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GPU-Accelerated Vecchia Approximations of Gaussian Processes for Geospatial Data using Batched Matrix Computations

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GPU-Accelerated Vecchia Approximations of Gaussian Processes...

ISC High Performance 2024 Research Paper Proceedings (39th International Conference)

作者： Qilong Pan Sameh Abdulah Marc G. Genton David E. Keyes Hatem Ltaief Ying Sun Division of Computer Electrical and Mathematical Sciences and Engineering (CEMSE) Statistics Program Extreme Computing Research Center King Abdullah University of Science and Technology Thuwal Jeddah Saudi Arabia

Gaussian processes (GPs) are commonly used for geospatial analysis, but they suffer from high computational complexity when dealing with massive data. For instance, the log-likelihood function required in estimating the statistical model parameters for geospatial data is a computationally intensive procedure that involves computing the inverse of a covariance matrix with size $n$ × n, where $n$ represents the number of geographical locations in the simplest case. As a result, in the literature, studies have shifted towards approximation methods to handle larger values of $n$ effectively while maintaining high accuracy. These methods encompass a range of techniques, including low-rank and sparse approximations. Among these techniques, Vecchia approximation is one of the most promising methods to speed up evaluating the log-likelihood function. This study presents a parallel implementation of the Vecchia approximation technique, utilizing batched matrix computations on contemporary GPUs. The proposed implementation relies on batched linear algebra routines to efficiently execute individual conditional distributions in the Vecchia algorithm. We rely on the KBLAS linear algebra library to perform batched linear algebra operations, reducing the time to solution compared to the state-of-the-art parallel implementation of the likelihood estimation operation in the ExaGeoStat software by up to 700X, 833X, 1380X on 32GB GV100, 80GB A100, and 80GB H100 GPUs, respectively, with the largest matrix dimension that can fully fit into the GPU memory in the dense Maximum Likelihood Estimation (MLE) case. We also successfully manage larger problem sizes on a single NVIDIA GPU, accommodating up to 1 million locations with 80GB A100 and H100 GPUs while maintaining the necessary application accuracy. We further assess the accuracy performance of the implemented algorithm, identifying the optimal settings for the Vecchia approximation algorithm to preserve accuracy on two real geos

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Design of a 100 Gb/s Ethernet Interface for a Silicon Photonics-based Data Acquisition System for Particle Physics Experiments

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Design of a 100 Gb/s Ethernet Interface for a Silicon Photon...

IEEE Symposium on Nuclear science (NSS/MIC)

作者： G. Lessard P. Arsenault P. Martel-Dion S. Prentice T. Rossignol F. Retière S. A. Charlebois J.-F. Pratte Department of Electrical and Computer Engineering Interdisciplinary Institute for Technological Innovation Université de Sherbrooke Sherbrooke Canada Science Technology Department Physical Science Division TRIUMF Vancouver Canada

Particle physics experiments, like nEXO and ARGO, require a large-scale data acquisition system capable of supporting high data rates. One can expect a total data rate of approximately 400 Gb/s for nEXO, whereas ARGO estimates are on a scale of Pb/s. To support those experiments, which require a low-power and high-bandwidth communication (≈1 Gb/s per link), a modular Silicon-Photonics (SiP) communication module is in development to connect the front-end electronics to the data acquisition system (DAQ). This research focuses on the interface between more than 100 optical transceivers and the DAQ. To eliminate the need for custom hardware in the servers of the DAQ, the system is compatible with a standard Ethernet network. Targetting an Ethernet interface allows the use of commodity off-the-shelf equipment to connect custom electronics to the DAQ and simplifies integration, deployment, and maintenance. This system is composed of a Zynq system-on-chip (SoC), where the FPGA receives data from a set of transceivers and wraps the frame received in UDP datagrams sent to the DAQ; the processor handles various configurations and commands. To match the requirements on data rates and modularity, this study proposes a proof of concept demonstrating a 100 Gb/s link using a FPGA to transfer the data from the custom SiP transceivers to a server running DAQ software, implemented using the MIDAS framework. Following this work, the implemented Ethernet link will constitute a system ready to integrate with the SiP communication module. This integration will provide a platform to deploy large-scale and high data-rate DAQs for the targeted experiments, namely nEXO and ARGO.

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Van der Waals device integration beyond the limits of van der Waals forces using adhesive matrix transfer

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Nature Electronics 2024年第1期7卷 17-28页

作者： Satterthwaite, Peter F. Zhu, Weikun Jastrzebska-Perfect, Patricia Tang, Melbourne Spector, Sarah O. Gao, Hongze Kitadai, Hikari Lu, Ang-Yu Tan, Qishuo Tang, Shin-Yi Chueh, Yu-Lun Kuo, Chia-Nung Lue, Chin Shan Kong, Jing Ling, Xi Niroui, Farnaz Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Research Laboratory of Electronics Massachusetts Institute of Technology CambridgeMA United States Department of Chemical Engineering Massachusetts Institute of Technology CambridgeMA United States Department of Physics Massachusetts Institute of Technology CambridgeMA United States Department of Chemistry Boston University BostonMA United States Department of Materials Science and Engineering National Tsing Hua University Hsinchu Taiwan Semiconductor Research Center Hon Hai Research Institute Taipei Taiwan College of Semiconductor Research National Tsing Hua University Hsinchu Taiwan Department of Physics National Cheng Kung University Tainan Taiwan Taiwan Consortium of Emergent Crystalline Materials National Science and Technology Council Taipei Taiwan Program on Key Materials Academy of Innovative Semiconductor and Sustainable Manufacturing National Cheng Kung University Tainan Taiwan Division of Materials Science and Engineering Boston University BostonMA United States The Photonics Center Boston University BostonMA United States

Pristine van der Waals (vdW) heterostructures formed between two-dimensional (2D) and other materials can be used to create optical and electronic devices. However, the weak vdW forces alone do not allow direct physical stacking of arbitrary layers. As a result, vdW heterostructure fabrication typically requires solvents, sacrificial layers or high temperatures, which can introduce damage and contaminants. Here, we show that adhesive matrix transfer can eliminate these limitations and can provide vdW integration beyond the limits of vdW forces. In the approach, a hybrid high- and low-adhesion surface is used to decouple the forces driving the transfer from the vdW forces defining the heterostructure of interest. We show that the technique can be used to achieve direct vdW integration of diverse 2D materials (MoS2, WSe2, PtS2 and GaS) with dielectrics (SiO2 and Al2O3), which is conventionally forbidden but critical for active devices and scalable, aligned heterostructure formation. The approach also allows single-step 2D material-to-device integration, which we illustrate by fabricating arrays of monolayer MoS2 transistors. As any exposure to solvents or polymers is avoided, the interfaces and surfaces remain pristine. Thus, intrinsic 2D material properties can be probed without the influence of processing steps. The materials can be further engineered through surface treatments and used to fabricate unconventional device form factors. © 2023, The Author(s), under exclusive licence to Springer Nature Limited.

关键词： Van der Waals forces

Spectral Extremal Connectivity of Two-State Seizure Brain Waves

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arXiv 2025年

作者： Talento, Mara Sherlin D. Richards, Jordan Pinto-Orellana, Marco Huser, Raphael Ombao, Hernando C. Statistics Program Computer Electrical and Mathematical Science & Engineering Division King Abdullah University of Science and Technology 23955 - 6900 Saudi Arabia Neuro-AI Laboratory Computer Electrical and Mathematical Science & Engineering Division King Abdullah University of Science and Technology 23955 - 6900 Saudi Arabia School of Mathematics Maxwell Institute for Mathematical Sciences University of Edinburgh EdinburghEH9 3FD United Kingdom Department of Biomedical Engineering University of California Irvine92697 United States

Coherence analysis plays a vital role in the study of functional brain connectivity. However, coherence captures only linear spectral associations, and thus can produce misleading findings when ignoring variations of connectivity in the tails of the distribution. This limitation becomes important when investigating extreme neural events that are characterized by large signal amplitudes. The focus of this paper is to examine connectivity in the tails of the distribution, as this reveals salient information that may be overlooked by standard methods. We develop a novel notion of spectral tail association of periodograms to study connectivity in the network of electroencephalogram (EEG) signals of seizure-prone neonates. We further develop a novel non-stationary extremal dependence model for multivariate time series that captures differences in extremal dependence during different brain phases, namely burst-suppression and non-burst-suppression. One advantage of our proposed approach is its ability to identify tail connectivity at key frequency bands that could be associated with outbursts of energy which may lead to seizures. We discuss these novel scientific findings alongside a comparison of the extremal behavior of brain signals for epileptic and non-epileptic patients. © 2025, CC BY.

关键词： Electroencephalography

Unbiased Parameter Estimation for Partially Observed Diffusions

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arXiv 2023年

作者： Awadelkarim, Elsiddig Jasra, Ajay Ruzayqat, Hamza Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this article we consider the estimation of static parameters for partially observed diffusion process with discrete-time observations over a fixed time interval. In particular, we assume that one must time-discretize the partially observed diffusion process and work with the model with bias and consider maximizing the resulting log-likelihood. Using a novel double randomization scheme, based upon Markovian stochastic approximation we develop a new method to unbiasedly estimate the static parameters, that is, to obtain the maximum likelihood estimator with no time discretization bias. Under assumptions we prove that our estimator is unbiased and investigate the method in several numerical examples, showing that it can empirically out-perform existing unbiased *** Codes 60J22, 62M05, 65C40, 62M20 © 2023, CC BY.

关键词： Parameter estimation

Antithetic Multilevel Particle Filters

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arXiv 2023年

作者： Jasra, Ajay Maama, Mohamed Ombao, Hernando Applied Mathematics and Computational Science Program United States Statistics Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this paper we consider the filtering of partially observed multi-dimensional diffusion processes that are observed regularly at discrete times. This is a challenging problem which requires the use of advanced numerical schemes based upon time-discretization of the diffusion process and then the application of particle filters. Perhaps the state-of-the-art method for moderate dimensional problems is the multilevel particle filter of [12]. This is a method that combines multilevel Monte Carlo and particle filters. The approach in that article is based intrinsically upon an Euler discretization method. We develop a new particle filter based upon the antithetic truncated Milstein scheme of [10]. We show that for a class of diffusion problems, for ϵ > 0 given, that the cost to produce a mean square error (MSE) in estimation of the filter, of O(ϵ2) is O(ϵ−2 log(ϵ)2). In the case of multidimensional diffusions with non-constant diffusion coefficient, the method of [12] has a cost of O(ϵ−2.5) to achieve the same MSE. We support our theory with numerical results in several examples. Copyright © 2023, The Authors. All rights reserved.

关键词： Mean square error

Bayesian Parameter Estimation for Partially Observed McKean-Vlasov Diffusions Using Multilevel Markov chain Monte Carlo

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arXiv 2025年

作者： Jasra, Ajay Wu, Amin School of Data Science The Chinese University of Hong Kong Shenzhen Shenzhen China Statistics Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this article we consider Bayesian estimation of static parameters for a class of partially observed McKean-Vlasov diffusion processes with discrete-time observations over a fixed time interval. This problem features several obstacles to its solution, which include that the posterior density is numerically intractable in continuous-time, even if the transition probabilities are available and even when one uses a time-discretization, the posterior still cannot be used by adopting well-known computational methods such as Markov chain Monte Carlo (MCMC). In this paper we provide a solution to this problem by using new MCMC algorithms which can solve the aforementioned issues. This MCMC algorithm is extended to use multilevel Monte Carlo (MLMC) methods. We prove convergence bounds on our parameter estimators and show that the MLMC-based MCMC algorithm reduces the computational cost to achieve a mean square error versus ordinary MCMC by an order of magnitude. We numerically illustrate our results on two models. Copyright © 2025, The Authors. All rights reserved.

关键词： Channel estimation

ReViT: A Hybrid Approach for BCLC Staging of Hepatocellular Carcinoma Using 3D CT with Multiple Instance Learning

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ReViT: A Hybrid Approach for BCLC Staging of Hepatocellular ...

2024 IEEE-EMBS International Conference on Biomedical and Health Informatics, BHI 2024

作者： Chang, Shun-Cheng Yu, Hsin-Pei Hsieh, Yi-Hsien Wang, Pochuang Wang, Weichung Su, Tung-Hung Kao, Jia-Horng Lin, Che Taipei10617 Taiwan Department of Computer Science and Information Engineering Ntu Taipei10617 Taiwan Institute of Applied Mathematical Sciences Ntu Taipei10617 Taiwan National Taiwan University Hospital Division of Gastroenterology and Hepatology Department of Internal Medicine Taipei10048 Taiwan Department of Electrical Engineering Ntu Taipei10617 Taiwan Center for Advanced Computing and Imaging in Biomedicine Ntu Taipei10617 Taiwan Smart Medicine and Health Informatics Program Ntu Taipei10617 Taiwan

ISBN: (纸本)9798350351552

Deep learning has revolutionized medical imaging, offering advanced methods for accurate diagnosis and treatment planning. The BCLC staging system is crucial for staging Hepatocellular Carcinoma (HCC), a high-mortality cancer. An automated BCLC staging system could significantly enhance diagnosis and treatment planning efficiency. However, we found that BCLC staging, which is directly related to the size and number of liver tumors, aligns well with the principles of the Multiple Instance Learning (MIL) framework. To effectively achieve this, we proposed a new preprocessing technique called Masked Cropping and Padding(MCP), which addresses the variability in liver volumes and ensures consistent input sizes. This technique preserves the structural integrity of the liver, facilitating more effective learning. Furthermore, we introduced Re ViT, a novel hybrid model that integrates the local feature extraction capabilities of Convolutional Neural Networks (CNNs) with the global context modeling of Vision Transformers (ViTs). Re ViT leverages the strengths of both architectures within the MIL framework, enabling a robust and accurate approach for BCLC staging. We will further explore the trade-off between performance and interpretability by employing TopK Pooling strategies, as our model focuses on the most informative instances within each bag. © 2024 IEEE.

关键词： Convolutional neural networks

A BCLC Staging System for Hepatocellular Carcinoma using Swin Transformer and CT Imaging 46

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A BCLC Staging System for Hepatocellular Carcinoma using Swi...

46th Annual International Conference of the IEEE engineering in Medicine and Biology Society, EMBC 2024

作者： Chang, Shun-Cheng Wang, Pochuang Wang, Weichung Su, Tung-Hung Kao, Jia-Horng Lin, Che Taipei10617 Taiwan Department of Computer Science and Information Engineering Ntu Taipei10617 Taiwan Institute of Applied Mathematical Sciences Ntu Taipei10617 Taiwan Division of Gastroenterology and Hepatology Department of Internal Medicine National Taiwan University Hospital Taipei10048 Taiwan Department of Electrical Engineering Ntu Taipei10617 Taiwan Center for Advanced Computing and Imaging in Biomedicine Ntu Taipei10617 Taiwan Smart Medicine and Health Informatics Program Ntu Taipei10617 Taiwan

ISBN: (纸本)9798350371499

The Barcelona Clinic Liver Cancer (BCLC) staging system plays a crucial role in clinical planning, offering valuable insights for effectively managing hepatocellular carcinoma. Accurate prediction of BCLC stages can significantly ease the workload on radiologists. However, few datasets are explicitly designed for discerning BCLC stages. Despite the common practice of appending BCLC labels to clinical data within datasets, the inherent imbalance in BCLC distribution is further amplified by the diverse purposes for which datasets are curated. In this study, we aim to develop a BCLC staging system using the advanced Swin Transformer model. Additionally, we explore the integration of two datasets, each originally intended for separate objectives, highlighting the critical challenge of preserving class distribution in practical study designs. This exploration is pivotal for ensuring the applicability of our developed staging system in the designed clinical settings. Our resulting BCLC staging system demonstrates an accuracy of 55.81% (±7.8%), contributing to advancing medical image-based research for predicting BCLC stages. © 2024 IEEE.

关键词： Distribution transformers