Approximation Algorithms for Bounded Degree Phylogenetic Roots

The Degree- Δ Closest Phylogenetic k th Root Problem (ΔCPR _k ) is the problem of finding a (phylogenetic) tree T from a given graph G=(V,E) such that (1) the degree of each internal node in T is at least 3 and at most Δ, (2) the external nodes (i.e. leaves) of T are exactly the elements of V, and (3) the number of disagreements, i.e., |E ⊕{{u,v} : u,v are leaves of T and d _T (u,v)≤k}|, is minimized, where d _T (u,v) denotes the distance between u and v in tree T. This problem arises from theoretical studies in evolutionary biology and generalizes several important combinatorial optimization problems such as the maximum matching problem. Unfortunately, it is known to be NP-hard for all fixed constants Δ,k such that either both Δ≥3 and k≥3, or Δ>3 and k=2. This paper presents a polynomial-time 8-approximation algorithm for Δ CPR ₂ for any fixed Δ>3, a quadratic-time 12-approximation algorithm for 3CPR ₃, and a polynomial-time approximation scheme for the maximization version of Δ CPR _k for any fixed Δ and k.     

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}| .     

Approximating Buy-at-Bulk and Shallow-Light <Emphasis Type="Italic">k</Emphasis>-Steiner Trees

We study two related network design problems with two cost functions. In the buy-at-bulk k-Steiner tree problem we are given a graph G(V,E) with a set of terminals T⊆V including a particular vertex s called the root, and an integer k≤|T|. There are two cost functions on the edges of G, a buy cost b:E→ℝ⁺ and a distance cost r:E→ℝ⁺. The goal is to find a subtree H of G rooted at s with at least k terminals so that the cost ∑ _e∈H b(e)+∑ _t∈T−s dist(t,s) is minimized, where dist(t,s) is the distance from t to s in H with respect to the r cost. We present an O(log ⁴ n)-approximation algorithm for the buy-at-bulk k-Steiner tree problem. The second and closely related one is bicriteria approximation algorithm for Shallow-light k-Steiner trees. In the shallow-light k-Steiner tree problem we are given a graph G with edge costs b(e) and distance costs r(e), and an integer k. Our goal is to find a minimum cost (under b-cost) k-Steiner tree such that the diameter under r-cost is at most some given bound D. We develop an (O(log n),O(log ³ n))-approximation algorithm for a relaxed version of Shallow-light k-Steiner tree where the solution has at least terminals. Using this we obtain an (O(log ² n),O(log ⁴ n))-approximation algorithm for the shallow-light k-Steiner tree and an O(log ⁴ n)-approximation algorithm for the buy-at-bulk k-Steiner tree problem. Our results are recently used to give the first polylogarithmic approximation algorithm for the non-uniform multicommodity buy-at-bulk problem (Chekuri, C., et al. in Proceedings of 47th Annual IEEE Symposium on Foundations of Computer Science (FOCS’06), pp. 677–686, 2006). A preliminary version of this paper appeared in the Proceedings of 9th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems (APPROX) 2006, LNCS 4110, pp. 153–163, 2006. M.T. Hajiaghayi supported in part by IPM under grant number CS1383-2-02. M.R. Salavatipour supported by NSERC grant No. G121210990, and a faculty start-up grant from University of Alberta.     

Minimum Cost Source Location Problems with Flow Requirements

In this paper, we consider source location problems and their generalizations with three connectivity requirements (arc-connectivity requirements λ and two kinds of vertex-connectivity requirements κ and ), where the source location problems are to find a minimum-cost set S⊆V in a given graph G=(V,A) with a capacity function u:A→ℝ₊ such that for each vertex v∈V, the connectivity from S to v (resp., from v to S) is at least a given demand d ⁻(v) (resp., d ⁺(v)). We show that the source location problem with edge-connectivity requirements in undirected networks is strongly NP-hard, which solves an open problem posed by Arata et al. (J. Algorithms 42: 54–68, 2002). Moreover, we show that the source location problems with three connectivity requirements are inapproximable within a ratio of cln D for some constant c, unless every problem in NP has an O(N ^{log log N} )-time deterministic algorithm. Here D denotes the sum of given demands. We also devise (1+ln D)-approximation algorithms for all the extended source location problems if we have the integral capacity and demand functions. By the inapproximable results above, this implies that all the source location problems are Θ(ln ∑ _v∈V (d ⁺(v)+d ⁻(v)))-approximable. An extended abstract of this paper appeared in Sakashita et al. (Proceedings of LATIN 2006, Chile, LNCS, vol. 3887, pp. 769–780, March 2006).     

All-Pairs Bottleneck Paths in Vertex Weighted Graphs

Let G=(V,E,w) be a directed graph, where w:V→ℝ is a weight function defined on its vertices. The bottleneck weight, or the capacity, of a path is the smallest weight of a vertex on the path. For two vertices u,v the capacity from u to v, denoted by c(u,v), is the maximum bottleneck weight of a path from u to v. In the All-Pairs Bottleneck Paths (APBP) problem the task is to find the capacities for all ordered pairs of vertices. Our main result is an O(n ^2.575) time algorithm for APBP. The exponent is derived from the exponent of fast matrix multiplication.     

Approximating Minimum-Power Degree and Connectivity Problems

Power optimization is a central issue in wireless network design. Given a graph with costs on the edges, the power of a node is the maximum cost of an edge incident to it, and the power of a graph is the sum of the powers of its nodes. Motivated by applications in wireless networks, we consider several fundamental undirected network design problems under the power minimization criteria. Given a graph G=(V,E)\mathcal{G}=(V,\mathcal{E}) with edge costs {c(e):e∈ℰ} and degree requirements {r(v):v∈V}, the Minimum-Power Edge-Multi-Cover\textsf{Minimum-Power Edge-Multi-Cover} (MPEMC\textsf{MPEMC} ) problem is to find a minimum-power subgraph G of G\mathcal{G} so that the degree of every node v in G is at least r(v). We give an O(log n)-approximation algorithms for MPEMC\textsf{MPEMC} , improving the previous ratio O(log ⁴ n). This is used to derive an O(log n+α)-approximation algorithm for the undirected $\textsf{Minimum-Power $\textsf{Minimum-Power ($\textsf{MP$\textsf{MP ) problem, where α is the best known ratio for the min-cost variant of the problem. Currently, _boxclosen-k)\alpha=O(\log k\cdot \log\frac{n}{n-k}) which is O(log k) unless k=n−o(n), and is O(log ² k)=O(log ² n) for k=n−o(n). Our result shows that the min-power and the min-cost versions of the $\textsf{$\textsf{ problem are equivalent with respect to approximation, unless the min-cost variant admits an o(log n)-approximation, which seems to be out of reach at the moment.     

Fast Algorithms for the Density Finding Problem

We study the problem of finding a specific density subsequence of a sequence arising from the analysis of biomolecular sequences. Given a sequence A=(a ₁,w ₁),(a ₂,w ₂),…,(a _n ,w _n ) of n ordered pairs (a _i ,w _i ) of numbers a _i and width w _i >0 for each 1≤i≤n, two nonnegative numbers ℓ, u with ℓ≤u and a number δ, the Density Finding Problem is to find the consecutive subsequence A(i ^*,j ^*) over all O(n ²) consecutive subsequences A(i,j) with width constraint satisfying ℓ≤w(i,j)=∑ _r=i ^j w _r ≤u such that its density is closest to δ. The extensively studied Maximum-Density Segment Problem is a special case of the Density Finding Problem with δ=∞. We show that the Density Finding Problem has a lower bound Ω(nlog n) in the algebraic decision tree model of computation. We give an algorithm for the Density Finding Problem that runs in optimal O(nlog n) time and O(nlog n) space for the case when there is no upper bound on the width of the sequence, i.e., u=w(1,n). For the general case, we give an algorithm that runs in O(nlog ² m) time and O(n+mlog m) space, where and w _min=min  _r=1 ⁿ w _r . As a byproduct, we give another O(n) time and space algorithm for the Maximum-Density Segment Problem. Grants NSC95-2221-E-001-016-MY3, NSC-94-2422-H-001-0001, and NSC-95-2752-E-002-005-PAE, and by the Taiwan Information Security Center (TWISC) under the Grants NSC NSC95-2218-E-001-001, NSC95-3114-P-001-002-Y, NSC94-3114-P-001-003-Y and NSC 94-3114-P-011-001.     

On Word Equations in One Variable

For a word equation E of length n in one variable x occurring # _x times in E a resolution algorithm of O(n+# _x log n) time complexity is presented here. This is the best result known and for the equations that feature #_x < \fracnlogn\#_{x}<\frac{n}{\log n} it yields time complexity of O(n) which is optimal. Additionally it is proven here that the set of solutions of any one-variable word equation is either of the form F or of the form F∪(uv)⁺ u where F is a set of O(log n) words and u, v are some words such that uv is a primitive word.     

Distributed Approximation of Capacitated Dominating Sets

We study local, distributed algorithms for the capacitated minimum dominating set (CapMDS) problem, which arises in various distributed network applications. Given a network graph G=(V,E), and a capacity cap(v)∈ℕ for each node v∈V, the CapMDS problem asks for a subset S⊆V of minimal cardinality, such that every network node not in S is covered by at least one neighbor in S, and every node v∈S covers at most cap(v) of its neighbors. We prove that in general graphs and even with uniform capacities, the problem is inherently non-local, i.e., every distributed algorithm achieving a non-trivial approximation ratio must have a time complexity that essentially grows linearly with the network diameter. On the other hand, if for some parameter ε>0, capacities can be violated by a factor of 1+ε, CapMDS becomes much more local. Particularly, based on a novel distributed randomized rounding technique, we present a distributed bi-criteria algorithm that achieves an O(log Δ)-approximation in time O(log ³ n+log (n)/ε), where n and Δ denote the number of nodes and the maximal degree in G, respectively. Finally, we prove that in geometric network graphs typically arising in wireless settings, the uniform problem can be approximated within a constant factor in logarithmic time, whereas the non-uniform problem remains entirely non-local.     

<Emphasis Type="Italic">f</Emphasis>-Sensitivity Distance Oracles and Routing Schemes

An f-sensitivity distance oracle for a weighted undirected graph G(V,E) is a data structure capable of answering restricted distance queries between vertex pairs, i.e., calculating distances on a subgraph avoiding some forbidden edges. This paper presents an efficiently constructible f-sensitivity distance oracle that given a triplet (s,t,F), where s and t are vertices and F is a set of forbidden edges such that |F|≤f, returns an estimate of the distance between s and t in G(V,E∖F). For an integer parameter k≥1, the size of the data structure is O(fkn ^1+1/k log (nW)), where W is the heaviest edge in G, the stretch (approximation ratio) of the returned distance is (8k−2)(f+1), and the query time is O(|F|⋅log ² n⋅log log n⋅log log d), where d is the distance between s and t in G(V,E∖F).     

Network Design with Edge-Connectivity and Degree Constraints

We consider the following network design problem; Given a vertex set V with a metric cost c on V, an integer k≥1, and a degree specification b, find a minimum cost k-edge-connected multigraph on V under the constraint that the degree of each vertex v∈V is equal to b(v). This problem generalizes metric TSP. In this paper, we show that the problem admits a ρ-approximation algorithm if b(v)≥2, v∈V, where ρ=2.5 if k is even, and ρ=2.5+1.5/k if k is odd. We also prove that the digraph version of this problem admits a 2.5-approximation algorithm and discuss some generalization of metric TSP.     

The edge-orientation problem and some of its variants on weighted graphs

Let G(V, E) be a connected undirected graph with n vertices and m edges, where each vertex v is associated with a cost C(v) and each edge e = (u, v) is associated with two weights, W(u → v) and W(v → u). The issue of assigning an orientation to each edge so that G becomes a directed graph is resolved in this paper. Determining a scheme to assign orientations of all edges such that max_x∈V{C(x)+∑_x→zW(x→z)} is minimized is the objective. This issue is called the edge-orientation problem (the EOP). Two variants of the EOP, the Out-Degree-EOP and the Vertex-Weighted EOP, are first proposed and then efficient algorithms for solving them on general graphs are designed. Ascertaining that the EOP is NP-hard on bipartite graphs and chordal graphs is the second result. Finally, an O(n log n)-time algorithm for the EOP on trees is designed. In general, the algorithmic results in this paper facilitate the implementation of the weighted fair queuing (WFQ) on real networks. The objective of the WFQ is to assign an effective weight for each flow to enhance link utilization. Our findings consequently can be easily extended to other classes of graphs, such as cactus graphs, block graphs, and interval graphs.     

A 2-approximation NC algorithm for connected vertex cover and tree cover

The connected vertex cover problem is a variant of the vertex cover problem, in which a vertex cover is additional required to induce a connected subgraph in a given connected graph. The problem is known to be NP-hard and to be at least as hard to approximate as the vertex cover problem is. While several 2-approximation NC algorithms are known for vertex cover, whether unweighted or weighted, no parallel algorithm with guaranteed approximation is known for connected vertex cover. Moreover, converting the existing sequential 2-approximation algorithms for connected vertex cover to parallel ones results in RNC algorithms of rather high complexity at best.In this paper we present a 2-approximation NC (and RNC) algorithm for connected vertex cover (and tree cover). The NC algorithm runs in O(log²n) time using O(Δ²(m+n)/logn) processors on an EREW-PRAM, while the RNC algorithm runs in O(logn) expected time using O(m+n) processors on a CRCW-PRAM, when a given graph has n vertices and m edges with maximum vertex degree of Δ.     

Minimum Weakly Fundamental Cycle Bases Are Hard To Find

In the last years, new variants of the minimum cycle basis (MCB) problem and new classes of cycle bases have been introduced, as motivated by several applications from disparate areas of scientific and technological inquiry. At present, the complexity status of the MCB problem is settled only for undirected, directed, and strictly fundamental cycle bases (SFCB’s). Weakly fundamental cycle bases (WFCB’s) form a natural superclass of SFCB’s. A cycle basis of a graph G is a WFCB iff ν=0 or there exists an edge e of G and a circuit C _i in such that is a WFCB of G∖e. WFCB’s still possess several of the nice properties offered by SFCB’s. At the same time, several classes of graphs enjoying WFCB’s of cost asymptotically inferior to the cost of the cheapest SFCB’s have been found and exhibited in the literature. Considered also the computational difficulty of finding cheap SFCB’s, these works advocated an in-depth study of WFCB’s. In this paper, we settle the complexity status of the MCB problem for WFCB’s (the MWFCB problem). The problem turns out to be -hard. However, in this paper, we also offer a simple and practical 2⌈log ₂ n⌉-approximation algorithm for the MWFCB problem. In O(n ν) time, this algorithm actually returns a WFCB whose cost is at most 2⌈log ₂ n⌉∑ _e∈E(G) w _e , thus allowing a fast 2⌈log ₂ n⌉-approximation also for the MCB problem. With this algorithm, we provide tight bounds on the cost of any MCB and MWFCB.     

On the partial terminal Steiner tree problem

We investigate a practical variant of the well-known graph Steiner tree problem. For a complete graph G = ( V,E ) with length function l:E → R ⁺ and two vertex subsets R ⊂ V and R ′ ⊆ R, a partial terminal Steiner tree is a Steiner tree which contains all vertices in R such that all vertices in R ∖ R ′ belong to the leaves of this Steiner tree. The partial terminal Steiner tree problem is to find a partial terminal Steiner tree T whose total lengths ∑ _{(u,v) ∈T} l ( u,v ) is minimum. In this paper, we show that the problem is both NP-complete and MAX SNP-hard when the lengths of edges are restricted to either 1 or 2. We also provide an approximation algorithm for the problem.

Improved Approximation Algorithm for Convex Recoloring of Trees

A pair (T,C) of a tree T and a coloring C is called a colored tree. Given a colored tree (T,C) any coloring C′ of T is called a recoloring of T. Given a weight function on the vertices of the tree the recoloring distance of a recoloring is the total weight of recolored vertices. A coloring of a tree is convex if for any two vertices u and v that are colored by the same color c, every vertex on the path from u to v is also colored by c. In the minimum convex recoloring problem we are given a colored tree and a weight function and our goal is to find a convex recoloring of minimum recoloring distance. The minimum convex recoloring problem naturally arises in the context of phylogenetic trees. Given a set of related species the goal of phylogenetic reconstruction is to construct a tree that would best describe the evolution of this set of species. In this context a convex coloring corresponds to perfect phylogeny. Since perfect phylogeny is not always possible the next best thing is to find a tree which is as close to convex as possible, or, in other words, a tree with minimum recoloring distance. We present a (2+ε)-approximation algorithm for the minimum convex recoloring problem, whose running time is O(n ²+n(1/ε)²4^1/ε ). This result improves the previously known 3-approximation algorithm for this NP-hard problem. We also present an algorithm for computing an optimal convex recoloring whose running time is , where n ^* is the number of colors that violate convexity in the input tree, and Δ is the maximum degree of vertices in the tree. The parameterized complexity of this algorithm is O(n ²+n⋅k⋅2 ^k ).     

Approximation Algorithms for <Emphasis Type="Italic">k</Emphasis>-hurdle Problems

The polynomial-time solvable k-hurdle problem is a natural generalization of the classical s-t minimum cut problem where we must select a minimum-cost subset S of the edges of a graph such that |p∩S|≥k for every s-t path p. In this paper, we describe a set of approximation algorithms for “k-hurdle” variants of the NP-hard multiway cut and multicut problems. For the k-hurdle multiway cut problem with r terminals, we give two results, the first being a pseudo-approximation algorithm that outputs a (k−1)-hurdle solution whose cost is at most that of an optimal solution for k hurdles. Secondly, we provide a 2(1-\frac1r)2(1-\frac{1}{r})-approximation algorithm based on rounding the solution of a linear program, for which we give a simple randomized half-integrality proof that works for both edge and vertex k-hurdle multiway cuts that generalizes the half-integrality results of Garg et al. for the vertex multiway cut problem. We also describe an approximation-preserving reduction from vertex cover as evidence that it may be difficult to achieve a better approximation ratio than 2(1-\frac1r)2(1-\frac{1}{r}). For the k-hurdle multicut problem in an n-vertex graph, we provide an algorithm that, for any constant ε>0, outputs a ⌈(1−ε)k⌉-hurdle solution of cost at most O(log n) times that of an optimal k-hurdle solution, and we obtain a 2-approximation algorithm for trees.     

Combinatorial Algorithms for Data Migration to Minimize Average Completion Time

The data migration problem is to compute an efficient plan for moving data stored on devices in a network from one configuration to another. It is modeled by a transfer graph, where vertices represent the storage devices, and edges represent data transfers required between pairs of devices. Each vertex has a non-negative weight, and each edge has a processing time. A vertex completes when all the edges incident on it complete; the constraint is that two edges incident on the same vertex cannot be processed simultaneously. The objective is to minimize the sum of weighted completion times of all vertices. Kim (J. Algorithms 55, 42–57, 2005) gave an LP-rounding 3-approximation algorithm when edges have unit processing times. We give a more efficient primal-dual algorithm that achieves the same approximation guarantee. When edges have arbitrary processing times we give a primal-dual 5.83-approximation algorithm. We also study a variant of the open shop scheduling problem. This is a special case of the data migration problem in which the transfer graph is bipartite and the objective is to minimize the sum of completion times of edges. We present a simple algorithm that achieves an approximation ratio of , thus improving the 1.796-approximation given by Gandhi et al. (ACM Trans. Algorithms 2(1), 116–129, 2006). We show that the analysis of our algorithm is almost tight. A preliminary version of the paper appeared in the Proceedings of the 9th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX 2006. Research of R. Gandhi partially supported by Rutgers University Research Council Grant. Research of J. Mestre done at the University of Maryland; supported by NSF Awards CCR-0113192 and CCF-0430650, and the University of Maryland Dean’s Dissertation Fellowship.     

Analysis of an adaptive algorithm to find the two nearest neighbors

Given a setS ofN distinct elements in random order and a pivotx ∈S, we study the problem of simultaneously finding the left and the right neighbors ofx, i.e.,L=max{u|u<x} andR=min{v|v>x}. We analyze an adaptive algorithm that solves this problem by scanning the setS while maintaining current values for the neighborsL andR. Each new element inspected is compared first against the neighbor in the most populous side, then (if necessary) against the neighbor in the other side, and finally (if necessary), against the pivot. This algorithm may require 3N comparisons in the worst case, but it performs well on the average. If the pivot has rankαN, where α is fixed and <1/2, the algorithm does (1+α)N+Θ(logN) comparisons on the average, with a variance of 3 lnN+Θ(1). However, in the case where the pivot is the median, the average becomes 3/2;N+Θ(√N), while the variance grows to (1/2−π/8)N+Θ(logN). We also prove that, in the αN case, the limit distribution is Gaussian. This work has been supported in part by Grant FONDECYT(Chile) 1950622 and 1981029. Online publication October 6, 2000.     

An efficient distributed algorithm for finding all hinge vertices in networks

Let G=(V, E) be a graph with vertex set V of size n and edge set E of size m. A vertex v∈V is called a hinge vertex if there exist two vertices in V\{v} such that their distance becomes longer when v is removed. In this paper, we present a distributed algorithm that finds all hinge vertices on an arbitrary graph. The proposed algorithm works for named static asynchronous networks and achieves O(n ²) time complexity and O(m) message complexity. In particular, the total messages exchanged during the algorithm are at most 2m(log n+nlog n+1) bits.