Search Results - Memory efficient graph algorithms

Memory efficient algorithms for cactus graphs and block graphs by Brimkov, Boris, Hicks, Illya V.

“… of cactus graphs and block graphs. For some of these problems we also present in-place algorithms, which perform faster than the corresponding constant-work-space algorithms…”
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Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs by Holley, Guillaume, Melsted, Páll

“… We present a parallel and memory-efficient algorithm enabling the direct construction of the compacted de Bruijn graph without producing the intermediate uncompacted graph…”
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A Scalable, Memory-Efficient Algorithm for Minimum Cycle Mean Calculation in Directed Graphs by Maji, Supriyo, Koh, Cheng-Kok

“… However, as an efficient implementation of YTO relies on data redundancy, its memory usage is higher and could be a prohibitive factor in large size problems…”
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A memory-efficient algorithm to obtain splicing graphs and de novoexpression estimates from de Bruijn graphs of RNA-Seq data by Sze, Sing-Hoi, Tarone, Aaron M

“… Results Since the de Bruijn graph contains all branching possibilities, we develop a memory-efficient algorithm to recover alternative splicing information and library-specific expression information…”
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A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data by Sze, Sing-Hoi, Tarone, Aaron M

“… Since the de Bruijn graph contains all branching possibilities, we develop a memory-efficient algorithm to recover alternative splicing information and library-specific expression information…”
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ODGI: understanding pangenome graphs by Guarracino, Andrea, Heumos, Simon, Nahnsen, Sven, Prins, Pjotr, Garrison, Erik

“… Results We wrote Optimized Dynamic Genome/Graph Implementation (ODGI), a novel suite of tools that implements scalable algorithms and has an efficient in-memory representation of DNA pangenome graphs in the form of variation graphs…”
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vGraph: Memory-Efficient Multicore Graph Processing for Traversal-Centric Algorithms by Jia, Menghan, Zhang, Yiming, Gan, Xinbiao, Li, Dongsheng, Xu, Erci, Wang, Ruibo, Lu, Kai

“… This paper presents v Graph, a NUMA-aware, memory-efficient multicore graph processing system for traversal-centric algorithms…”
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Memory Efficient Edge Addition Designs for Large and Dynamic Social Networks by Santos, Eunice E., Murugappan, Vairavan, Korah, John

“… In addition, the size of these information sources is constantly increasing, therefore we need designs that can perform analysis that are memory efficient in order to address resource constraints. In this paper, we show how our anytime anywhere framework can be used to construct memory-efficient closeness centrality algorithms. In particular, we will show how dynamic edge additions can be efficiently handled in the proposed scheme…”
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Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs by Kundeti, Vamsi K, Rajasekaran, Sanguthevar, Dinh, Hieu, Vaughn, Matthew, Thapar, Vishal

“… Efficient algorithms for building these massive de Bruijn graphs are very essential in large sequencing projects based on short reads…”
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I/O-Efficient Algorithms for Degeneracy Computation on Massive Networks by Li, Rong-Hua, Song, Qiushuo, Xiao, Xiaokui, Qin, Lu, Wang, Guoren, Yu, Jeffrey Xu, Mao, Rui

“… In this paper, we propose an I/O-efficient algorithm to compute the degeneracy of the massive graph that cannot be fully kept in the main memory…”
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Time and Memory Efficient Parallel Algorithm for Structural Graph Summaries and two Extensions to Incremental Summarization and \(k\)-Bisimulation for Long \(k\)-Chaining by Blume, Till, Rau, Jannik, Richerby, David, Scherp, Ansgar

“…We developed a flexible parallel algorithm for graph summarization based on vertex-centric programming and parameterized message passing…”
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GraphLily: Accelerating Graph Linear Algebra on HBM-Equipped FPGAs by Hu, Yuwei, Du, Yixiao, Ustun, Ecenur, Zhang, Zhiru

“…Graph processing is typically memory bound due to low compute to memory access ratio and irregular data access pattern…”
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Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data by Dhapola, Parashar, Rodhe, Johan, Olofzon, Rasmus, Bonald, Thomas, Erlandsson, Eva, Soneji, Shamit, Karlsson, Göran

“… Scarf wraps memory-efficient implementations of a graph-based t-stochastic neighbour embedding and hierarchical clustering algorithm…”
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Memory and communication efficient algorithm for decentralized counting of nodes in networks by Saha, Arindam, Marshall, James A. R., Reina, Andreagiovanni

“…, such as collective robotics and distributed sensor networks. Thus several stochastic and naïve deterministic algorithms for distributed graph size estimation or calculation have been provided…”
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A fast and memory efficient MLCS algorithm by character merging for DNA sequences alignment by Liu, Sen, Wang, Yuping, Tong, Wuning, Wei, Shiwei

“… With the increasing in sequence length and number of sequences, the existing dynamic programming algorithms and the dominant point-based algorithms become ineffective and inefficient, especially…”
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SimRank: effective and scalable pairwise similarity search based on graph topology by Yu, Weiren, Lin, Xuemin, Zhang, Wenjie, Pei, Jian, McCann, Julie A.

“…Given a graph, how can we quantify similarity between two nodes in an effective and scalable way…”
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A Graph Theoretic Framework of Recomputation Algorithms for Memory-Efficient Backpropagation by Kusumoto, Mitsuru, Inoue, Takuya, Watanabe, Gentaro, Akiba, Takuya, Koyama, Masanori

“…Recomputation algorithms collectively refer to a family of methods that aims to reduce the memory consumption of the backpropagation by selectively discarding the intermediate results of the forward…”
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Efficient Distributed Graph Algorithms for High Performance Computing Contexts by Bogle, Ian

“…There exists a rich and long-standing body of literature on the topic of efficient, parallel graph algorithms…”
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Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections by Khan, Jamshed, Patro, Rob

“… analyses on these genomes. Therefore, time- and memory-efficient construction of the graph from reference sequences is an important problem…”
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I/O efficient Core Graph Decomposition at web scale by Dong Wen, Lu Qin, Ying Zhang, Xuemin Lin, Yu, Jeffrey Xu

“… Nevertheless, many real-world graphs are big and may not reside in memory. In the literature, there is only one work for I/O efficient core decomposition that avoids loading the whole graph in memory…”
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