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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

An Online Plug-and-Play Algorithm for Regularized Image Reconstruction

Plug-and-play priors (PnP) is a powerful framework for regularizing imaging inverse problems by using advanced denoisers within an iterative algorithm. Recent experimental evidence suggests that PnP algorithms achieve state-of-the-art performance in a range of imaging applications. Here, we introduce a new online PnP algorithm based on the proximal gradient method (PGM). The proposed algorithm uses only a subset of measurements at every iteration, which makes it scalable to very large datasets. We present a new theoretical convergence analysis, for both batch and online variants of PnP-PGM, for denoisers that do not necessarily correspond to proximal operators. We also present simulations illustrating the applicability of the algorithm to image reconstruction in diffraction tomography. Finally, the results in this paper have the potential to expand the applicability of the PnP framework to very large datasets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Automated isotope identification algorithm using artificial neural networks

There is a need to develop an algorithm that can determine the relative activities of radio-isotopes in a large dataset of low-resolution gamma-ray spectra that contains a mixture of many radio-isotopes. Low-resolution gamma-ray spectra that contain mixtures of radio-isotopes often exhibit feature over-lap, requiring algorithms that can analyze these features when overlap occurs. While machine learning and pattern recognition algorithms have shown promise for the problem of radio-isotope identification, their ability to identify and quantify mixtures of radio-isotopes has not been studied. Because machine learning algorithms use abstract features of the spectrum, such as the shape of overlapping peaks and Compton continuum, they are a natural choice for analyzing radio-isotope mixtures. An artificial neural network (ANN) has be trained to calculate the relative activities of 32 radio-isotopes in a spectrum. Furthermore, the ANN is trained with simulated gamma-ray spectra, allowing easy expansion of the library of target radio-isotopes. In this paper we present our initial algorithms based on an ANN and evaluate them against a series measured and simulated spectra.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Distributed Finite-Time Termination for Consensus Algorithm in Switching Topologies

Here, in this article, we present a finite-time stopping criterion for consensus algorithms in networks with dynamic communication topology. Prior state of the art has established convergence to the consensus value; however, the asymptotic convergence of these algorithms poses a challenge in practical settings where the response from agents is required in finite time. To this end, we propose a maximum-minimum protocol that propagates the global maximum and minimum values of agent states (while running the consensus algorithm) in the network. This article focuses on establishing that the global maximum and minimum values are strictly monotonic even for a dynamic topology, and they can be used to distributively ascertain the closeness to convergence in finite time. We rigorously show that each node can have access to the global maximum and minimum by running the proposed maximum-minimum protocol to realize a finite-time stopping criterion for the otherwise asymptotic consensus algorithm. The practical utility of the algorithm is illustrated through experiments where each agent is instantiated by a NodeJS socket.io server.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Electromagnetic Transient (EMT) Simulation Algorithms for Evaluation of Large-Scale Extreme Fast Charging Systems (T&D Models)

Simulation of high-fidelity models of extreme fast charging (XFC) systems and large-area power grids with many XFCs can be time consuming in traditional simulators. Traditional simulators use a single method of discretization for all the components that results in imposing a large computational burden of inverting a large matrix as well as increased computations related to single method of discretization (that is typically a trapezoidal method). To overcome the problem of simulating large-area power grids with many XFCs, in this paper, advanced numerical simulation algorithms are applied for the first time together to reduce the dimension of matrix inversion. Here, the algorithms include numerical stiffness-based segregation, time constant-based segregation, clustering and aggregation on differential algebraic equations (DAEs), and multi-order integration approaches. These algorithms apply multiple discretization algorithms rather than a single discretization algorithm that further reduces the computational burden. The approaches mentioned here have resulted in speed-up of up to 18x in the simulation of a single distribution system with 15 XFCs and of up to 271x in the simulation of a transmission-distribution system with 300 XFCs in multiple distribution feeders with respect to conventional simulators (like power systems computer aided design [PSCAD]).

42 ENGINEERING↗
DOE OSTI2016

Fast Parallel Stochastic Subspace Algorithms for Large-Scale Ambient Oscillation Monitoring

With the installation of synchrophasors widely across the power grid, measurement-based oscillation monitoring algorithms are becoming increasingly useful in identifying the real-time oscillatory modal properties in power systems. When the number of phasor measurement unit (PMU) channels grows, the computational time of many PMU data based algorithms is dominated by the computational burden in processing large-scale dense matrices. In order to overcome this limitation, this paper presents new formulations and computational strategies for speeding up an ambient oscillation monitoring algorithm, namely, stochastic subspace identification (SSI). Based on previous work, two fast singular value decomposition (SVD) approaches are first applied to the SVD evaluation within the SSI algorithm. Next, block structures are exploited so that the large-scale dense matrix computations can be processed in parallel. This helps in memory savings as well as in overall computational time. Experimental results from three sets of archived data of the western interconnection demonstrate that the new approaches can provide significant speedups while retaining modal estimation accuracy. With proposed fast parallel algorithms, the real-time oscillation monitoring of the large-scale system using hundreds of PMU measurements becomes feasible.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

A Survey of Distributed Optimization and Control Algorithms for Electric Power Systems

Historically, centrally computed algorithms have been the primary means of power system optimization and control. With increasing penetrations of distributed energy resources requiring optimization and control of power systems with many controllable devices, distributed algorithms have been the subject of significant research interest. Here, this paper surveys the literature of distributed algorithms with applications to optimization and control of power systems. In particular, this paper reviews distributed algorithms for offline solution of optimal power flow (OPF) problems as well as online algorithms for real-time solution of OPF, optimal frequency control, optimal voltage control, and optimal wide-area control problems.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

A comparison of histopathology imaging comprehension algorithms based on multiple instance learning

Whole slide imaging (WSI), also called digital virtual microscopy, is a new imaging modality. It allows for the application of AI and machine learning methods to cancer pathology to help establish a means for the automatic diagnosis of cancer cases. However, designing machine-learning models for WSI is computationally challenging due to its required ultra-high resolution. The current state-of-the-art models use multiple instance learning (MIL). MIL is a weakly-supervised learning method in which the model uses an array of inferences from many smaller instances to make a final classification about the entire set. In the context of WSI, researchers divide the ultra-high-resolution image into many patches. The model then classifies the slide based on an array of inferences from the patches. Among several ways of making the final classification, attention-based mechanisms have resulted in superb accuracy scores. The Transformer, one attention-based algorithm, has reported substantial improvements for WSI comprehension tasks. In this project, we studied and compared several WSI comprehension algorithms. We used the following three datasets: CAMELYON16+17, TCGALung, and TCGA-Kidney. We found that attention-based MIL algorithms performed better than standard MIL algorithms for classifying WSI images, achieving a higher mean accuracy and AUC. However, none of the attention-based algorithms performed significantly better than the others, reporting accuracy scores that varied widely. Presumably, it is due to the limited availability of training samples in the data corpus. Since it is not easy to increase the samples from human subjects, some machine learning techniques like transfer learning could help mitigate this issue.

Saunders, Adam↗
DOE OSTI2024

Evidence of scaling advantage for the quantum approximate optimization algorithm on a classically intractable problem

The quantum approximate optimization algorithm (QAOA) is a leading candidate algorithm for solving optimization problems on quantum computers. However, the potential of QAOA to tackle classically intractable problems remains unclear. Here, we perform an extensive numerical investigation of QAOA on the low autocorrelation binary sequences (LABS) problem, which is classically intractable even for moderately sized instances. We perform noiseless simulations with up to 40 qubits and observe that the runtime of QAOA with fixed parameters scales better than branch-and-bound solvers, which are the state-of-the-art exact solvers for LABS. The combination of QAOA with quantum minimum finding gives the best empirical scaling of any algorithm for the LABS problem. We demonstrate experimental progress in executing QAOA for the LABS problem using an algorithm-specific error detection scheme on Quantinuum trapped-ion processors. Our results provide evidence for the utility of QAOA as an algorithmic component that enables quantum speedups.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

A Sequential Quadratic Programming Algorithm for Nonsmooth Problems with Upper- \({\boldsymbol{\mathcal{C}^2}}\) Objective

An optimization algorithm for nonsmooth nonconvex constrained optimization problems with upper- \({\boldsymbol{\mathcal{C}^2}}\) objective functions is proposed and analyzed. Upper- \({\boldsymbol{\mathcal{C}^2}}\) is a weakly concave property that exists in difference of convex (DC) functions and arises naturally in many applications, particularly certain classes of solutions to parametric optimization problems e.g., recourse of stochastic programming and projection onto closed sets. The algorithm can be viewed as an extension of sequential quadratic programming (SQP) to nonsmooth problems with upper- \({\boldsymbol{\mathcal{C}^2}}\) objectives or a simplified bundle method. It is globally convergent with bounded algorithm parameters that are updated with a trust-region criterion. The algorithm handles general smooth constraints through linearization and uses a line search to ensure progress. The potential inconsistencies from the linearization of the constraints are addressed through a penalty method. In conclusion, the capabilities of the algorithm are demonstrated by solving both simple upper- \({\boldsymbol{\mathcal{C}^2}}\) problems and a real-world optimal power flow problem used in current power grid industry practices.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

An Incremental Tensor Train Decomposition Algorithm

We present a new algorithm for incrementally updating the tensor train decomposition of a stream of tensor data. This new algorithm, called the tensor train incremental core expansion (TT-ICE) improves upon the current state-of-the-art algorithms for compressing in tensor train format by developing a new adaptive approach that incurs significantly slower rank growth and guarantees compression accuracy. This capability is achieved by limiting the number of new vectors appended to the TT-cores of an existing accumulation tensor after each data increment. These vectors represent directions orthogonal to the span of existing cores and are limited to those needed to represent a newly arrived tensor to a target accuracy. We provide two versions of the algorithm: TT-ICE and TT-ICE accelerated with heuristics (TT-ICE*). Here, we provide a proof of correctness for TT-ICE and empirically demonstrate the performance of the algorithms in compressing large-scale video and scientific simulation datasets. Compared to existing approaches that also use rank adaptation, TT-ICE* achieves 57× higher compression and up to 95% reduction in computational time.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Discrete Event Execution with One-Sided and Two-Sided GVT Algorithms on 216,000 Processor Cores

Global virtual time (GVT) computation is a key determinant of the efficiency and runtime dynamics of parallel discrete event simulations (PDES), especially on large-scale parallel platforms. Here, three execution modes of a generalized GVT computation algorithm are studied on high-performance parallel computing systems: (1) a synchronous GVT algorithm that affords ease of implementation, (2) an asynchronous GVT algorithm that is more complex to implement but can relieve blocking latencies, and (3) a variant of the asynchronous GVT algorithm to exploit one-sided communication in extant supercomputing platforms. Performance results are presented of implementations of these algorithms on up to 216,000 cores of a Cray XT5 system, exercised on a range of parameters: optimistic and conservative synchronization, fine- to medium-grained event computation, synthetic and non-synthetic applications, and different lookahead values. Performance of up to 54 billion events executed per second is registered. Detailed PDES-specific runtime metrics are presented to further the understanding of tightly-coupled discrete event dynamics on massively parallel platforms.

Perumalla, Kalyan S↗
DOE OSTI2016

A high-performance parallel algorithm for nonnegative matrix factorization

Non-negative matrix factorization (NMF) is the problem of determining two non-negative low rank factors W and H, for the given input matrix A, such that A ≈ WH. NMF is a useful tool for many applications in different domains such as topic modeling in text mining, background separation in video analysis, and community detection in social networks. Despite its popularity in the data mining community, there is a lack of efficient distributed algorithms to solve the problem for big data sets. We propose a high-performance distributed-memory parallel algorithm that computes the factorization by iteratively solving alternating non-negative least squares (NLS) subproblems for W and H. It maintains the data and factor matrices in memory (distributed across processors), uses MPI for interprocessor communication, and, in the dense case, provably minimizes communication costs (under mild assumptions). As opposed to previous implementations, our algorithm is also flexible: (1) it performs well for both dense and sparse matrices, and (2) it allows the user to choose any one of the multiple algorithms for solving the updates to low rank factors W and H within the alternating iterations. We demonstrate the scalability of our algorithm and compare it with baseline implementations, showing significant performance improvements.

Kannan, Ramakrishnan↗
DOE OSTI2023

Fast tree-based algorithms for DBSCAN for low-dimensional data on GPUs

DBSCAN is a well-known density-based clustering algorithm to discover arbitrary shape clusters. While conceptually simple in serial, the algorithm is challenging to efficiently parallelize on manycore GPU architectures. Common pitfalls, such as asynchronous range query calls, result in high thread execution divergence in many implementations. In this paper, we propose a new framework for GPU-accelerated DBSCAN, and describe two tree-based algorithms within that framework. Both algorithms fuse the search for neighbors with updating cluster information, but differ in their treatment of dense regions of the data. We show that the time taken to compute clusters is at most twice that of determination of the neighbors. We compare the proposed algorithms with existing CPU and GPU implementations, and demonstrate their competitiveness and performance using a fast traversal structure (bounding volume hierarchy) for low dimensional data. We also show that the memory usage can be reduced by processing object neighbors dynamically without storing them.

Prokopenko, Andrey↗
DOE OSTI2019

Effective Cloud Detection and Segmentation Using a Gradient-Based Algorithm for Satellite Imagery: Application to Improve PERSIANN-CCS

The effective identification of clouds and monitoring of their evolution are important toward more accurate quantitative precipitation estimation and forecast. In this study, a new gradient-based cloud-image segmentation algorithm is developed using image processing techniques. This method integrates morphological image gradient magnitudes to separate cloud systems and patches boundaries. A varying scale kernel is implemented to reduce the sensitivity of image segmentation to noise and to capture objects with various finenesses of the edges in remote sensing images. The proposed method is flexible and extendable from single to multispectral imagery. Case studies were carried out to validate the algorithm by applying the proposed segmentation algorithm to synthetic radiances for channels of the Geostationary Operational Environmental Satellite ( GOES-16) simulated by a high-resolution weather prediction model. The proposed method compares favorably with the existing cloud-patch-based segmentation technique implemented in the Precipitation Estimation from Remotely Sensed Information Using Artificial Neural Networks–Cloud Classification System (PERSIANN-CCS) rainfall retrieval algorithm. Evaluation of event-based images indicates that the proposed algorithm has potentials comparing to the conventional segmentation technique used in PERSIANN-CCS to improve rain detection and estimation skills with an accuracy rate of up to 98% in identifying cloud regions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, many algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom mappings? For more than four thousand metabolic reactions in the latest human metabolic reconstruction, Recon 3D, we compared the atom mappings predicted by six atom mapping algorithms. We also compared these predictions to those obtained by manual curation of atom mappings for over five hundred reactions distributed among all top level Enzyme Commission number classes. Five of the evaluated algorithms had similarly high prediction accuracy of over 91% when compared to manually curated atom mapped reactions. On average, the accuracy of the prediction was highest for reactions catalysed by oxidoreductases and lowest for reactions catalysed by ligases. In addition to prediction accuracy, the algorithms were evaluated on their accessibility, their advanced features, such as the ability to identify equivalent atoms, and their ability to map hydrogen atoms. In addition to prediction accuracy, we found that software accessibility and advanced features were fundamental to the selection of an atom mapping algorithm in practice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Stochastic characterization of phase detection algorithms in phase-shifting interferometry

Phase-shifting interferometry (PSI) is the preferred non-contact method for profiling sub-nanometer surfaces. Based on monochromatic light interference, the method computes the surface profile from a set of interferograms collected at separate stepping positions. Errors in the estimated profile are introduced when these positions are not located correctly. In order to cope with this problem, various algorithms that minimize the effects of certain types of stepping errors (linear, sinusoidal, etc.) have been developed. Despite the relatively large number of algorithms suggested in the literature, there is no unified way of characterizing their performance when additional unaccounted random errors are present. Here, we suggest a procedure for quantifying the expected behavior of each algorithm in the presence of independent and identically distributed (i.i.d.) random stepping errors, which can occur in addition to the systematic errors for which the algorithm has been designed. As a result, the usefulness of this method derives from the fact that it can guide the selection of the best algorithm for specific measurement situations.

42 ENGINEERING↗
DOE OSTI2021

Efficient ptychographic phase retrieval via a matrix-free Levenberg-Marquardt algorithm

The phase retrieval problem, where one aims to recover a complex-valued image from far-field intensity measurements, is a classic problem encountered in a range of imaging applications. Modern phase retrieval approaches usually rely on gradient descent methods in a nonlinear minimization framework. Calculating closed-form gradients for use in these methods is tedious work, and formulating second order derivatives is even more laborious. Additionally, second order techniques often require the storage and inversion of large matrices of partial derivatives, with memory requirements that can be prohibitive for data-rich imaging modalities. We use a reverse-mode automatic differentiation (AD) framework to implement an efficient matrix-free version of the Levenberg-Marquardt (LM) algorithm, a longstanding method that finds popular use in nonlinear least-square minimization problems but which has seen little use in phase retrieval. Furthermore, we extend the basic LM algorithm so that it can be applied for more general constrained optimization problems (including phase retrieval problems) beyond just the least-square applications. Since we use AD, we only need to specify the physics-based forward model for a specific imaging application; the first and second-order derivative terms are calculated automatically through matrix-vector products, without explicitly forming the large Jacobian or Gauss-Newton matrices typically required for the LM method. We demonstrate that this algorithm can be used to solve both the unconstrained ptychographic object retrieval problem and the constrained “blind” ptychographic object and probe retrieval problems, under the popular Gaussian noise model as well as the Poisson noise model. We compare this algorithm to state-of-the-art first order ptychographic reconstruction methods to demonstrate empirically that this method outperforms best-in-class first-order methods: it provides excellent convergence guarantees with (in many cases) a superlinear rate of convergence, all with a computational cost comparable to, or lower than, the tested first-order algorithms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families

Comparative network analysis provides effective computational means for gaining novel insights into the structural and functional compositions of biological networks. In recent years, various methods have been developed for biological network alignment, whose main goal is to identify important similarities and critical differences between networks in terms of their topology and composition. A major impediment to advancing network alignment techniques has been the lack of gold-standard benchmarks that can be used for accurate and comprehensive performance assessment of such algorithms. The original NAPAbench (network alignment performance assessment benchmark) was developed to address this problem, and it has been widely utilized by many researchers for the development, evaluation, and comparison of novel network alignment techniques. In this work, we introduce NAPAbench 2—a major update of the original NAPAbench that was introduced in 2012. NAPAbench 2 includes a completely redesigned network synthesis algorithm that can generate protein-protein interaction (PPI) network families whose characteristics closely match those of the latest real PPI networks. Furthermore, the network synthesis algorithm comes with an intuitive GUI that allows users to easily generate PPI network families with an arbitrary number of networks of any size, according to a flexible user-defined phylogeny. In addition, NAPAbench 2 provides updated benchmark datasets—created using the redesigned network synthesis algorithm—which can be used for comprehensive performance assessment of network alignment algorithms and their scalability.

42 ENGINEERING↗