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An Updated Experimental Evaluation of Graph Bipartization Methods [article]

Timothy D. Goodrich, Eric Horton, Blair D. Sullivan
2021 arXiv   pre-print
We experimentally evaluate the practical state-of-the-art in graph bipartization (Odd Cycle Transversal), motivated by recent advances in near-term quantum computing hardware and the related embedding  ...  In total, over 8000 graph instances are evaluated, compared to the previous canonical corpus of 100 graphs.  ...  In this work, we combine richer data with various timeout scenarios in order to provide a modernized evaluation of OCT methods.  ... 
arXiv:1805.01041v4 fatcat:iyhfmqnzkbbn5lfkfal227qzbm

Algorithm Engineering for Optimal Graph Bipartization

Falk Hüffner
2009 Journal of Graph Algorithms and Applications  
We examine exact algorithms for the NP-hard Graph Bipartization problem. The task is, given a graph, to find a minimum set of vertices to delete to make it bipartite.  ...  Based on the "iterative compression" method introduced by Reed, Smith, and Vetta in 2004, we present new algorithms and experimental results. The worst-case time complexity is improved.  ...  Algorithms We describe two conventional approaches and the iterative compression method. Branch-and-Bound. Wernicke [36] presents an algorithm for Graph Bipartization based on branch-and-bound.  ... 
doi:10.7155/jgaa.00177 fatcat:4lrmvfxhcndsfjtajfcql2hyme

Algorithm Engineering for Optimal Graph Bipartization [chapter]

Falk Hüffner
2005 Lecture Notes in Computer Science  
We examine exact algorithms for the NP-hard Graph Bipartization problem. The task is, given a graph, to find a minimum set of vertices to delete to make it bipartite.  ...  Based on the "iterative compression" method introduced by Reed, Smith, and Vetta in 2004, we present new algorithms and experimental results. The worst-case time complexity is improved.  ...  Graph Bipartization by Iterative Compression In this section, we give an alternative presentation of the algorithm for Graph Bipartization by Reed et al. [33] .  ... 
doi:10.1007/11427186_22 fatcat:qzxhojrswrf45ks4zntpoacnsm

An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations

Y. Pirola, P. Bonizzoni, Tao Jiang
2012 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Finally, we present an extensive experimental evaluation and comparison of our heuristic algorithm with several other state-of-the-art methods for HI on pedigrees.  ...  Secondly, we propose an efficient and accurate heuristic algorithm for MCHC based on an L-reduction to a well-known coding problem.  ...  Part of the work was done when YP was visiting at University of California, Riverside.  ... 
doi:10.1109/tcbb.2011.51 pmid:21383417 fatcat:odi7abhfv5eylp4abhkjdoroum

Towards Online Shortest Path Computation

Leong Hou U, Hong Jun Zhao, Man Lung Yiu, Yuhong Li, Zhiguo Gong
2014 IEEE Transactions on Knowledge and Data Engineering  
An impressive result is that the driver can compute/update their shortest path result by receiving only a small fraction of the index.  ...  This approach has excellent scalability with the number of clients.  ...  It remains, however, an evaluated factor for OSP.  ... 
doi:10.1109/tkde.2013.176 fatcat:e2id3tfmrngutkjgqxhz5nwiri

Fixed-Parameter Algorithms in Analysis of Heuristics for Extracting Networks in Linear Programs [chapter]

Gregory Gutin, Daniel Karapetyan, Igor Razgon
2009 Lecture Notes in Computer Science  
In particular, the FPT algorithm can be used to evaluate the quality of approximation of heuristic approaches.  ...  methods are faster.  ...  The work of G. Gutin was supported in part by a grant from EPSRC. The work of I. Razgon was supported by Science Foundation Ireland grant 05/IN/I886.  ... 
doi:10.1007/978-3-642-11269-0_18 fatcat:upc4576yo5a6ncpspebvjk2vu4

Layout decomposition for double patterning lithography

Andrew B. Kahng, Chul-Hong Park, Xu Xu, Hailong Yao
2008 2008 IEEE/ACM International Conference on Computer-Aided Design  
Experimental results show that our proposed layout decomposition method effectively decomposes given layouts to satisfy the key goals of minimized line-ends and maximized overlap margin.  ...  We evaluate our technique on both real-world and artificially generated testcases in 45nm technology.  ...  method obtains a conflict graph which is 2-colorable.  ... 
doi:10.1109/iccad.2008.4681616 dblp:conf/iccad/KahngPXY08 fatcat:iqkdhiiisves3o3fcvdrweoy4i

Solving #SAT and MAXSAT by Dynamic Programming

Sigve Hortemo Sæther, Jan Arne Telle, Martin Vatshelle
2015 The Journal of Artificial Intelligence Research  
We present some limited experimental results, comparing implementations of our algorithms to state-of-the-art #SAT and MaxSAT solvers, as a proof of concept that warrants further research.  ...  We show that our algorithms extend all previous results for MaxSAT and #SAT achieved by dynamic programming along structural decompositions of the incidence graph of the input formula.  ...  There are 3 tables involved in this update, one at each child and one at the parent. A pair of entries, one from each child table, may lead to an update of an entry in the parent table.  ... 
doi:10.1613/jair.4831 fatcat:akaeiy75tbaibdntc7bwuojr44

More Recent Advances in (Hyper)Graph Partitioning [article]

Ümit V. Çatalyürek, Karen D. Devine, Marcelo Fonseca Faraj, Lars Gottesbüren, Tobias Heuer, Henning Meyerhenke, Peter Sanders, Sebastian Schlag, Christian Schulz, Daniel Seemaier, Dorothea Wagner
2022 arXiv   pre-print
In recent years, significant advances have been made in the design and evaluation of balanced (hyper)graph partitioning algorithms.  ...  Our work serves as an update to a previous survey on the topic.  ...  We would like to thank Ilya Safro for feedback and additional references on an early version of the manuscript.  ... 
arXiv:2205.13202v3 fatcat:xgz5hgqgireojelyaegrbyxoua

The Link Prediction Problem in Bipartite Networks [article]

Jérôme Kunegis and Ernesto W. De Luca and Sahin Albayrak
2010 arXiv   pre-print
In a graph, a link prediction function of two vertices denotes the similarity or proximity of the vertices.  ...  Since in a bipartite graph adjacency vertices can only be connected by paths of odd lengths, these functions do not apply to bipartite graphs.  ...  Measures for the level of bipartivity exist in several forms [4, 27] , and spectral transformations offer another method.  ... 
arXiv:1006.5367v1 fatcat:3k2ox2b3vfa25f37wjuzkafdhe

A graph-based clustering method for a large set of sequences using a graph partitioning algorithm

H Kawaji, Y Yamaguchi, H Matsuda, A Hashimoto
2001 Genome Informatics Series  
A graph-based clustering method is proposed to cluster protein sequences into families, which automatically improves clusters of the conventional single linkage clustering method.  ...  Our approach formulates sequence clustering problem as a kind of graph partitioning problem in a weighted linkage graph, which vertices correspond to sequences, edges correspond to higher similarities  ...  (9) Update SLT for new W LG, and N for new SLT . An example of clustering process is showed in Figure 3 .  ... 
pmid:11791228 fatcat:uwrojme7evgodc4xm3tdfmux5a

Combinatorial clustering and Its Application to 3D Polygonal Traffic Sign Reconstruction From Multiple Images

B. Vallet, B. Soheilian, M. Brédif
2014 ISPRS Annals of the Photogrammetry, Remote Sensing and Spatial Information Sciences  
The proposed method is applied to the reconstruction of 3D traffic signs from their 2D detections to demonstrate its capacity to solve ambiguities.  ...  This paper formulates a framework to use the geometric quality of the reconstruction as a hint to do a proper clustering.  ...  ACKNOWLEDGEMENTS This study has been performed as part of the Cap Digital Business Cluster TerraMobilita Project.  ... 
doi:10.5194/isprsannals-ii-3-165-2014 fatcat:sum4cmvfyjaffae3zyatnc7jh4

Scalable Hypergraph Embedding System [article]

Sepideh Maleki, Donya Saless, Dennis P. Wall, Keshav Pingali
2022 arXiv   pre-print
While hypergraphs are a generalization of graphs, state-of-the-art graph embedding techniques are not adequate for solving prediction and classification tasks on large hypergraphs accurately in reasonable  ...  However, it is difficult to use graphs to capture non-binary relations such as communities of nodes. These kinds of complex relations are expressed more naturally as hypergraphs.  ...  Prior works such as HyperGCN and Hyper-SAGNN have been evaluated for one or the other of these tasks but not both. Experimental settings. We implement HyperNetVec in Galois 6.0 [23] .  ... 
arXiv:2103.09660v5 fatcat:ewhwt22v3nbk5emcovwiwtx2ya

Topological network measures for drug repositioning

Apurva Badkas, Sébastien De Landtsheer, Thomas Sauter
2020 Briefings in Bioinformatics  
Computational approaches are significantly contributing to these efforts, of which, network-based methods play a key role.  ...  This review gives a broad overview of the topic, and offers perspectives on the application of topological measures for network analysis.  ...  In order to control for experimental/methodological biases, the design and selection of appropriate control graphs is an important aspect.  ... 
doi:10.1093/bib/bbaa357 pmid:33348366 pmcid:PMC8294518 fatcat:zc2wwglvxbeb3fxxjypukchpzq

Layout Decomposition Approaches for Double Patterning Lithography

Andrew B. Kahng, Chul-Hong Park, Xu Xu, Hailong Yao
2010 IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems  
We evaluate our methods on both real and artificial 45 nm testcases.  ...  Experimental results show that our proposed layout decomposition approaches effectively decompose given layouts to satisfy the key goals of minimized line-ends and maximized overlap margin.  ...  More precisely, given a layout, the steps of "layout fracturing," "graph construction," "node splitting," and "graph update" are the same as in the CCD approach, and yield an updated conflict graph on  ... 
doi:10.1109/tcad.2010.2048374 fatcat:fe4trk6oxbbntacag7icyrkkuq
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