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Scaling iterative graph computations with GraphMap

Kisung Lee, Ling Liu, Karsten Schwan, Calton Pu, Qi Zhang, Yang Zhou, Emre Yigitoglu, Pingpeng Yuan
2015 Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '15  
This paper presents GraphMap, a distributed iterative graph computation framework that maximizes access locality and speeds up distributed iterative graph computations by effectively utilizing secondary  ...  Extensive experiments on several real-world graphs show that GraphMap outperforms existing distributed memory-based systems for various iterative graph algorithms.  ...  Considerable research effort on scaling large graph computations has been devoted to two different directions: One is to deploy a super powerful many-core computer with memory capac-Permission to make  ... 
doi:10.1145/2807591.2807604 dblp:conf/sc/LeeLSPZZYY15 fatcat:sxwjv6iq6beexlz5tz2qb5od5e

GraphMaps: Browsing Large Graphs as Interactive Maps [article]

Lev Nachmanson, Roman Prutkin, Bongshin Lee, Nathalie Henry Riche, Alexander E. Holroyd, Xiaoji Chen
2015 arXiv   pre-print
Our case studies indicate that GraphMaps is useful in gaining an overview of a large graph, and also in exploring a graph on a finer level of detail.  ...  GraphMaps preprocesses a graph in such a way that during browsing, the geometry of the entities is stable, and the viewer is responsive.  ...  We are grateful to Roberto Sonnino for the useful discussions on the rendering of the tile images in a background thread, and to Itzhak Benenson for sharing with us his ideas on the visualization style  ... 
arXiv:1506.06745v1 fatcat:odb4rzlftzhtxao4gdqxbl23da

GraphMaps: Browsing Large Graphs as Interactive Maps [chapter]

Lev Nachmanson, Roman Prutkin, Bongshin Lee, Nathalie Henry Riche, Alexander E. Holroyd, Xiaoji Chen
2015 Lecture Notes in Computer Science  
Our case studies indicate that GraphMaps is useful in gaining an overview of a large graph, and also in exploring a graph on a finer level of detail.  ...  GraphMaps preprocesses a graph in such a way that during browsing, the geometry of the entities is stable, and the viewer is responsive.  ...  We are grateful to Roberto Sonnino for the useful discussions on the rendering of the tile images in a background thread, and to Itzhak Benenson for sharing with us his ideas on the visualization style  ... 
doi:10.1007/978-3-319-27261-0_1 fatcat:fbr7r7antzgrzonw2xnyljrh7e

A New Approach to GraphMaps, a System Browsing Large Graphs as Interactive Maps [article]

Debajyoti Mondal, Lev Nachmanson
2018 arXiv   pre-print
We think that keeping this change small facilitates smooth browsing of the graph. We also propose new node selection techniques to cope with some of the challenges of the GraphMaps approach.  ...  GraphMaps reveals the structural properties of the graph and enables users to explore the graph in a natural way by using the standard zoom and pan operations.  ...  By browsing a graph with GraphMaps, the user obtains a quick overview of the important elements. Navigation through different zoom levels reveals the structure of the graph.  ... 
arXiv:1705.05479v2 fatcat:il6xzsmjgbhebfzqz6aotkvjie

Metric-topological maps from laser scans adjusted with incremental tree network optimizer

Dario Lodi Rizzini, Stefano Caselli
2009 Robotics and Autonomous Systems  
The second map builder stores a hybrid metric-topological representation: the map consists of a graph whose nodes contain local occupancy grid maps and whose edges are labeled with relative pose between  ...  After a preliminary selection of pose constraints candidates, relative pose is computed through standard scan matching techniques.  ...  GraphMap GraphMap consists of a graph whose nodes store poses with a local map and whose edges correspond to constraints between pairs of nodes like in ScanMap.  ... 
doi:10.1016/j.robot.2009.07.022 fatcat:bggkziihvfgyxpkpq3d3bwzl7u

Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap [article]

Ivan Sovic, Mile Sikic, Andreas Wilm, Shannon Nicole Fenlon, Swaine Chen, Niranjan Nagarajan
2015 bioRxiv   pre-print
We present the first nanopore read mapper (GraphMap) that uses a read-funneling paradigm to robustly handle variable error rates and fast graph traversal to align long reads with speed and very high precision  ...  GraphMap alignments are the first to demonstrate consensus calling with <1 error in 100,000 bases, variant calling on the human genome with 76% improvement in sensitivity over the next best mapper (BWA-MEM  ...  GraphMap retains BLAST's sensitivity while scaling well with genome size.  ... 
doi:10.1101/020719 fatcat:zby4yboit5crpkvpmd4z6xx64i

MABP: an optimal resource allocation approach in data center networks

XiaoLing Li, HuaiMin Wang, Bo Ding, XiaoYong Li
2014 Science China Information Sciences  
Furthermore, SN consists of a large number of servers connecting via physical links, while WKs are service demands made to the cloud by cloud users/tenants, which are modeled as graph with a set of processes  ...  with communication between them [5].  ...  Along with the increase in the scale of SN and the number of variables in WK, the computation cost becomes larger.  ... 
doi:10.1007/s11432-014-5164-y fatcat:ttjoe7bbzbdcfn6a4rayeg7ozm

Overlapping long sequence reads: Current innovations and challenges in developing sensitive, specific and scalable algorithms [article]

Justin Chu, Hamid Mohamadi, Rene Warren, Chen Yang, Inanc Birol
2016 bioRxiv   pre-print
We benchmarked these tools, tracking their resource needs and computational performance, and assessed the specificity and precision of each.  ...  The concepts surveyed may apply to future sequencing technologies, as scalability is becoming more relevant with increased sequencing throughput.  ...  Acknowledgements The authors would like to thank Sergey Koren, Ivan Sović for their help and suggestions when running MHAP and GraphMap, respectively, as well as their insights into the behaviour and results  ... 
doi:10.1101/081596 fatcat:bft5rd5svrhh5mgnaozkh35nue

Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design [article]

Damla Senol Cali
2021 arXiv   pre-print
However, the analysis of genome sequencing data is currently bottlenecked by the computational power and memory bandwidth limitations of existing systems.  ...  Fourth, we propose SeGraM, the first hardware acceleration framework for sequence-to-graph mapping and alignment.  ...  using specialized compute units that we design to exploit data locality, and (3) scales linearly in performance with the number of parallel compute units that we add to the system.  ... 
arXiv:2111.01916v1 fatcat:lbwk74jcbjgqzeqk7gnb77asja

Minimum Congestion Mapping in a Cloud

Nikhil Bansal, Kang-Won Lee, Viswanath Nagarajan, Murtaza Zafer
2015 SIAM journal on computing (Print)  
The physical network of the cloud is represented as a graph with vertices denoting servers and edges corresponding to communication links.  ...  We study a basic resource allocation problem that arises in cloud computing environments.  ...  By scaling edge capacities in the substrate graph, we can assume that the workload H is a complete graph K r with unit demand between every pair of vertices.  ... 
doi:10.1137/110845239 fatcat:qxgk7egqmfanrmzf4ngot6akge

Minimum congestion mapping in a cloud

Nikhil Bansal, Kang-Won Lee, Viswanath Nagarajan, Murtaza Zafer
2011 Proceedings of the 30th annual ACM SIGACT-SIGOPS symposium on Principles of distributed computing - PODC '11  
The physical network of the cloud is represented as a graph with vertices denoting servers and edges corresponding to communication links.  ...  We study a basic resource allocation problem that arises in cloud computing environments.  ...  By scaling edge capacities in the substrate graph, we can assume that the workload H is a complete graph K r with unit demand between every pair of vertices.  ... 
doi:10.1145/1993806.1993854 dblp:conf/podc/BansalLNZ11 fatcat:4mlwruw4w5fkdjldvuyumbjaji

Multi-GPU Graph Analytics [article]

Yuechao Pan, Yangzihao Wang, Yuduo Wu, Carl Yang, John D. Owens
2017 arXiv   pre-print
We present a single-node, multi-GPU programmable graph processing library that allows programmers to easily extend single-GPU graph algorithms to achieve scalable performance on large graphs with billions  ...  We analyze the theoretical and practical limits to scalability in the context of varying graph primitives and datasets.  ...  Except for DOBFS and for graphs that have too little computation to fill the GPU on an iteration, most primitives are bounded by computation.  ... 
arXiv:1504.04804v4 fatcat:o2g3vpa6andmnfh33uwu4t3nle

A long read mapping method for highly repetitive reference sequences [article]

Chirag Jain, Arang Rhie, Nancy Hansen, Sergey Koren, Adam M. Phillippy
2020 bioRxiv   pre-print
We mathematically define MCASs and discuss an exact algorithm as well as a practical heuristic to compute them.  ...  MCASs are formulated as minimal length substrings of a read that have unique alignments to a reference locus with sufficient mapping confidence (i.e., a mapping quality score above a user-specified threshold  ...  GRAPHMAP Illustrating allelic bias Figure 2 shows an IGV visualization of primary alignments computed by Winnowmap2 and three other long read mapping tools NGMLR, minimap2 and graphmap.  ... 
doi:10.1101/2020.11.01.363887 fatcat:eq5il5khhzfdphfb7zylffnknu

Multi-level tree based approach for interactive graph visualization with semantic zoom [article]

Felice De Luca, Iqbal Hossain, Kathryn Gray, Stephen Kobourov, Katy Börner
2019 arXiv   pre-print
With this in mind, we propose the Zoomable Multi-Level Tree (ZMLT) algorithm for multi-level tree-based, map-like visualization of large graphs.  ...  of details; (2) The embedded trees represent the underlying graph appropriately at different levels of details; (3) At every level of detail we show real vertices and real paths from the underlying graph  ...  Note that this approach reduces label overlap iteratively.  ... 
arXiv:1906.05996v2 fatcat:z4g6l2c6xbal5pxznxglbmnfya

Fast and accurate de novo genome assembly from long uncorrected reads [article]

Robert Vaser, Ivan Sovic, Niranjan Nagarajan, Mile Sikic
2016 biorxiv/medrxiv   pre-print
Based on tests with PacBio and Oxford Nanopore datasets we show that Racon coupled with Miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order  ...  We show that the error correction step can be omitted and high quality consensus sequences can be generated efficiently with a SIMD accelerated, partial order alignment based stand-alone consensus module  ...  These sequences can be further polished with Quiver or Nanopolish or by applying Racon for more iterations.  ... 
doi:10.1101/068122 fatcat:gfeomkurbvgcfe6gpu4izufwoi
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