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name="searchtype"><option value="all">All fields</option><option value="title">Title</option><option selected value="author">Author(s)</option><option value="abstract">Abstract</option><option value="comments">Comments</option><option value="journal_ref">Journal reference</option><option value="acm_class">ACM classification</option><option value="msc_class">MSC classification</option><option value="report_num">Report number</option><option value="paper_id">arXiv identifier</option><option value="doi">DOI</option><option value="orcid">ORCID</option><option value="license">License (URI)</option><option value="author_id">arXiv author ID</option><option value="help">Help pages</option><option value="full_text">Full text</option></select> <input id="query" name="query" type="text" value="Chacon, A"> <ul id="abstracts"><li><input checked id="abstracts-0" name="abstracts" type="radio" value="show"> <label for="abstracts-0">Show abstracts</label></li><li><input id="abstracts-1" 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is-small is-link">Go</button> </div> </div> </form> </div> </div> <ol class="breathe-horizontal" start="1"> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2411.11547">arXiv:2411.11547</a> <span> [<a href="https://arxiv.org/pdf/2411.11547">pdf</a>, <a href="https://arxiv.org/format/2411.11547">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Distributed, Parallel, and Cluster Computing">cs.DC</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Genomics">q-bio.GN</span> </div> </div> <p class="title is-5 mathjax"> gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/cs?searchtype=author&query=Schmidt%2C+B">Bertil Schmidt</a>, <a href="/search/cs?searchtype=author&query=Kallenborn%2C+F">Felix Kallenborn</a>, <a href="/search/cs?searchtype=author&query=Wichmann%2C+A">Alexander Wichmann</a>, <a href="/search/cs?searchtype=author&query=Chacon%2C+A">Alejandro Chacon</a>, <a href="/search/cs?searchtype=author&query=Hundt%2C+C">Christian Hundt</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2411.11547v1-abstract-short" style="display: inline;"> The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a key component in DNA variant calling tools such as the GATK HaplotypeCaller but can be highly time consuming due to its quadratic time complexity and the large n… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2411.11547v1-abstract-full').style.display = 'inline'; document.getElementById('2411.11547v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2411.11547v1-abstract-full" style="display: none;"> The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a key component in DNA variant calling tools such as the GATK HaplotypeCaller but can be highly time consuming due to its quadratic time complexity and the large number of pairs to be aligned. Unfortunately, previous approaches to accelerate this task using the massively parallel processing capabilities of modern GPUs are limited by inefficient memory access schemes. This established the need for significantly faster solutions. We address this need by presenting gpuPairHMM -- a novel GPU-based parallelization scheme for the dynamic-programming based Pair-HMM forward algorithm based on wavefronts and warp-shuffles. It gains efficiency by minimizing both memory accesses and instructions. We show that our approach achieves close-to-peak performance on several generations of modern CUDA-enabled GPUs (Volta, Ampere, Ada, Hopper). It also outperforms prior implementations on GPUs, CPUs, and FPGAs by a factor of at least 8.6, 10.4, and 14.5, respectively. gpuPairHMM is publicly available at https://github.com/asbschmidt/gpuPairHMM. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2411.11547v1-abstract-full').style.display = 'none'; document.getElementById('2411.11547v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 18 November, 2024; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> November 2024. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2210.00058">arXiv:2210.00058</a> <span> [<a href="https://arxiv.org/pdf/2210.00058">pdf</a>, <a href="https://arxiv.org/format/2210.00058">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Cryptography and Security">cs.CR</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Hardware Architecture">cs.AR</span> </div> </div> <p class="title is-5 mathjax"> Hardware Trojan Threats to Cache Coherence in Modern 2.5D Chiplet Systems </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/cs?searchtype=author&query=Chacon%2C+G+A">Gino A. Chacon</a>, <a href="/search/cs?searchtype=author&query=Williams%2C+C">Charles Williams</a>, <a href="/search/cs?searchtype=author&query=Knechtel%2C+J">Johann Knechtel</a>, <a href="/search/cs?searchtype=author&query=Sinanoglu%2C+O">Ozgur Sinanoglu</a>, <a href="/search/cs?searchtype=author&query=Gratz%2C+P+V">Paul V. Gratz</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2210.00058v1-abstract-short" style="display: inline;"> As industry moves toward chiplet-based designs, the insertion of hardware Trojans poses a significant threat to the security of these systems. These systems rely heavily on cache coherence for coherent data communication, making coherence an attractive target. Critically, unlike prior work, which focuses only on malicious packet modifications, a Trojan attack that exploits coherence can modify dat… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2210.00058v1-abstract-full').style.display = 'inline'; document.getElementById('2210.00058v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2210.00058v1-abstract-full" style="display: none;"> As industry moves toward chiplet-based designs, the insertion of hardware Trojans poses a significant threat to the security of these systems. These systems rely heavily on cache coherence for coherent data communication, making coherence an attractive target. Critically, unlike prior work, which focuses only on malicious packet modifications, a Trojan attack that exploits coherence can modify data in memory that was never touched and is not owned by the chiplet which contains the Trojan. Further, the Trojan need not even be physically between the victim and the memory controller to attack the victim's memory transactions. Here, we explore the fundamental attack vectors possible in chiplet-based systems and provide an example Trojan implementation capable of directly modifying victim data in memory. This work aims to highlight the need for developing mechanisms that can protect and secure the coherence scheme from these forms of attacks. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2210.00058v1-abstract-full').style.display = 'none'; document.getElementById('2210.00058v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 30 September, 2022; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> October 2022. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2111.02493">arXiv:2111.02493</a> <span> [<a href="https://arxiv.org/pdf/2111.02493">pdf</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Signal Processing">eess.SP</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Artificial Intelligence">cs.AI</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Computer Vision and Pattern Recognition">cs.CV</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Instrumentation and Detectors">physics.ins-det</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1088/1361-6501/ac2dbd">10.1088/1361-6501/ac2dbd <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> Roadmap on Signal Processing for Next Generation Measurement Systems </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/cs?searchtype=author&query=Iakovidis%2C+D+K">D. K. Iakovidis</a>, <a href="/search/cs?searchtype=author&query=Ooi%2C+M">M. Ooi</a>, <a href="/search/cs?searchtype=author&query=Kuang%2C+Y+C">Y. C. Kuang</a>, <a href="/search/cs?searchtype=author&query=Demidenko%2C+S">S. Demidenko</a>, <a href="/search/cs?searchtype=author&query=Shestakov%2C+A">A. Shestakov</a>, <a href="/search/cs?searchtype=author&query=Sinitsin%2C+V">V. Sinitsin</a>, <a href="/search/cs?searchtype=author&query=Henry%2C+M">M. Henry</a>, <a href="/search/cs?searchtype=author&query=Sciacchitano%2C+A">A. Sciacchitano</a>, <a href="/search/cs?searchtype=author&query=Discetti%2C+A">A. Discetti</a>, <a href="/search/cs?searchtype=author&query=Donati%2C+S">S. Donati</a>, <a href="/search/cs?searchtype=author&query=Norgia%2C+M">M. Norgia</a>, <a href="/search/cs?searchtype=author&query=Menychtas%2C+A">A. Menychtas</a>, <a href="/search/cs?searchtype=author&query=Maglogiannis%2C+I">I. Maglogiannis</a>, <a href="/search/cs?searchtype=author&query=Wriessnegger%2C+S+C">S. C. Wriessnegger</a>, <a href="/search/cs?searchtype=author&query=Chacon%2C+L+A+B">L. A. Barradas Chacon</a>, <a href="/search/cs?searchtype=author&query=Dimas%2C+G">G. Dimas</a>, <a href="/search/cs?searchtype=author&query=Filos%2C+D">D. Filos</a>, <a href="/search/cs?searchtype=author&query=Aletras%2C+A+H">A. H. Aletras</a>, <a href="/search/cs?searchtype=author&query=T%C3%B6ger%2C+J">J. T枚ger</a>, <a href="/search/cs?searchtype=author&query=Dong%2C+F">F. Dong</a>, <a href="/search/cs?searchtype=author&query=Ren%2C+S">S. Ren</a>, <a href="/search/cs?searchtype=author&query=Uhl%2C+A">A. Uhl</a>, <a href="/search/cs?searchtype=author&query=Paziewski%2C+J">J. Paziewski</a>, <a href="/search/cs?searchtype=author&query=Geng%2C+J">J. Geng</a>, <a href="/search/cs?searchtype=author&query=Fioranelli%2C+F">F. Fioranelli</a> , et al. (9 additional authors not shown) </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2111.02493v3-abstract-short" style="display: inline;"> Signal processing is a fundamental component of almost any sensor-enabled system, with a wide range of applications across different scientific disciplines. Time series data, images, and video sequences comprise representative forms of signals that can be enhanced and analysed for information extraction and quantification. The recent advances in artificial intelligence and machine learning are shi… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2111.02493v3-abstract-full').style.display = 'inline'; document.getElementById('2111.02493v3-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2111.02493v3-abstract-full" style="display: none;"> Signal processing is a fundamental component of almost any sensor-enabled system, with a wide range of applications across different scientific disciplines. Time series data, images, and video sequences comprise representative forms of signals that can be enhanced and analysed for information extraction and quantification. The recent advances in artificial intelligence and machine learning are shifting the research attention towards intelligent, data-driven, signal processing. This roadmap presents a critical overview of the state-of-the-art methods and applications aiming to highlight future challenges and research opportunities towards next generation measurement systems. It covers a broad spectrum of topics ranging from basic to industrial research, organized in concise thematic sections that reflect the trends and the impacts of current and future developments per research field. Furthermore, it offers guidance to researchers and funding agencies in identifying new prospects. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2111.02493v3-abstract-full').style.display = 'none'; document.getElementById('2111.02493v3-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 28 January, 2022; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 3 November, 2021; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> November 2021. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">48 pages, https://iopscience.iop.org/article/10.1088/1361-6501/ac2dbd</span> </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> Measurement Science and Technology 33(1) (2022) 1-48 </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/1610.04121">arXiv:1610.04121</a> <span> [<a href="https://arxiv.org/pdf/1610.04121">pdf</a>, <a href="https://arxiv.org/format/1610.04121">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Computer Vision and Pattern Recognition">cs.CV</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1016/j.procs.2016.05.305">10.1016/j.procs.2016.05.305 <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> Embedded real-time stereo estimation via Semi-Global Matching on the GPU </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/cs?searchtype=author&query=Hernandez-Juarez%2C+D">Daniel Hernandez-Juarez</a>, <a href="/search/cs?searchtype=author&query=Chac%C3%B3n%2C+A">Alejandro Chac贸n</a>, <a href="/search/cs?searchtype=author&query=Espinosa%2C+A">Antonio Espinosa</a>, <a href="/search/cs?searchtype=author&query=V%C3%A1zquez%2C+D">David V谩zquez</a>, <a href="/search/cs?searchtype=author&query=Moure%2C+J+C">Juan Carlos Moure</a>, <a href="/search/cs?searchtype=author&query=L%C3%B3pez%2C+A+M">Antonio Manuel L贸pez</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="1610.04121v1-abstract-short" style="display: inline;"> Dense, robust and real-time computation of depth information from stereo-camera systems is a computationally demanding requirement for robotics, advanced driver assistance systems (ADAS) and autonomous vehicles. Semi-Global Matching (SGM) is a widely used algorithm that propagates consistency constraints along several paths across the image. This work presents a real-time system producing reliable… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1610.04121v1-abstract-full').style.display = 'inline'; document.getElementById('1610.04121v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="1610.04121v1-abstract-full" style="display: none;"> Dense, robust and real-time computation of depth information from stereo-camera systems is a computationally demanding requirement for robotics, advanced driver assistance systems (ADAS) and autonomous vehicles. Semi-Global Matching (SGM) is a widely used algorithm that propagates consistency constraints along several paths across the image. This work presents a real-time system producing reliable disparity estimation results on the new embedded energy-efficient GPU devices. Our design runs on a Tegra X1 at 42 frames per second (fps) for an image size of 640x480, 128 disparity levels, and using 4 path directions for the SGM method. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1610.04121v1-abstract-full').style.display = 'none'; document.getElementById('1610.04121v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 13 October, 2016; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> October 2016. </p> </li> </ol> <div class="is-hidden-tablet">  <span class="help" style="display: inline-block;"><a href="https://github.com/arXiv/arxiv-search/releases">Search v0.5.6 released 2020-02-24</a>  </span> </div> </div> </main> <footer> <div class="columns is-desktop" role="navigation" aria-label="Secondary">  <div class="column"> <div class="columns"> <div class="column"> <ul 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