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DOE OSTI2019

A sparse Gaussian sigmoid basis function approximation of hyperspectral data for detection of solids

We define a new characterization of emissivity and reflectance curves for compositional exploitation of hyperspectral data. Here, our method decomposes each spectrum into a sparse set of Gaussian sigmoid components using penalized regression. Detection is based on the combination of Gaussian sigmoid components unique to a target material. Focusing on the presence of spectral upslopes and downslopes rather than spectral correlations makes detection more robust to both target variation and spectral variability from atmosphere and background encountered during the collection process. We present simulation studies that demonstrate the potential to reduce false positive rates without compromising sensitivity. Characterization of long–wave infrared (LWIR) experimental data validates our method using minerals of different particle sizes, measurement angles, and collection conditions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

powersqueeze

powersqueeze (psqz) is a truncated power iteration library intended for high-performance computing platforms. psqz efficiently produces low-dimensional, linear measurements of graph matrix spectra by combining classical power iteration with sparse Johnson-Lindenstrauss transforms. psqz is intended to produce high-quality, fast, data-oblivious low-dimensional representations of high-dimensional sparse data such as graphs and term-document matrices. psqz is intended to replace similar workflows that depend on directly approximating a truncated eigendecomposition (e.g., the first step of spectral clustering), which is a much more expensive operation.

Priest, BenjaminW [Lawrence Livermore National Lab↗

DOE OSTI2022

Phase curves of small bodies from the SLOAN Moving Objects Catalog

Extensive photometric surveys continue to produce enormous stores of data on small bodies. These data are typically sparsely obtained at arbitrary (or unknown) rotational phases. Therefore, new methods for processing such data need to be developed to make the most of these vast catalogs. We aim to produce a method of recreating the phase curves of small bodies by considering the uncertainties introduced by the nominal errors in the magnitudes and the effect introduced by rotational variations. Here, we use the SLOAN Moving Objects Catalog data as a benchmark to construct phase curves of all small bodies in u', g', r', i', and z' filters. From the phase curves, we obtain the absolute magnitudes and we use them to set up the absolute colors, which are the colors of the asteroids that are not affected by changes in the phase angle. We selected objects with ≥3 observations taken in at least one filter and spanning over a minimum of 5 degrees in the phase angle. We developed a method that combines Monte Carlo simulations and Bayesian inference to estimate the absolute magnitudes using the HG 12 * photometric system. We obtained almost 15 000 phase curves, with about 12 000 of these including all five filters. The absolute magnitudes and absolute colors are compatible with previously published data that support our method. The method we developed is fully automatic and well suited for a run based on large amounts of data. Moreover, it includes the nominal uncertainties in the magnitudes and the whole distribution of possible rotational states of the objects producing what are possibly less precise values, that is, larger uncertainties, but more accurate, namely, closer to the actual value. To our knowledge, this work is the first to include the effect of rotational variations in such a manner.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

Compact video content representation for video coding using low multi-linear tensor rank approximation with dynamic core tensor order

Tensor is a multi-way representation of an entity that is widely used in many applications of mathematics and physics. The wide range of tensor algebra operations attract the researchers of graphical and vision field to identify unique methods for various applications such as segmentation, compression, indexing and so on. In this paper, low multi-linear rank approximation of a tensor is used for decomposition so as to perform compression on a video that is represented as a 4D tensor. Thus, the encoder has blocks for (1) multilinear rank approximation method so as to aid decomposition, (2) sparsity removal of residual data to reduce the required memory storage to a small level, (3) quantization on the sparse less residual data and (4) LZ77 dictionary coding for the video. The decoder uses a tensor reconstruction block along with residual error correction block that reduces loss/error in the reconstructed video. The size of core tensor is an important factor in rank approximation. It is identified at run time depending on the video contents. This size is determined adaptively using Tikhonov’s regularization method. The best value of core tensor size is identified with the corner of L-curve which preserves the video contents from heavy loss/error. Experimental results of the proposed work on comparison with H.264/AVC compression method indicate that the proposed method achieves up to 10% improvement in compression ratio with the least amount of loss and a maximum signal to noise ratio of 0.14. The proposed system gives better compression ratio than H.265 for videos with more number of frames without compromising quality.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implements sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Fast 2D Bicephalous Convolutional Autoencoder for Compressing 3D Time Projection Chamber Data

High-energy large-scale particle colliders produce data at high speed in the order of 1 terabytes per second in nuclear physics and petabytes per second in high energy physics. Developing real-time data compression algorithms to reduce such data at high throughput to fit permanent storage has drawn increasing attention. Specifically, at the newly constructed sPHENIX experiment at the Relativistic Heavy Ion Collider (RHIC), a time projection chamber is used as the main tracking detector, which records particle trajectories in a volume of three-dimensional (3D) cylinder. The resulting data are usually very sparse with occupancy around 10.8%. Such sparsity presents a challenge to conventional learning-free lossy compression algorithms, such as SZ, ZFP, and MGARD. The 3D convolutional neural network (CNN)-based approach, Bicephalous Convolutional Autoencoder (BCAE), outperforms traditional methods both in compression rate and reconstruction accuracy. BCAE can also utilize the computation power of graphical processing units suitable for deployment in a modern heterogeneous highperformance computing environment. This work introduces two BCAE variants: BCAE++ and BCAE-2D. BCAE++ achieves a 15% better compression ratio and a 77% better reconstruction accuracy measured in mean absolute error compared with BCAE. BCAE-2D treats the radial direction as the channel dimension of an image, resulting in a 3× speedup in compression throughput. In addition, we demonstrate an unbalanced autoencoder with a larger decoder can improve reconstruction accuracy without significantly sacrificing throughput. Lastly, we observe both the BCAE++ and BCAE-2D can benefit more from using half-precision mode in throughput (76 - 79% increase) without loss in reconstruction accuracy. The source code and links to data and pretrained models can be found at https://github.com/BNL-DAQ-LDRD/NeuralCompression_v2

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks

Studies of microbial communities by targeted sequencing of rRNA genes lead to recovering numerous rare low-abundance taxa with unknown biological roles. We propose to study associations of such rare organisms with their environments by a computational framework based on transformation of the data into qualitative variables. Namely, we analyze the sparse table of putative species or OTUs (operational taxonomic units) and samples generated in such studies, also known as an OTU table, by collecting statistics on co-occurrences of the species and on shared species richness across samples. Based on the statistics we built two association networks, of the rare putative species and of the samples respectively, using a known computational technique, Association networks (Anets) developed for analysis of qualitative data. Clusters of samples and clusters of OTUs are then integrated and combined with metadata of the study to produce a map of associated putative species in their environments. We tested and validated the framework on two types of microbiomes, of human body sites and that of the Populus tree root systems. We show that in both studies the associations of OTUs can separate samples according to environmental or physiological characteristics of the studied systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication

Writing large amounts of data concurrently to stable storage is a typical I/O pattern of many HPC workflows. This pattern introduces high I/O overheads and results in increased storage space utilization especially for workflows that need to capture the evolution of data structures with high frequency as checkpoints. In this context, many applications, such as graph pattern matching, perform sparse updates to large data structures between checkpoints. For these applications, incremental checkpointing techniques that save only the differences from one checkpoint to another can dramatically reduce the checkpoint sizes, I/O bottlenecks, and storage space utilization. However, such techniques are not without challenges: it is non-trivial to transparently determine what data has changed since a previous checkpoint and assemble the differences in a compact fashion that does not result in excessive metadata. State-of-art data reduction techniques (e.g., compression and de-duplication) have significant limitations when applied to modern HPC applications that leverage GPUs: slow at detecting the differences, generate a large amount of metadata to keep track of the differences, and ignore crucial spatiotemporal checkpoint data redundancy. This paper addresses these challenges by proposing a Merkle tree-based incremental checkpointing method to exploit GPUs' high memory bandwidth and massive parallelism. Experimental results at scale show a significant reduction of the I/O overhead and space utilization of checkpointing compared with state-of-the-art incremental checkpointing and compression techniques.

Tan, Nigel↗

DOE OSTI2018

Sparse modeling of space- and time-varying diffraction response of a progressively loaded aluminum alloy

Highlights: • Plasticity induces crystal orientation and lattice spacing heterogeneity. • High energy x-ray diffraction spot broadening typically accompanies plasticity. • Method quantifies spot broadening in difficult, mixed microstructure data. • Algorithm finds sparse combination of entries from dictionary of peak functions. • Approach showed asymmetric plastic response in preprocessed AA7075 T651 sample. - Abstract: High energy X-ray diffraction data collected in situ during loading experiments permits probing of the crystal structure of a plastically deforming material sample. An elastoplastic deformation is associated with heterogeneity in both crystal orientation and lattice spacing—each manifesting as azimuthal broadening and radial broadening of diffraction peaks respectively. Quantifying the spreading effect is challenging, especially in cases where the sample has a granularity between that of a single crystal and fine grain or powder material. The approach developed in this paper begins by modeling the intensity signal in the vicinity of a Debye-Scherrer ring as a sparse, nonnegative superposition of Gaussian basis functions drawn from an over-complete dictionary. Processing automatically selects from the dictionary basis functions whose widths and amplitudes are representative of the data. The chosen basis functions are used to compute scalar measures of radial and azimuthal broadening for the set of diffraction peaks composing a Debye-Scherrer ring. To demonstrate the utility of the approach, we show that analysis of diffraction peak shape information from an aluminum alloy 7075 T651 (AA7075 T651) sample provides insight into the origin of material state that would have otherwise have been difficult if not impossible to extract using conventional methods. Furthermore, the extracted information revealed a deformation response linked to the processing history of the sample.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network

Abstract Single-cell RNA sequencing (scRNA-seq) permits researchers to study the complex mechanisms of cell heterogeneity and diversity. Unsupervised clustering is of central importance for the analysis of the scRNA-seq data, as it can be used to identify putative cell types. However, due to noise impacts, high dimensionality and pervasive dropout events, clustering analysis of scRNA-seq data remains a computational challenge. Here, we propose a new deep structural clustering method for scRNA-seq data, named scDSC, which integrate the structural information into deep clustering of single cells. The proposed scDSC consists of a Zero-Inflated Negative Binomial (ZINB) model-based autoencoder, a graph neural network (GNN) module and a mutual-supervised module. To learn the data representation from the sparse and zero-inflated scRNA-seq data, we add a ZINB model to the basic autoencoder. The GNN module is introduced to capture the structural information among cells. By joining the ZINB-based autoencoder with the GNN module, the model transfers the data representation learned by autoencoder to the corresponding GNN layer. Furthermore, we adopt a mutual supervised strategy to unify these two different deep neural architectures and to guide the clustering task. Extensive experimental results on six real scRNA-seq datasets demonstrate that scDSC outperforms state-of-the-art methods in terms of clustering accuracy and scalability. Our method scDSC is implemented in Python using the Pytorch machine-learning library, and it is freely available at https://github.com/DHUDBlab/scDSC.

Gan, Yanglan↗

DOE OSTI2019

Software Defined Architectures for Data Analytics

Data analytics applications increasingly are complex workflows composed of phases with very different program behaviors (e.g., graph algorithms and machine learning, algorithms operating on sparse an dense data structures, etc). To reach the levels of efficiency required to process these workflows in real time, upcoming architectures will need to leverage even more workload specialization. If, at one end, we may find even more heterogenous processors composed by a myriad of specialized processing elements, at the other end we may see novel reconfigurable architectures, composed of sets of functional units and memories interconnected with (re)configurable on-chip networks, able to adapt dynamically to adapt the workload characteristics. Field Programmable Gate Arrays are more and more used for accelerating various workloads and, in particular, inferencing in machine learning, providing higher efficiency than other solutions. However, their fine grained nature still leads to issues for the design software and still makes dynamic reconfiguration impractical. Future, more coarse-grained architectures could offer the features to execute diverse workloads at high efficiency while providing better reconfiguration mechanisms for dynamic adaptability. Nevertheless, we argue that the challenges for reconfigurable computing remain in the software. In this position paper, we describe a possible toolchain for reconfigurable architectures targeted at data analytics.

FPGA, Dataflow, Reconfigurable Architectures, Soft↗

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

Prong Segmentation using Point Set Transformers in Multiple View Neutrino Detectors

NOvA is a long-baseline neutrino experiment studying neutrino oscillations by detecting neutrinos from the NuMI beam at Fermilab. Its physics analysis relies on accurate prong segmentation, which involves matching each hit to its source particle and identifying the particle type. This task has commonly been addressed using a combination of traditional clustering algorithms and convolutional neural networks (CNNs). However, NOvA’s detector design presents data as two sparse and decoupled 2D images (XZ and YZ views) rather than a native 3D representation, posing a significant challenge for traditional CNN-based models. In this talk, we propose a novel neural network based on the Point Set Transformer. By treating detector hits as sparse point clouds and implementing a cross-view attention mechanism, our model enables efficient information mixing between both views. Evaluated on NOvA simulated data, our model achieves superior accuracy while requiring significantly fewer computational resources compared to other models. Furthermore, the model demonstrates great performance when applied to Liquid Argon Time Projection Chamber (LArTPC) data, which shows its potential as a universal prong segmentation algorithm for multiple view neutrino detectors.

Liu, Jiaxi [UC, Irvine]↗

DOE OSTI2022

Poisson hurdle model-based method for clustering microbiome features

Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Physics-based shape matching for intraoperative image guidance

Purpose: Soft-tissue deformations can severely degrade the validity of preoperative planning data during computer assisted interventions. Intraoperative imaging such as stereo endoscopic, time-of-flight or, laser range scanner data can be used to compensate these movements. In this context, the intraoperative surface has to be matched to the preoperative model. The shape matching is especially challenging in the intraoperative setting due to noisy sensor data, only partially visible surfaces, ambiguous shape descriptors, and real-time requirements. Methods: A novel physics-based shape matching (PBSM) approach to register intraoperatively acquired surface meshes to preoperative planning data is proposed. The key idea of the method is to describe the nonrigid registration process as an electrostatic–elastic problem, where an elastic body (preoperative model) that is electrically charged slides into an oppositely charged rigid shape (intraoperative surface). It is shown that the corresponding energy functional can be efficiently solved using the finite element (FE) method. It is also demonstrated how PBSM can be combined with rigid registration schemes for robust nonrigid registration of arbitrarily aligned surfaces. Furthermore, it is shown how the approach can be combined with landmark based methods and outline its application to image guidance in laparoscopic interventions. Results: A profound analysis of the PBSM scheme based on in silico and phantom data is presented. Simulation studies on several liver models show that the approach is robust to the initial rigid registration and to parameter variations. The studies also reveal that the method achieves submillimeter registration accuracy (mean error between 0.32 and 0.46 mm). An unoptimized, single core implementation of the approach achieves near real-time performance (2 TPS, 7–19 s total registration time). It outperforms established methods in terms of speed and accuracy. Furthermore, it is shown that the method is able to accurately match partial surfaces. Finally, a phantom experiment demonstrates how the method can be combined with stereo endoscopic imaging to provide nonrigid registration during laparoscopic interventions. Conclusions: The PBSM approach for surface matching is fast, robust, and accurate. As the technique is based on a preoperative volumetric FE model, it naturally recovers the position of volumetric structures (e.g., tumors and vessels). It cannot only be used to recover soft-tissue deformations from intraoperative surface models but can also be combined with landmark data from volumetric imaging. In addition to applications in laparoscopic surgery, the method might prove useful in other areas that require soft-tissue registration from sparse intraoperative sensor data (e.g., radiation therapy)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

A Comparative Study of Multi-material Data Structures for Computational Physics Applications

The data structures used to represent the multi-material state of a computational physics application can have a drastic impact on the performance of the application. We look at efficient data structures for sparse applications where there may be many materials, but only one or few in most computational cells. We develop simple performance models for use in selecting possible data structures and programming patterns. We verify the analytic models of performance through a small test program of the representative cases.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Discrete Regularization for Calibration of Geologic Facies Against Dynamic Flow Data

Abstract Subsurface flow model calibration involves many more unknowns than measurements, leading to ill‐posed problems with nonunique solutions. To alleviate nonuniqueness, the problem is regularized by constraining the solution space using prior knowledge. In certain sedimentary environments, such as fluvial systems, the contrast in hydraulic properties of different facies types tends to dominate the flow and transport behavior, making the effect of within facies heterogeneity less significant. Hence, flow model calibration in those formations reduces to delineating the spatial structure and connectivity of different lithofacies types and their boundaries. A major difficulty in calibrating such models is honoring the discrete, or piecewise constant, nature of facies distribution. The problem becomes more challenging when complex spatial connectivity patterns with higher‐order statistics are involved. This paper introduces a novel formulation for calibration of complex geologic facies by imposing appropriate constraints to recover plausible solutions that honor the spatial connectivity and discreteness of facies models. To incorporate prior connectivity patterns, plausible geologic features are learned from available training models. This is achieved by learning spatial patterns from training data, e.g., ‐SVD sparse learning or the traditional Principal Component Analysis. Discrete regularization is introduced as a penalty functions to impose solution discreteness while minimizing the mismatch between observed and predicted data. An efficient gradient‐based alternating directions algorithm is combined with variable splitting to minimize the resulting regularized nonlinear least squares objective function. Numerical results show that imposing learned facies connectivity and discreteness as regularization functions leads to geologically consistent solutions that improve facies calibration quality.

Khaninezhad, Mohammad‐Reza↗

DOE OSTI2026

Machine Learning Based Metamodel for Faster Life Cycle Assessment of Large Portfolio of Buildings

Managing a large portfolio of buildings involves decisions on reuse, retrofit, renovation, rehabilitation, and new construction, influenced by trade-offs between performance metrics such as cost, time, and operational flexibility over the building's life cycle. Traditional life cycle assessment tools for evaluating these metrics can be labor- and compute-intensive, requiring extensive data and modeling for each building. Metamodels (or surrogate models) using machine learning have been explored as faster alternatives, but training these models has been hindered by the limited availability of comprehensive data on key life cycle metrics. Recent advancements in machine learning, particularly deep learning techniques like zero-shot and few-shot learning, allow models to learn from sparse or limited data. We propose a machine learning-based metamodel that leverages these techniques for rapid estimation of key building life cycle metrics. This presentation will cover the model architecture, data collection, training, and validation processes, along with an ongoing case study applied to a large portfolio of buildings. We will discuss the model's performance in terms of accuracy, compute time, limitations, and its potential for expanding to additional life cycle metrics. This data-driven approach offers a promising direction for the rapid evaluation of large building portfolios.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗