Parallel integer sorting and simulation amongst CRCW models

 In this paper a general technique for reducing processors in simulation without any increase in time is described. This results in an O(√log n) time algorithm for simulating one step of PRIORITY on TOLERANT with processor-time product of O(n log log n); the same as that for simulating PRIORITY on ARBITRARY. This is used to obtain an O(log n/log log n+√log n (log log m− log log n)) time algorithm for sorting n integers from the set {0,…, m−1}, m≧n, with a processor-time product of O(n log log m log log n) on a TOLERANT CRCW PRAM. New upper and lower bounds for ordered chaining problem on an allocated COMMON CRCW model are also obtained. The algorithm for ordered chaining takes O(log n/log log n) time on an allocated PRAM of size n. It is shown that this result is best possible (upto a constant multiplicative factor) by obtaining a lower bound of Ω(r log n/(log r+log log n)) for finding the first (leftmost one) live processor on an allocated-COMMON PRAM of size n of r-slow virtual processors (one processor simulates r processors of allocated PRAM). As a result, for ordered chaining problem, “processor-time product” has to be at least Ω(n log n/log log n) for any poly-logarithmic time algorithm. Algorithm for ordered-chaining problem results in an O(log N/log log N) time algorithm for (stable) sorting of n integers from the set {0,…, m−1} with n-processors on a COMMON CRCW PRAM; here N=max(n, m). In particular if, m=n ^O(1) , then sorting takes Θ(log n/log log n) time on both TOLERANT and COMMON CRCW PRAMs. Processor-time product for TOLERANT is O(n(log log n)²). Algorithm for COMMON uses n processors. Received August 13, 1992/June 30, 1995     

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.     

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.     

<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).     

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).     

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.     

Strong-Diameter Decompositions of Minor Free Graphs

We provide the first sparse covers and probabilistic partitions for graphs excluding a fixed minor that have strong diameter bounds; i.e. each set of the cover/partition has a small diameter as an induced sub-graph. Using these results we provide improved distributed name-independent routing schemes. Specifically, given a graph excluding a minor on r vertices and a parameter ρ>0 we obtain the following results: (1) a polynomial algorithm that constructs a set of clusters such that each cluster has a strong-diameter of O(r ² ρ) and each vertex belongs to 2 ^O(r) r! clusters; (2) a name-independent routing scheme with a stretch of O(r ²), headers of O(log n+rlog r) bits, and tables of size 2 ^O(r) r! log ⁴ n/log log n bits; (3) a randomized algorithm that partitions the graph such that each cluster has strong-diameter O(r6 ^r ρ) and the probability an edge (u,v) is cut is O(r  d(u,v)/ρ).     

Minimum Weight Convex Steiner Partitions

New tight bounds are presented on the minimum length of planar straight line graphs connecting n given points in the plane and having convex faces. Specifically, we show that the minimum length of a convex Steiner partition for n points in the plane is at most O(log n/log log n) times longer than a Euclidean minimum spanning tree (EMST), and this bound is the best possible. Without Steiner points, the corresponding bound is known to be Θ(log n), attained for n vertices of a pseudo-triangle. We also show that the minimum length convex Steiner partition of n points along a pseudo-triangle is at most O(log log n) times longer than an EMST, and this bound is also the best possible. Our methods are constructive and lead to O(nlog n) time algorithms for computing convex Steiner partitions having O(n) Steiner points and weight within the above worst-case bounds in both cases.     

Combining Markov-Chain Analysis and Drift Analysis

In their seminal article Droste, Jansen, and Wegener (Theor. Comput. Sci. 276:51–82, 2002) consider a basic direct-search heuristic with a global search operator, namely the so-called (1+1) Evolutionary Algorithm ((1+1) EA). They present the first theoretical analysis of the (1+1) EA’s expected runtime for the class of linear functions over the search space {0,1} ⁿ . In a rather long and involved proof they show that, for any linear function, the expected runtime is O(nlog n), i.e., that there are two constants c and n′ such that, for n≥n′, the expected number of iterations until a global optimum is generated is bounded above by c⋅nlog ₂ n. However, neither c nor n′ are specified—they would be pretty large. Here we reconsider this optimization scenario to demonstrate the potential of an analytical method that makes use of the distribution of the evolving candidate solution over the search space {0,1} ⁿ . Actually, an invariance property of this distribution is proved, which is then used to obtain a significantly improved bound on the drift, namely the expected change of a potential function, here the number of bits set correctly. Finally, this better estimate of the drift enables an upper bound on the expected number of iterations of 3.8nlog ₂ n+7.6log ₂ n for n≥2.     

Online Dynamic Programming Speedups

Consider the dynamic program h(n)=min _1≤j≤n a(n,j), where a(n,j) is some formula that may (online) or may not (offline) depend on the previously computed h(i), for i<n. The goal is to compute all h(n), for 1≤n≤N. It is well known that, if a(n,j) satisfy the Monge property, then the SMAWK algorithm (Aggarwal et al., Algorithmica 2(1):195–208, 1987) can solve the offline problem in O(N) time; a Θ(N) speedup over the naive algorithm. In this paper we extend this speedup to the online case, that is, to compute h(n) in the order n=1,2,…,N when (i) we do not know the values of a(n′,j) for n′>n before h(n) has been computed and (ii) do not know the problem size N in advance. We show that if a(n,j) satisfy a stronger, but sometimes still natural, property than the Monge one, then each h(n) can be computed in online fashion in O(1) amortized time. This maintains the speedup online, in the sense that the total time to compute all h(n) is O(N). We also show how to compute each h(n) in the worst case O(log N) time, while maintaining the amortized time bound. For a(n,j) satisfying our stronger property, our algorithm is also simpler than the standard SMAWK algorithm for solving the offline case. We illustrate our technique on two examples from the literature; the first is the D-median problem on a line, and the second comes from mobile wireless paging. The research of the first author was partially supported by the NSF program award CNS-0626606; the research of the second and third authors was partially supported by Hong Kong RGC CERG grant HKUST6312/04E.     

Exact and Approximate Truthful Mechanisms for the Shortest Paths Tree Problem

Let a communication network be modeled by an undirected graph G=(V,E) of n nodes and m edges, and assume that edges are controlled by selfish agents. In this paper we analyze the problem of designing a truthful mechanism for computing one of the most popular structures in communication networks, i.e., the single-source shortest paths tree. More precisely, we will study several realistic scenarios, in which each agent can own either a single or multiple edges of G. In particular, for the single-edge case, we will show that: (i) in the classic utilitarian case, the problem can be solved efficiently in O(mnlog α(m,n)) time, where α(m,n) is the inverse of the Ackermann’s function; (ii) in a meaningful non-utilitarian case, namely that in which agents’ valuation functions only depend on the edge lengths, the problem can be solved in O(m+nlog n) time. Conversely, for the multiple-edges case, we will show in the utilitarian case an O(mP+nPlog n) time truthful mechanism, where P=O(n) denotes the number of agents participating in the solution, while in the same non-utilitarian case we will prove a general lower bound to the approximation ratio that can be achieved by any truthful mechanism, by showing that no c-approximate mechanism can exist, for any fixed . Work partially supported by the Research Project GRID.IT, funded by the Italian Ministry of Education, University and Research. Part of the results herein contained was presented at the 11th International Euro-Par Conference (Euro-Par’05), Lisbon, Portugal, 2005.     

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.     

Kinetic Collision Detection for Convex Fat Objects

We design compact and responsive kinetic data structures for detecting collisions between n convex fat objects in 3-dimensional space that can have arbitrary sizes. Our main results are:

Linearized Suffix Tree: an Efficient Index Data Structure with the Capabilities of Suffix Trees and Suffix Arrays

Suffix trees and suffix arrays are fundamental full-text index data structures to solve problems occurring in string processing. Since suffix trees and suffix arrays have different capabilities, some problems are solved more efficiently using suffix trees and others are solved more efficiently using suffix arrays. We consider efficient index data structures with the capabilities of both suffix trees and suffix arrays without requiring much space. When the size of an alphabet is small, enhanced suffix arrays are such index data structures. However, when the size of an alphabet is large, enhanced suffix arrays lose the power of suffix trees. Pattern searching in an enhanced suffix array takes O(m|Σ|) time while pattern searching in a suffix tree takes O(mlog |Σ|) time where m is the length of a pattern and Σ is an alphabet. In this paper, we present linearized suffix trees which are efficient index data structures with the capabilities of both suffix trees and suffix arrays even when the size of an alphabet is large. A linearized suffix tree has all the functionalities of the enhanced suffix array and supports the pattern search in O(mlog |Σ|) time. In a different point of view, it can be considered a practical implementation of the suffix tree supporting O(mlog |Σ|)-time pattern search. In addition, we also present two efficient algorithms for computing suffix links on the enhanced suffix array and the linearized suffix tree. These are the first algorithms that run in O(n) time without using the range minima query. Our experimental results show that our algorithms are faster than the previous algorithms.     

In-place Algorithm for Erasing a Connected Component in a Binary Image

Removing noise in a given binary image is a common operation. A generalization of the operation is to erase an arbitrarily specified component by reversing pixel values in the component. This paper shows that this operation can be done without using any data structure like a stack or queue, or more exactly using only constant extra memory (consisting of a constant number of words of O(log n) bits for an image of n pixels) in O(mlog m) time for a component consisting of m pixels. This is an in-place algorithm, but the image matrix cannot be used as work space since it has just one bit for each pixel. Whenever we flip a pixel value in a target component, the component shape is also deformed, which causes some difficulty. The main idea for our constant work space algorithm is to deform a component so that its connectivity is preserved.     

An O(n 3(log log n/log n)5/4) Time Algorithm for All Pairs Shortest Path

We present an O(n ³(log log n/log n)^5/4) time algorithm for all pairs shortest paths. This algorithm improves on the best previous result of O(n ³/log n) time. Research supported in part by NSF grant 0310245.     

Optimal External Memory Planar Point Enclosure

In this paper we study the external memory planar point enclosure problem: Given N axis-parallel rectangles in the plane, construct a data structure on disk (an index) such that all K rectangles containing a query point can be reported I/O-efficiently. This problem has important applications in e.g. spatial and temporal databases, and is dual to the important and well-studied orthogonal range searching problem. Surprisingly, despite the fact that the problem can be solved optimally in internal memory with linear space and O(log N+K) query time, we show that one cannot construct a linear sized external memory point enclosure data structure that can be used to answer a query in O(log  _B N+K/B) I/Os, where B is the disk block size. To obtain this bound, Ω(N/B ^1−ε ) disk blocks are needed for some constant ε>0. With linear space, the best obtainable query bound is O(log ₂ N+K/B) if a linear output term O(K/B) is desired. To show this we prove a general lower bound on the tradeoff between the size of the data structure and its query cost. We also develop a family of structures with matching space and query bounds. An extended abstract of this paper appeared in Proceedings of the 12th European Symposium on Algorithms (ESA’04), Bergen, Norway, September 2004, pp. 40–52. L. Arge’s research was supported in part by the National Science Foundation through RI grant EIA–9972879, CAREER grant CCR–9984099, ITR grant EIA–0112849, and U.S.-Germany Cooperative Research Program grant INT–0129182, as well as by the US Army Research Office through grant W911NF-04-01-0278, by an Ole Roemer Scholarship from the Danish National Science Research Council, a NABIIT grant from the Danish Strategic Research Council and by the Danish National Research Foundation. V. Samoladas’ research was supported in part by a grant co-funded by the European Social Fund and National Resources-EPEAEK II-PYTHAGORAS. K. Yi’s research was supported in part by the National Science Foundation through ITR grant EIA–0112849, U.S.-Germany Cooperative Research Program grant INT–0129182, and Hong Kong Direct Allocation Grant (DAG07/08).     

A Fast Algorithm for Adaptive Prefix Coding

In this paper we present a new algorithm for adaptive prefix coding. Our algorithm encodes a text S of m symbols in O(m) time, i.e., in O(1) amortized time per symbol. The length of the encoded string is bounded above by (H+1)m+O(nlog ² m) bits where n is the alphabet size and H is the entropy. This is the first algorithm that adaptively encodes a text in O(m) time and achieves an almost optimal bound on the encoding length in the worst case. Besides that, our algorithm does not depend on an explicit code tree traversal. A preliminary version of this paper appeared in the Proceedings of the 2006 IEEE International Symposium on Information Theory (ISIT 2006). M. Karpinski’s work partially supported by a DFG grant, Max-Planck Research Prize, and IST grant 14036 (RAND-APX). Y. Nekrich’s work partially supported by IST grant 14036 (RAND-APX).     

On Metric Clustering to Minimize the Sum of Radii

Given an n-point metric (P,d) and an integer k>0, we consider the problem of covering P by k balls so as to minimize the sum of the radii of the balls. We present a randomized algorithm that runs in n ^{O(log n⋅log Δ)} time and returns with high probability the optimal solution. Here, Δ is the ratio between the maximum and minimum interpoint distances in the metric space. We also show that the problem is NP-hard, even in metrics induced by weighted planar graphs and in metrics of constant doubling dimension.     

OTIS-MOT: an efficient interconnection network for parallel processing

Mesh of trees (MOT) is well known for its small diameter, high bisection width, simple decomposability and area universality. On the other hand, OTIS (Optical Transpose Interconnection System) provides an efficient optoelectronic model for massively parallel processing system. In this paper, we present OTIS-MOT as a competent candidate for a two-tier architecture that can take the advantages of both the OTIS and the MOT. We show that an n⁴_-n^{4}_{-} processor OTIS-MOT has diameter 8log n ^∗+1 (The base of the logarithm is assumed to be 2 throughout this paper.) and fault diameter 8log n+2 under single node failure. We establish other topological properties such as bisection width, multiple paths and the modularity. We show that many communication as well as application algorithms can run on this network in comparable time or even faster than other similar tree-based two-tier architectures. The communication algorithms including row/column-group broadcast and one-to-all broadcast are shown to require O(log n) time, multicast in O(n ²log n) time and the bit-reverse permutation in O(n) time. Many parallel algorithms for various problems such as finding polynomial zeros, sales forecasting, matrix-vector multiplication and the DFT computation are proposed to map in O(log n) time. Sorting and prefix computation are also shown to run in O(log n) time.