Reordering of Genomic Data for Improved Compression-Based Inference.
Abstract not provided.
Caswell, Jacob↗
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Results for “data compression”
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Reordering of Genomic Data for Improved Compression-Based Inference.
Abstract not provided.
Gooding, Renee Lynne↗
STZ: A High Quality and High Speed Streaming Lossy Compression Framework for Scientific Data
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97 MATHEMATICS AND COMPUTING↗
The compression–error trade-off for large gridded data sets
The netCDF-4 format is widely used for large gridded scientific data sets and includes several compression methods: lossy linear scaling and the non-lossy deflate and shuffle algorithms. Many multidimensional geoscientific data sets exhibit considerable variation over one or several spatial dimensions (e.g., vertically) with less variation in the remaining dimensions (e.g., horizontally). On such data sets, linear scaling with a single pair of scale and offset parameters often entails considerable loss of precision. We introduce an alternative compression method called "layer-packing" that simultaneously exploits lossy linear scaling and lossless compression. Layer-packing stores arrays (instead of a scalar pair) of scale and offset parameters. An implementation of this method is compared with lossless compression, storing data at fixed relative precision (bit-grooming) and scalar linear packing in terms of compression ratio, accuracy and speed. When viewed as a trade-off between compression and error, layer-packing yields similar results to bit-grooming (storing between 3 and 4 significant figures). Bit-grooming and layer-packing offer significantly better control of precision than scalar linear packing. Relative performance, in terms of compression and errors, of bit-groomed and layer-packed data were strongly predicted by the entropy of the exponent array, and lossless compression was well predicted by entropy of the original data array. Layer-packed data files must be "unpacked" to be readily usable. The compression and precision characteristics make layer-packing a competitive archive format for many scientific data sets.
58 GEOSCIENCES↗
Verification of conventional equations of state for tantalum under quasi-isentropic compression
Shock Hugoniot data have been widely used to calibrate analytic equations of state (EOSs) of condensed matter at high pressures. However, the suitability of particular analytic EOSs under off-Hugoniot states has not been sufficiently verified using experimental data. We have conducted quasi-isentropic compression experiments (ICEs) of tantalum using the compact pulsed power generator CQ-4, and explored the relation of longitudinal stress versus volume of tantalum under quasi-isentropic compression using backward integration and characteristic inverse methods. By subtracting the deviatoric stress and additional pressure caused by irreversible plastic dissipation, the isentropic pressure can be extracted from the longitudinal stress. Several theoretical isentropes are deduced from analytic EOSs and compared with ICE results to validate the suitability of these analytic EOSs in isentropic compression states. The comparisons show that the Gruneisen EOS with Gruneisen Gamma proportional to volume is accurate, regardless whether the Hugoniot or isentrope is used as the reference line. The Vinet EOS yields better accuracy in isentropic compression states. Theoretical isentropes derived from Tillotson, PUFF, and Birch-Murnaghan EOSs well agree with the experimental isentrope in the range of 0–100 GPa, but deviate gradually with pressure increasing further.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Analyzing acoustic emission data to identify cracking modes in cement paste using an artificial neural network
This research is focused on the identification of cracking mechanisms for cement paste using acoustic emission data, recorded from compression and notched four-point bending tests. A procedure is developed for analyzing the data by employing an agglomerative hierarchical clustering method, an artificial neural network, and a ray-tracing source location algorithm. An agglomerative hierarchical clustering method is utilized to cluster the AE data from a compression test using frequency-dependent features. A neural network is trained using the compression test data and applied to the AE data emitted during the four-point bending test. The clustered data from the four-point bending test is localized using a ray-tracing algorithm. Based on the occurrence and locations of the clustered events and signal feature analyses, potential cracking mechanisms are identified and assigned.
36 MATERIALS SCIENCE↗
Applying Compression-Based Metrics to Seismic Data in Support of Global Nuclear Explosion Monitoring
The analysis of seismic data for evidence of possible nuclear explosion testing is a critical global security mission that relies heavily on human expertise to identify and mark seismic signals embedded in background noise. To assist analysts in making these determinations, we adapted two compression distance metrics for use with seismic data. First, we demonstrated that the Normalized Compression Distance (NCD) metric can be adapted for use with waveform data and can identify the arrival times of seismic signals. Then we tested an approximation for the NCD called Sliding Information Distance (SLID), which can be computed much faster than NCD. We assessed the accuracy of the SLID output by comparing it to both the Akaike Information Criterion (AIC) and the judgments of expert seismic analysts. Our results indicate that SLID effectively identifies arrival times and provides analysts with useful information that can aid their analysis process.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
CODARcode/MGARD
MGARD is a software providing error-controlled lossy compression and data refactoring based on multi-grid theories. It transforms floating-point scientific data into a multilevel representation, followed by quantization and lossless encoding processes, resulting in a self-describing compressed buffer. It supports diverse data topologies, error control norms, and computing architectures.
Chen, Jieyang [University of Oregon]↗
Pass-efficient methods for compression of high-dimensional turbulent flow data
The future of high-performance computing, specifically on future Exascale computers, will presumably see memory capacity and bandwidth fail to keep pace with data generated, for instance, from massively parallel partial differential equation (PDE) systems. Current strategies proposed to address this bottleneck entail the omission of large fractions of data, as well as the incorporation of in situ compression algorithms to avoid overuse of memory. To ensure that post-processing operations are successful, this must be done in a way that a sufficiently accurate representation of the solution is stored. Moreover, in situations where the input/output system becomes a bottleneck in analysis, visualization, etc., or the execution of the PDE solver is expensive, the number of passes made over the data must be minimized. In the interest of addressing this problem, this work focuses on the utility of pass-efficient, parallelizable, low-rank, matrix decomposition methods in compressing high-dimensional simulation data from turbulent flows. Additionally, a particular emphasis is placed on using coarse representation of the data – compatible with the PDE discretization grid – to accelerate the construction of the low-rank factorization. This includes the presentation of a novel single-pass matrix decomposition algorithm for computing the so-called interpolative decomposition. The methods are described extensively and numerical experiments on two turbulent channel flow data are performed. In the first (unladen) channel flow case, compression factors exceeding 400 are achieved while maintaining accuracy with respect to first- and second-order flow statistics. In the particle-laden case, compression factors of 100 are achieved and the compressed data is used to recover particle velocities. These results show that these compression methods can enable efficient computation of various quantities of interest in both the carrier and disperse phases.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Maximizing efficiency of dataset compression for machine learning potentials with information theory
Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.
36 MATERIALS SCIENCE↗
Error-controlled, progressive, and adaptable retrieval of scientific data with multilevel decomposition
Extreme-scale simulations and high-resolution instruments have been generating an increasing amount of data, which poses significant challenges to not only data storage during the run, but also post-processing where data will be repeatedly retrieved and analyzed for a long period of time. The challenges in satisfying a wide range of post-hoc analysis needs while minimizing the I/O overhead caused by inappropriate and/or excessive data retrieval should never be left unmanaged. In this paper, we propose a data refactoring, compressing, and retrieval framework capable of 1) fine-grained data refactoring with regard to precision; 2) incrementally retrieving and recomposing the data in terms of various error bounds; and 3) adaptively retrieving data in multi-precision and multi-resolution with respect to different analysis. With the progressive data re-composition and the adaptable retrieval algorithms, our framework significantly reduces the amount of data retrieved when multiple incremental precision are requested and/or the downstream analysis time when coarse resolution is used. Experiments show that the amount of data retrieved under the same progressively requested error bound using our framework is 64% less than that using state-of-the-art single-error-bounded approaches. Parallel experiments with up to 1, 024 cores and ~ 600 GB data in total show that our approach yields 1.36× and 2.52× performance over existing approaches in writing to and reading from persistent storage systems, respectively.
Liang, Xin↗
CHIPFoam Modification to Allow for Modelling SWIFT Foams
SWIFT (Silicon-water in Familiar Template) foams are silicone foams that have a continuous porosity without having any obvious spherical or ellipsoidal pore shapes. Like other foamed rubber, SWIFT foams can experience large reversible deformations. Because of their microstructure, SWIFT foams have a stiffering behavior in compression that is very abrupt compared to most other foamed rubbers. Work by Benedikt reported by Miller showed that fitting compressive test data with the CHIPFoam model in its current form is impractical and inaccurate. This report describes an extension made to CHIPFoam to allow the modeling of SWIFT foams. While the extension allows the modeling of SWIFT foams, it also extends the range of porosity of foams that can be modelled with CHIPFoam to include very high porosity (>99%) foamed rubber. The previous model was unstable for porosities greater than 70%. The changes made to CHIPFoam include the introduction of a critical porosity at which the compressible Danielsson strain energy function that couples volumetric and deviatoric mechanical behavior begins to increase with compression. This new feature also required the introduction of a third term in the multiplicative decomposition of the relative volume, J . The organization of this report is described here. The first section, SWIFT Foam Structure and Mechanical Behavior, describes the structure of SWIFT foams as contrasted to other foamed rubbers. It also contrasts the mechanical behavior of SWIFT foams to other more traditional foamed rubbers. The second section, CHIPFoam Modifications, describes the specific modifications done to be able to modify the delayed rapid compressive stiffening seen in SWIFT foams. The third section, Results, demonstrates the use of the modified model to fit compressive loading response data from a SWIFT foam sample. The fourth section, Conclusions and Further Work, puts the work in perspective and presents likely further work.
36 MATERIALS SCIENCE↗
FRaZ: A Generic High-Fidelity Fixed-Ratio Lossy Compression Framework for Scientific Floating-point Data
With ever-increasing volumes of scientific floating-point data being produced by high-performance computing applications, significantly reducing scientific floating-point data size is critical, and error-controlled lossy compressors have been developed for years. None of the existing scientific floating-point lossy data compressors, however, support effective fixed-ratio lossy compression. Yet fixed-ratio lossy compression for scientific floating-point data not only compresses to the requested ratio but also respects a user-specified error bound with higher fidelity. In this paper, we present FRaZ: a generic fixed-ratio lossy compression framework respecting user-specified error constraints. The contribution is twofold. (1) We develop an efficient iterative approach to accurately determine the appropriate error settings for different lossy compressors based on target compression ratios. (2) We perform a thorough performance and accuracy evaluation for our proposed fixed-ratio compression framework with multiple state-of-the-art error-controlled lossy compressors, using several real-world scientific floating-point datasets from different domains. Experiments show that FRaZ effectively identifies the optimum error setting in the entire error setting space of any given lossy compressor. While fixed-ratio lossy compression is slower than fixed-error compression, it provides an important new lossy compression technique for users of very large scientific floating-point datasets.
Underwood, Robert↗
A dictionary learning algorithm for compression and reconstruction of streaming data in preset order
There has been an emerging interest in developing and applying dictionary learning (DL) to process massive datasets in the last decade. Many of these efforts, however, focus on employing DL to compress and extract a set of important features from data, while considering restoring the original data from this set a secondary goal. On the other hand, although several methods are able to process streaming data by updating the dictionary incrementally as new snapshots pass by, most of those algorithms are designed for the setting where the snapshots are randomly drawn from a probability distribution. In this paper, we present a new DL approach to compress and denoise massive dataset in real time, in which the data are streamed through in a preset order (instances are videos and temporal experimental data), so at any time, we can only observe a biased sample set of the whole data. Here, our approach incrementally builds up the dictionary in a relatively simple manner: if the new snapshot is adequately explained by the current dictionary, we perform a sparse coding to find its sparse representation; otherwise, we add the new snapshot to the dictionary, with a Gram-Schmidt process to maintain the orthogonality. To compress and denoise noisy datasets, we apply the denoising to the snapshot directly before sparse coding, which deviates from traditional dictionary learning approach that achieves denoising via sparse coding. Compared to full-batch matrix decomposition methods, where the whole data is kept in memory, and other mini-batch approaches, where unbiased sampling is often assumed, our approach has minimal requirement in data sampling and storage: i) each snapshot is only seen once then discarded, and ii) the snapshots are drawn in a preset order, so can be highly biased. Through experiments on climate simulations and scanning transmission electron microscopy (STEM) data, we demonstrate that the proposed approach performs competitively to those methods in data reconstruction and denoising.
97 MATHEMATICS AND COMPUTING↗
A novel method may reveal bulk metallic glass compressive ductility trends in high data rate nanoindentation
Recent methods allow novel amorphous alloy compositions to be rapidly manufactured at small scale; however, obtaining materials properties such as compressive ductility from these smaller specimens has remained a challenge. Here, we suggest a potential high-throughput nanoindentation method that may be able to rapidly characterize the relative compressive ductility between these alloys based on their serration characteristics. The properties of emergent serrations, when interpreted in a simple micromechanical stress relaxation model, may order these materials by their compressive plastic strain to failure. These results are consistent with the ordering obtained from compressed specimens as well as with model simulations, suggesting that this model may be broadly useful for interpreting compressive ductility from nanoindentation serrations. After it is validated on more materials, this new method will match the rapid pace of amorphous alloy development, thus allowing metallic glass properties to be fine-tuned for each application prior to scale prototyping.
36 MATERIALS SCIENCE↗
Elastic-Waveform Inversion with Compressive Sensing for Sparse Seismic Data
Accurate velocity models of compressional- and shear-waves are essential for geothermal reservoir characterization and microseismic imaging. Elastic-waveform inversion of multi-component seismic data can provide high-resolution inversion results of subsurface geophysical properties. However, the method requires seismic data acquired using dense source and receiver arrays. In practice, seismic sources and/or geophones are often sparsely distributed on the surface and/or in a borehole, such as 3D vertical seismic profiling (VSP) surveys. We develop a novel elastic-waveform inversion method with compressive sensing for inversion of sparse seismic data. We employ an alternating-minimization algorithm to solve the optimization problem of our new waveform inversion method. We validate our new method using synthetic VSP data for a geophysical model built using geologic features found at the Raft River enhanced-geothermal-system (EGS) field. We apply our method to synthetic VSP data with a sparse source array and compare the results with those obtained with a dense source array. Our numerical results demonstrate that the velocity models produced with our new method using a sparse source array are almost as accurate as those obtained using a dense source array.
58 GEOSCIENCES↗
Scalable Data Management, Analysis, and Visualization (SDAV) Institute
Analytics-driven data layout optimizations and compression (NCSU): We have developed solutions that address challenges related to scientific data indexing, compression, and storage layout problems. Moreover, in addition to focusing on mainstream uniform mesh data, we have also addressed Adaptive Mesh Refinement (AMR) data.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
MPI-Bash: Parallel scripting right from the Bourne-Again Shell (Bash)
Parallel, scientific applications running on massively parallel supercomputers commonly produce large numbers of large data files. While parallel filesystems improve the performance of file generation, postprocessing activities such as archiving and compressing the data are often run sequentially (and therefore slowly), squandering the supercomputer's vast performance. Consequently, data that take hours to generate may take days to postprocess. Writing and debugging parallel postprocessing programs is often too time-consuming to be worthwhile, especially for one-off postprocessing operations. What the community needs is a simple mechanism for cobbling together scripts that distribute postprocessing work across a supercomputer's many nodes. MPI-Bash attempts to supply that mechanism by augmenting the GNU project's command shell, Bash, with support for the Message Passing Interface (MPI) and, if available, the Libcircle library for work distribution and load balancing. MPI-Bash makes it easy to parallelize bash scripts that run a set of Linux commands independently over a large number of input files. Because MPI-Bash includes various MPI functions for data transfer and synchronization, it is not limited to embarrassingly parallel workloads but can incorporate phased operations (i.e., all workers must finish operation X before any worker is allowed to begin operation Y).
97 MATHEMATICS AND COMPUTING↗