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.     

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).     

Modulo Constraints and the Complexity of Typechecking XML Views

The typechecking problem for transformations of relational data into tree data is the following: given a relational-to-XML transformation P, and an XML type d, decide whether for every database instance the result of the transformation P on satisfies d. TreeQL programs with projection-free conjunctive queries (see Alon et al. in ACM Trans. Comput. Log. 4(3):315–354, 2003) are considered as transformations and DTDs with arbitrary regular expressions as XML types. A non-elementary upper bound for the typechecking problem was already given by Alon et al. (ACM Trans. Comput. Log. 4(3):315–354, 2003) (although in a more general setting, where equality and negation in projection-free conjunctive queries and additional universal integrity constraints are allowed). In this paper we show that the typechecking problem is coNEXPTIME-complete. As an intermediate step we consider the following problem, which can be formulated independently of XML notions. Given a set of triples of the form (φ,k,j), where φ is a projection-free conjunctive query and k,j are natural numbers, decide whether there exists a database such that, for each triple (φ,k,j) in the set, there exists a natural number α, such that there are exactly k+j*α tuples satisfying the query φ in . Our main technical contribution consists of a NEXPTIME algorithm for the last problem. Partially supported by Polish Ministry of Science and Higher Education research project N206 022 31/3660, 2006/2009. This paper is an extended version of 20, where the coNEXPTIME upper bound was shown.     

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.     

Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions

We present a method to speed up the dynamic program algorithms used for solving the HMM decoding and training problems for discrete time-independent HMMs. We discuss the application of our method to Viterbi’s decoding and training algorithms (IEEE Trans. Inform. Theory IT-13:260–269, 1967), as well as to the forward-backward and Baum-Welch (Inequalities 3:1–8, 1972) algorithms. Our approach is based on identifying repeated substrings in the observed input sequence. Initially, we show how to exploit repetitions of all sufficiently small substrings (this is similar to the Four Russians method). Then, we describe four algorithms based alternatively on run length encoding (RLE), Lempel-Ziv (LZ78) parsing, grammar-based compression (SLP), and byte pair encoding (BPE). Compared to Viterbi’s algorithm, we achieve speedups of Θ(log n) using the Four Russians method, using RLE, using LZ78, using SLP, and Ω(r) using BPE, where k is the number of hidden states, n is the length of the observed sequence and r is its compression ratio (under each compression scheme). Our experimental results demonstrate that our new algorithms are indeed faster in practice. We also discuss a parallel implementation of our algorithms. A preliminary version of this paper appeared in Proc. 18th Annual Symposium on Combinatorial Pattern Matching (CPM), pp. 4–15, 2007. Y. Lifshits’ research was supported by the Center for the Mathematics of Information and the Lee Center for Advanced Networking. S. Mozes’ work conducted while visiting MIT.     

Approximating the Bandwidth of Caterpillars

A caterpillar is a tree in which all vertices of degree three or more lie on one path, called the backbone. We present a polynomial time algorithm that produces a linear arrangement of the vertices of a caterpillar with bandwidth at most O(log n/log log n) times the local density of the caterpillar, where the local density is a well known lower bound on the bandwidth. This result is best possible in the sense that there are caterpillars whose bandwidth is larger than their local density by a factor of Ω(log n/log log n). The previous best approximation ratio for the bandwidth of caterpillars was O(log n). We show that any further improvement in the approximation ratio would require using linear arrangements that do not respect the order of the vertices of the backbone. We also show how to obtain a (1+ε) approximation for the bandwidth of caterpillars in time . This result generalizes to trees, planar graphs, and any family of graphs with treewidth .     

Applying Approximate Counting for Computing the Frequency Moments of Long Data Streams

This paper takes up a remark in the well-known paper of Alon, Matias, and Szegedy (J. Comput. Syst. Sci. 58(1):137–147, 1999) about the computation of the frequency moments of data streams and shows in detail how any F _k with k≥1 can be approximately computed using space O(km ^1−1/k (k+log m+log log  n)) based on approximate counting. An important building block for this, which may be interesting in its own right, is a new approximate variant of reservoir sampling using space O(log log  n) for constant error parameters.     

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.     

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.     

Resource scheduling with variable requirements over time

The problem of scheduling resources for tasks with variable requirements over time can be stated as follows. We are given two sequences of vectors A=A ₁,…,A _n and R=R ₁,…,R _m . Sequence A represents resource availability during n time intervals, where each vector A _i has q elements. Sequence R represents resource requirements of a task during m intervals, where each vector R _i has q elements. We wish to find the earliest time interval i, termed latency, such that for 1≤k≤m, 1≤j≤q: A _i+k−1 ^j ≥R _k ^j , where A _i+k−1 ^j and R _k ^j are the jth elements of vectors A _i+k−1 and R _k , respectively. One application of this problem is I/O scheduling for multimedia presentations. The fastest known algorithm to compute the optimal solution of this problem has computation time (Amir and Farach, in Proceedings of the ACM-SIAM symposium on discrete algorithms (SODA), San Francisco, CA, pp. 212–223, 1991; Inf. Comput. 118(1):1–11, 1995). We propose a technique that approximates the optimal solution in linear time: . We evaluated the performance of our algorithm when used for multimedia I/O scheduling. Our results show that 95% of the time, our solution is within 5% of the optimal.     

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.     

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).     

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.     

Communication-Aware Processor Allocation for Supercomputers: Finding Point Sets of Small Average Distance

We give processor-allocation algorithms for grid architectures, where the objective is to select processors from a set of available processors to minimize the average number of communication hops. The associated clustering problem is as follows: Given n points in ℜ ^d , find a size-k subset with minimum average pairwise L ₁ distance. We present a natural approximation algorithm and show that it is a -approximation for two-dimensional grids; in d dimensions, the approximation guarantee is , which is tight. We also give a polynomial-time approximation scheme (PTAS) for constant dimension d, and we report on experimental results.     

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.     

Approximately Fair Cost Allocation in Metric Traveling Salesman Games

A traveling salesman game is a cooperative game . Here N, the set of players, is the set of cities (or the vertices of the complete graph) and c _D is the characteristic function where D is the underlying cost matrix. For all S⊆N, define c _D (S) to be the cost of a minimum cost Hamiltonian tour through the vertices of S∪{0} where is called as the home city. Define Core as the core of a traveling salesman game . Okamoto (Discrete Appl. Math. 138:349–369, [2004]) conjectured that for the traveling salesman game with D satisfying triangle inequality, the problem of testing whether Core is empty or not is -hard. We prove that this conjecture is true. This result directly implies the -hardness for the general case when D is asymmetric. We also study approximately fair cost allocations for these games. For this, we introduce the cycle cover games and show that the core of a cycle cover game is non-empty by finding a fair cost allocation vector in polynomial time. For a traveling salesman game, let and ∀ S⊆N, x(S)≤ε⋅c _D (S)} be an ε-approximate core, for a given ε>1. By viewing an approximate fair cost allocation vector for this game as a sum of exact fair cost allocation vectors of several related cycle cover games, we provide a polynomial time algorithm demonstrating the non-emptiness of the log ₂(|N|−1)-approximate core by exhibiting a vector in this approximate core for the asymmetric traveling salesman game. We improve it further by finding a -approximate core in polynomial time for some constant c. We also show that there exists an ε ₀>1 such that it is -hard to decide whether ε ₀-Core is empty or not. A preliminary version of the paper appeared in the third Workshop on Approximation and Online Algorithms (WAOA), 2005.     

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.