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It is an unsupervised representation algorithm used to learn morphometric properties from cellular objects. Many similar/identical open source implementations are widely available in tensorflow, pytorch, etc. And ours is implemented in matlab.
Even though it is well known that binary values are common in graph applications (e.g., adjacency matrix), how to leverage the phenomenon for efficiency has not yet been adequately explored. This paper presents a systematic study on how to unlock the potential of the bit-level optimizations of graph computations that involve binary values. It proposes a two-level representation named Bit-Block Compressed Sparse Row (B2SR) and presents a series of optimizations to the graph operations on B2SR by the intrinsics of modern GPUs. It additionally introduces Deep Reinforcement Learning (DRL) as an efficient way to best configure the bit-level optimizations on the fly. Additionally, the DQN-based adaptive tile size selector with dedicated model training can reach 68% prediction accuracy. Evaluations on NVIDIA Pascal and Volta GPUs show that the optimizations bring up to 40× and 6555× for essential GraphBLAS kernels SpMV and SpGEMM, respectively, making GraphBLAS-based BFS accelerate up to 433×, SSSP, PR, and CC up to 35×, and TC up to 52×.
Remedy selection, implementation, and coordination with tank farm activities for adjacent waste sites need to be facilitated by a technically defensible description of sources and their relative strength and temporal contributions to groundwater contamination. Detailed data describing contaminant source releases are typically not available, so source locations are highly uncertain. Furthermore, data on sources and model parameters are not readily available through direct measurements. Instead, source data are often derived by extrapolation from a few direct and/or indirect measurements, while model parameters are commonly estimated using inverse modeling or calibration methods. Because the conceptual model of sources will influence the mass and timing of the flux of contaminants to groundwater, uncertainty in the source terms should be considered. Even though a best-fit model can often be identified, it may not be the best representation of the sources given the sparse, uncertain nature of the data used for estimating source terms. To support future feasibility studies, a systematic approach is needed for identifying remediation and monitoring activities appropriate under conditions of uncertainty. In this study, an integrated assessment of alternative conceptual model elements has been examined using the B-Complex site in the Hanford Central Plateau to demonstrate how multiple sources in a waste management complex can be described to identify their relative contributions to groundwater. The heterogeneous structure of the system is modeled based on available field information on the lithological data for both the vadose zone and aquifer. The approach includes a simulation assessment and linkages to site data, with an uncertainty analysis applied to evaluate the effects of source term uncertainty on contaminant mass flux to groundwater. An integrated assessment of alternative conceptual model elements was evaluated to identify how parameter uncertainty impacts both temporal and spatial uncertainties associated with vadose zone source terms. Modeling scenarios identify important characteristics of remediation target zones to provide context for how surface barriers, in situ remedies, and water-table treatment zones can be designed to account for source dynamics. Ramifications for remediation and monitoring are discussed within the context of the source term uncertainty. The described approach facilitates systematically addressing alternative conceptual model questions in relation to remediation and monitoring and supports the remedial investigation/ feasibility study process and the remediation strategy development for the Hanford Central Plateau.
Remedy selection, implementation, and coordination with tank farm activities for adjacent waste sites need to be facilitated by a technically defensible description of sources and their relative strength and temporal contributions to groundwater contamination. Detailed data describing contaminant source releases are typically not available, so source locations are highly uncertain. Furthermore, data on sources and model parameters are not readily available through direct measurements. Instead, source data are often derived by extrapolation from a few direct and/or indirect measurements, while model parameters are commonly estimated using inverse modeling or calibration methods. Because the conceptual model of sources will influence the mass and timing of the flux of contaminants to groundwater, uncertainty in the source terms should be considered. Even though a best-fit model can often be identified, it may not be the best representation of the sources given the sparse, uncertain nature of the data used for estimating source terms. To support future feasibility studies, a systematic approach is needed for identifying remediation and monitoring activities appropriate under conditions of uncertainty. In this study, an integrated assessment of alternative conceptual model elements has been examined using the B-Complex site in the Hanford Central Plateau to demonstrate how multiple sources in a waste management complex can be described to identify their relative contributions to groundwater. The heterogeneous structure of the system is modeled based on available field information on the lithological data for both the vadose zone and aquifer. The approach includes a simulation assessment and linkages to site data, with an uncertainty analysis applied to evaluate the effects of source term uncertainty on contaminant mass flux to groundwater. An integrated assessment of alternative conceptual model elements was evaluated to identify how parameter uncertainty impacts both temporal and spatial uncertainties associated with vadose zone source terms. Modeling scenarios identify important characteristics of remediation target zones to provide context for how surface barriers, in situ remedies, and water-table treatment zones can be designed to account for source dynamics. Ramifications for remediation and monitoring are discussed within the context of the source term uncertainty. The described approach facilitates systematically addressing alternative conceptual model questions in relation to remediation and monitoring and supports the remedial investigation/ feasibility study process and the remediation strategy development for the Hanford Central Plateau. (authors)
Background Histopathology images of tumor biopsies present unique challenges for applying machine learning to the diagnosis and treatment of cancer. The pathology slides are high resolution, often exceeding 1GB, have non-uniform dimensions, and often contain multiple tissue slices of varying sizes surrounded by large empty regions. The locations of abnormal or cancerous cells, which may constitute a small portion of any given tissue sample, are not annotated. Cancer image datasets are also extremely imbalanced, with most slides being associated with relatively common cancers. Since deep representations trained on natural photographs are unlikely to be optimal for classifying pathology slide images, which have different spectral ranges and spatial structure, we here describe an approach for learning features and inferring representations of cancer pathology slides based on sparse coding. Results We show that conventional transfer learning using a state-of-the-art deep learning architecture pre-trained on ImageNet (RESNET) and fine tuned for a binary tumor/no-tumor classification task achieved between 85% and 86% accuracy. However, when all layers up to the last convolutional layer in RESNET are replaced with a single feature map inferred via a sparse coding using a dictionary optimized for sparse reconstruction of unlabeled pathology slides, classification performance improves to over 93%, corresponding to a 54% error reduction. Conclusions We conclude that a feature dictionary optimized for biomedical imagery may in general support better classification performance than does conventional transfer learning using a dictionary pre-trained on natural images.
This paper presents a GPU-accelerated simulation package, TRED, for next-generation neutrino detectors with pixelated charge readout, leveraging community-driven software ecosystems to ensure adaptability and extensibility. We introduce two generic contributions: (i) an effective-charge representation based on Gaussian quadrature rules, in which the linear- interpolation factors for the field response inside each voxel are absorbed into the effective charge, and (ii) a sparse, block- binned tensor representation that enables efficient FFT-based computation of induced signals on readout electrodes for sparsely activated detector volumes. The former captures structure inside a voxel without dense sampling, while the latter achieves low memory usage and scalable runtime, as demonstrated in bench- mark studies. The underlying data representation is applicable to large-scale detectors and to other computational problems involving sparse activity.
NOvA is a long-baseline neutrino oscillation experiment that detects neutrino particles from the NuMI beam at Fermilab. Before data from this experiment can be used in analyses, raw hits in the detector must be matched to their source particles, and the type of each particle must be identified. This task has commonly been done using a mix of traditional clustering approaches and convolutional neural networks (CNNs). Due to the construction of the detector, the data is presented as two sparse 2D images: an XZ and a YZ view of the detector, rather than a 3D representation. We propose a point set neural network that operates on the sparse matrices with an operation that mixes information from both views. Our model uses less than 10% of the memory required using previous methods while achieving a 96.8% AUC score, a higher score than obtained when both views are processed independently (85.4%).
This study demonstrates the maturing ability of the half-hourly precipitation estimates from the Integrated Multi-satellitE Retrievals for GPM (IMERG) for use in global analyses of the diurnal cycle. The refined intercalibration and interpolation between the sensors in V06 leads to greater consistency in the precipitation retrievals over different hours of the day. Evaluation against ground measurements suggests a slight lag in the diurnal phase of only +0.59 h. We demonstrate the diurnal cycle over different regions around the globe, including the Maritime Continent, where accurate representation of precipitation variability in global models remains a challenge. Using examples over Singapore, Bangladesh, and Lake Victoria, we reveal the intricate interplay between diurnal and seasonal variability. This study demonstrates the unprecedented capability of IMERG in capturing the diurnal cycle of precipitation globally, potentially advancing our understanding in regions of sparse ground measurements and supporting improvements in its representation in global models.
Tensor-based methods are receiving renewed attention in recent years due to their prevalence in diverse real-world applications. There is considerable literature on tensor representations and algorithms for tensor decompositions, both for dense and sparse tensors. Many applications in hypergraph analytics, machine learning, psychometry, and signal processing result in tensors that are both sparse and symmetric, making them an important class for further study. Similar to the critical Tensor Times Matrix chain operation (TTM c ) in general sparse tensors, the $\underline{S}$ parse $\underline{S}$ ymmetric $\underline{T}$ ensor $\underline{T}$ imes $\underline{S}$ ame $\underline{M}$ atrix $\underline{c}$ hain (S 3 TTM c ) operation is compute and memory intensive due to high tensor order and the associated factorial explosion in the number of non-zeros. We present the novel Compressed Sparse Symmetric (CSS) format for sparse symmetric tensors, along with an efficient parallel algorithm for the S 3 TTM c operation. We theoretically establish that S 3 TTM c on CSS achieves a better memory versus run-time trade-off compared to state-of-the-art implementations, and visualize the variation of the performance gap over the parameter space. We demonstrate experimental findings that confirm these results and achieve up to 2.72× speedup on synthetic and real datasets. The scaling of the algorithm on different test architectures is also showcased to highlight the effect of machine characteristics on algorithm performance.
High–dimensional datasets are becoming ubiquitous in many applications and therefore unsupervised tensor methods to interrogate them are needed. Here, we report a new unsupervised machine learning (ML) approach (NTFk) based on nonnegative tensor factorization integrated with a custom k–means clustering. We demonstrate the ability of NTFk to extracting temporal and spatial features of phase separation of copolymers as they are modeled by self–consistent field theory. Microphase separation of block copolymers has been extensively studied both experimentally and theoretically. However, the interpretation of computer simulations and/or experimental data, representing temporal and spatial changes of molecular species concentration is still a challenging task. Thus, extracting the phase diagram from simulations or experimental data as well as the interpretation of data requires discernment of the model/experimental parameters (such as, temperature, concentrations, the number of molecular species and the interaction between species) impact on the microphase separation process. An attractive and unique aspect of the introduced ML method is that it ensures the nonnegativity of the extracted latent features. Nonnegativity is an essential constraint needed to obtain interpretable and sparse latent features that are parts–based representation of the data. The custom clustering in NTFk serves to estimate the number of latent features in the data.
Here, we present a graph-based methodology to reduce the computational cost of obtaining first passage times through sparse fracture networks. We also derive graph representations of generic three-dimensional discrete fracture networks (DFNs) using the DFN topology and flow boundary conditions. Subgraphs corresponding to the union of the k shortest paths between the inflow and outflow boundaries are identified and transport on their equivalent subnetworks is compared to transport through the full network. The number of paths included in the subgraphs is based on the scaling behavior of the number of edges in the graph with the number of shortest paths. First passage times through the subnetworks are in good agreement with those obtained in the full network, both for individual realizations and in distribution. We obtain accurate estimates of first passage times with an order of magnitude reduction of CPU time and mesh size using the proposed method.
Key components of CEED software development involve fast finite element operator storage and evaluation, architecture optimizations, performant algorithms for all orders, global kernels for finite element operators, efficient use of the memory sub-system, optimal data locality and motion, enhanced scalability and parallelism, and fast tensor contractions. As ultimate goals of the project, CEED is exploring and identifying the best algorithms for the full range of discretizations and applying algorithmic and software development to support ECP applications’ needs. In this milestone, we initiated the development and implementation of a common CEED API consisting of two main components: low-level and high-level APIs. We accomplished the goal of having the low-level component ready for the release of CEED v1.0 in the next quarter, see CEED-MS13. In this report we also provide a highlight from CEED’s integration with the MARBL app and the corresponding Laghos miniapp. A main theme in this work has been the systematic transition of advanced algorithms, developed and tested in Laghos, to the large-scale multi-physics settings of the MARBL code. The low-level CEED API provides a set of FE kernels and components for writing new low-level kernels. Examples include: vector and sparse linear algebra, element matrix assembly over a batch of elements, partial assembly and action for efficient high-order operators like mass, diffusion, advection, etc. The main goal of the low-level API is to establish the basis for the high-level API. Also, identifying such low-level kernels and providing a reference implementation for them serves as the basis for collaboration with vendors and STs. Another goal for the low-level API is to make it easy for applications with their own discretization infrastructure, who do not want to switch directly to using the high-level CEED API, to still evaluate and use the core operations provided by the low-level API. One of the challenges with high-order methods is that a global sparse matrix is no longer a good representation of a high-order linear operator, both with respect to the FLOPs needed for its evaluation, as well as the memory transfer needed for a matvec. Thus, another important question we tried to address while developing the low-level API is: is it possible to abstract out in a natural and efficient way the different implementations and data structures that arise when dealing with various computational device types: CPUs, GPUs, etc. Fully answering this question is beyond the scope of this particular milestone, since that requires longer time as we develop and expand the devices we support. The future high-level API will be the frontend provided by CEED consisting of high-level abstractions such as meshes, finite element spaces and solutions, bilinear forms, solvers, etc. At this high-level, an important aspect of the API will be to provide a uniform abstraction layer for writing code in a portable manner. To achieve that, we plan to utilize the MPI programming model combined with a device abstraction layer (DAL) for finite element computations that we will develop. The DAL will serve as the bridge between the low- and the high-level APIs, allowing a variety of programming models to be used for the low-level kernel implementations. The software artifacts delivered as part of this milestone include an initial CEED API software implementation (libCEED) provided through the CEED website, http://ceed.exascaleproject.org and the CEED GitHub organization, http://github.com/ceed. In addition to details and results from the above R&D efforts, in this document we are also reporting on other project-wide activities performed in Q1 of FY18, including: the Nek5000 v17.0 MFEM v3.3.2 and PETSc v3.8 releases, collaborations with ECP/ST and SciDAC projects, the inaugural Nek5000 hackathon and various outreach activities.
Handling large graphs in a distributed environment requires effective partitioning across processors and efficient management of local partitions. In 2D partitioning, local graphs often become too sparse, making memory-efficient data structures crucial. Using the Compressed Sparse Row (CSR) format wastes space, especially for > 83% of vertices with empty edges for the sparse graphs. This study explores bit-CSR (BCSR), a modified CSR representation, on GPUs to reduce memory usage in graph computations. We achieved 16.67% memory savings on a sparse rmat dataset with 268 million vertices and 357 million edges, without performance degradation, supported by both theoretical and experimental storage savings of 33%. However, we observed a 1.7× slowdown in degree lookup times due to bitwise operations on AMD CPUs. This analysis highlights the potential of BCSR on GPUs for improving Graph500 benchmark performance on GPU-accelerated systems, such as the Frontier supercomputer.
Tensor based methods are receiving renewed attention in recent years due to their prevalence in diverse real-world applications. There is considerable literature on tensor representations and algorithms for tensor decompositions, both for dense and sparse tensors. Many applications in hypergraph analytics, machine learning, psychometry, and signal processing result in tensors that are both sparse and symmetric, making it an important class for further study. Similar to the critical Tensor Times Matrix chain operation (TTMc) in general sparse tensors, the Sparse Symmetric Tensor Times Same Matrix chain (S3TTMc) operation is compute and memory intensive due to high tensor order and the associated factorial explosion in the number of non-zeros. In this work, we present a novel compressed storage format CSS for sparse symmetric tensors, along with an efficient parallel algorithm for the S3TTMc operation. We theoretically establish that S3TTMc on CSS achieves a better memory versus run-time trade-off compared to state-of-the-art implementations. We demonstrate experimental findings that confirm these results and achieve up to 2.9× speedup on synthetic and real datasets.
Reanalyses are regularly gridded, retrospective depictions of the physical earth system, which are produced through the correction of a short-term forecast to available observations. In the Arctic, reanalyses are particularly well suited to marshal the sparse observing network to provide a plausible, multivariate representation of conditions. Atmospheric reanalyses such as MERRA-2 (NASA Modern-Era Retrospective analysis for Research and Applications, version 2) and ocean reanalyses such as SODA3 (Univ. Maryland Simple Ocean Data Assimilation version 3) are widely used in Arctic research for diagnostic studies of circulation, model evaluation, and as boundary conditions for a variety of process models. Here, we provide examples that illustrate the utility of reanalyses for providing information on the spatial and temporal scales of recent, rapid changes in the Arctic. Recent trends in Arctic surface temperatures, surface melt over Greenland and Arctic glaciers, and evolving freshwater conditions in the Arctic Ocean are examples where reanalyses can provide information that cannot easily be obtained via other means. These examples provide information on the scale, magnitude, and the uncertainty of recent Arctic change and provide a context for future scenarios. We further quantify uncertainties in key reanalyses variables and approaches for addressing these issues.
The DECOVALEX Project is an on-going international research collaboration, established in 1992, to advance the understanding and modeling of coupled Thermal (T), Hydrological (H), Mechanical (M) and Chemical (C) processes in geological in geological systems. This document is the final report of Task G which was proposed by the Swedish Radiation Safety Authority (SSM) and coordinated by geomecon GmbH, presenting the technical definitions of the problems studied, approaches applied, achievements made and outstanding issues for future research. Task G in DECOVALEX-2019 is primarily concerned with the evolution of transmissivity throughout the lifetime of a repository for radioactive waste, and in particular of spent nuclear fuel, in sparsely fractured and competent crystalline rock masses, and the representation of these processes via numerical simulation. The numerical simulations were to be evaluated for their suitability, and to be validated. Over the course of the work presented here, not only were transmissivity changes and the best approaches to simulate those change examined, but also strategies were to be developed on how to monitor transmissivity change. Guidelines on what a control program and a monitoring system for a repository should include and be able to measure, and how this can be done in practice, was a key objective of the research project.
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.
A method for the parallel solution of triangular sets of equations is described that is appropriate when there are many right-handed sides. By preprocessing, the method can reduce the number of parallel steps required to solve Lx = b compared to parallel forward or backsolve. Applications are to iterative solvers with triangular preconditioners, to structural analysis, or to power systems applications, where there may be many right-handed sides (not all available a priori). The inverse of L is represented as a product of sparse triangular factors. The problem is to find a factored representation of this inverse of L with the smallest number of factors (or partitions), subject to the requirement that no new nonzero elements be created in the formation of these inverse factors. A method from an earlier reference is shown to solve this problem. This method is improved upon by constructing a permutation of the rows and columns of L that preserves triangularity and allow for the best possible such partition. A number of practical examples and algorithmic details are presented. The parallelism attainable is illustrated by means of elimination trees and clique trees.