Fixed-Parameter Algorithms for CLOSEST STRING and Related Problems

CLOSEST STRING is one of the core problems in the field of consensus word analysis with particular importance for computational biology. Given k strings of the same length and a nonnegative integer d , find a ``center string'' s such that none of the given strings has the Hamming distance greater than d from s . CLOSEST STRING is NP-complete. In biological applications, however, d is usually very small. We show how to solve CLOSEST STRING in linear time for fixed d —the exponential growth in d is bounded by O(dd) . We extend this result to the closely related problems d -MISMATCH and DISTINGUISHING STRING SELECTION. Moreover, we also show that CLOSEST STRING is solvable in linear time when k is fixed and d is arbitrary. In summary, this means that CLOSEST STRING is fixed-parameter tractable with respect to parameter d and with respect to parameter k . Finally, the practical usefulness of our findings is substantiated by some experimental results.     

A Fixed-Parameter Approach to 2-Layer Planarization

A bipartite graph is biplanar if the vertices can be placed on two parallel lines (layers) in the plane such that there are no edge crossings when edges are drawn as line segments between the layers. In this paper we study the 2-Layer Planarization problem: Can k edges be deleted from a given graph G so that the remaining graph is biplanar? This problem is NP-complete, and remains so if the permutation of the vertices in one layer is fixed (the 1-Layer Planarization problem). We prove that these problems are fixed-parameter tractable by giving linear-time algorithms for their solution (for fixed k). In particular, we solve the 2-Layer Planarization problem in O(k · 6^k + |G|) time and the 1-Layer Planarization problem in O(3^k · |G|) time. We also show that there are polynomial-time constant-approximation algorithms for both problems.     

Going weighted: Parameterized algorithms for cluster editing

The goal of the Cluster Editing problem is to make the fewest changes to the edge set of an input graph such that the resulting graph is a disjoint union of cliques. This problem is NP-complete but recently, several parameterized algorithms have been proposed. In this paper, we present a number of surprisingly simple search tree algorithms for Weighted Cluster Editing assuming that edge insertion and deletion costs are positive integers. We show that the smallest search tree has size O(1.82^k) for edit cost k, resulting in the currently fastest parameterized algorithm, both for this problem and its unweighted counterpart. We have implemented and compared our algorithms, and achieved promising results.¹     

Two fixed-parameter algorithms for Vertex Covering by Paths on Trees

Vertex Covering by Paths on Trees with applications in machine translation is the task to cover all vertices of a tree T=(V,E) by choosing a minimum-weight subset of given paths in the tree. The problem is NP-hard and has recently been solved by an exact algorithm running in O(C⁴⋅²|V|) time, where C denotes the maximum number of paths covering a tree vertex. We improve this running time to O(C²⋅C⋅|V|). On the route to this, we introduce the problem Tree-like Weighted Hitting Set which might be of independent interest. In addition, for the unweighted case of Vertex Covering by Paths on Trees, we present an exact algorithm using a search tree of size O(k²⋅k!), where k denotes the number of chosen covering paths. Finally, we briefly discuss the existence of a size-O(k²) problem kernel.     

Fixed Parameter Algorithms for DOMINATING SET and Related Problems on Planar Graphs

Abstract. We present an algorithm that constructively produces a solution to the k -DOMINATING SET problem for planar graphs in time O(c^ \sqrt k n) , where c=4^ 6\sqrt 34 . To obtain this result, we show that the treewidth of a planar graph with domination number γ (G) is O(\sqrt \rule 0pt 4pt \smash γ (G) ) , and that such a tree decomposition can be found in O(\sqrt \rule 0pt 4pt \smash γ (G) n) time. The same technique can be used to show that the k -FACE COVER problem (find a size k set of faces that cover all vertices of a given plane graph) can be solved in O(c ₁ ^ \sqrt k n) time, where c ₁ =3^ 36\sqrt 34 and k is the size of the face cover set. Similar results can be obtained in the planar case for some variants of k -DOMINATING SET, e.g., k -INDEPENDENT DOMINATING SET and k -WEIGHTED DOMINATING SET.     

A fixed-parameter tractability result for multicommodity demand flow in trees

We study an NP-hard (and MaxSNP-hard) problem in trees—Multicommodity Demand Flow—dealing with demand flows between pairs of nodes and trying to maximize the value of the routed flows. This problem has been intensively studied for trees as well as for general graphs mainly from the viewpoint of polynomial-time approximation algorithms. By way of contrast, we provide an exact dynamic programming algorithm for this problem that works well whenever some natural problem parameter is small, a reasonable assumption in several applications. More specifically, we prove fixed-parameter tractability with respect to the maximum number of the input flows at any tree node.     

A refined search tree technique for Dominating Set on planar graphs

We establish a refined search tree technique for the parameterized DOMINATING SET problem on planar graphs. Here, we are given an undirected graph and we ask for a set of at most k vertices such that every other vertex has at least one neighbor in this set. We describe algorithms with running times O(8^kn) and O(8^kk+n³), where n is the number of vertices in the graph, based on bounded search trees. We describe a set of polynomial time data-reduction rules for a more general “annotated” problem on black/white graphs that asks for a set of k vertices (black or white) that dominate all the black vertices. An intricate argument based on the Euler formula then establishes an efficient branching strategy for reduced inputs to this problem. In addition, we give a family examples showing that the bound of the branching theorem is optimal with respect to our reduction rules. Our final search tree algorithm is easy to implement; its analysis, however, is involved.     

Applying Modular Decomposition to Parameterized Cluster Editing Problems

A graph G is said to be a bicluster graph if G is a disjoint union of bicliques (complete bipartite subgraphs), and a cluster graph if G is a disjoint union of cliques (complete subgraphs). In this work, we study the parameterized versions of the NP-hard Bicluster Graph Editing and Cluster Graph Editing problems. The former consists of obtaining a bicluster graph by making the minimum number of modifications in the edge set of an input bipartite graph. When at most k modifications are allowed (Bicluster(k) Graph Editing problem), this problem is FPT, and can be solved in O(4 ^k nm) time by a standard search tree algorithm. We develop an algorithm of time complexity O(4 ^k +n+m), which uses a strategy based on modular decomposition techniques; we slightly generalize the original problem as the input graph is not necessarily bipartite. The algorithm first builds a problem kernel with O(k ²) vertices in O(n+m) time, and then applies a bounded search tree. We also show how this strategy based on modular decomposition leads to a new way of obtaining a problem kernel with O(k ²) vertices for the Cluster(k) Graph Editing problem, in O(n+m) time. This problem consists of obtaining a cluster graph by modifying at most k edges in an input graph. A previous FPT algorithm of time O(1.92 ^k +n ³) for this problem was presented by Gramm et al. (Theory Comput. Syst. 38(4), 373–392, 2005, Algorithmica 39(4), 321–347, 2004). In their solution, a problem kernel with O(k ²) vertices is built in O(n ³) time.     

Simple Algorithms for the On-Line Multidimensional Dictionary and Related Problems

The on-line multidimensional dictionary problem consists of executing on-line any sequence of the following operations: INSERT(p) , DELETE(p) , and MEM-BER-SHIP(p) , where p is any (ordered) d -tuple (or string with d elements, or points in d -space where the dimensions have been ordered). We introduce a clean structure based on balanced binary search trees, which we call multidimensional balanced binary search trees, to represent the set of d -tuples. We present algorithms for each of the above operations that take O(d + log n) time, where n is the current number of d -tuples in the set, and each INSERT and DELETE operation requires no more than a constant number of rotations. Our structure requires dn words to represent the input, plus O(n) pointers and data indicating the first component where pairs of d -tuples differ. This information, which can be easily updated, enables us to test for MEMBERSHIP efficiently. Other operations that can be performed efficiently in our multidimensional balanced binary search trees are: print in lexicographic order (O(dn) time), find the (lexicographically) smallest or largest d -tuple (O( log n) time), and concatenation (O(d + log n) time). Finding the (lexicographically) k th smallest or largest d -tuple can also be implemented efficiently (O( log n) time), at the expense of adding an integer value at each node. Received June 13, 1997; revised September 3, 1998.     

Isolation concepts for clique enumeration: Comparison and computational experiments

We do computational studies concerning the enumeration of isolated cliques in graphs. Isolation, as recently introduced, measures the degree of connectedness of the cliques to the rest of the graph. Isolation helps both in getting faster algorithms for the enumeration of maximal general cliques and in filtering out cliques with special semantics. We compare three isolation concepts and their combination with two enumeration modi for maximal cliques (“isolated maximal” vs “maximal isolated”). All studied concepts exhibit the fixed-parameter tractability of the enumeration task with respect to the parameter “degree of isolation”. We provide a first systematic experimental study of the corresponding enumeration algorithms, using synthetic graphs (in the _Gn,m,p$G_{n,m,p}$ model), financial networks, and a music artist similarity network, proposing the enumeration of isolated cliques as a useful instrument in analyzing financial and social networks.     

Automated Generation of Search Tree Algorithms for Hard Graph Modification Problems

We present a framework for an automated generation of exact search tree algorithms for NP-hard problems. The purpose of our approach is twofold—rapid development and improved upper bounds. Many search tree algorithms for various problems in the literature are based on complicated case distinctions. Our approach may lead to a much simpler process of developing and analyzing these algorithms. Moreover, using the sheer computing power of machines it may also lead to improved upper bounds on search tree sizes (i.e., faster exact solving algorithms) in comparison with previously developed hand-made search trees. Among others, such an example is given with the NP-complete Cluster Editing problem (also known as Correlation Clustering on complete unweighted graphs), which asks for the minimum number of edge additions and deletions to create a graph which is a disjoint union of cliques. The hand-made search tree for Cluster Editing had worst-case size O(2.27^k), which now is improved to O(1.92^k) due to our new method. (Herein, k denotes the number of edge modifications allowed.)     

Error Compensation in Leaf Power Problems

The k-Leaf Power recognition problem is a particular case of graph power problems: For a given graph it asks whether there exists an unrooted tree—the k-leaf root—with leaves one-to-one labeled by the graph vertices and where the leaves have distance at most k iff their corresponding vertices in the graph are connected by an edge. Here we study "error correction" versions of k-Leaf Power recognition—that is, adding or deleting at most l edges to generate a graph that has a k-leaf root. We provide several NP-completeness results in this context, and we show that the NP-complete Closest 3-Leaf Power problem (the error correction version of 3-Leaf Power) is fixed-parameter tractable with respect to the number of edge modifications or vertex deletions in the given graph. Thus, we provide the seemingly first nontrivial positive algorithmic results in the field of error compensation for leaf power problems with k > 2. To this end, as a result of independent interest, we develop a forbidden subgraph characterization of graphs with 3-leaf roots.     

Fixed-parameter algorithms for Kemeny rankings

The computation of Kemeny rankings is central to many applications in the context of rank aggregation. Given a set of permutations (votes) over a set of candidates, one searches for a “consensus permutation” that is “closest” to the given set of permutations. Unfortunately, the problem is NP-hard. We provide a broad study of the parameterized complexity for computing optimal Kemeny rankings. Besides the three obvious parameters “number of votes”, “number of candidates”, and solution size (called Kemeny score), we consider further structural parameterizations. More specifically, we show that the Kemeny score (and a corresponding Kemeny ranking) of an election can be computed efficiently whenever the average pairwise distance between two input votes is not too large. In other words, Kemeny Score is fixed-parameter tractable with respect to the parameter “average pairwise Kendall–Tau distance _da$d_a$”. We describe a fixed-parameter algorithm with running time 16^⌈_da⌉⋅poly$16^{\lceil d_a\rceil }\cdot poly$. Moreover, we extend our studies to the parameters “maximum range” and “average range” of positions a candidate takes in the input votes. Whereas Kemeny Score remains fixed-parameter tractable with respect to the parameter “maximum range”, it becomes NP-complete in the case of an average range of two. This excludes fixed-parameter tractability with respect to the parameter “average range” unless P=NP. Finally, we extend some of our results to votes with ties and incomplete votes, where in both cases one no longer has permutations as input.     

Parallel Algorithms for Maximum Matching in Complements of Interval Graphs and Related Problems

Given a set of n intervals representing an interval graph, the problem of finding a maximum matching between pairs of disjoint (nonintersecting) intervals has been considered in the sequential model. In this paper we present parallel algorithms for computing maximum cardinality matchings among pairs of disjoint intervals in interval graphs in the EREW PRAM and hypercube models. For the general case of the problem, our algorithms compute a maximum matching in O( log ³ n) time using O(n/ log ² n) processors on the EREW PRAM and using n processors on the hypercubes. For the case of proper interval graphs, our algorithm runs in O( log n ) time using O(n) processors if the input intervals are not given already sorted and using O(n/ log n ) processors otherwise, on the EREW PRAM. On n -processor hypercubes, our algorithm for the proper interval case takes O( log n log log n ) time for unsorted input and O( log n ) time for sorted input. Our parallel results also lead to optimal sequential algorithms for computing maximum matchings among disjoint intervals. In addition, we present an improved parallel algorithm for maximum matching between overlapping intervals in proper interval graphs. Received November 20, 1995; revised September 3, 1998.     

Approximation Algorithms for Degree-Constrained Minimum-Cost Network-Design Problems

We study network-design problems with two different design objectives: the total cost of the edges and nodes in the network and the maximum degree of any node in the network. A prototypical example is the degree-constrained node-weighted Steiner tree problem: We are given an undirected graph G(V,E) , with a nonnegative integral function d that specifies an upper bound d(v) on the degree of each vertex v ∈ V in the Steiner tree to be constructed, nonnegative costs on the nodes, and a subset of k nodes called terminals. The goal is to construct a Steiner tree T containing all the terminals such that the degree of any node v in T is at most the specified upper bound d(v) and the total cost of the nodes in T is minimum. Our main result is a bicriteria approximation algorithm whose output is approximate in terms of both the degree and cost criteria—the degree of any node v ∈ V in the output Steiner tree is O(d(v) log k) and the cost of the tree is O(log k) times that of a minimum-cost Steiner tree that obeys the degree bound d(v) for each node v . Our result extends to the more general problem of constructing one-connected networks such as generalized Steiner forests. We also consider the special case in which the edge costs obey the triangle inequality and present simple approximation algorithms with better performance guarantees. Received December 21, 1998; revised September 24, 1999.     

Improved Algorithms and Complexity Results for Power Domination in Graphs

The NP-complete Power Dominating Set problem is an “electric power networks variant” of the classical domination problem in graphs: Given an undirected graph G=(V,E), find a minimum-size set P?V such that all vertices in V are “observed” by the vertices in P. Herein, a vertex observes itself and all its neighbors, and if an observed vertex has all but one of its neighbors observed, then the remaining neighbor becomes observed as well. We show that Power Dominating Set can be solved by “bounded-treewidth dynamic programs.” For treewidth being upper-bounded by a constant, we achieve a linear-time algorithm. In particular, we present a simplified linear-time algorithm for Power Dominating Set in trees. Moreover, we simplify and extend several NP-completeness results, particularly showing that Power Dominating Set remains NP-complete for planar graphs, for circle graphs, and for split graphs. Specifically, our improved reductions imply that Power Dominating Set parameterized by |P| is W[2]-hard and it cannot be better approximated than Dominating Set.