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Reflections on multivariate algorithmics and problem parameterization
 PROC. 27TH STACS
, 2010
"... Research on parameterized algorithmics for NPhard problems has steadily grown over the last years. We survey and discuss how parameterized complexity analysis naturally develops into the field of multivariate algorithmics. Correspondingly, we describe how to perform a systematic investigation and e ..."
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Research on parameterized algorithmics for NPhard problems has steadily grown over the last years. We survey and discuss how parameterized complexity analysis naturally develops into the field of multivariate algorithmics. Correspondingly, we describe how to perform a systematic investigation and exploitation of the “parameter space” of computationally hard problems.
Parameterized Algorithmics for Finding Connected Motifs in Biological Networks
 IEEE TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
"... We study the NPhard LISTCOLORED GRAPH MOTIF problem which, given an undirected listcolored graph G = (V, E) and a multiset M of colors, asks for maximumcardinality sets S ⊆ V and M ′ ⊆ M such that G[S] is connected and contains exactly (with respect to multiplicity) the colors in M ′. LISTCOLO ..."
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We study the NPhard LISTCOLORED GRAPH MOTIF problem which, given an undirected listcolored graph G = (V, E) and a multiset M of colors, asks for maximumcardinality sets S ⊆ V and M ′ ⊆ M such that G[S] is connected and contains exactly (with respect to multiplicity) the colors in M ′. LISTCOLORED GRAPH MOTIF has applications in the analysis of biological networks. We study LISTCOLORED GRAPH MOTIF with respect to three different parameterizations. For the parameters motif size M  and solution size S  we present fixedparameter algorithms, whereas for the parameter V −M  we show W[1]hardness for general instances and achieve fixedparameter tractability for a special case of LISTCOLORED GRAPH MOTIF. We implemented the fixedparameter algorithms for parameters M  and S, developed further speedup heuristics for these algorithms, and applied them in the context of querying proteininteraction networks, demonstrating their usefulness for realistic instances. Furthermore, we show that extending the request for motif connectedness to stronger demands such as biconnectedness or bridgeconnectedness leads to W[1]hard problems when the parameter is the motif size M.
Parameterized algorithmics for computational social choice: nine research challenges
 Tsinghua Science and Technology
, 2014
"... Computational Social Choice is an interdisciplinary research area involving Economics, Political Science, and Social Science on the one side, and Mathematics and Computer Science (including Artificial Intelligence and Multiagent Systems) on the other side. Typical computational problems studied in ..."
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Computational Social Choice is an interdisciplinary research area involving Economics, Political Science, and Social Science on the one side, and Mathematics and Computer Science (including Artificial Intelligence and Multiagent Systems) on the other side. Typical computational problems studied in this field include the vulnerability of voting procedures against attacks, or preference aggregation in multiagent systems. Parameterized Algorithmics is a subfield of Theoretical Computer Science seeking to exploit meaningful problemspecific parameters in order to identify tractable special cases of in general computationally hard problems. In this paper, we propose nine of our favorite research challenges concerning the parameterized complexity of problems appearing in this context.
Parameterized Enumeration of Neighbour Strings and Kemeny Aggregations
, 2013
"... I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii In this thesis, we consider approaches to enumeration ..."
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I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii In this thesis, we consider approaches to enumeration problems in the parameterized complexity setting. We obtain competitive parameterized algorithms to enumerate all, as well as several of, the solutions for two related problems Neighbour String and Kemeny Rank Aggregation. In both problems, the goal is to find a solution that is as close as possible to a set of inputs (strings and total orders, respectively) according to some distance measure. We also introduce a notion of enumerative kernels for which there is a bijection between solutions to the original instance and solutions to the kernel, and provide such a kernel for Kemeny Rank Aggregation, improving a previous kernel for the problem. We demonstrate how several of the algorithms and notions discussed in this thesis are extensible to a group of parameterized problems, improving published results for some other problems. iii Acknowledgements I would like to thank my supervisor, Professor Naomi Nishimura, for her generous support and invaluable advice on my research. I would also like to thank Professor Jonathan Buss and Professor Timothy Chan for their helpful comments on the direction of my research. I wish to thank Professor Bin Ma for fruitful discussions on some of the results in this work. I am also grateful to my thesis committee for spending their valuable time reading this thesis, and for their suggestions which improved the content and presentation of my work. Special thanks to my family for their encouragement and love, and to the many friends I met in Waterloo, for making my PhD experience really enjoyable. iv