2 Search Results for "Kreutzer, Christoph"


Document
Online Transitivity Clustering of Biological Data with Missing Values

Authors: Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, and Jan Baumbach

Published in: OASIcs, Volume 26, German Conference on Bioinformatics 2012


Abstract
Motivation: Equipped with sophisticated biochemical measurement techniques we generate a massive amount of biomedical data that needs to be analyzed computationally. One long-standing challenge in automatic knowledge extraction is clustering. We seek to partition a set of objects into groups such that the objects within the clusters share common traits. Usually, we have given a similarity matrix computed from a pairwise similarity function. While many approaches for biomedical data clustering exist, most methods neglect two important problems: (1) Computing the similarity matrix might not be trivial but resource-intense. (2) A clustering algorithm itself is not sufficient for the biologist, who needs an integrated online system capable of performing preparative and follow-up tasks as well. Results: Here, we present a significantly extended version of Transitivity Clustering. Our first main contribution is its’ capability of dealing with missing values in the similarity matrix such that we save time and memory. Hence, we reduce one main bottleneck of computing all pairwise similarity values. We integrated this functionality into the Weighted Graph Cluster Editing model underlying Transitivity Clustering. By means of identifying protein (super)families from incomplete all-vs-all BLAST results we demonstrate the robustness of our approach. While most tools concentrate on the partitioning process itself, we present a new, intuitive web interface that aids with all important steps of a cluster analysis: (1) computing and post-processing of a similarity matrix, (2) estimation of a meaningful density parameter, (3) clustering, (4) comparison with given gold standards, and (5) fine-tuning of the clustering by varying the parameters. Availability: Transitivity Clustering, the new Cost Matrix Creator, all used data sets as well as an online documentation are online available at http://transclust.mmci.uni-saarland.de/.

Cite as

Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, and Jan Baumbach. Online Transitivity Clustering of Biological Data with Missing Values. In German Conference on Bioinformatics 2012. Open Access Series in Informatics (OASIcs), Volume 26, pp. 57-68, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)


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@InProceedings{rottger_et_al:OASIcs.GCB.2012.57,
  author =	{R\"{o}ttger, Richard and Kreutzer, Christoph and Vu, Thuy Duong and Wittkop, Tobias and Baumbach, Jan},
  title =	{{Online Transitivity Clustering of Biological Data with Missing Values}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{57--68},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{B\"{o}cker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2012.57},
  URN =		{urn:nbn:de:0030-drops-37189},
  doi =		{10.4230/OASIcs.GCB.2012.57},
  annote =	{Keywords: Transitivity Clustering, Large Scale clustering, Missing Values, Web Interface}
}
Document
Lower Bounds on the Complexity of MSO_1 Model-Checking

Authors: Robert Ganian, Petr Hlineny, Alexander Langer, Jan Obdržálek, Peter Rossmanith, and Somnath Sikdar

Published in: LIPIcs, Volume 14, 29th International Symposium on Theoretical Aspects of Computer Science (STACS 2012)


Abstract
One of the most important algorithmic meta-theorems is a famous result by Courcelle, which states that any graph problem definable in monadic second-order logic with edge-set quantifications (MSO2) is decidable in linear time on any class of graphs of bounded tree-width. In the parlance of parameterized complexity, this means that MSO2 model-checking is fixed-parameter tractable with respect to the tree-width as parameter. Recently, Kreutzer and Tazari proved a corresponding complexity lower-bound---that MSO2 model-checking is not even in XP wrt the formula size as parameter for graph classes that are subgraph-closed and whose tree-width is poly-logarithmically unbounded. Of course, this is not an unconditional result but holds modulo a certain complexity-theoretic assumption, namely, the Exponential Time Hypothesis (ETH). In this paper we present a closely related result. We show that even MSO1 model-checking with a fixed set of vertex labels, but without edge-set quantifications, is not in XP wrt the formula size as parameter for graph classes which are subgraph-closed and whose tree-width is poly-logarithmically unbounded unless the non-uniform ETH fails. In comparison to Kreutzer and Tazari, (1) we use a stronger prerequisite, namely non-uniform instead of uniform ETH, to avoid the effectiveness assumption and the construction of certain obstructions used in their proofs; and (2) we assume a different set of problems to be efficiently decidable, namely MSO1-definable properties on vertex labeled graphs instead of MSO2-definable properties on unlabeled graphs. Our result has an interesting consequence in the realm of digraph width measures: Strengthening a recent result, we show that no subdigraph-monotone measure can be algorithmically useful, unless it is within a poly-logarithmic factor of (undirected) tree-width.

Cite as

Robert Ganian, Petr Hlineny, Alexander Langer, Jan Obdržálek, Peter Rossmanith, and Somnath Sikdar. Lower Bounds on the Complexity of MSO_1 Model-Checking. In 29th International Symposium on Theoretical Aspects of Computer Science (STACS 2012). Leibniz International Proceedings in Informatics (LIPIcs), Volume 14, pp. 326-337, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)


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@InProceedings{ganian_et_al:LIPIcs.STACS.2012.326,
  author =	{Ganian, Robert and Hlineny, Petr and Langer, Alexander and Obdr\v{z}\'{a}lek, Jan and Rossmanith, Peter and Sikdar, Somnath},
  title =	{{Lower Bounds on the Complexity of MSO\underline1 Model-Checking}},
  booktitle =	{29th International Symposium on Theoretical Aspects of Computer Science (STACS 2012)},
  pages =	{326--337},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-35-4},
  ISSN =	{1868-8969},
  year =	{2012},
  volume =	{14},
  editor =	{D\"{u}rr, Christoph and Wilke, Thomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2012.326},
  URN =		{urn:nbn:de:0030-drops-34185},
  doi =		{10.4230/LIPIcs.STACS.2012.326},
  annote =	{Keywords: Monadic Second-Order Logic, Treewidth, Lower Bounds, Exponential Time Hypothesis, Parameterized Complexity}
}
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