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**Published in:** LIPIcs, Volume 285, 18th International Symposium on Parameterized and Exact Computation (IPEC 2023)

Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. We consider an extension of PD to phylogenetic networks. Given a phylogenetic network with weighted edges and a subset S of leaves, the all-paths phylogenetic diversity of S is the summed weight of all edges on a path from the root to some leaf in S. The problem of finding a bounded-size set S that maximizes this measure is polynomial-time solvable on trees, but NP-hard on networks. We study the latter from a parameterized perspective.
While this problem is W[2]-hard with respect to the size of S (and W[1]-hard with respect to the size of the complement of S), we show that it is FPT with respect to several other parameters, including the phylogenetic diversity of S, the acceptable loss of phylogenetic diversity, the number of reticulations in the network, and the treewidth of the underlying graph.

Mark Jones and Jannik Schestag. How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks. In 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 285, pp. 30:1-30:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{jones_et_al:LIPIcs.IPEC.2023.30, author = {Jones, Mark and Schestag, Jannik}, title = {{How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks}}, booktitle = {18th International Symposium on Parameterized and Exact Computation (IPEC 2023)}, pages = {30:1--30:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-305-8}, ISSN = {1868-8969}, year = {2023}, volume = {285}, editor = {Misra, Neeldhara and Wahlstr\"{o}m, Magnus}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2023.30}, URN = {urn:nbn:de:0030-drops-194496}, doi = {10.4230/LIPIcs.IPEC.2023.30}, annote = {Keywords: Phylogenetic Networks, Phylogenetic Diversity, Parameterized Complexity, W-hierarchy, FPT algorithms} }

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**Published in:** LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the network class ideal for capturing evolutionary histories that involve horizontal gene transfers. Here, we study the minimum number of additional leaves needed to make a network orchard. We demonstrate that computing this proximity measure for a given network is NP-hard and describe a tight upper bound. We also give an equivalent measure based on vertex labellings to construct a mixed integer linear programming formulation. Our experimental results, which include both real-world and synthetic data, illustrate the efficiency of our implementation.

Leo van Iersel, Mark Jones, Esther Julien, and Yukihiro Murakami. Making a Network Orchard by Adding Leaves. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 7:1-7:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{vaniersel_et_al:LIPIcs.WABI.2023.7, author = {van Iersel, Leo and Jones, Mark and Julien, Esther and Murakami, Yukihiro}, title = {{Making a Network Orchard by Adding Leaves}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {7:1--7:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-294-5}, ISSN = {1868-8969}, year = {2023}, volume = {273}, editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.7}, URN = {urn:nbn:de:0030-drops-186333}, doi = {10.4230/LIPIcs.WABI.2023.7}, annote = {Keywords: Phylogenetics, Network, Orchard Networks, Proximity Measures, NP-hardness} }

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**Published in:** LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)

Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called Tree Containment, arises when validating networks constructed by phylogenetic inference methods. We present the first algorithm for (rooted) Tree Containment using the treewidth t of the input network N as parameter, showing that the problem can be solved in 2^O(t²)⋅|N| time and space.

Leo van Iersel, Mark Jones, and Mathias Weller. Embedding Phylogenetic Trees in Networks of Low Treewidth. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 69:1-69:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)

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@InProceedings{vaniersel_et_al:LIPIcs.ESA.2022.69, author = {van Iersel, Leo and Jones, Mark and Weller, Mathias}, title = {{Embedding Phylogenetic Trees in Networks of Low Treewidth}}, booktitle = {30th Annual European Symposium on Algorithms (ESA 2022)}, pages = {69:1--69:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-247-1}, ISSN = {1868-8969}, year = {2022}, volume = {244}, editor = {Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva and Herman, Grzegorz}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2022.69}, URN = {urn:nbn:de:0030-drops-170070}, doi = {10.4230/LIPIcs.ESA.2022.69}, annote = {Keywords: fixed-parameter tractability, treewidth, phylogenetic tree, phylogenetic network, display graph, tree containment, embedding} }

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**Published in:** LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)

In the NP-hard Longest Common Subsequence problem (LCS), given a set of strings, the task is to find a string that can be obtained from every input string using as few deletions as possible. LCS is one of the most fundamental string problems with numerous applications in various areas, having gained a lot of attention in the algorithms and complexity research community. Significantly improving on an algorithm by Irving and Fraser [CPM'92], featured as a research challenge in a 2014 survey paper, we show that LCS is fixed-parameter tractable (FPT) when parameterized by the maximum number of deletions per input string. Given the relatively moderate running time of our algorithm (linear time when the parameter is a constant) and small parameter values to be expected in several applications, we believe that our purely theoretical analysis could finally pave the way to a new, exact and practically useful algorithm for this notoriously hard string problem.

Laurent Bulteau, Mark Jones, Rolf Niedermeier, and Till Tantau. An FPT-Algorithm for Longest Common Subsequence Parameterized by the Maximum Number of Deletions. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 6:1-6:11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bulteau_et_al:LIPIcs.CPM.2022.6, author = {Bulteau, Laurent and Jones, Mark and Niedermeier, Rolf and Tantau, Till}, title = {{An FPT-Algorithm for Longest Common Subsequence Parameterized by the Maximum Number of Deletions}}, booktitle = {33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)}, pages = {6:1--6:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-234-1}, ISSN = {1868-8969}, year = {2022}, volume = {223}, editor = {Bannai, Hideo and Holub, Jan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.6}, URN = {urn:nbn:de:0030-drops-161338}, doi = {10.4230/LIPIcs.CPM.2022.6}, annote = {Keywords: NP-hard string problems, multiple sequence alignment, center string, parameterized complexity, search tree algorithms, enumerative algorithms} }

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**Published in:** LIPIcs, Volume 43, 10th International Symposium on Parameterized and Exact Computation (IPEC 2015)

Let c, k be two positive integers. Given a graph G=(V,E), the c-Load Coloring problem asks whether there is a c-coloring varphi: V => [c] such that for every i in [c], there are at least k edges with both endvertices colored i. Gutin and Jones (IPL 2014) studied this problem with c=2. They showed 2-Load Coloring to be fixed-parameter tractable (FPT) with parameter k by obtaining a kernel with at most 7k vertices. In this paper, we extend the study to any fixed c by giving both a linear-vertex and a linear-edge kernel. In the particular case of c=2, we obtain a kernel with less than 4k vertices and less than 8k edges. These results imply that for any fixed c >= 2, c-Load Coloring is FPT and the optimization version of c-Load Coloring (where k is to be maximized) has an approximation algorithm with a constant ratio.

Florian Barbero, Gregory Gutin, Mark Jones, and Bin Sheng. Parameterized and Approximation Algorithms for the Load Coloring Problem. In 10th International Symposium on Parameterized and Exact Computation (IPEC 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 43, pp. 43-54, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{barbero_et_al:LIPIcs.IPEC.2015.43, author = {Barbero, Florian and Gutin, Gregory and Jones, Mark and Sheng, Bin}, title = {{Parameterized and Approximation Algorithms for the Load Coloring Problem}}, booktitle = {10th International Symposium on Parameterized and Exact Computation (IPEC 2015)}, pages = {43--54}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-92-7}, ISSN = {1868-8969}, year = {2015}, volume = {43}, editor = {Husfeldt, Thore and Kanj, Iyad}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2015.43}, URN = {urn:nbn:de:0030-drops-55703}, doi = {10.4230/LIPIcs.IPEC.2015.43}, annote = {Keywords: Load Coloring, fixed-parameter tractability, kernelization} }

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**Published in:** LIPIcs, Volume 43, 10th International Symposium on Parameterized and Exact Computation (IPEC 2015)

A workflow specification defines sets of steps and users. An authorization policy determines for each user a subset of steps the user is allowed to perform. Other security requirements, such as separation-of-duty, impose constraints on which subsets of users may perform certain subsets of steps. The workflow satisfiability problem (WSP) is the problem of determining whether there exists an assignment of users to workflow steps that satisfies all such authorizations and constraints. An algorithm for solving WSP is important, both as a static analysis tool for workflow specifications, and for the construction of run-time reference monitors for workflow management systems. Given the computational difficulty of WSP, it is important, particularly for the second application, that such algorithms are as efficient as possible.
We introduce class-independent constraints, enabling us to model scenarios where the set of users is partitioned into groups, and the identities of the user groups are irrelevant to the satisfaction of the constraint. We prove that solving WSP is fixed-parameter tractable (FPT) for this class of constraints and develop an FPT algorithm that is useful in practice. We compare the performance of the FPT algorithm with that of SAT4J (a pseudo-Boolean SAT solver) in computational experiments, which show that our algorithm significantly outperforms SAT4J for many instances of WSP. User-independent constraints, a large class of constraints including many practical ones, are a special case of class-independent constraints for which WSP was proved to be FPT (Cohen et al., J. Artif. Intel. Res. 2014). Thus our results considerably extend our knowledge of the fixed-parameter tractability of WSP.

Jason Crampton, Andrei Gagarin, Gregory Gutin, and Mark Jones. On the Workflow Satisfiability Problem with Class-independent Constraints. In 10th International Symposium on Parameterized and Exact Computation (IPEC 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 43, pp. 66-77, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{crampton_et_al:LIPIcs.IPEC.2015.66, author = {Crampton, Jason and Gagarin, Andrei and Gutin, Gregory and Jones, Mark}, title = {{On the Workflow Satisfiability Problem with Class-independent Constraints}}, booktitle = {10th International Symposium on Parameterized and Exact Computation (IPEC 2015)}, pages = {66--77}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-92-7}, ISSN = {1868-8969}, year = {2015}, volume = {43}, editor = {Husfeldt, Thore and Kanj, Iyad}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2015.66}, URN = {urn:nbn:de:0030-drops-55727}, doi = {10.4230/LIPIcs.IPEC.2015.66}, annote = {Keywords: Workflow Satisfiability Problem; Constraint Satisfaction Problem; fixed-parameter tractability; user-independent constraints} }

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**Published in:** LIPIcs, Volume 24, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2013)

Poljak and Turzik (Discrete Mathematics 1986) introduced the notion of
lambda-extendible properties of graphs as a generalization of the property of being bipartite. They showed that for any 0<lambda<1 and
lambda-extendible property Pi, any connected graph G on n vertices and m edges contains a spanning subgraph H in Pi with at least lambda*m+(1-lambda)(n-1)/2 edges. The property of being bipartite is
lambda-extendible for lambda =1/2, and so the Poljak-Turzik bound
generalizes the well-known Edwards-Erdos bound for Max Cut. Other examples of lambda-extendible properties include: being an acyclic oriented graph, a balanced signed graph, or a q-colorable graph for some q in N.
Mnich et al. (FSTTCS 2012) defined the closely related notion of strong lambda-extendibility. They showed that the problem of finding a subgraph satisfying a given strongly lambda-extendible property Pi is fixed-parameter tractable (FPT) when parameterized above the Poljak-Turzik bound---does there exist a spanning subgraph H of a connected graph G such that H in Pi and H has at least lambda*m+(1-lambda)(n-1)/2+k edges?---subject to the condition that the problem is FPT on a certain simple class of graphs called almost-forests of cliques. This generalized an earlier result of Crowston et al. (ICALP 2012) for Max Cut, to all strongly lambda-extendible properties which satisfy the additional criterion.
In this paper we settle the kernelization complexity of nearly all problems parameterized above Poljak-Turzik bounds, in the affirmative. We show that these problems admit quadratic kernels (cubic when lambda=1/2), without using the assumption that the problem is FPT on almost-forests of cliques. Thus our results not only remove the technical condition of being FPT on almost-forests of cliques from previous results, but also unify and extend previously known kernelization results in this direction. Our results add to the select list of generic kernelization results known in the literature.

Robert Crowston, Mark Jones, Gabriele Muciaccia, Geevarghese Philip, Ashutosh Rai, and Saket Saurabh. Polynomial Kernels for lambda-extendible Properties Parameterized Above the Poljak-Turzik Bound. In IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2013). Leibniz International Proceedings in Informatics (LIPIcs), Volume 24, pp. 43-54, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2013)

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@InProceedings{crowston_et_al:LIPIcs.FSTTCS.2013.43, author = {Crowston, Robert and Jones, Mark and Muciaccia, Gabriele and Philip, Geevarghese and Rai, Ashutosh and Saurabh, Saket}, title = {{Polynomial Kernels for lambda-extendible Properties Parameterized Above the Poljak-Turzik Bound}}, booktitle = {IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2013)}, pages = {43--54}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-64-4}, ISSN = {1868-8969}, year = {2013}, volume = {24}, editor = {Seth, Anil and Vishnoi, Nisheeth K.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2013.43}, URN = {urn:nbn:de:0030-drops-43599}, doi = {10.4230/LIPIcs.FSTTCS.2013.43}, annote = {Keywords: Kernelization, Lambda Extension, Above-Guarantee Parameterization, MaxCut} }

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**Published in:** LIPIcs, Volume 18, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012)

An oriented graph is a directed graph without directed 2-cycles. Poljak and Turzik (1986) proved that every connected oriented graph G on n vertices and m arcs contains an acyclic subgraph with at least m/2+(n-1)/4 arcs. Raman and Saurabh (2006) gave another proof of this result and left it as an open question to establish the parameterized complexity of the following problem: does G have an acyclic subgraph with least m/2 + (n-1)/4 + k arcs, where k is the parameter? We answer this question by showing that the problem can be solved by an algorithm of runtime (12k)!n^{O(1)}. Thus, the problem is fixed-parameter tractable. We also prove that there is a polynomial time algorithm that either establishes that the input instance of the problem is a Yes-instance or reduces the input instance to an equivalent one of size O(k^2).

Robert Crowston, Gregory Gutin, and Mark Jones. Directed Acyclic Subgraph Problem Parameterized above the Poljak-Turzik Bound. In IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012). Leibniz International Proceedings in Informatics (LIPIcs), Volume 18, pp. 400-411, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2012)

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@InProceedings{crowston_et_al:LIPIcs.FSTTCS.2012.400, author = {Crowston, Robert and Gutin, Gregory and Jones, Mark}, title = {{Directed Acyclic Subgraph Problem Parameterized above the Poljak-Turzik Bound}}, booktitle = {IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012)}, pages = {400--411}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-47-7}, ISSN = {1868-8969}, year = {2012}, volume = {18}, editor = {D'Souza, Deepak and Radhakrishnan, Jaikumar and Telikepalli, Kavitha}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2012.400}, URN = {urn:nbn:de:0030-drops-38765}, doi = {10.4230/LIPIcs.FSTTCS.2012.400}, annote = {Keywords: Acyclic Subgraph, Fixed-parameter tractable, Polynomial Kernel} }

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**Published in:** LIPIcs, Volume 13, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2011)

In the parameterized problem MaxLin2-AA[$k$], we are given a system with variables x_1,...,x_n consisting of equations of the form Product_{i in I}x_i = b, where x_i,b in {-1, 1} and I is a nonempty subset of {1,...,n}, each equation has a positive integral weight, and we are to decide whether it is possible to simultaneously satisfy equations of total weight at least W/2+k, where W is the total weight of all equations and k is the parameter (if k=0, the possibility is assured). We show that MaxLin2-AA[k] has a kernel with at most O(k^2 log k) variables and can be solved in time 2^{O(k log k)}(nm)^{O(1)}. This solves an open problem of Mahajan et al. (2006).
The problem Max-r-Lin2-AA[k,r] is the same as MaxLin2-AA[k] with two
differences: each equation has at most r variables and r is the second parameter. We prove a theorem on Max-$r$-Lin2-AA[k,r] which implies that Max-r-Lin2-AA[k,r] has a kernel with at most (2k-1)r variables, improving a number of results including one by Kim and Williams (2010). The theorem also implies a lower bound on the maximum of a function f that maps {-1,1}^n to the set of reals and whose Fourier expansion (which is a multilinear polynomial) is of degree r. We show applicability of the lower bound by giving a new proof of the Edwards-Erdös bound (each connected graph on n vertices and m edges has a bipartite subgraph with at least m/2 +(n-1)/4 edges) and obtaining a generalization.

Robert Crowston, Michael Fellows, Gregory Gutin, Mark Jones, Frances Rosamond, Stéphan Thomassé, and Anders Yeo. Simultaneously Satisfying Linear Equations Over F_2: MaxLin2 and Max-r-Lin2 Parameterized Above Average. In IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2011). Leibniz International Proceedings in Informatics (LIPIcs), Volume 13, pp. 229-240, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2011)

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@InProceedings{crowston_et_al:LIPIcs.FSTTCS.2011.229, author = {Crowston, Robert and Fellows, Michael and Gutin, Gregory and Jones, Mark and Rosamond, Frances and Thomass\'{e}, St\'{e}phan and Yeo, Anders}, title = {{Simultaneously Satisfying Linear Equations Over F\underline2: MaxLin2 and Max-r-Lin2 Parameterized Above Average}}, booktitle = {IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2011)}, pages = {229--240}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-34-7}, ISSN = {1868-8969}, year = {2011}, volume = {13}, editor = {Chakraborty, Supratik and Kumar, Amit}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2011.229}, URN = {urn:nbn:de:0030-drops-33416}, doi = {10.4230/LIPIcs.FSTTCS.2011.229}, annote = {Keywords: MaxLin, fixed-parameter tractability, kernelization, pseudo-boolean functions} }

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