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International Symposium on Parallel and Distributed Processing (IPDPS)

作者： Wai Teng Tang Wen Jun Tan Ratna Krishnamoorthy Yi Wen Wong Shyh-Hao Kuo Rick Siow Mong Goh Stephen John Turner Weng-Fai Wong School of Computer Engineering Nanyang Technological University Singapore Department of Computer Science School of Computing National University of Singapore Singapore Institute of High Performance Computing Agency for Science Technology and Research Singapore

ISBN: (纸本)9781467360661

Stencils represent an important class of computations that are used in many scientific disciplines. Increasingly, many of the stencil computations in scientific applications are being offloaded to GPUs to improve running times. Since a large part of the simulation time is spent inside the stencil kernels, optimizing the kernel is therefore important in the context of achieving greater computation efficiencies and reducing simulation time. In this work, we proposed a novel in-plane method for stencil computations on GPUs and compared its performance with the conventional method implemented in the Nvidia SDK. We also implemented an auto-tuning framework for our method to select the optimal parameters for different GPU architectures. A performance model was developed for our proposed method, and is used to speed up the auto-tuning process. Our results show that a speedup of nearly 2× can be achieved compared to Nvidia's implementation.

关键词： Kernel Instruction sets Loading Graphics processing units computer architecture Bandwidth Registers

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On the Impact of Widening Vector Registers on Sequence Alignment

On the Impact of Widening Vector Registers on Sequence Align...

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International Conference on Parallel Processing (ICPP)

作者： Jeffrey Daily Ananth Kalyanaraman Sriram Krishnamoorthy Bin Ren High Performance Computing Group Pacific Northwest National Laboratory School of Electrical Engineering and Computer Science Washington State University

ISBN: (纸本)9781509028245

Vector extensions, such as SSE, have been part of the x86 since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. In this paper, we demonstrate that the trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. We present a practically efficient SIMD implementation of a parallel scan based sequence alignment algorithm that can better exploit wider SIMD units. We conduct comprehensive workload and use case analyses to characterize the relative behavior of the striped and scan approaches and identify the best choice of algorithm based on input length and SIMD width.

关键词： Algorithm design and analysis Databases Heuristic algorithms Dynamic programming Bioinformatics Registers Signal processing algorithms

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Span-based localizing network for natural language video localization

arXiv

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arXiv 2020年

作者： Zhang, Hao Sun, Aixin Jing, Wei Zhou, Joey Tianyi School of Computer Science and Engineering Nanyang Technological University Institute of High Performance Computing A*STAR Institute for Infocomm Research A*STAR

Given an untrimmed video and a text query, natural language video localization (NLVL) is to locate a matching span from the video that semantically corresponds to the query. Exist-ing Solutions formulate NLVL either as a rank-ing task and apply multimodal matching ar-chitecture, or as a regression task to directly regress the target video span. In this work, we address NLVL task with a span-based QA approach by treating the input video as text passage. We propose a video span localizing network (VSLNet), on top of the Standard span-based QA framework, to address NLVL. The proposed VSLNet tackles the differences between NLVL and span-based QA through a simple and yet effective query-guided high-lighting (QGH) strategy. The QGH guides VSLNet to search for matching video span within a highlighted region. Through extensive experiments on three benchmark datasets, we show that the proposed VSLNet outper-forms the state-of-the-art methods;and adopt-ing span-based QA framework is a promising direction to solve NLVL. Copyright © 2020, The Authors. All rights reserved.

关键词： Machine learning

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performance modeling for runtime kernel adaptation: A case study on infectious disease simulation

Performance modeling for runtime kernel adaptation: A case s...

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International Workshop on Grid computing

作者： Jiangming Jin Stephen John Turner Bu-Sung Lee Shyh-hao Kuo Rick Siow Mong Goh Terence Hung School of Computer Engineering Nanyang Technological University Singapore Institute of High Performance Computing Agency of Science Agency for Science Technology and Research Singapore

In many large-scale scientific applications, there may be a compute intensive kernel that largely determines the overall performance of the application. Sometimes algorithmic variations of the kernel may be available and a performance benefit can then be gained by choosing the optimal kernel at runtime. However, it is sometimes difficult to choose the most efficient kernel as the kernel algorithms have varying performance under different execution conditions. This paper shows how to construct a set of performance models to explore and analyze the bottleneck of an application. Furthermore, based on the performance models, a theoretical method is proposed to guide the kernel adaptation at runtime. A component-based large-scale infectious disease simulation is used to illustrate the method. The performance models of the different kernels are validated by a range of experiments. The use of runtime kernel adaptation shows a significant performance gain.

关键词： Kernel Adaptation model Diseases Computational modeling Runtime Mathematical model Object oriented modeling

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Health Care and Management based on Block chain and Machine Learning

Health Care and Management based on Block chain and Machine ...

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2023 International Conference on Artificial Intelligence and Knowledge Discovery in Concurrent engineering, ICECONF 2023

作者： Bakh, Ruhi Sarkar, VeenaNair Auguskani, Jerlin Priya Lovelin Poornima, Galiveeti Shetty, Monali N. Raj, Meerjumla Govind Dr. Ambedkar Institute of Management Studies and Research India Iihmr University India Department of Nursing College Aldrab Jazan University Saudi Arabia High Performance Computing Lab School of Computer Science and Information Science Presidency University Bengaluru India Computer Science Engineering Fr. Crce India St. Martin and #39 s Engineering College Survey No. 563 Dulapally Kompally Telangana Secunderabad500100 India

ISBN: (纸本)9798350334357

With the coming of technology, we currently have an immense measure of information accessible in each field, making it conceivable to offer responses to many issues. We will utilize machine learning and block chain technology to resolve issues with healthcare information the executives in this review. With the guide of machine learning, separating just the relevant information from the data is plausible. Using prepared calculations, this is finished. The reliability of information trade turns into a test after this information has been put away. This is where block chain technology is valuable. Block chain technology's agreement guarantees that information is credible and exchanges are secure. By putting the patient at the focal point of the healthcare framework and upgrading the security and interoperability of health information, block chain technology can possibly further develop health care organization. This article fundamentally centres around settling issues with healthcare information the board using Block chain technology and including a few urgent highlights utilizing Machine Learning. The freshest technology, block chain, offers a strong and secure groundwork. With these offices, block chain has gotten some momentum in an assortment of use areas, including the food business, store network the board, energy, government support offices, and healthcare. © 2023 IEEE.

关键词： Health care

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Implementation of an RFID-based biological sample identification and tracking system

Implementation of an RFID-based biological sample identifica...

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2011 2nd IEEE RFID Technologies and Applications Conference, RFID-TA 2011, Collocated with the 2011 IEEE MTT-S International Microwave Workshop Series on Millimeter Wave Integration Technologies, IMWS 2011

作者： Zarabzadeh, Atieh Hayati, Farzad Watson, R. William G. Bradley, Geoff Grimson, Jane Centre for Health Informatics Department of Computer Science Trinity College Dublin Ireland Department of Electronic Electrical and Computer Engineering University of Birmingham United Kingdom UCD School of Medicine and Medical Science UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin Ireland Trinity Centre for High Performance Computing Trinity College Dublin Ireland

ISBN: (纸本)9781457700279

Collection, processing, storage and maintenance of samples to facilitate long-term cohort studies in biobanks, requires a system to manage samples in an effective way to prevent sample mix up and loss. Sample identification and tracking system aims to reserve data on the samples at all the times, hence RFID technology is employed. This technology allows information to be stored on the tags attached to tubes containing samples. A system is proposed, designed and prototype in the Prostate Cancer Research Consortium biobank. © 2011 IEEE.

关键词： Radio frequency identification (RFID)

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An Efficient Sparse LSTM Accelerator on Embedded FPGAs with Bandwidth-Oriented Pruning

An Efficient Sparse LSTM Accelerator on Embedded FPGAs with ...

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International Conference on Field Programmable Logic and Applications

作者： Shiqing Li Shien Zhu Xiangzhong Luo Tao Luo Weichen Liu School of Computer Science and Engineering Nanyang Technological University Singapore Institute of High Performance Computing Agency for Science Technology and Research (A*STAR) Singapore

Long short-term memory (LSTM) networks have been widely used in natural language processing applications. Although over 80% weights can be pruned to reduce the memory requirement with little accuracy loss, the pruned model still cannot be buffered on-chip for small embedded FPGAs. Considering that weights are stored in the off-chip DDR, the performance of LSTM is bounded by the available memory bandwidth. However, current pruning strategies did not consider bandwidth utilization and thus lead to bad performance in this situation. In this work, we propose an efficient sparse LSTM accelerator on embedded FPGAs with bandwidth-oriented pruning. The key idea is that data sequences can be compressed if items can be represented by a linear function of their indices in the sequences. Inspired by this idea, we first propose a column-wise pruning strategy that removes all the column indices and around 75% row indices of the remaining weights. Based on the strategy, we design a dedicated compressed format to fill the bandwidth. Further, we propose a fully pipelined hardware accelerator, which achieves the workload balance and shortens the critical path. Finally, we train the LSTM model using the TIMIT dataset and implement the accelerator on the Xilinx PYNQ-Z1 platform. The experimental result shows that our design achieves around 0.3% accuracy improvement, a 2.18x performance speedup, and a 1.96x power efficiency compared to the state-of-the-art work.

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Identification of Key Genes as Potential Drug Targets for Gastric Cancer

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Tsinghua science and Technology 2023年第4期28卷 649-664页

作者： Md.Tofazzal Hossain Md.Selim Reza Yin Peng Shengzhong Feng Yanjie Wei Center for High Performance Computing Joint Engineering Research Center for Health Big Data Intelligent Analysis TechnologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China School of Computer Science and Technology University of Chinese Academy of SciencesBeijing 100049China Department of Statistics Bangabandhu Sheikh Mujibur Rahman Science and Technology UniversityGopalganj 8100Bangladesh Guangdong Provincial Key Laboratory for Genome Stability and Disease Prevention and Regional Immunity and Diseases Department of PathologyShenzhen UniversityShenzhen 518060China

Gastric cancer(GC)is one of the most common cancers and ranks the third in cancer mortality all over the *** goal of this study was to identify potential hub-genes,highlighting their functions,signaling pathways,and candidate drugs for the treatment of GC *** used publicly available next generation sequencing(NGS)data to identify differentially expressed(DE)*** top DE genes were mapped to STRING database to construct the protein-protein interaction(PPI)network and top hub genes were selected for further *** found a total of 1555 DE genes with 870 upregulated and 685 downregulated genes in *** selected the top 400(200 upregulated and 200 downregulated)genes to construct a PPI network and extracted the top 15 hub *** gene ontology(GO)term and kyoto encyclopedia of genes and genomes(KEGG)pathway enrichment analyses of the 15 hub genes exposed some important functions and signaling pathways that were significantly associated with GC *** survival analysis of the hub genes disclosed that the lower expressions of the three hub genes CDH2,COL4A1,and COL5A2 were associated with better survival of GC *** three genes might be the candidate biomarkers for the diagnosis and treatment of ***,we considered 3 key proteins(genomic biomarkers)(COL4A1,CDH2,and CO5A2)as the drug target proteins(receptors),performed their docking analysis with the 102 meta-drug agents,and found Everolimus,Docetaxel,Lanreotide,Venetoclax,Temsirolimus,and Nilotinib as the top ranked 6 candidate drugs with respect to our proposed target proteins for the treatment against GC ***,the proposed drugs might play vital role for the treatment against GC patients.

关键词： gastric cancer hub genes candidate genes molecular docking candidate drugs

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Comparison of high Level FPGA Hardware Design for Solving Tri-diagonal Linear Systems

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Procedia computer science 2014年 29卷 95-101页

作者： David J. Warne Neil A. Kelson Ross F. Hayward High Performance Computing and Research Support Queensland University of Technology Brisbane Queensland Australia School of Electrical Engineering and Computer Science Queensland University of Technology Brisbane Queensland Australia

Reconfigurable computing devices can increase the performance of compute intensive algorithms by implementing application specific co-processor architectures. The power cost for this performance gain is often an order of magnitude less than that of modern CPUs and GPUs. Exploiting the potential of reconfigurable devices such as Field-Programmable Gate Arrays (FPGAs) is typically a complex and tedious hardware engineering task. Recently the major FPGA vendors (Altera, and Xilinx) have released their own high-level design tools, which have great potential for rapid development of FPGA based custom accelerators. In this paper, we will evaluate Altera's OpenCL Software Development Kit, and Xilinx's Vivado high Level Sythesis tool. These tools will be compared for their performance, logic utilisation, and ease of development for the test case of a tri-diagonal linear system solver.

关键词： Reconfigurable computing Field Programmable Gate Arrays high Level Synthesis Open computing Language Numerical Linear Algebra Tri-diagonal Linear Systems

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Smith-Purcell radiation from time grating

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Newton 2025年第2期1卷

作者： Juan-Feng Zhu Ayan Nussupbekov Yudi Fan Wenjie Zhou Zicheng Song Xuchen Wang Zi-Wen Zhang Chao-Hai Du Xianlong Wei Ping Bai Ching Eng Png Cheng-Wei Qiu Lin Wu Science Mathematics and Technology Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore Institute of High Performance Computing Agency for Science Technology and Research (A∗STAR) 1 Fusionopolis Way #16-16 Connexis Singapore 138632 Singapore Department of Electrical and Computer Engineering National University of Singapore 4 Engineering Drive 3 Singapore 117583 Singapore Center for Composite Materials and Structures School of Astronautics Harbin Institute of Technology Harbin China Institute of Nanotechnology Karlsruhe Institute of Technology Karlsruhe Germany Optical Communication Systems and Networks School of Electronics Peking University Beijing China Key Laboratory for the Physics and Chemistry of Nanodevices School of Electronics Peking University Beijing China

Smith-Purcell radiation (SPR) arises when an electron moves above a spatial grating, where fixed momentum compensation constrains the emission wavelength. In contrast, temporal SPR ( t -SPR) utilizes a time grating to leverage temporal periodicity for energy compensation, enabling more flexible radiation control. We introduce a generalized dispersion equation for t -SPR that predicts the interplay between radiation frequency, direction, electron velocity, modulation period, and harmonic orders. t -SPR offers several advantages over conventional SPR: robustness ( t -SPR maintains stable emission intensity without rapid decay as the electron moves away from the time grating), versatility ( t -SPR enables precise control via temporal modulation of period, amplitude, and waveform), and amplified emission (temporal modulation introduces additional energy channels, boosting emission). These features make t -SPR highly promising for advanced applications in on-chip light sources and electron accelerators.

关键词： Smith-Purcell radiation time grating photonic time crystal free-electron radiation

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