-Engine v0.1.0

Given a pre-trained neural network, Inference-Engine performs maps network inputs to outputs by executing the forward pass through the provided network. Although the predominant programming language for machine-learning is Python, most high-performance computing (HPC) applications are written in Fortran, C, or C++. Inference-Engine aims to support HPC programs and is written in Fortran, a language with a large feature set supporting interoperability with C. This software exposes concurrency in a portable way by using standard language features that some modern Fortran compilers can exploit with various optimizations, including offloading computation to a Graphics Processing Unit (GPU). In particular, this software makes extensive use of Fortran's "do concurrent" parallel loop construct, implicitly parallel array statements, and pure procedures that can be invoked inside "do concurrent" blocks. Inference-Engine also supports dynamic choice of inference methods at runtime. Two current options include one method that uses Fortran's "dot_product" intrinsic function inside "do concurrent" blocks and another method that instead uses Fortran' "matmul" array intrinsic function. We plan to investigate automatic compiler offloading of "do concurrent" calculations to GPUs and compile-time substitution of optimized libraries such as the Basic Linear Algebra Library (BLAS) for "matmul" invocations. We also envision the potential for the choice of which method to use could happen at program launch based on in situ performance measurements on any given platform.

Rouson, Damian↗
DOE OSTI2019

CosmoGAN: creating high-fidelity weak lensing convergence maps using Generative Adversarial Networks

Abstract Inferring model parameters from experimental data is a grand challenge in many sciences, including cosmology. This often relies critically on high fidelity numerical simulations, which are prohibitively computationally expensive. The application of deep learning techniques to generative modeling is renewing interest in using high dimensional density estimators as computationally inexpensive emulators of fully-fledged simulations. These generative models have the potential to make a dramatic shift in the field of scientific simulations, but for that shift to happen we need to study the performance of such generators in the precision regime needed for science applications. To this end, in this work we apply Generative Adversarial Networks to the problem of generating weak lensing convergence maps. We show that our generator network produces maps that are described by, with high statistical confidence, the same summary statistics as the fully simulated maps.

Mustafa, Mustafa (ORCID:0000000291770283)↗
DOE OSTI2025

Automatically parallelizing batch inference on deep neural networks using Fiats and Fortran 2023 `do concurrent`

This paper introduces novel programming strategies that leverage features of the Fortran 2023 standard of the International Standards Organization (ISO) to automatically parallelize computations on deep neural networks. The paper focuses on the interplay of object-oriented, parallel, and functional programming paradigms in the Fiats deep learning library. We demonstrate how several infrequently used language features play a role in enabling efficient, parallel execution. Specifically, the ability to explicitly declare that a procedure is pure facilitates inference in the context of the language’s loop-parallelism construct `do concurrent`. Also, explicitly prohibiting the overriding of a parent type’s type-bound procedures eliminates the need for dynamic dispatch in performance-critical code. Finally, this paper uses batch inference calculations on a neural network surrogate for atmospheric aerosol dynamics to demonstrate that LLVM Flang compiler’s automatic parallelization of `do concurrent` achieves roughly the same performance and scalability as achieved by OpenMP compiler directives. We also demonstrate that double-precision inference costs 37–72% longer runtime than default-real precision with most values in the range 57-60%.

Rouson, Damian↗
DOE OSTI2021

Hierarchical Inference with Bayesian Neural Networks: An Application to Strong Gravitational Lensing

In the past few years, approximate Bayesian Neural Networks (BNNs) have demonstrated the ability to produce statistically consistent posteriors on a wide range of inference problems at unprecedented speed and scale. However, any disconnect between training sets and the distribution of real-world objects can introduce bias when BNNs are applied to data. This is a common challenge in astrophysics and cosmology, where the unknown distribution of objects in our universe is often the science goal. In this work, we incorporate BNNs with flexible posterior parameterizations into a hierarchical inference framework that allows for the reconstruction of population hyperparameters and removes the bias introduced by the training distribution. We focus on the challenge of producing posterior PDFs for strong gravitational lens mass model parameters given Hubble Space Telescope–quality single-filter, lens-subtracted, synthetic imaging data. We show that the posterior PDFs are sufficiently accurate (statistically consistent with the truth) across a wide variety of power-law elliptical lens mass distributions. We then apply our approach to test data sets whose lens parameters are drawn from distributions that are drastically different from the training set. We show that our hierarchical inference framework mitigates the bias introduced by an unrepresentative training set's interim prior. Simultaneously, we can precisely reconstruct the population hyperparameters governing our test distributions. Our full pipeline, from training to hierarchical inference on thousands of lenses, can be run in a day. The framework presented here will allow us to efficiently exploit the full constraining power of future ground- and space-based surveys (https://github.com/swagnercarena/ovejero).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Disentangling direct from indirect relationships in association networks

Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in Escherichia coli also revealed considerably higher prediction power than the best-performing approaches in the DREAM5 (Dialogue on Reverse Engineering Assessment and Methods project, #5) Network Inference Challenge. In addition, applying iDIRECT to highly diverse grassland soil microbial communities in response to climate warming showed that the iDIRECT-processed networks were significantly different from the original networks, with considerably fewer nodes, links, and connectivity, but higher relative modularity. Further analysis revealed that the iDIRECT-processed network was more complex under warming than the control and more robust to both random and target species removal ( P < 0.001). As a general approach, iDIRECT has great advantages for network inference, and it should be widely applicable to infer direct relationships in association networks across diverse disciplines in science and engineering.

59 BASIC BIOLOGICAL SCIENCES↗