Exact exponential-time algorithms for finding bicliques

Due to a large number of applications, bicliques of graphs have been widely considered in the literature. This paper focuses on non-induced bicliques. Given a graph G=(V,E) on n vertices, a pair (X,Y), with X,Y⊆V, X∩Y=∅, is a non-induced biclique if {x,y}∈E for any x∈X and y∈Y. The NP-complete problem of finding a non-induced (k₁,k₂)-biclique asks to decide whether G contains a non-induced biclique (X,Y) such that |X|=k₁ and |Y|=k₂. In this paper, we design a polynomial-space O(n^1.6914)-time algorithm for this problem. It is based on an algorithm for bipartite graphs that runs in time O(n^1.30052). In deriving this algorithm, we also exhibit a relation to the spare allocation problem known from memory chip fabrication. As a byproduct, we show that the constraint bipartite vertex cover problem can be solved in time O(n^1.30052).     

A Cubic-Vertex Kernel for Flip Consensus Tree

Given a bipartite graph G=(V _c ,V _t ,E) and a nonnegative integer k, the NP-complete Minimum-Flip Consensus Tree problem asks whether G can be transformed, using up to k edge insertions and deletions, into a graph that does not contain an induced P ₅ with its first vertex in V _t (a so-called M-graph or Σ-graph). This problem plays an important role in computational phylogenetics, V _c standing for the characters and V _t standing for taxa. Chen et al. (IEEE/ACM Trans. Comput. Biol. Bioinform. 3:165–173, 2006). showed that Minimum-Flip Consensus Tree is NP-complete and presented a parameterized algorithm with running time O(6 ^k ?|V _t |?|V _c |). Subsequently, Böcker et al. (ACM Trans. Algorithms 8:7:1–7:17, 2012) presented a refined search tree algorithm with running time O(4.42 ^k (|V _t |+|V _c |)+|V _t |?|V _c |). We continue the study of Minimum-Flip Consensus Tree parameterized by k. Our main contribution are polynomial-time executable data reduction rules yielding a problem kernel with O(k ³) vertices. In addition, we present an improved search tree algorithm with running time O(3.68 ^k ?|V _c |²|V _t |).     

Bandwidth on AT-free graphs

We study the classical Bandwidth problem from the viewpoint of parametrised algorithms. Given a graph G=(V,E) and a positive integer k, the Bandwidth problem asks whether there exists a bijective function β:{1,…,∣V∣}→V such that for every edge uv∈E, ∣β⁻¹(u)−β⁻¹(v)∣≤k. It is known that under standard complexity assumptions, no algorithm for Bandwidth with running time of the form f(k)n^O(1) exists, even when the input is restricted to trees. We initiate the search for classes of graphs where such algorithms do exist. We present an algorithm with running time n⋅2^O(klogk) for Bandwidth on AT-free graphs, a well-studied graph class that contains interval, permutation, and cocomparability graphs. Our result is the first non-trivial algorithm that shows fixed-parameter tractability of Bandwidth on a graph class on which the problem remains NP-complete.     

Minimal proper interval completions

Given an arbitrary graph G=(V,E) and a proper interval graph H=(V,F) with E⊆F we say that H is a proper interval completion of G. The graph H is called a minimal proper interval completion of G if, for any sandwich graph H^′=(V,F^′) with E⊆F^′⊂F, H^′ is not a proper interval graph. In this paper we give a O(n+m) time algorithm computing a minimal proper interval completion of an arbitrary graph. The output is a proper interval model of the completion.     

A linear-time algorithm for finding a sparsek-connected spanning subgraph of ak-connected graph

We show that anyk-connected graphG = (V, E) has a sparsek-connected spanning subgraphG′ = (V, E′) with ¦E′¦ =O(k¦V¦) by presenting anO(¦E¦)-time algorithm to find one such subgraph, where connectivity stands for either edge-connectivity or node-connectivity. By using this algorithm as preprocessing, the time complexities of some graph problems related to connectivity can be improved. For example, the current best time boundO(max{k ²¦V¦^1/2,k¦V¦}¦E¦) to determine whether node-connectivityK(G) of a graphG = (V, E) is larger than a given integerk or not can be reduced toO(max{k ³¦V¦^3/2,k ²¦V¦²}).     

Enumerating Minimal Subset Feedback Vertex Sets

The Subset Feedback Vertex Set problem takes as input a pair (G,S), where G=(V,E) is a graph with weights on its vertices, and S?V. The task is to find a set of vertices of total minimum weight to be removed from G, such that in the remaining graph no cycle contains a vertex of S. We show that this problem can be solved in time O(1.8638 ⁿ ), where n=|V|. This is a consequence of the main result of this paper, namely that all minimal subset feedback vertex sets of a graph can be enumerated in time O(1.8638 ⁿ ).     

A note on finding all homogeneous set sandwiches

A module is a set of vertices H of a graph G=(V,E) such that each vertex of V?H is either adjacent to all vertices of H or to none of them. A homogeneous set is a nontrivial module. A graph G_s=(V,E_s) is a sandwich for a pair of graphs G_t=(V,E_t) and G=(V,E) if E_t⊆E_s⊆E. In a recent paper, Tang et al. [Inform. Process. Lett. 77 (2001) 17-22] described an O(Δn²) algorithm for testing the existence of a homogeneous set in sandwich graphs of G_t=(V,E_t) and G=(V,E) and then extended it to an enumerative algorithm computing all these possible homogeneous sets. In this paper, we invalidate this latter algorithm by proving there are possibly exponentially many such sets, even if we restrict our attention to strong modules. We then give a correct characterization of a homogeneous set of a sandwich graph.     

Multilevelk-way Partitioning Scheme for Irregular Graphs

In this paper, we present and study a class of graph partitioning algorithms that reduces the size of the graph by collapsing vertices and edges, we find ak-way partitioning of the smaller graph, and then we uncoarsen and refine it to construct ak-way partitioning for the original graph. These algorithms compute ak-way partitioning of a graphG= (V,E) inO(|E|) time, which is faster by a factor ofO(logk) than previously proposed multilevel recursive bisection algorithms. A key contribution of our work is in finding a high-quality and computationally inexpensive refinement algorithm that can improve upon an initialk-way partitioning. We also study the effectiveness of the overall scheme for a variety of coarsening schemes. We present experimental results on a large number of graphs arising in various domains including finite element methods, linear programming, VLSI, and transportation. Our experiments show that this new scheme produces partitions that are of comparable or better quality than those produced by the multilevel bisection algorithm and requires substantially smaller time. Graphs containing up to 450,000 vertices and 3,300,000 edges can be partitioned in 256 domains in less than 40 s on a workstation such as SGI's Challenge. Compared with the widely used multilevel spectral bisection algorithm, our new algorithm is usually two orders of magnitude faster and produces partitions with substantially smaller edge-cut.     

On vertex ranking of a starlike graph

A vertex coloring c:V→{1,2,…,t} of a graph G=(V,E) is a vertex t-ranking if for any two vertices of the same color every path between them contains a vertex of larger color. The vertex ranking number χ_r(G) is the smallest value of t such that G has a vertex t-ranking. A χ_r(G)-ranking of G is said to be an optimal vertex ranking. In this paper, we present an O(|V|+|E|) time algorithm for finding an optimal vertex ranking of a starlike graph G=(V,E). Our result implies that an optimal vertex ranking of a split graph can be computed in linear time.     

On the cubicity of bipartite graphs

A unit cube in k-dimension (or a k-cube) is defined as the Cartesian product R₁×R₂×?×Rk, where each Ri is a closed interval on the real line of the form [ai,ai+1]. The cubicity of G, denoted as cub(G), is the minimum k such that G is the intersection graph of a collection of k-cubes. Many NP-complete graph problems can be solved efficiently or have good approximation ratios in graphs of low cubicity. In most of these cases the first step is to get a low dimensional cube representation of the given graph.It is known that for a graph G, . Recently it has been shown that for a graph G, cub(G)?4(Δ+1)lnn, where n and Δ are the number of vertices and maximum degree of G, respectively. In this paper, we show that for a bipartite graph G=(A∪B,E) with |A|=n₁, |B|=n₂, n₁?n₂, and Δ^′=min{ΔA,ΔB}, where ΔA=maxa∈Ad(a) and ΔB=maxb∈Bd(b), d(a) and d(b) being the degree of a and b in G, respectively, cub(G)?2(Δ^′+2)⌈lnn₂⌉. We also give an efficient randomized algorithm to construct the cube representation of G in 3(Δ^′+2)⌈lnn₂⌉ dimensions. The reader may note that in general Δ^′ can be much smaller than Δ.     

Parameterizing cut sets in a graph by the number of their components

For a connected graph G=(V,E), a subset U⊆V is a disconnected cut if U disconnects G and the subgraph G[U] induced by U is disconnected as well. A cut U is a k-cut if G[U] contains exactly k(≥1) components. More specifically, a k-cut U is a (k,?)-cut if V?U induces a subgraph with exactly ?(≥2) components. The Disconnected Cut problem is to test whether a graph has a disconnected cut and is known to be NP-complete. The problems k-Cut and (k,?)-Cut are to test whether a graph has a k-cut or (k,?)-cut, respectively. By pinpointing a close relationship to graph contractibility problems we show that (k,?)-Cut is in P for k=1 and any fixed constant ?≥2, while it is NP-complete for any fixed pair k,?≥2. We then prove that k-Cut is in P for k=1 and NP-complete for any fixed k≥2. On the other hand, for every fixed integer g≥0, we present an FPT algorithm that solves (k,?)-Cut on graphs of Euler genus at most g when parameterized by k+?. By modifying this algorithm we can also show that k-Cut is in FPT for this graph class when parameterized by k. Finally, we show that Disconnected Cut is solvable in polynomial time for minor-closed classes of graphs excluding some apex graph.     

Minimum Augmentation of Edge-Connectivity between Vertices and Sets of Vertices in Undirected Graphs

Given an undirected multigraph G=(V,E), a family $\mathcal{W}Given an undirected multigraph G=(V,E), a family W\mathcal{W} of areas W⊆V, and a target connectivity k≥1, we consider the problem of augmenting G by the smallest number of new edges so that the resulting graph has at least k edge-disjoint paths between v and W for every pair of a vertex v∈V and an area W ? WW\in \mathcal{W} . So far this problem was shown to be NP-complete in the case of k=1 and polynomially solvable in the case of k=2. In this paper, we show that the problem for k≥3 can be solved in O(m+n(k ³+n ²)(p+kn+nlog n)log k+pkn ³log (n/k)) time, where n=|V|, m=|{{u,v}|(u,v)∈E}|, and p=|W|p=|\mathcal{W}| .     

Constrained minimum vertex cover in bipartite graphs: complexity and parameterized algorithms

Motivated by the research in reconfigurable memory array structures, this paper studies the complexity and algorithms for the constrained minimum vertex cover problem on bipartite graphs (min-cvcb) defined as follows: given a bipartite graph G=(V,E) with vertex bipartition V=U∪L and two integers k_u and k_l, decide whether there is a minimum vertex cover in G with at most k_u vertices in U and at most k_l vertices in L. It is proved in this paper that the min-cvcb problem is NP-complete. This answers a question posed by Hasan and Liu. A parameterized algorithm is developed for the problem, in which classical results in matching theory and recently developed techniques in parameterized computation theory are nicely combined and extended. The algorithm runs in time O(1.26^k_u+k_l+(k_u+k_l)|G|) and significantly improves previous algorithms for the problem.     

On the bi-enhancement of chordal-bipartite probe graphs

Given a class C of graphs, a graph G=(V,E) is said to be a C-probe graph if there exists a stable (i.e., independent) set of vertices X⊆V and a set F of pairs of vertices of X such that the graph G^′=(V,E∪F) is in the class C. Recently, there has been increasing interest and research on a variety of C-probe graph classes, such as interval probe graphs, chordal probe graphs and chain probe graphs.In this paper we focus on chordal-bipartite probe graphs. We prove a structural result that if B is a bipartite graph with no chordless cycle of length strictly greater than 6, then B is chordal-bipartite probe if and only if a certain “enhanced” graph B^∗ is a chordal-bipartite graph. This theorem is analogous to a result on interval probe graphs in Zhang (1994) [18] and to one on chordal probe graphs in Golumbic and Lipshteyn (2004) [11].     

On the Rainbow Connectivity of Graphs: Complexity and FPT Algorithms

For a graph G=(V,E) and a color set C, let f:E→C be an edge-coloring of G in which two adjacent edges may have the same color. Then, the graph G edge-colored by f is rainbow connected if every two vertices of G have a path in which all edges are assigned distinct colors. Chakraborty et al. defined the problem of determining whether the graph colored by a given edge-coloring is rainbow connected. Chen et al. introduced the vertex-coloring version of the problem as a variant, and we introduce the total-coloring version in this paper. We settle the precise computational complexities of all the three problems with regards to graph diameters, and also characterize these with regards to certain graph classes: cacti, outer planer and series-parallel graphs. We then give FPT algorithms for the three problems on general graphs when parameterized by the number of colors in C; our FPT algorithms imply that all the three problems can be solved in polynomial time for any graph with n vertices if |C|=O(logn).     

Exact Algorithms for <Emphasis Type="Italic">L</Emphasis>(2,1)-Labeling of Graphs

The notion of distance constrained graph labelings, motivated by the Frequency Assignment Problem, reads as follows: A mapping from the vertex set of a graph G=(V,E) into an interval of integers {0,…,k} is an L(2,1)-labeling of G of span k if any two adjacent vertices are mapped onto integers that are at least 2 apart, and every two vertices with a common neighbor are mapped onto distinct integers. It is known that for any fixed k≥4, deciding the existence of such a labeling is an NP-complete problem. We present exact exponential time algorithms that are faster than the naive O ^*((k+1) ⁿ ) algorithm that would try all possible mappings. The improvement is best seen in the first NP-complete case of k=4, where the running time of our algorithm is O(1.3006 ⁿ ). Furthermore we show that dynamic programming can be used to establish an O(3.8730 ⁿ ) algorithm to compute an optimal L(2,1)-labeling.     

Computing the Map of Geometric Minimal Cuts

In this paper we consider the following problem of computing a map of geometric minimal cuts (called MGMC problem): Given a graph G=(V,E) and a planar rectilinear embedding of a subgraph H=(V _H ,E _H ) of G, compute the map of geometric minimal cuts induced by axis-aligned rectangles in the embedding plane. The MGMC problem is motivated by the critical area extraction problem in VLSI designs and finds applications in several other fields. In this paper, we propose a novel approach based on a mix of geometric and graph algorithm techniques for the MGMC problem. Our approach first shows that unlike the classic min-cut problem on graphs, the number of all rectilinear geometric minimal cuts is bounded by a low polynomial, O(n ³). Our algorithm for identifying geometric minimal cuts runs in O(n ³logn(loglogn)³) expected time which can be reduced to O(nlogn(loglogn)³) when the maximum size of the cut is bounded by a constant, where n=|V _H |. Once geometric minimal cuts are identified we show that the problem can be reduced to computing the L _∞ Hausdorff Voronoi diagram of axis aligned rectangles. We present the first output-sensitive algorithm to compute this diagram which runs in O((N+K)log² NloglogN) time and O(Nlog² N) space, where N is the number of rectangles and K is the complexity of the Hausdorff Voronoi diagram. Our approach settles several open problems regarding the MGMC problem.     

An SDP Primal-Dual Algorithm for Approximating the Lovász-Theta Function

The Lovász ?-function (Lovász in IEEE Trans. Inf. Theory, 25:1–7, 1979) of a graph G=(V,E) can be defined as the maximum of the sum of the entries of a positive semidefinite matrix X, whose trace Tr(X) equals 1, and X _ij =0 whenever {i,j}∈E. This function appears as a subroutine for many algorithms for graph problems such as maximum independent set and maximum clique. We apply Arora and Kale’s primal-dual method for SDP to design an algorithm to approximate the ?-function within an additive error of δ>0, which runs in time $O(\frac{\vartheta ^{2} n^{2}}{\delta^{2}} \log n \cdot M_{e})$ , where ?=?(G) and M _e =O(n ³) is the time for a matrix exponentiation operation. It follows that for perfect graphs G, our primal-dual method computes ?(G) exactly in time O(? ² n ⁵logn). Moreover, our techniques generalize to the weighted Lovász ?-function, and both the maximum independent set weight and the maximum clique weight for vertex weighted perfect graphs can be approximated within a factor of (1+?) in time O(? ^?2 n ⁵logn).     

On Reversible Cascades in Scale-Free and Erdős-Rényi Random Graphs

Consider the following cascading process on a simple undirected graph G(V,E) with diameter Δ. In round zero, a set S?V of vertices, called the seeds, are active. In round i+1, i∈?, a non-isolated vertex is activated if at least a ρ∈(0,1] fraction of its neighbors are active in round i; it is deactivated otherwise. For k∈?, let min-seed^(k)(G,ρ) be the minimum number of seeds needed to activate all vertices in or before round k. This paper derives upper bounds on min-seed^(k)(G,ρ). In particular, if G is connected and there exist constants C>0 and γ>2 such that the fraction of degree-k vertices in G is at most C/k ^γ for all k∈?⁺, then min-seed^(Δ)(G,ρ)=O(?ρ ^γ?1|V|?). Furthermore, for n∈?⁺, p=Ω((ln(e/ρ))/(ρn)) and with probability 1?exp(?n ^Ω(1)) over the Erd?s-Rényi random graphs G(n,p), min-seed⁽¹⁾(G(n,p),ρ)=O(ρn).     

Finding Maximum Edge Bicliques in Convex Bipartite Graphs

A bipartite graph G=(A,B,E) is convex on B if there exists an ordering of the vertices of B such that for any vertex v??A, vertices adjacent to v are consecutive in?B. A complete bipartite subgraph of a graph G is called a biclique of G. Motivated by an application to analyzing DNA microarray data, we study the problem of finding maximum edge bicliques in convex bipartite graphs. Given a bipartite graph G=(A,B,E) which is convex on B, we present a new algorithm that computes a maximum edge biclique of G in O(nlog?³ nlog?log?n) time and O(n) space, where n=|A|. This improves the current O(n ²) time bound available for the problem. We also show that for two special subclasses of convex bipartite graphs, namely for biconvex graphs and bipartite permutation graphs, a maximum edge biclique can be computed in O(n??(n)) and O(n) time, respectively, where n=min?(|A|,|B|) and ??(n) is the slowly growing inverse of the Ackermann function.