Scientific applications generate an unprecedented volume of data, overwhelming the network and file systems’ bandwidth and posing challenges for efficient and scalable data retrieval and analysis. Progressive data compression offers a promising solution by enabling on-demand retrieval at reduced size. However, existing progressive methods either fail to bound the errors in essential quantities of interest (QoIs) derived from raw data or suffer from suboptimal retrieval efficiency. In this work, we propose QProR, an efficient QoI-based progressive framework that optimizes progressive retrieval for target QoIs. Our key contributions include: (1) a systematic framework that integrates error-controlled lossy compressors with bitplane encoding while decoupling the two processes for high flexibility and adaptability; (2) a novel weighted bitplane encoding method which incorperates QoI knowledge into data refactoring to enhance retrieval efficiency; (3) an optimized retrieval strategy that accounts for the varying impacts of different variables on multivariate QoIs; (4) comprehensive evaluations using six real-world datasets from multiple scientific applications and thorough comparisons against state of the arts. Experimental results demonstrate that QProR achieves up to \(80.38\%\) reduction in the retrieval size under the same requested QoI error tolerance, when compared with the best-performing existing methods. When transferring 384 GB of scientific data to remote sites, QProR delivers up to 1.68 × speedup in the end-to-end data transfer performance.

Alzheimer's disease (AD) is characterized by progressive brain network disintegration, yet quantifying this process at an individual level remains challenging. This study explores the potential of an individualized differential structural covariance network (IDSCN) as a graph theory-based biomarker to capture disease-specific network reorganization. We found that throughout the AD spectrum, significant progressive atrophy occurred in multiple brain regions, especially the hippocampus. At the same time, the brain underwent a profound structural covariant reorganization, and this reorganization was significantly centered on the hippocampus. Graph theory analysis revealed a significant enhancement in nodal strength and nodal efficiency across widespread brain regions, with the hippocampus, amygdala, middle temporal gyrus, and entorhinal cortex emerging as core hubs of pathological impact. Importantly, betweenness centrality selectively increased only in the bilateral hippocampus, highlighting their critical role as bridges in the pathological propagation network. Machine learning validation confirmed that this individualized network biomarker performs excellently in distinguishing AD patients from cognitively normal individuals, demonstrates comparable efficacy to traditional morphological models in capturing early disease-related changes, and shows potential in differentiating between mild cognitive impairment converters and non-converters. Our study establishes the hippocampus-centered IDSCN as an effective, individualized graph theory-based biomarker, providing new insights into the network pathophysiology of AD and holding significant potential for early diagnosis and prognostic stratification.

Data compression is becoming critical for storing scientific data because many scientific applications need to store large amounts of data and post process this data for scientific discovery. Unlike image and video compression algorithms that limit errors to primary data (PD), scientists require compression techniques that accurately preserve derived quantities of interest (QoIs). This paper presents a physics-informed compression technique implemented as an end-to-end, scalable, GPU-based pipeline for data compression that addresses this requirement. Our hybrid compression technique combines machine learning techniques and standard compression methods. Specifically, we combine an autoencoder, an error-bounded lossy compressor to provide guarantees on raw data error, and a constraint satisfaction post-processing step to preserve the QoIs within a minimal error (generally less than floating point error). The effectiveness of the data compression pipeline is demonstrated by compressing nuclear fusion simulation data generated by a large-scale fusion code, XGC, which produces hundreds of terabytes of data in a single day. Our approach works within the ADIOS framework and results in compression by a factor of more than 150 while requiring only a few percent of the computational resources necessary for generating the data, making the overall approach highly effective for practical scenarios.

Neural networks are increasingly integrated into scientific discovery, where input data reduction and model quantization play a key role in accelerating inference. However, understanding and mitigating the impact of these techniques on output error is critical for ensuring reliable results, particularly in tasks demanding high numerical precision. This paper introduces a comprehensive framework for optimizing neural network inference in scientific computing by combining data reduction and model quantization while maintaining error-controlled outcomes. We develop theoretical analyses to bound error propagation under these techniques and propose a framework that balances computational performance with error constraints. Evaluation on real-world learning-based combustion simulations and satellite image classification shows that our derived error bounds accurately predict observed errors while enabling significant computational speedup under our framework. This work highlights the potential for further leveraging advancements in modern lossy compression algorithms and hardware accelerators that support lower-precision formats.

The rapid growth in scientific data generation is outpacing advancements in computing systems necessary for efficient storage, transfer, and analysis, particularly in the context of exascale computing. With the deployment of first-generation exascale computing systems and next-generation experimental facilities, this gap is widening and necessitates effective data reduction techniques to manage enormous data volumes. Over the past decade, various data reduction methods, including lossless compression, error-controlled lossy compression, and data refactoring, have been developed to accelerate I/O in scientific workflows. Despite significant reductions in data volume, these methods introduce considerable computational overhead, which can become the new bottleneck in data processing. To mitigate this, GPU-accelerated data reduction algorithms have been introduced. However, challenges remain in their integration into exascale workflows, including limited portability across different GPU architectures, substantial memory transfer overhead, and reduced scalability on dense multi-GPU systems. To address these challenges, we propose HPDR, a high-performance and portable data reduction framework. HPDR is designed to enable the execution of state-of-the-art reduction algorithms across diverse processor architectures while reducing memory transfer overhead to 2.3 % of the original, resulting in up to$3.5 \times$faster throughput compared to existing solutions. It also achieves up to 96% of the theoretical speedup in multi-GPU settings. In addition, evaluations on accelerating I/O operations at scale up to 1,024 nodes of the Frontier supercomputer demonstrate that HPDR can achieve up to$103\ \text{TB} / \mathrm{s}$reduction throughput, providing up to$4 \times$acceleration in parallel I/O performance compared to existing data reduction routines. This work highlights the potential of HPDR to significantly enhance data reduction efficiency in exascale computing environments.

Checkpoint/Restart (C/R) strategies are vital for fault tolerance in PDE-based scientific simulations, yet traditional checkpointing incurs significant I/O overhead. Lossy compression offers a scalable solution by reducing checkpoint data size, but conventional methods often lack control over physical invariants (e.g., energy), leading to instability such as oscillations or divergence in Partial Differential Equations (PDE) systems. This paper introduces a stability-preserving compression approach tailored for PDE simulations by explicitly controlling kinetic and potential energy perturbations to ensure stable restarts. Extensive experiments conducted across diverse PDE configurations demonstrate that our method maintains numerical stability with minimal error magnification—even across multiple checkpoint-restart cycles—outperforming state-of-the-art lossy compressors. Parallel evaluations on the Frontier supercomputer show up to 8.4× improvement in checkpoint write performance and 6.3× in read performance, while maintaining relative L2 errors ∼ 2e-6 throughout continued simulation. These results provide practical guidance for balancing compression accuracy, stability, and computational efficiency in large-scale PDE applications.

Scientific applications produce vast amounts of data, posing grand challenges in the underlying data management and analytic tasks. Progressive compression is a promising way to address this problem, as it allows for on-demand data retrieval with significantly reduced data movement cost. However, most existing progressive methods are designed for CPUs, leaving a gap for them to unleash the power of today’s heterogeneous computing systems with GPUs.In this work, we propose HP-MDR, a high-performance and portable data refactoring and progressive retrieval framework for GPUs. Our contributions are four-fold: (1) We carefully optimize the bitplane encoding and lossless encoding, two key stages in progressive methods, to achieve high performance on GPUs; (2) We propose pipeline optimization and incorporate it with data refactoring and progressive retrieval workflows to further enhance the performance for large data process; (3) We leverage our framework to enable high-performance data retrieval with guaranteed error control for common Quantities of Interest; (4) We evaluate HP-MDR and compare it with state of the arts using five real-world datasets. Experimental results demonstrate that HP-MDR delivers an average 13.68 × and 6.31 × throughput in data refactoring and progressive retrieval tasks, respectively. It also leads to 11.22 × throughput for recomposing required data representations under Quantity-of-Interest error control and 6.04 × performance for the corresponding end-to-end data retrieval, when compared with state-of-the-art solutions.

This paper presents a novel end-to-end framework for closed-form computation and visualization of critical point uncertainty in 2D uncertain scalar fields. Critical points are fundamental topological descriptors used in the visualization and analysis of scalar fields. The uncertainty inherent in data (e.g., observational and experimental data, approximations in simulations, and compression), however, creates uncertainty regarding critical point positions. Uncertainty in critical point positions, therefore, cannot be ignored, given their impact on downstream data analysis tasks. In this work, we study uncertainty in critical points as a function of uncertainty in data modeled with probability distributions. Although Monte Carlo (MC) sampling techniques have been used in prior studies to quantify critical point uncertainty, they are often expensive and are infrequently used in production-quality visualization software. We, therefore, propose a new end-to-end framework to address these challenges that comprises a threefold contribution. First, we derive the critical point uncertainty in closed form, which is more accurate and efficient than the conventional MC sampling methods. Specifically, we provide the closed-form and semianalytical (a mix of closed-form and MC methods) solutions for parametric (e.g., uniform, Epanechnikov) and nonparametric models (e.g., histograms) with finite support. Second, we accelerate critical point probability computations using a parallel implementation with the VTK-m library, which is platform portable. Finally, we demonstrate the integration of our implementation with the ParaView software system to demonstrate near-real-time results for real datasets.

In the compression of scientific data, error-controlled compressors enable to considerably decrease the size of the dataset while maintaining adequate levels of accuracy. In this paper, we note that multi-level refactoring scheme such as MGARD i) rely on an approximation of the data based on the interpolation of coefficients, ii) estimate the resulting error with global metrics on the dataset. To improve on these two aspects, we propose a method that aims to divide the original dataset into blocks based on their smoothness and refactors each block separately with the most relevant interpolation order. We show the relevance of such a method on tailored datasets and the benefits and challenges when applying it to large scientific data.

We present a general framework for compressing unstructured scientific data with known local connectivity. A common application is simulation data defined on arbitrary finite element meshes. The framework employs a greedy topology preserving reordering of original nodes which allows for seamless integration into existing data processing pipelines. This reordering process depends solely on mesh connectivity and can be performed offline for optimal efficiency. However, the algorithm’s greedy nature also supports on-the-fly implementation. The proposed method is compatible with any compression algorithm that leverages spatial correlations within the data. The effectiveness of this approach is demonstrated on a large-scale real dataset using several compression methods, including MGARD, SZ, and ZFP.

Scientists conduct large-scale simulations to compute derived quantities from primary data. Thus, it is crucial that data compression techniques maintain bounded errors on these derived quantities or quantities of interest (QOI). For many spatiotemporal applications, these QOIs are binary in nature and represent presence or absence of a physical phenomenon. In this work, we propose to use a hybrid approah for differential compression for such applications. We use a neural network (NN) approach to determine regions-of-interest (ROIs) where the binary QOIs are going to be prevalent. This is then used with traditional approaches that compress at a lower level (and higher accuracy) for these ROIs as compared to other regions.

Data compression plays a key role in reducing storage and I/O costs. Traditional lossy methods primarily target data on rectilinear grids and cannot leverage the spatial coherence in unstructured mesh data, leading to suboptimal compression ratios. We present a multi-component, error-bounded compression framework designed to enhance the compression of floating-point unstructured mesh data, which is common in scientific applications. Our approach involves interpolating mesh data onto a rectilinear grid and then separately compressing the grid interpolation and the interpolation residuals. This method is general, independent of mesh types and typologies, and can be seamlessly integrated with existing lossy compressors for improved performance. We evaluated our framework across twelve variables from two synthetic datasets and two real-world simulation datasets. The results indicate that the multi-component framework consistently outperforms state-of-the-art lossy compressors on unstructured data, achieving, on average, a 2.3 − 3.5× improvement in compression ratios, with error bounds ranging from 1 × 10 the−6to 1×10−2. We further investigate impact of hyperparameters, such as grid spacing and error allocation, to deliver optimal compression ratios in diverse datasets.

The ever-increasing volume of data produced by HPC simulations necessitates scalable methods for data exploration and knowledge extraction. Scientific data analysis often involves complex queries across distributed datasets, requiring manipulation of multiple primary variables and generating derived data that needs to be handled efficiently, creating challenges for applications that need to parse many large datasets. Relying on individual applications to handle all intermediate data generally leads to redundant computations across studies and unnecessary data transfers. In this paper, we investigate the performance of different approaches where applications define derived variables as quantities of interest (QoIs) and offload the computation and transfer of these QoIs to the I/O library. This significantly reduces redundancy and optimizes data movement across the distributed storage and processing infrastructure by allowing control over when and where derived variables are computed. We present a detailed analysis of the performance-storage trade-offs associated with different solutions and showcase results for our study on two large-scale datasets created from climate and combustion simulations.

The unprecedented amount of scientific data has introduced heavy pressure on the current data storage and transmission systems. Progressive compression has been proposed to mitigate this problem, which offers data access with on-demand precision. However, existing approaches only consider precision control on primary data, leaving uncertainties on the quantities of interest (QoIs) derived from it. In this work, we present a progressive data retrieval framework with guaranteed error control on derivable QoIs. Our contributions are three-fold. (1) We carefully derive the theories to strictly control QoI errors during progressive retrieval. Our theory is generic and can be applied to any QoIs that can be composited by the basis of derivable QoIs proved in the paper. (2) We design and develop a generic progressive retrieval framework based on the proposed theories, and optimize it by exploring feasible progressive representations. (3) We evaluate our framework using five real-world datasets with a diverse set of QoIs. Experiments demonstrate that our framework can faithfully respect any user-specified QoI error bounds in the evaluated applications. This leads to over $2.02 \times$ performance gain in data transfer tasks compared to transferring the primary data while guaranteeing a QoI error that is less than 1E-5.

Data compression is becoming critical for data-intensive scientific applications. Scientists require compression techniques that accurately preserve derived quantities of interest (QoIs). Prior work has shown that a pipeline can be built to guarantee error on the primary data (PD) within user-defined bounds and achieve near-floating point QoI errors. In this paper, we present novel computational approaches for accelerating the pipeline and demonstrate results that enable concurrent execution of compression in parallel with the simulation nodes. This allows compression, including the writing of the required compression data, for the previous time step to be completed while the simulation proceeds with the current time step. Overall, the approach presented in this paper results in a 6–8 times improvement in computational overhead compared to previous work. These results were obtained using data generated by a large-scale fusion code called XGC, which produces hundreds of terabytes of data in a single day.

Scientific discoveries are increasingly constrained by limited storage space and I/O capacities. For time-series simulations and experiments, their data often need to be decimated over timesteps to accommodate storage and I/O limitations. In this paper, we propose a technique that addresses storage costs while improving post-analysis accuracy through spatiotemporal adaptive, error-controlled lossy compression. We investigate the trade-off between data precision and temporal output rates, revealing that reducing data precision and increasing timestep frequency lead to more accurate analysis outcomes. Additionally, we integrate spatiotemporal feature detection with data compression and demonstrate that performing adaptive error-bounded compression in higher dimensional space enables greater compression ratios, leveraging the error propagation theory of a transformation-based compressor. To evaluate our approach, we conduct experiments using the well-known E3SM climate simulation code and apply our method to compress variables used for cyclone tracking. Our results show a significant reduction in storage size while enhancing the quality of cyclone tracking analysis, both quantitatively and qualitatively, in comparison to the prevalent timestep decimation approach. Compared to three state-of-the-art lossy compressors lacking feature preservation capabilities, our adaptive compression framework improves perfectly matched cases in TC tracking by 26.4-51.3% at medium compression ratios and by 77.3-571.1% at large compression ratios, with a merely 5–11% computational overhead.

Many scientific simulations and experiments generate terabytes to petabytes of data daily, necessitating data compression techniques. Unlike video and image compression, scientists require methods that accurately preserve primary data (PD) and derived quantities of interest (QoIs). In our previous work, we demonstrated the effectiveness of hybrid compression techniques that combine machine learning with traditional approaches. This paper presents innovative computational techniques aimed at expediting the compression pipeline. Our experiments, conducted on two distinct platforms with a large-scale XGC-based fusion simulation, demonstrate that the overhead incurred by these new approaches is less than one percent of the computational resources needed for the simulation.

In modern science, big data plays an increasingly important role. Many scientific applications, such as running simulations on supercomputers or conducting experiments on advanced instruments, produce huge amount of data at unprecedented speed. Analyzing and understanding such big data is the key for scientists to make scientific breakthroughs. However, data might become unavailable for scientists to access when outages or maintenance of the storage system occur, which severely hinders scientific discovery. To improve the data availability, data duplication and erasure coding (EC) are often used. But as the scientific data gets larger, using these two methods can cause considerable storage and network overhead.

As the disparity between compute and I/O on high-performance computing systems has continued to widen, it has become increasingly difficult to perform post-hoc data analytics on full-resolution scientific simulation data due to the high I/O cost. Error-bounded data decomposition and progressive data retrieval framework has recently been developed to address such a challenge by performing data decomposition before storage and reading only part of the decomposed data when necessary. However, the performance of the progressive retrieval framework has been suffering from the over-pessimistic error control theory, such that the achieved maximum error of recomposed data is significantly lower than the required error. Therefore, more data than required is fetched for recomposition, incurring additional I/O overhead. In order to tackle this issue, we propose a DNN-based progressive retrieval framework that can better identify the minimum amount of data to be retrieved. Our contributions are as follows: 1) We provide an in-depth investigation of the recently developed progressive retrieval framework; 2) We propose two designs of prediction models (named D-MGARD and E-MGARD) to estimate the amount of retrieved data size based on error bounds. 3) We evaluate our proposed solutions using scientific datasets generated by real-world simulations from two domains. Evaluation results demonstrate the effectiveness of our solution in accurately predicting the amount of retrieval data size, as well as the advantages of our solution over the traditional approach to reducing the I/O overhead. Based on our evaluation, our solution is shown to read significantly less data (5% - 40% with D-MGARD, 20% - 80% with E-MGARD).

Efficient data compression is becoming increasingly critical for storing scientific data because many scientific applications produce vast amounts of data. This paper presents an end-to-end algorithmic and software pipeline for data compression that guarantees both error bounds on primary data (PD) and derived data, known as Quantities of Interest (QoI).We demonstrate the effectiveness of the pipeline by compressing fusion data generated by a large-scale fusion code, XGC, which produces tens of petabytes of data in a single day. We demonstrate that the compression is conducted by setting aside computational resources known as staging nodes, and does not impact the simulation performance. For efficient parallel I/O, the pipeline uses ADIOS2, which many codes such as XGC already use for their parallel I/O. We show that our approach can compress the data by two orders of magnitude while guaranteeing high accuracy on both the PD and the QoIs. Further, the amount of resources required by compression is a few percent of the resources required by simulation while ensuring that the compression time for each stage is less than the corresponding simulation time.This pipeline consists of three main steps. The first step decomposes the data using domain decomposition into small subdomains. Each subdomain is then compressed independently to achieve a high level of parallelism. The second step uses existing techniques that guarantee error bounds on the primary data for each subdomain. The third step uses a post-processing optimization technique based on Lagrange multipliers to reduce the QoI errors for data corresponding to each subdomain. The Lagrange multipliers generated can be further quantized or truncated to increase the compression level. All of the above characteristics of our approach make it highly practical to apply on-the-fly compression while guaranteeing errors on QoIs that are critical to the scientists.

The increase of computer processing speed is significantly outpacing improvements in network and storage bandwidth, leading to the big data challenge in modern science, where scientific applications can quickly generate much more data than that can be transferred and stored. As a result, big scientific data must be reduced by a few orders of magnitude while the accuracy of the reduced data needs to be guaranteed for further scientific explorations. Moreover, scientists are often interested in some specific spatial/temporal regions in their data, where higher accuracy is required. The locations of the regions requiring high accuracy can sometimes be prescribed based on application knowledge, while other times they must be estimated based on general spatial/temporal variation. In this paper, we develop a novel multilevel approach which allows users to impose region-wise compression error bounds. Our method utilizes the byproduct of a multilevel compressor to detect regions where details are rich and we provide the theoretical underpinning for region-wise error control. With spatially varying precision preservation, our approach can achieve significantly higher compression ratios than single-error bounded compression approaches and control errors in the regions of interest.

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.

High-performance packet analysis systems have attracted great interest as tools to deal with security concerns in high-speed networks. Recently, researchers have utilized GPUs to improve packet processing performance. However, most existing work has been targeted at per-packet analysis level. Flow-centric operations have been challenging for GPUs because they require sequential operations and large buffers for flow reassembly. In this work, we present the GoldenEye GPU Packet Processing System (GoldenEye), a deep packet inspection (DPI) system that tracks out-of-order TCP packets and provides stream-based signature matching. When a batch of packets arrives, GoldenEye sorts packets into flow-reassembled streams and normalizes retransmission through a GPU-implemented reordering module. For signatures that straddle batch boundaries, GoldenEye couples a small set of metadata with a functionally-equivalent minimal regular expression retrieval algorithm to connect the partial matches. Results show that GoldenEye can reassemble tens of millions of packets/sec and conduct stateful DPI operations on TCP streams at multi-ten Gbit/sec rates.

Many state-of-the-art general object detection methods make use of shared full-image convolutional features (as in Faster R-CNN). This achieves a reasonable test-phase computation time while enjoys the discriminative power provided by large Convolutional Neural Network (CNN) models. Such designs excel on benchmarks1which contain natural images but which have very unnatural distributions, i.e. they have an unnaturally high-frequency of the target classes and a bias towards a “friendly” or “dominant” object scale. In this paper we present further study of the use and adaptation of the Faster R-CNN object detection method for datasets presenting natural scale distribution and unbiased real-world object frequency. In particular, we show that better alignment of the detector scale sensitivity to the extant distribution improves vehicle detection performance. We do this by modifying both the selection of Region Proposals, and through using more scale-appropriate full-image convolution features within the CNN model. By selecting better scales in the region proposal input and by combining feature maps through careful design of the convolutional neural network, we improve performance on smaller objects. We significantly increase detection AP for the KITTI dataset car class from 76.3% on our baseline Faster R-CNN detector to 83.6% in our improved detector.

We have established a new concept for creating ordered arrays of quantum dots by self-organized epitaxy. The concept is based on self-organized anisotropic strain engineering of strained layer templates and is demonstrated for (In,Ga)As/GaAs superlattice structures on GaAs (100) and strain-induced (In,Ga)As growth instability on GaAs (311)B. The well-defined one- and two-dimensional networks of InAs quantum dots grown on top of these templates are of excellent structural and optical quality. This breakthrough, thus, allows for novel fundamental studies and device operation principles based on single and multiple carrier- and photon-, and coherent quantum interference effects.