2 Search Results for "Shamir, Ron"

Document
DOI: 10.4230/LIPIcs.SEA.2023.14
A Graph-Theoretic Formulation of Exploratory Blockmodeling

Authors: Alexander Bille, Niels Grüttemeier, Christian Komusiewicz, and Nils Morawietz

Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)

Abstract
We present a new simple graph-theoretic formulation of the exploratory blockmodeling problem on undirected and unweighted one-mode networks. Our formulation takes as input the network G and the maximum number t of blocks for the solution model. The task is to find a minimum-size set of edge insertions and deletions that transform the input graph G into a graph G' with at most t neighborhood classes. Herein, a neighborhood class is a maximal set of vertices with the same neighborhood. The neighborhood classes of G' directly give the blocks and block interactions of the computed blockmodel. We analyze the classic and parameterized complexity of the exploratory blockmodeling problem, provide a branch-and-bound algorithm, an ILP formulation and several heuristics. Finally, we compare our exact algorithms to previous ILP-based approaches and show that the new algorithms are faster for t ≥ 4.
Cite as

Alexander Bille, Niels Grüttemeier, Christian Komusiewicz, and Nils Morawietz. A Graph-Theoretic Formulation of Exploratory Blockmodeling. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 14:1-14:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{bille_et_al:LIPIcs.SEA.2023.14,
  author =	{Bille, Alexander and Gr\"{u}ttemeier, Niels and Komusiewicz, Christian and Morawietz, Nils},
  title =	{{A Graph-Theoretic Formulation of Exploratory Blockmodeling}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{14:1--14:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.14},
  URN =		{urn:nbn:de:0030-drops-183648},
  doi =		{10.4230/LIPIcs.SEA.2023.14},
  annote =	{Keywords: Clustering, Exact Algorithms, ILP-Formulation, Branch-and-Bound, Social Networks}
}
Document
DOI: 10.4230/LIPIcs.CPM.2016.16
A Linear-Time Algorithm for the Copy Number Transformation Problem

Authors: Ron Shamir, Meirav Zehavi, and Ron Zeira

Published in: LIPIcs, Volume 54, 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)

Abstract
Problems of genome rearrangement are central in both evolution and cancer. Most evolutionary scenarios have been studied under the assumption that the genome contains a single copy of each gene. In contrast, tumor genomes undergo deletions and duplications, and thus the number of copies of genes varies. The number of copies of each gene along a chromosome is called its copy number profile. Understanding copy number profile changes can assist in predicting disease progression and treatment. To date, questions related to distances between copy number profiles gained little scientific attention. Here we focus on the following fundamental problem, introduced by Schwarz et al. (PLOS Comp. Biol., 2014): given two copy number profiles, u and v, compute the edit distance from u to v, where the edit operations are segmental deletions and amplifications. We establish the computational complexity of this problem, showing that it is solvable in linear time and constant space.
Cite as

Ron Shamir, Meirav Zehavi, and Ron Zeira. A Linear-Time Algorithm for the Copy Number Transformation Problem. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 16:1-16:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2016)

Copy BibTex To Clipboard

@InProceedings{shamir_et_al:LIPIcs.CPM.2016.16,
  author =	{Shamir, Ron and Zehavi, Meirav and Zeira, Ron},
  title =	{{A Linear-Time Algorithm for the Copy Number Transformation Problem}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{16:1--16:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-012-5},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{54},
  editor =	{Grossi, Roberto and Lewenstein, Moshe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.16},
  URN =		{urn:nbn:de:0030-drops-60789},
  doi =		{10.4230/LIPIcs.CPM.2016.16},
  annote =	{Keywords: Genome Rearrangement, Copy Number}
}
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