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All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the influence of conformational uncertainty in biomolecular solvation

Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansion, we construct a surrogate model of the target property with respect to varying conformational states. We also propose a method to increase the sparsity of the gPC expansion by defining a set of conformational “active space” random variables. With the increased sparsity, we employ the compressive sensing method to accurately construct the surrogate model. We demonstrate the performance of the surrogate model by evaluating fluctuation-induced uncertainty in solvent-accessible surface area for the bovine trypsin inhibitor protein system and show that the new approach offers more accurate statistical information than standard Monte Carlo approaches. Further more, the constructed surrogate model also enables us to directly evaluate the target property under various conformational states, yielding a more accurate response surface than standard sparse grid collocation methods. In particular, the new method provides higher accuracy in high-dimensional systems, such as biomolecules, where sparse grid performance is limited by the accuracy of the computed quantity of interest. Our new framework is generalizable and can be used to investigate the uncertainty of a wide variety of target properties in biomolecular systems.

coarse graining↗
DOE OSTI2019

A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness

The challenge of quantifying uncertainty propagation in real-world systems is rooted in the high-dimensionality of the stochastic input and the frequent lack of explicit knowledge of its probability distribution. Traditional approaches show limitations for such problems, especially when the size of the training data is limited. To address these diculties, we have developed a general framework of constructing surrogate models on spaces of stochastic input with arbitrary probability measure irrespective of the mutual dependencies between individual components of the random inputs and the analytical form. The present Data-driven Sparsity-enhancing Rotation for Arbitrary Randomness (DSRAR) framework includes a data-driven construction of multivariate polynomial basis for arbitrary mutually dependent probability measure and a sparsity enhancement rotation procedure. This sparsity-enhancing rotation method was initially proposed in our previous work [1] for Gaussian density distributions, which may not be feasible for non-Gaussian distributions due to the loss of orthogonality after the rotation. To remedy such diculties, we developed a new data-driven approach to construct orthonormal polynomials for polynomials for arbitrary mutually dependent (amdP) randomness, ensuring the constructed basis maintains the orthogonality/near-orthogonality with respect to the density of the rotated random vector, where directly applying the regular polynomial chaos including arbitrary polynomial chaos (aPC) [2] shows limitations due to the assumption of the mutual independence between the components of the random inputs. The developed DSRAR framework leads to accurate recovery, with only limited training data, of a sparse representation of the target functions. The eectiveness of our method is demonstrated in challenging problems such as PDEs and realistic molecular systems within high-dimensional conformational space (O(10)) where the underlying density is implicitly represented by a large collection of sample data, as well as systems with explicitly given non-Gaussian probabilistic measures.

Lei, Huan↗
DOE OSTI2025

Accelerating GNNs on GPU Sparse Tensor Cores through N:M Sparsity-Oriented Graph Reordering

Recent advancements in GPU hardware support have introduced the capability to leverage N:M sparse patterns for substantial performance gains. Graphs in Graph Neural Networks (GNNs) are typically sparse, but the sparsity is often irregular, not conforming to such sparse patterns. In this paper, we propose a novel graph reordering algorithm, the first of its kind, to reshape irregular graph data into the N:M structured sparse pattern at the tile level, allowing linear-algebra-based graph operations in GNNs to benefit from the N:M sparse hardware. The optimization is lossless, maintaining the accuracy of GNN. It can remove 98-100\% violations of the N:M sparse patterns at the vector level, and increase the proportion of conforming graphs in SuiteSparse collection from 5-9\% to 88.7-93.5\%. On A100 GPUs, the optimization accelerates Sparse Matrix Matrix (SpMM) by up to 43X (2.3X -- 7.5X on average) and speeds up the key graph operations in GNNs on real graphs by as much as 8.6X (3.5X on average).

artificial intelligence, graph neural networks↗
DOE OSTI2026

Sparsity Applications for Gradient‐Based Optimization of Wind Farms

Optimizing wind farms is essential for designing efficient energy systems, especially as farms grow larger and span multiple sites. However, this optimization becomes increasingly challenging due to the rising computational cost associated with more turbines. Gradient‐based optimization methods scale better than gradient‐free approaches for large problems, but the most computationally expensive component remains the calculation of gradients for the objective function and constraint Jacobians. To address this, we propose leveraging sparsity to accelerate gradient evaluations and reduce the size of the constraint Jacobian. Wind farms naturally exhibit sparsity—many turbines do not influence each other under certain wind directions. However, unlike traditional sparse problems with fixed patterns, wind farm sparsity is dynamic, requiring new strategies to handle changing interactions efficiently. This paper presents a study of sparsity in wind farm optimization and introduces several methods to exploit it. These strategies are tested on multiple farms using the analytic Cumulative Curl model, with gradients computed via automatic differentiation (AD). The same sparsity‐aware techniques are also applicable to finite difference (FD) methods, where they can yield even greater speedups due to the high cost of directional evaluations. Results show that sparse methods achieve up to a 10x speedup with less than ± 5% variance in optimized wake losses compared to traditional methods. These findings suggest that sparsity‐aware optimization not only maintains solution quality but also scales efficiently with farm size, enabling more comprehensive design exploration at reduced computational cost.

17 WIND ENERGY↗
DOE OSTI2015

Group‐sparsity regularization for ill‐posed subsurface flow inverse problems

Abstract Sparse representations provide a flexible and parsimonious description of high‐dimensional model parameters for reconstructing subsurface flow property distributions from limited data. To further constrain ill‐posed inverse problems, group‐sparsity regularization can take advantage of possible relations among the entries of unknown sparse parameters when: (i) groups of sparse elements are either collectively active or inactive and (ii) only a small subset of the groups is needed to approximate the parameters of interest. Since subsurface properties exhibit strong spatial connectivity patterns they may lead to sparse descriptions that satisfy the above conditions. When these conditions are established, a group‐sparsity regularization can be invoked to facilitate the solution of the resulting inverse problem by promoting sparsity across the groups. The proposed regularization penalizes the number of groups that are active without promoting sparsity within each group. Two implementations are presented in this paper: one based on the multiresolution tree structure of Wavelet decomposition, without a need for explicit prior models, and another learned from explicit prior model realizations using sparse principal component analysis (SPCA). In each case, the approach first classifies the parameters of the inverse problem into groups with specific connectivity features, and then takes advantage of the grouped structure to recover the relevant patterns in the solution from the flow data. Several numerical experiments are presented to demonstrate the advantages of additional constraining power of group‐sparsity in solving ill‐posed subsurface model calibration problems.

Golmohammadi, Azarang↗
DOE OSTI2023

Sparsity of the electron repulsion integral tensor using different localized virtual orbital representations in local second-order Møller–Plesset theory

Utilizing localized orbitals, local correlation theory can reduce the unphysically high system-size scaling of post-Hartree–Fock (post-HF) methods to linear scaling in insulating molecules. The sparsity of the four-index electron repulsion integral (ERI) tensor is central to achieving this reduction. For second-order Møller–Plesset theory (MP2), one of the simplest post-HF methods, only the (ia|jb) ERIs are needed, coupling occupied orbitals i, j and virtuals a, b. In this paper, we compare the numerical sparsity (called the “ragged list”) and two other approaches revealing the low-rank sparsity of the ERI. The ragged list requires only one set of (localized) virtual orbitals, and we find that the orthogonal valence virtual-hard virtual set of virtuals originally proposed by Subotnik et al. gives the sparsest ERI tensor. To further compress the ERI tensor, the pair natural orbital (PNO) type representation uses different sets of virtual orbitals for different occupied orbital pairs, while the occupied-specific virtual (OSV) approach uses different virtuals for each occupied orbital. Here, our results indicate that while the low-rank PNO representation achieves significant rank reduction, it also requires more memory than the ragged list. The OSV approach requires similar memory to that of the ragged list, but it involves greater algorithmic complexity. An approximation (called the “fixed sparsity pattern”) for solving the local MP2 equations using the numerically sparse ERI tensor is proposed and tested to be sufficiently accurate and to have highly controllable error. A low-scaling local MP2 algorithm based on the ragged list and the fixed sparsity pattern is therefore promising.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

SU-E-T-446: Group-Sparsity Based Angle Generation Method for Beam Angle Optimization

Purpose: This work is to develop the effective algorithm for beam angle optimization (BAO), with the emphasis on enabling further improvement from existing treatment-dependent templates based on clinical knowledge and experience. Methods: The proposed BAO algorithm utilizes a priori beam angle templates as the initial guess, and iteratively generates angular updates for this initial set, namely angle generation method, with improved dose conformality that is quantitatively measured by the objective function. That is, during each iteration, we select “the test angle” in the initial set, and use group-sparsity based fluence map optimization to identify “the candidate angle” for updating “the test angle”, for which all the angles in the initial set except “the test angle”, namely “the fixed set”, are set free, i.e., with no group-sparsity penalty, and the rest of angles including “the test angle” during this iteration are in “the working set”. And then “the candidate angle” is selected with the smallest objective function value from the angles in “the working set” with locally maximal group sparsity, and replaces “the test angle” if “the fixed set” with “the candidate angle” has a smaller objective function value by solving the standard fluence map optimization (with no group-sparsity regularization). Similarly other angles in the initial set are in turn selected as “the test angle” for angular updates and this chain of updates is iterated until no further new angular update is identified for a full loop. Results: The tests using the MGH public prostate dataset demonstrated the effectiveness of the proposed BAO algorithm. For example, the optimized angular set from the proposed BAO algorithm was better the MGH template. Conclusion: A new BAO algorithm is proposed based on the angle generation method via group sparsity, with improved dose conformality from the given template. Hao Gao was partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000) and the Shanghai Pujiang Talent Program (#14PJ1404500)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Two-level structural sparsity regularization for identifying lattices and defects in noisy images

Here, this paper presents a regularized regression model with a two-level structural sparsity penalty applied to locate individual atoms in a noisy scanning transmission electron microscopy image (STEM). In crystals, the locations of atoms is symmetric, condensed into a few lattice groups. Therefore, by identifying the underlying lattice in a given image, individual atoms can be accurately located. We propose to formulate the identification of the lattice groups as a sparse group selection problem. Furthermore, real atomic scale images contain defects and vacancies, so atomic identification based solely on a lattice group may result in false positives and false negatives. To minimize error, model includes an individual sparsity regularization in addition to the group sparsity for a within-group selection, which results in a regression model with a two-level sparsity regularization. We propose a modification of the group orthogonal matching pursuit (gOMP) algorithm with a thresholding step to solve the atom finding problem. The convergence and statistical analyses of the proposed algorithm are presented. The proposed algorithm is also evaluated through numerical experiments with simulated images. The applicability of the algorithm on determination of atom structures and identification of imaging distortions and atomic defects was demonstrated using three real STEM images. In conclusion, we believe this is an important step toward automatic phase identification and assignment with the advent of genomic databases for materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Exact Gaussian processes for massive datasets via non-stationary sparsity-discovering kernels

Abstract A Gaussian Process (GP) is a prominent mathematical framework for stochastic function approximation in science and engineering applications. Its success is largely attributed to the GP’s analytical tractability, robustness, and natural inclusion of uncertainty quantification. Unfortunately, the use of exact GPs is prohibitively expensive for large datasets due to their unfavorable numerical complexity of $$O(N^3)$$ O ( N 3 ) in computation and $$O(N^2)$$ O ( N 2 ) in storage. All existing methods addressing this issue utilize some form of approximation—usually considering subsets of the full dataset or finding representative pseudo-points that render the covariance matrix well-structured and sparse. These approximate methods can lead to inaccuracies in function approximations and often limit the user’s flexibility in designing expressive kernels. Instead of inducing sparsity via data-point geometry and structure, we propose to take advantage of naturally-occurring sparsity by allowing the kernel to discover—instead of induce—sparse structure. The premise of this paper is that the data sets and physical processes modeled by GPs often exhibit natural or implicit sparsities, but commonly-used kernels do not allow us to exploit such sparsity. The core concept of exact, and at the same time sparse GPs relies on kernel definitions that provide enough flexibility to learn and encode not only non-zero but also zero covariances. This principle of ultra-flexible, compactly-supported, and non-stationary kernels, combined with HPC and constrained optimization, lets us scale exact GPs well beyond 5 million data points.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Resolution enhancement of lung 4D-CT via group-sparsity

Purpose: 4D-CT typically delivers more accurate information about anatomical structures in the lung, over 3D-CT, due to its ability to capture visual information of the lung motion across different respiratory phases. This helps to better determine the dose during radiation therapy for lung cancer. However, a critical concern with 4D-CT that substantially compromises this advantage is the low superior-inferior resolution due to less number of acquired slices, in order to control the CT radiation dose. To address this limitation, the authors propose an approach to reconstruct missing intermediate slices, so as to improve the superior-inferior resolution.Methods: In this method the authors exploit the observation that sampling information across respiratory phases in 4D-CT can be complimentary due to lung motion. The authors’ approach uses this locally complimentary information across phases in a patch-based sparse-representation framework. Moreover, unlike some recent approaches that treat local patches independently, the authors’ approach employs the group-sparsity framework that imposes neighborhood and similarity constraints between patches. This helps in mitigating the trade-off between noise robustness and structure preservation, which is an important consideration in resolution enhancement. The authors discuss the regularizing ability of group-sparsity, which helps in reducing the effect of noise and enables better structural localization and enhancement.Results: The authors perform extensive experiments on the publicly available DIR-Lab Lung 4D-CT dataset [R. Castillo, E. Castillo, R. Guerra, V. Johnson, T. McPhail, A. Garg, and T. Guerrero, “A framework for evaluation of deformable image registration spatial accuracy using large landmark point sets,” Phys. Med. Biol. 54, 1849–1870 (2009)]. First, the authors carry out empirical parametric analysis of some important parameters in their approach. The authors then demonstrate, qualitatively as well as quantitatively, the ability of their approach to achieve more accurate and better localized results over bicubic interpolation as well as a related state-of-the-art approach. The authors also show results on some datasets with tumor, to further emphasize the clinical importance of their method.Conclusions: The authors have proposed to improve the superior-inferior resolution of 4D-CT by estimating intermediate slices. The authors’ approach exploits neighboring constraints in the group-sparsity framework, toward the goal of achieving better localization and noise robustness. The authors’ results are encouraging, and positively demonstrate the role of group-sparsity for 4D-CT resolution enhancement.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

TH-EF-BRB-05: 4pi Non-Coplanar IMRT Beam Angle Selection by Convex Optimization with Group Sparsity Penalty

Purpose: Integrated beam orientation and fluence map optimization is expected to be the foundation of robust automated planning but existing heuristic methods do not promise global optimality. We aim to develop a new method for beam angle selection in 4π non-coplanar IMRT systems based on solving (globally) a single convex optimization problem, and to demonstrate the effectiveness of the method by comparison with a state of the art column generation method for 4π beam angle selection. Methods: The beam angle selection problem is formulated as a large scale convex fluence map optimization problem with an additional group sparsity term that encourages most candidate beams to be inactive. The optimization problem is solved using an accelerated first-order method, the Fast Iterative Shrinkage-Thresholding Algorithm (FISTA). The beam angle selection and fluence map optimization algorithm is used to create non-coplanar 4π treatment plans for several cases (including head and neck, lung, and prostate cases) and the resulting treatment plans are compared with 4π treatment plans created using the column generation algorithm. Results: In our experiments the treatment plans created using the group sparsity method meet or exceed the dosimetric quality of plans created using the column generation algorithm, which was shown superior to clinical plans. Moreover, the group sparsity approach converges in about 3 minutes in these cases, as compared with runtimes of a few hours for the column generation method. Conclusion: This work demonstrates the first non-greedy approach to non-coplanar beam angle selection, based on convex optimization, for 4π IMRT systems. The method given here improves both treatment plan quality and runtime as compared with a state of the art column generation algorithm. When the group sparsity term is set to zero, we obtain an excellent method for fluence map optimization, useful when beam angles have already been selected. NIH R43CA183390, NIH R01CA188300, Varian Medical Systems; Part of this research took place while D. O’Connor was a summer intern at RefleXion Medical.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Sparsity for Gradient-Based Optimization of Wind Farm Layouts

Optimizing wind farm layouts is an important step in designing an efficient wind farm. Optimizing wind farm layouts is also a difficult task due to computation times increasing with the number of turbines present in the farm. The most computationally expensive part of gradient-based optimization is calculating the gradient. In order to reduce the expense of gradient calculation, we performed a study on the use of sparsity in wind farm layout optimization. This paper presents the findings of the sparsity study and provides a method to use sparsity in wind farm layout optimization. We tested this sparsity method by optimizing multiple farms with sparse methods and compared the results to optimizations of the same farms using traditional methods. By using the sparse method to optimize multiple farms, we found that the objective results were comparable between sparse and traditional methods and that sparse methods were 4 times faster than traditional methods on average. We expect more speedups with improved methodology and larger wind farms. By using sparse methods, it is possible to solve the wind farm layout optimization problem more efficiently, thus allowing for a more thorough study of the wind farm layout design space without excessive computational costs. Further work is required to refine the method and prepare for testing on real-world wind farm layout applications.

gradient↗
DOE OSTI2017

Adaptive OFDM Waveform Design for Spatio-Temporal-Sparsity Exploited STAP Radar

In this chapter, we describe a sparsity-based space-time adaptive processing (STAP) algorithm to detect a slowly moving target using an orthogonal frequency division multiplexing (OFDM) radar. The motivation of employing an OFDM signal is that it improves the target-detectability from the interfering signals by increasing the frequency diversity of the system. However, due to the addition of one extra dimension in terms of frequency, the adaptive degrees-of-freedom in an OFDM-STAP also increases. Therefore, to avoid the construction a fully adaptive OFDM-STAP, we develop a sparsity-based STAP algorithm. We observe that the interference spectrum is inherently sparse in the spatio-temporal domain, as the clutter responses occupy only a diagonal ridge on the spatio-temporal plane and the jammer signals interfere only from a few spatial directions. Hence, we exploit that sparsity to develop an efficient STAP technique that utilizes considerably lesser number of secondary data compared to the other existing STAP techniques, and produces nearly optimum STAP performance. In addition to designing the STAP filter, we optimally design the transmit OFDM signals by maximizing the output signal-to-interference-plus-noise ratio (SINR) in order to improve the STAP performance. The computation of output SINR depends on the estimated value of the interference covariance matrix, which we obtain by applying the sparse recovery algorithm. Therefore, we analytically assess the effects of the synthesized OFDM coefficients on the sparse recovery of the interference covariance matrix by computing the coherence measure of the sparse measurement matrix. Our numerical examples demonstrate the achieved STAP-performance due to sparsity-based technique and adaptive waveform design.

Sen, Satyabrata↗
DOE OSTI2024

Jacobian sparsity detection using Bloom filters

Determining Jacobian sparsity structure is an important step in the efficient computation of sparse Jacobians. We introduce a new method for determining Jacobian sparsity patterns by combining bit vector probing with Bloom filters. In conclusion, we further refine Bloom filter probing by combining it with hierarchical probing to yield a highly effective strategy for Jacobian sparsity pattern determination.

Bloom filter↗
DOE OSTI2016

Sparsity Prior Computed Tomography Reconstruction Using a Nonstandard Simultaneous X-ray Acquisition Model

In this article we systematically evaluate the performance of several state-of-the-art, sparsity prior computed tomography (CT) reconstruction algorithms, using a nonstandard simultaneous x-ray acquisition method. Sparsity prior is an efficient strategy in CT reconstruction, relying on iterative algorithms such as the algebraic reconstruction technique to produce a crude reconstruction, based on which sparse approximation is performed. The simultaneous x-ray acquisition model ensures rapid capture of x-rays; however, it captures a significantly fewer number of attenuation measurements, and the projections are nonuniform. We propose a weighted average filter in the reconstruction framework to ensure better quality reconstruction by minimizing the effect of nonuniform projections. The performance of the state-of-the-art algorithms is analyzed with and without weighted averaging before sparse approximation, in simulated and real environments. Experiments in the simulated environment are conducted with and without the presence of noise. From the results, it is evident that sparsity prior algorithms are capable of producing cross-sectional reconstruction using the simultaneous x-ray acquisition model, and better reconstruction quality is achievable with the incorporation of weighted averaging in the reconstruction framework.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

SU-G-IeP1-13: Sub-Nyquist Dynamic MRI Via Prior Rank, Intensity and Sparsity Model (PRISM)

Purpose: Accelerated dynamic MRI is important for MRI guided radiotherapy. Inspired by compressive sensing (CS), sub-Nyquist dynamic MRI has been an active research area, i.e., sparse sampling in k-t space for accelerated dynamic MRI. This work is to investigate sub-Nyquist dynamic MRI via a previously developed CS model, namely Prior Rank, Intensity and Sparsity Model (PRISM). Methods: The proposed method utilizes PRISM with rank minimization and incoherent sampling patterns for sub-Nyquist reconstruction. In PRISM, the low-rank background image, which is automatically calculated by rank minimization, is excluded from the L1 minimization step of the CS reconstruction to further sparsify the residual image, thus allowing for higher acceleration rates. Furthermore, the sampling pattern in k-t space is made more incoherent by sampling a different set of k-space points at different temporal frames. Results: Reconstruction results from L1-sparsity method and PRISM method with 30% undersampled data and 15% undersampled data are compared to demonstrate the power of PRISM for dynamic MRI. Conclusion: A sub- Nyquist MRI reconstruction method based on PRISM is developed with improved image quality from the L1-sparsity method.

60 APPLIED LIFE SCIENCES↗