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.     

A Metropolis-Type Optimization Algorithm on the Infinite Tree

Let S(v) be a function defined on the vertices v of the infinite binary tree. One algorithm to seek large positive values of S is the Metropolis-type Markov chain (X _n ) defined by for each neighbor w of v , where b is a parameter (``1/temperature") which the user can choose. We introduce and motivate study of this algorithm under a probability model for the objective function S , in which S is a ``tree-indexed simple random walk," that is, the increments (e) = S(w)-S(v) along parent—child edges e = (v,w) are independent and P ( = 1) = p , P( = -1) = 1-p . This algorithm has a ``speed" r(p,b) = lim _n n ^-1 ES(X _n ) . We study the speed via a mixture of rigorous arguments, nonrigorous arguments, and Monte Carlo simulations, and compare with a deterministic greedy algorithm which permits rigorous analysis. Formalizing the nonrigorous arguments presents a challenging problem. Mathematically, the subject is in part analogous to recent work of Lyons et al. [19], [20] on the speed on random walk on Galton—Watson trees. A key feature of the model is the existence of a critical point p _crit below which the problem is infeasible; we study the behavior of algorithms as p p _crit. This provides a novel analogy between optimization algorithms and statistical physics. Received September 8, 1997; revised February 15, 1998.     

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.     

两元指纹向量聚类问题的复杂性与改进启发式算法

证明丢失值位数不超过2的指纹向量聚类问题为NP-Hard,并给出Figueroa等人指纹向量聚类启发式算法的改进算法.主要改进了算法的实现方法.以链表存储相容顶点集合,并以逐位扫描指纹向量的方法产生相容点集链表,可将产生相容点集的时间复杂性由O(m·n·2p)减小为O(m·(n·p 1)·2p),可使划分一个唯一极大团或最大团的时间复杂性由O(m·p·2p)减小为O(m·2p).实际测试显示,改进算法的空间复杂性平均减少为原算法的49%以下,平均可用原算法20%的时间求解与原算法相同的实例.当丢失值位数超过6时,改进算法几乎总可用不超过原算法11%的时间计算与原算法相同的实例.     

A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences through Alignment

The nested arc-annotation of a sequence is an important model used to represent structural information for RNA and protein sequences. Given two sequences S₁ and S₂ and a nested arc-annotation P₁ for S₁, this paper considers the problem of inferring the nested arc-annotation P₂ for S₂ such that (S₁, P₁) and (S₂, P₂) have the largest common substructure. The problem has a direct application in predicting the secondary structure of an RNA sequence given a closely related sequence with known secondary structure. The currently most efficient algorithm for this problem requires O(nm³) time and O(nm²) space where n is the length of the sequence with known arc-annotation and m is the length of the sequence whose arc-annotation is to be inferred. By using sparsification on a new recursive dynamic programming algorithm and applying a Hirschberg-like traceback technique with compression, we obtain an improved algorithm that runs in min{O(nm² + n²m),O(nm² log n), O(nm³)} time and min{O(m² + mn), O(m² log n + n)} space.     

Detecting Holes and Antiholes in Graphs

In this paper we study the problems of detecting holes and antiholes in general undirected graphs, and we present algorithms for these problems. For an input graph G on n vertices and m edges, our algorithms run in O(n + m²) time and require O(n m) space; we thus provide a solution to the open problem posed by Hayward et al. asking for an O(n⁴)-time algorithm for finding holes in arbitrary graphs. The key element of the algorithms is the use of the depth-first-search traversal on appropriate auxiliary graphs in which moving between any two adjacent vertices is equivalent to walking along a P₄ (i.e., a chordless path on four vertices) of the input graph or on its complement, respectively. The approach can be generalized so that for a fixed constant k ≥ 5 we obtain an O(n^k-1)-time algorithm for the detection of a hole (antihole resp.) on at least k vertices. Additionally, we describe a different approach which allows us to detect antiholes in graphs that do not contain chordless cycles on five vertices in O(n + m²) time requiring O(n + m) space. Again, for a fixed constant k ≥ 6, the approach can be extended to yield O(n^k-2)-time and O(n²)-space algorithms for detecting holes (antiholes resp.) on at least k vertices in graphs which do not contain holes (antiholes resp.) on k - 1 vertices. Our algorithms are simple and can be easily used in practice. Finally, we also show how our detection algorithms can be augmented so that they return a hole or an antihole whenever such a structure is detected in the input graph; the augmentation takes O(n + m) time and space.     

Time-Space Tradeoff in Derandomizing Probabilistic Logspace

Nisan showed that any randomized logarithmic space algorithm (running in polynomial time and with two-sided error) can be simulated by a deterministic algorithm that runs simultaneously in polynomial time and Θ(log² n) space. Subsequently Saks and Zhou improved the space complexity and showed that a deterministic simulation can be carried out in space Θ(log^1.5n). However, their simulation runs in time n^{Θ(log^{0.5}n)}. We prove a time--space tradeoff that interpolates these two simulations. Specifically, we prove that, for any 0 ≤ α ≤ 0.5, any randomized logarithmic space algorithm (running in polynomial time and with two-sided error) can be simulated deterministically in time n^{O(log^{0.5-α}n)} and space O(log^{1.5+α}n). That is, we prove that BPL ⊆ DTISP[n^{O(log^{0.5-α}n)}, O(log^1.5+αn)].     

Searching a Polygonal Region by Two Guards

We study the problem of searching for a mobile intruder in a polygonal region P by two guards. The objective is to decide whether there should exist a search schedule for the two guards to detect the intruder, no matter how fast the intruder moves, and if so, generate a search schedule. During the search, the two guards are required to walk on the boundary of P continuously and be mutually visible all the time. We present a characterization of the class of polygons searchable by two guards in terms of non-redundant components, and thus solve a long-standing open problem in computational geometry. Also, we give an optimal O(n) time algorithm to determine the two-guard searchability in a polygon, and an O(nlog n m) time algorithm to generate a search schedule, if it exists, where n is the number of vertices of P and m (≤n2) is the number of search instructions reported.     

Polynomial algorithms for finding the asymptotically optimum plan of the multiindex axial assignment problem

To construct the asymptotically optimum plan of the p-index axial assignment problem of order n, p algorithms α₀, α₁, ..., α _p−1 with complexities equal to O(n^p+1), O(n^p), ..., O(n²) operations, respectively, are proposed and substantiated under some additional conditions imposed on the coefficients of the objective function. __________ Translated from Kibernetika i Sistemnyi Analiz, No. 6, pp. 176–181, November–December 2005.     

An optimal visibility graph algorithm for triangulated simple polygons

LetP be a triangulated simple polygon withn sides. The visibility graph ofP has an edge between every pair of polygon vertices that can be connected by an open segment in the interior ofP. We describe an algorithm that finds the visibility graph ofP inO(m) time, wherem is the number of edges in the visibility graph. Becausem can be as small asO(n), the algorithm improves on the more general visibility algorithms of Asanoet al. [AAGHI] and Welzl [W], which take (n ²) time, and on Suri'sO(m logn) visibility graph algorithm for simple polygons [S].This work was supported in part by a U.S. Army Research Office fellowship under agreement DAAG29-83-G-0020.     

A Randomized Algorithm for the Voronoi Diagram of Line Segments on Coarse-Grained Multiprocessors

We present a randomized algorithm for computing the Voronoi diagram of line segments using coarse-grained parallel machines. Operating on P processors, for any input of n line segments, this algorithm performs O((n log n)/P) local operations per processor, O(n/P) messages per processor, and O(1) communication phases, with high probability for n=Ω(P ^3+ε ) . Received June 1, 1997; revised March 10, 1998.     

A space and time efficient algorithm for SimRank computation

SimRank has become an important similarity measure to rank web documents based on a graph model on hyperlinks. The existing approaches for conducting SimRank computation adopt an iteration paradigm. The most efficient deterministic technique yields O(n³)O\left(n^3\right) worst-case time per iteration with the space requirement O(n²)O\left(n^2\right), where n is the number of nodes (web documents). In this paper, we propose novel optimization techniques such that each iteration takes O (min{ n ·m , n^r })O \left(\min \left\{ n \cdot m , n^r \right\}\right) time and O ( n + m )O \left( n + m \right) space, where m is the number of edges in a web-graph model and r ≤ log₂ 7. In addition, we extend the similarity transition matrix to prevent random surfers getting stuck, and devise a pruning technique to eliminate impractical similarities for each iteration. Moreover, we also develop a reordering technique combined with an over-relaxation method, not only speeding up the convergence rate of the existing techniques, but achieving I/O efficiency as well. We conduct extensive experiments on both synthetic and real data sets to demonstrate the efficiency and effectiveness of our iteration techniques.     

On Minimum-Area Hulls

We study some minimum-area hull problems that generalize the notion of convex hull to star-shaped and monotone hulls. Specifically, we consider the minimum-area star-shaped hull problem: Given an n -vertex simple polygon P , find a minimum-area, star-shaped polygon P ^* containing P . This problem arises in lattice packings of translates of multiple, nonidentical shapes in material layout problems (e.g., in clothing manufacture), and has been recently posed by Daniels and Milenkovic. We consider two versions of the problem: the restricted version, in which the vertices of P ^* are constrained to be vertices of P , and the unrestricted version, in which the vertices of P ^* can be anywhere in the plane. We prove that the restricted problem falls in the class of ``3sum-hard' (sometimes called ``n ² -hard') problems, which are suspected to admit no solutions in o(n ² ) time. Further, we give an O(n ² ) time algorithm, improving the previous bound of O(n ⁵ ) . We also show that the unrestricted problem can be solved in O(n ² p(n)) time, where p(n) is the time needed to find the roots of two equations in two unknowns, each a polynomial of degree O(n) . We also consider the case in which P ^* is required to be monotone, with respect to an unspecified direction; we refer to this as the minimum-area monotone hull problem. We give a matching lower and upper bound of Θ(n log n) time for computing P ^* in the restricted version, and an upper bound of O(n q(n)) time in the unrestricted version, where q(n) is the time needed to find the roots of two polynomial equations in two unknowns with degrees 2 and O(n) . Received November 1996; revised March 1997.     

Spreading of Messages in Random Graphs

Consider the following model on the spreading of messages. A message initially convinces a set of vertices, called the seeds, of the Erdős-Rényi random graph G(n,p). Whenever more than a ρ∈(0,1) fraction of a vertex v’s neighbors are convinced of the message, v will be convinced. The spreading proceeds asynchronously until no more vertices can be convinced. This paper derives lower bounds on the minimum number of initial seeds, min-seed(n,p,d,r)\mathrm{min\hbox{-}seed}(n,p,\delta,\rho), needed to convince a δ∈{1/n,…,n/n} fraction of vertices at the end. In particular, we show that (1) there is a constant β>0 such that min-seed(n,p,d,r)=W(min{d,r}n)\mathrm{min\hbox{-}seed}(n,p,\delta,\rho)=\Omega(\min\{\delta,\rho\}n) with probability 1−n ^−Ω(1) for p≥β (ln (e/min {δ,ρ}))/(ρ n) and (2) min-seed(n,p,d,1/2)=W(dn/ln(e/d))\mathrm{min\hbox{-}seed}(n,p,\delta,1/2)=\Omega(\delta n/\ln(e/\delta)) with probability 1−exp (−Ω(δ n))−n ^−Ω(1) for all p∈[ 0,1 ]. The hidden constants in the Ω notations are independent of p.     

Polynomial Time Algorithms for 2-Edge-Connectivity Augmentation Problems

Abstract. Given a 2-edge-connected, real weighted graph G with n vertices and m edges, the 2-edge-connectivity augmentation problem is that of finding a minimum weight set of edges of G to be added to a spanning subgraph H of G to make it 2-edge-connected. While the general problem is NP-hard and 2 -approximable, in this paper we prove that it becomes polynomial time solvable if H is a depth-first search tree of G . More precisely, we provide an efficient algorithm for solving this special case which runs in O (M · α(M,n)) time, where α is the classic inverse of Ackermann's function and M=m · α(m,n) . This algorithm has two main consequences: first, it provides a faster 2 -approximation algorithm for the general 2 -edge-connectivity augmentation problem; second, it solves in O (m · α(m,n)) time the problem of restoring, by means of a minimum weight set of replacement edges, the 2 -edge-connectivity of a 2-edge-connected communication network undergoing a link failure.     

A simple nc algorithm to recognize weakly triangulated graphs

Let S be a set of n closed intervals on the x-axis. A ranking assigns to each interval, s, a distinct rank, p(s)? [1, 2,…,n]. We say that s can see t if p(s)<p(t) and there is a point p?s∩t so that p?u for all u with p(s)<p(u)<p(t). It is shown that a ranking can be found in time O(n log n) such that each interval sees at most three other intervals. It is also shown that a ranking that minimizes the average number of endpoints visible from an interval can be computed in time O(n ^5/2). The results have applications to intersection problems for intervals, as well as to channel routing problems which arise in layouts of VLSI circuits.     

On Approximating Polygonal Curves in Two and Three Dimensions

Given a polygonal curve P =[p₁, p₂, . . . , p_n], the polygonal approximation problem considered calls for determining a new curve P′ = [p′₁, p′₂, . . . , p′_m] such that (i) m is significantly smaller than n, (ii) the vertices of P′ are an ordered subset of the vertices of P, and (iii) any line segment [p′_A, p′_{A + 1} of P′ that substitutes a chain [p_B, . . . , p_C] in P is such that for all i where B ≤ i ≤ C, the approximation error of p_i with respect to [p′_A, p′_{A + 1}], according to some specified criterion and metric, is less than a predetermined error tolerance. Using the parallel-strip error criterion, we study the following problems for a curve P in R^d, where d = 2, 3: (i) minimize m for a given error tolerance and (ii) given m, find the curve P′ that has the minimum approximation error over all curves that have at most m vertices. These problems are called the min-# and min-ϵ problems, respectively. For R² and with any one of the L₁, L₂, or L_∞ distance metrics, we give algorithms to solve the min-# problem in O(n²) time and the min-ϵ problem in O(n² log n) time, improving the best known algorithms to date by a factor of log n. When P is a polygonal curve in R³ that is strictly monotone with respect to one of the three axes, we show that if the L₁ and L_∞ metrics are used then the min-# problem can be solved in O(n²) time and the min-ϵ problem can be solved in O(n³) time. If distances are computed using the L₂ metric then the min-# and min-ϵ problems can be solved in O(n³) and O(n³ log n) time, respectively. All of our algorithms exhibit O(n²) space complexity. Finally, we show that if it is not essential to minimize m, simple modifications of our algorithms afford a reduction by a factor of n for both time and space.     

Simple and Improved Parameterized Algorithms for Multiterminal Cuts

Given a graph G=(V,E) with n vertices and m edges, and a subset T of k vertices called terminals, the Edge (respectively, Vertex) Multiterminal Cut problem is to find a set of at most l edges (non-terminal vertices), whose removal from G separates each terminal from all the others. These two problems are NP-hard for k≥3 but well-known to be polynomial-time solvable for k=2 by the flow technique. In this paper, based on a notion farthest minimum isolating cut, we design several simple and improved algorithms for Multiterminal Cut. We show that Edge Multiterminal Cut can be solved in O(2 ^l kT(n,m)) time and Vertex Multiterminal Cut can be solved in O(k ^l T(n,m)) time, where T(n,m)=O(min?(n ^2/3,m ^1/2)m) is the running time of finding a minimum (s,t) cut in an unweighted graph. Furthermore, the running time bounds of our algorithms can be further reduced for small values of k: Edge 3-Terminal Cut can be solved in O(1.415 ^l T(n,m)) time, and Vertex {3,4,5,6}-Terminal Cuts can be solved in O(2.059 ^l T(n,m)), O(2.772 ^l T(n,m)), O(3.349 ^l T(n,m)) and O(3.857 ^l T(n,m)) time respectively. Our results on Multiterminal Cut can also be used to obtain faster algorithms for Multicut: $O((\min(\sqrt{2k},l)+1)^{2k}2^{l}T(n,m))Given a graph G=(V,E) with n vertices and m edges, and a subset T of k vertices called terminals, the Edge (respectively, Vertex) Multiterminal Cut problem is to find a set of at most l edges (non-terminal vertices), whose removal from G separates each terminal from all the others. These two problems are NP-hard for k≥3 but well-known to be polynomial-time solvable for k=2 by the flow technique. In this paper, based on a notion farthest minimum isolating cut, we design several simple and improved algorithms for Multiterminal Cut. We show that Edge Multiterminal Cut can be solved in O(2 ^l kT(n,m)) time and Vertex Multiterminal Cut can be solved in O(k ^l T(n,m)) time, where T(n,m)=O(min (n ^2/3,m ^1/2)m) is the running time of finding a minimum (s,t) cut in an unweighted graph. Furthermore, the running time bounds of our algorithms can be further reduced for small values of k: Edge 3-Terminal Cut can be solved in O(1.415 ^l T(n,m)) time, and Vertex {3,4,5,6}-Terminal Cuts can be solved in O(2.059 ^l T(n,m)), O(2.772 ^l T(n,m)), O(3.349 ^l T(n,m)) and O(3.857 ^l T(n,m)) time respectively. Our results on Multiterminal Cut can also be used to obtain faster algorithms for Multicut: O((min(?{2k},l)+1)^2k2^lT(n,m))O((\min(\sqrt{2k},l)+1)^{2k}2^{l}T(n,m)) -time algorithm for Edge Multicut and O((2k) ^k+l/2 T(n,m))-time algorithm for Vertex Multicut.     

The Fully Polynomial Approximation Algorithm for the 0-1 Knapsack Problem

A modified fast approximation algorithm for the 0-1 knapsack problem with improved complexity is presented, based on the schemes of Ibarra, Kim and Babat. By using a new partition of items, the algorithm solves the n -item 0-1 knapsack problem to any relative error tolerance ε > 0 in the scaled profit space P ^* /K = O ( 1/ ε ^1+δ ) with time O(n log(1/ ε )+1/ ε^{2+2δ}) and space O(n +1/ ɛ^{2+δ}), where P^{*} and b are the maximal profit and the weight capacity of the knapsack problem, respectively, K is a problem-dependent scaling factor, δ={α}/(1+α) and α=O( log b ). This algorithm reduces the exponent of the complexity bound in [5].     

Fast 3-coloring Triangle-Free Planar Graphs

Although deciding whether the vertices of a planar graph can be colored with three colors is NP-hard, the widely known Grötzsch’s theorem states that every triangle-free planar graph is 3-colorable. We show the first o(n ²) algorithm for 3-coloring vertices of triangle-free planar graphs. The time complexity of the algorithm is $\mathcal{O}(n\log n)Although deciding whether the vertices of a planar graph can be colored with three colors is NP-hard, the widely known Gr?tzsch’s theorem states that every triangle-free planar graph is 3-colorable. We show the first o(n ²) algorithm for 3-coloring vertices of triangle-free planar graphs. The time complexity of the algorithm is O(nlogn)\mathcal{O}(n\log n) .