Improved Approximate String Matching Using Compressed Suffix Data Structures

Approximate string matching is about finding a given string pattern in a text by allowing some degree of errors. In this paper we present a space efficient data structure to solve the 1-mismatch and 1-difference problems. Given a text T of length n over an alphabet A, we can preprocess T and give an -bit space data structure so that, for any query pattern P of length m, we can find all 1-mismatch (or 1-difference) occurrences of P in O(|A|mlog log n+occ) time, where occ is the number of occurrences. This is the fastest known query time given that the space of the data structure is o(nlog ² n) bits. The space of our data structure can be further reduced to O(nlog |A|) with the query time increasing by a factor of log  ^ε n, for 0<ε≤1. Furthermore, our solution can be generalized to solve the k-mismatch (and the k-difference) problem in O(|A| ^k m ^k (k+log log n)+occ) and O(log  ^ε n(|A| ^k m ^k (k+log log n)+occ)) time using an -bit and an O(nlog |A|)-bit indexing data structures, respectively. We assume that the alphabet size |A| is bounded by for the -bit space data structure.     

Two-Dimensional Packet Classification and Filter Conflict Resolution in the Internet

In this paper, we study the packet classification problem and the filter conflict resolution problem, both motivated by applications in the routing of packets in an IP network. For the first problem, we focus on the static 2-dimensional conflict-free (i.e., nested) filters. We design a linear space data structure with O(T _w (n)+(log log n)²) query time on a RAM with word size O(w) bits where n is the number of filters in the router, w is the number of bits in an IP address and

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.     

The Directed Orienteering Problem

This paper studies vehicle routing problems on asymmetric metrics. Our starting point is the directed k-TSP problem: given an asymmetric metric (V,d), a root r∈V and a target k≤|V|, compute the minimum length tour that contains r and at least k other vertices. We present a polynomial time O(\fraclog² nloglogn·logk)O(\frac{\log^{2} n}{\log\log n}\cdot\log k)-approximation algorithm for this problem. We use this algorithm for directed k-TSP to obtain an O(\fraclog² nloglogn)O(\frac{\log^{2} n}{\log\log n})-approximation algorithm for the directed orienteering problem. This answers positively, the question of poly-logarithmic approximability of directed orienteering, an open problem from Blum et al. (SIAM J. Comput. 37(2):653–670, 2007). The previously best known results were quasi-polynomial time algorithms with approximation guarantees of O(log ² k) for directed k-TSP, and O(log n) for directed orienteering (Chekuri and Pal in IEEE Symposium on Foundations in Computer Science, pp. 245–253, 2005). Using the algorithm for directed orienteering within the framework of Blum et al. (SIAM J. Comput. 37(2):653–670, 2007) and Bansal et al. (ACM Symposium on Theory of Computing, pp. 166–174, 2004), we also obtain poly-logarithmic approximation algorithms for the directed versions of discounted-reward TSP and vehicle routing problem with time-windows.     

Approximate Pattern Matching with the <Emphasis Type="Italic">L</Emphasis><Subscript>1</Subscript>, <Emphasis Type="Italic">L</Emphasis><Subscript>2</Subscript> and <Emphasis Type="Italic">L</Emphasis><Subscript>∞</Subscript> Metrics

Given an alphabet Σ={1,2,…,|Σ|} text string T∈Σ ⁿ and a pattern string P∈Σ ^m , for each i=1,2,…,n−m+1 define L _p (i) as the p-norm distance when the pattern is aligned below the text and starts at position i of the text. The problem of pattern matching with L _p distance is to compute L _p (i) for every i=1,2,…,n−m+1. We discuss the problem for d=1,2,∞. First, in the case of L ₁ matching (pattern matching with an L ₁ distance) we show a reduction of the string matching with mismatches problem to the L ₁ matching problem and we present an algorithm that approximates the L ₁ matching up to a factor of 1+ε, which has an O(\frac1e²nlogmlog|S|)O(\frac{1}{\varepsilon^{2}}n\log m\log|\Sigma|) run time. Then, the L ₂ matching problem (pattern matching with an L ₂ distance) is solved with a simple O(nlog m) time algorithm. Finally, we provide an algorithm that approximates the L _∞ matching up to a factor of 1+ε with a run time of O(\frac1enlogmlog|S|)O(\frac{1}{\varepsilon}n\log m\log|\Sigma|) . We also generalize the problem of String Matching with mismatches to have weighted mismatches and present an O(nlog ⁴ m) algorithm that approximates the results of this problem up to a factor of O(log m) in the case that the weight function is a metric.     

Reoptimization of constraint satisfaction problems with approximation resistant predicates

If k = O(log n) and a predicate P is approximation resistant for the reoptimization of the Max-EkCSP-P problem, then, after inserting a truth-value into the predicate and imposing some constraint, there exists a polynomial algorithm with the approximation ratio q(P) = \frac12 - d(P) q(P) = \frac{1}{{2 - d(P)}} , where d(P) = 2 ^{- k}| P ^{- 1}(1) | d(P) = {2^{ - k}}\left| {{P^{ - 1}}(1)} \right| is a “random” threshold approximation ratio of the predicate P. The ratio q(P) is a threshold approximation ratio.     

Parallel merging with restriction

In this paper, we study the merging of two sorted arrays and on EREW PRAM with two restrictions: (1) The elements of two arrays are taken from the integer range [1,n], where n=Max(n ₁,n ₂). (2) The elements are taken from either uniform distribution or non-uniform distribution such that , for 1≤i≤p (number of processors). We give a new optimal deterministic algorithm runs in time using p processors on EREW PRAM. For ; the running time of the algorithm is O(log ^(g) n) which is faster than the previous results, where log ^(g) n=log log ^(g−1) n for g>1 and log ⁽¹⁾ n=log n. We also extend the domain of input data to [1,n ^k ], where k is a constant.

Space Efficient Dynamic Orthogonal Range Reporting

In this paper we present new space efficient dynamic data structures for orthogonal range reporting. The described data structures support planar range reporting queries in time O(log n+klog log (4n/(k+1))) and space O(nlog log n), or in time O(log n+k) and space O(nlog  ^ε n) for any ε>0. Both data structures can be constructed in O(nlog n) time and support insert and delete operations in amortized time O(log ² n) and O(log nlog log n) respectively. These results match the corresponding upper space bounds of Chazelle (SIAM J. Comput. 17, 427–462, 1988) for the static case. We also present a dynamic data structure for d-dimensional range reporting with search time O(log  ^d−1 n+k), update time O(log  ^d n), and space O(nlog  ^d−2+ε n) for any ε>0. The model of computation used in our paper is a unit cost RAM with word size log n. A preliminary version of this paper appeared in the Proceedings of the 21st Annual ACM Symposium on Computational Geometry 2005. Work partially supported by IST grant 14036 (RAND-APX).     

Approximate hotlink assignment

Consider a directed rooted tree T=(V,E) of maximal degree d representing a collection V of web pages connected via a set E of links all reachable from a source home page, represented by the root of T. Each leaf web page carries a weight representative of the frequency with which it is visited. By adding hotlinks, shortcuts from a node to one of its descendents, we are interested in minimizing the expected number of steps needed to visit the leaf pages from the home page. We give an O(N²) time algorithm for assigning hotlinks so that the expected number of steps to reach the leaves from the root of the tree is at most H(p)/(log(d+1)−(d/(d+1))logd)+(d+1)/d, where H(p) is the entropy of the probability (frequency) distribution p=〈p₁,p₂,…,p_N〉 on the N leaves of the given tree, i.e., p_i is the weight on the ith leaf. The best known lower bound for this problem is H(p)/log(d+1). We also show how to adapt our algorithm to complete trees of a given degree d and in this case we prove it is optimal, asymptotically in d.     

Faster Approximate String Matching for Short Patterns

We study the classical approximate string matching problem, that is, given strings P and Q and an error threshold k, find all ending positions of substrings of Q whose edit distance to P is at most k. Let P and Q have lengths m and n, respectively. On a standard unit-cost word RAM with word size w≥log n we present an algorithm using time

Dynamic Hotlinks

Consider a directed rooted tree T=(V,E) representing a collection V of n web pages connected via a set E of links all reachable from a source home page, represented by the root of T. Each web page i carries a weight w _i representative of the frequency with which it is visited. By adding hotlinks, shortcuts from a node to one of its descendants, we are interested in minimizing the expected number of steps needed to visit pages from the home page. We give the first linear time algorithm for assigning hotlinks so that the number of steps to access a page i from the root of the tree reaches the entropy bound, i.e. is at most O(log (W/w _i )) where W=∑ _i∈T w _i . The best previously known algorithm for this task runs in time O(n ²). We also give the first efficient data structure for maintaining hotlinks when nodes are added, deleted or their weights modified, in amortized time O(log (W/w _i )) per update. The data structure can be made adaptive, i.e. reaches the entropy bound in the amortized sense without knowing the weights w _i in advance.     

Faster Deterministic Communication in Radio Networks

We study the communication primitives of broadcasting (one-to-all communication) and gossiping (all-to-all communication) in known topology radio networks, i.e., where for each primitive the schedule of transmissions is precomputed based on full knowledge about the size and the topology of the network. We show that gossiping can be completed in time units in any radio network of size n, diameter D, and maximum degree Δ=Ω(log n). This is an almost optimal schedule in the sense that there exists a radio network topology, specifically a Δ-regular tree, in which the radio gossiping cannot be completed in less than units of time. Moreover, we show a schedule for the broadcast task. Both our transmission schemes significantly improve upon the currently best known schedules by Gąsieniec, Peleg, and Xin (Proceedings of the 24th Annual ACM SIGACT-SIGOPS PODC, pp. 129–137, 2005), i.e., a O(D+Δlog n) time schedule for gossiping and a D+O(log ³ n) time schedule for broadcast. Our broadcasting schedule also improves, for large D, a very recent O(D+log ² n) time broadcasting schedule by Kowalski and Pelc. A preliminary version of this paper appeared in the proceedings of ISAAC’06. F. Cicalese supported by the Sofja Kovalevskaja Award 2004 of the Alexander von Humboldt Stiftung. F. Manne and Q. Xin supported by the Research Council of Norway through the SPECTRUM project.     

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.     

On Locating Disjoint Segments with Maximum Sum of Densities

Given a sequence A of n real numbers and two positive integers l and k, where , we study the problem of locating k disjoint segments of A, each of length at least l, such that the sum of their densities is maximized. The best previously known algorithm, due to Bergkvist and Damaschke, runs in O(nl+k ² l ²) time. In this paper, we propose an O(n+k ² llog l)-time algorithm for it. We also give an optimal algorithm for a related problem raised by Lin et al. in 2003, where the goal is to locate k disjoint maximum-density segments in a given sequence. A preliminary version of this work appeared in Proceedings of the 17th International Symposium on Algorithms and Computation, India, 2006.     

Complexity of Hard-Core Set Proofs

We study a fundamental result of Impagliazzo (FOCS’95) known as the hard-core set lemma. Consider any function f:{0,1}ⁿ?{0,1}{f:\{0,1\}^n\to\{0,1\}} which is “mildly hard”, in the sense that any circuit of size s must disagree with f on at least a δ fraction of inputs. Then, the hard-core set lemma says that f must have a hard-core set H of density δ on which it is “extremely hard”, in the sense that any circuit of size s￠=O(s/(\frac1e²log(\frac1ed))){s'=O(s/(\frac{1}{\epsilon^2}\log(\frac{1}{\epsilon\delta})))} must disagree with f on at least (1-e)/2{(1-\epsilon)/2} fraction of inputs from H.     

Compressed Indexes for Approximate String Matching

We revisit the problem of indexing a string S[1..n] to support finding all substrings in S that match a given pattern P[1..m] with at most k errors. Previous solutions either require an index of size exponential in k or need Ω(m ^k ) time for searching. Motivated by the indexing of DNA, we investigate space efficient indexes that occupy only O(n) space. For k=1, we give an index to support matching in O(m+occ+log nlog log n) time. The previously best solution achieving this time complexity requires an index of O(nlog n) space. This new index can also be used to improve existing indexes for k≥2 errors. Among others, it can support 2-error matching in O(mlog nlog log n+occ) time, and k-error matching, for any k>2, in O(m ^k−1log nlog log n+occ) time.     

Many-to-Many Communication in Radio Networks

Radio networks model wireless data communication when the bandwidth is limited to one wave frequency. The key restriction of such networks is mutual interference of packets arriving simultaneously at a node. The many-to-many (m2m) communication primitive involves p participant nodes from among n nodes in the network, where the distance between any pair of participants is at most d. The task is to have all the participants get to know all the input messages. We consider three cases of the m2m communication problem. In the ad-hoc case, each participant knows only its name and the values of n, p and d. In the partially centralized case, each participant knows the topology of the network and the values of p and d, but does not know the names of the other participants. In the centralized case, each participant knows the topology of the network and the names of all the participants. For the centralized m2m problem, we give deterministic protocols, for both undirected and directed networks, working in time, which is provably optimal. For the partially centralized m2m problem, we give a randomized protocol for undirected networks working in time with high probability (whp), and we show that any deterministic protocol requires time. For the ad-hoc m2m problem, we develop a randomized protocol for undirected networks that works in time whp. We show two lower bounds for the ad-hoc m2m problem. One lower bound states that any randomized protocol for the m2m ad hoc problem requires expected time. Another lower bound states that for any deterministic protocol for the m2m ad hoc problem, there is a network on which the protocol requires time when n−p(n)=Ω(n) and d>1, and that it requires Ω(n) time when n−p(n)=o(n). The results of this paper appeared in a preliminary form in “On many-to-many communication in packet radio networks” in Proceedings of the 10th Conference on Principles of Distributed Systems (OPODIS), Bordeaux, France, 2006, Lecture Notes in Computer Science 4305, Springer, Heidelberg, pp. 258–272. The work of B.S. Chlebus was supported by NSF Grant 0310503.     

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.     

A New Algorithm for Finding Trees with Many Leaves

We present an algorithm that finds out-trees and out-branchings with at least k leaves in directed graphs. These problems are known as Directed Maximum Leaf Out-Tree and Directed Maximum Leaf Out-Branching, respectively, and—in the case of undirected graphs—as Maximum Leaf Spanning Tree. The run time of our algorithm is O(4 ^k nm) on directed graphs and O(poly(n)+4 ^k k ²) on undirected graphs. This improves over the previously fastest algorithms for these problems with run times of 2 ^O(klog k) poly(n) and O(poly(n)+6.75 ^k poly(k)) respectively.