An improved algorithm for generalized comparison of minisatellites

One of the most important objects in genetic mapping and forensic studies are minisatellites. They consist of a heterogeneous tandem array of short repeat units called variants. The evolution of minisatellites is realized by tandem duplication and tandem deletion of variants. Jeffrey et al. proposed a method to obtain the sequence of variants, called maps. Bérard and Rivals designed the first algorithm of comparison of two minisatellite maps under an evolutionary model including deletion, insertion, mutation, amplification and contraction. The complexity of this first algorithm was O(n⁴) in time and O(n³) in space where n is the size of the maps. In this paper we propose a more efficient algorithm using the same generic evolutionary model which is O(n³) in time and O(n²) in space. Our algorithm with this better efficiency can even solve generalized and more refined models.     

Chaining algorithms for multiple genome comparison

Given n fragments from k>2 genomes, Myers and Miller showed how to find an optimal global chain of colinear non-overlapping fragments in O(nlog^kn) time and O(nlog^k−1n) space. For gap costs in the L₁-metric, we reduce the time complexity of their algorithm by a factor and the space complexity by a factor logn. For the sum-of-pairs gap cost, our algorithm improves the time complexity of their algorithm by a factor . A variant of our algorithm finds all significant local chains of colinear non-overlapping fragments. These chaining algorithms can be used in a variety of problems in comparative genomics: the computation of global alignments of complete genomes, the identification of regions of similarity (candidate regions of conserved synteny), the detection of genome rearrangements, and exon prediction.     

Constructing suffix arrays in linear time

The time complexity of suffix tree construction has been shown to be equivalent to that of sorting: O(n) for a constant-size alphabet or an integer alphabet and O(nlogn) for a general alphabet. However, previous algorithms for constructing suffix arrays have the time complexity of O(nlogn) even for a constant-size alphabet.

In this paper we present a linear-time algorithm to construct suffix arrays for integer alphabets, which do not use suffix trees as intermediate data structures during its construction. Since the case of a constant-size alphabet can be subsumed in that of an integer alphabet, our result implies that the time complexity of directly constructing suffix arrays matches that of constructing suffix trees.     

Constrained tree inclusion

The tree matching problem is considered of given labeled trees P and T, determining if the pattern tree P can be obtained from the text tree T by deleting degree-one and degree-two nodes and, in the case of unordered trees, by also permuting siblings. The constrained tree inclusion problem is more sensitive to the structure of the pattern tree than the general tree inclusion problem. Further, it can be solved in polynomial time for both unordered and ordered trees. Algorithms based on the restricted subtree homeomorphism algorithm of M.-J. Chung [J. Algorithms 8 (1) (1987) 106–112] are presented that solve the constrained tree inclusion problem in O(m^1.5n) time on unordered trees with m and n nodes, and in O(mn) time on ordered trees, using O(mn) additional space.     

Extracting approximate patterns

In this paper, we define a family of patterns with don't cares occurring in a text. We call them primitive patterns. The set of primitive patterns forms a basis for all the maximal patterns occurring in the text. The number of primitive patterns is smaller than other known basis.

We present an incremental algorithm that computes the primitive patterns occurring at least q times in a text of length n, given the N primitive patterns occurring at least q−1 times, in time O(|Σ|Nn²logn), where Σ is the alphabet. In the particular case where q=2, the complexity in time is only O(|Σ|n²logn). We also give an algorithm that decides if a given pattern is primitive in a given text. These algorithms are generalized, taking many sequences in input. Finally, we give a solution for reducing the number of patterns of interest by using scoring techniques, as we show that the number of primitive patterns is exponential.     

Sparse geometric graphs with small dilation

Given a set S of n points in , and an integer k such that 0k<n, we show that a geometric graph with vertex set S, at most n−1+k edges, maximum degree five, and dilation O(n/(k+1)) can be computed in time O(nlogn). For any k, we also construct planar n-point sets for which any geometric graph with n−1+k edges has dilation Ω(n/(k+1)); a slightly weaker statement holds if the points of S are required to be in convex position.     

Linear time isotonic and unimodal regression in the and norms

We consider L₁-isotonic regression and L_∞ isotonic and unimodal regression. For L₁-isotonic regression, we present a linear time algorithm when the number of outputs are bounded. We extend the algorithm to construct an approximate isotonic regression in linear time when the output range is bounded. We present linear time algorithms for L_∞ isotonic and unimodal regression.     

Proximity problems on line segments spanned by points

Finding the closest or farthest line segment (line) from a point are fundamental proximity problems. Given a set S of n points in the plane and another point q, we present optimal O(nlogn) time, O(n) space algorithms for finding the closest and farthest line segments (lines) from q among those spanned by the points in S. We further show how to apply our techniques to find the minimum (maximum) area triangle with a vertex at q and the other two vertices in S{q} in optimal O(nlogn) time and O(n) space. Finally, we give an O(nlogn) time, O(n) space algorithm to find the kth closest line from q and show how to find the k closest lines from q in O(nlogn+k) time and O(n+k) space.     

On minimizing pattern splitting in multi-track string matching

Given a pattern string P=p₁p₂p_m and K parallel text strings over an integer alphabet Σ, our task is to find the smallest integer κ>0 such that P can be split into κ pieces P=P¹…P^κ, where each Pⁱ has an occurrence in some text track T^k_i and these partial occurrences retain the order. We study some variations of this minimum splitting problem, such as splittings with limited gaps and transposition invariance, and show how to use sparse dynamic programming to solve the variations efficiently. In particular, we show that the minimum splitting problem can be interpreted as a shortest path problem on line segments.     

Computing homotopic shortest paths efficiently

We give deterministic and randomized algorithms to find shortest paths homotopic to a given collection Π of disjoint paths that wind amongst n point obstacles in the plane. Our deterministic algorithm runs in time , and the randomized algorithm runs in expected time O(k_out+k_inlogn+n(logn)^1+ε). Here k_in is the number of edges in all the paths of Π, and k_out is the number of edges in the output paths.     

Visibility maps of segments and triangles in 3D

Let T be a set of n triangles in three-dimensional space, let s be a line segment, and let t be a triangle, both disjoint from T. We consider the subdivision of T based on (in)visibility from s; this is the visibility map of the segment s with respect to T. The visibility map of the triangle t is defined analogously. We look at two different notions of visibility: strong (complete) visibility, and weak (partial) visibility. The trivial Ω(n²) lower bound for the combinatorial complexity of the strong visibility map of both s and t is almost tight: we prove an O(n²(n)) upper bound for both structures, where (n) is the extremely slowly increasing inverse Ackermann function. Furthermore, we prove that the weak visibility map of s has complexity Θ(n⁵), and the weak visibility map of t has complexity Θ(n⁷). If T is a polyhedral terrain, the complexity of the weak visibility map is Ω(n⁴) and O(n⁵), both for a segment and a triangle. We also present efficient algorithms to compute all discussed structures.     

A loop-free two-close Gray-code algorithm for listing k-ary Dyck words

P. Chase and F. Ruskey each published a Gray code for length n binary strings with m occurrences of 1, coding m-combinations of n objects, which is two-close—that is, in passing from one binary string to its successor a single 1 exchanges positions with a 0 which is either adjacent to the 1 or separated from it by a single 0. If we impose the restriction that any suffix of a string contains at least k−1 times as many 0's as 1's, we obtain k-suffixes: suffixes of k-ary Dyck words. Combinations are retrieved as special case by setting k=1 and k-ary Dyck words are retrieved as a special case by imposing the additional condition that the entire string has exactly k−1 times as many 0's as 1's. We generalize Ruskey's Gray code to the first two-close Gray code for k-suffixes and we provide a loop-free implementation for k2. For k=1 we use a simplified version of Chase's loop-free algorithm for generating his two-close Gray code for combinations. These results are optimal in the sense that there does not always exist a Gray code, either for combinations or Dyck words, in which the 1 and the 0 that exchange positions are adjacent.     

Bit-parallel approximate string matching algorithms with transposition

Using bit-parallelism has resulted in fast and practical algorithms for approximate string matching under Levenshtein edit distance, which permits a single edit operation to insert, delete or substitute a character. Depending on the parameters of the search, currently the fastest non-filtering algorithms in practice are the O(km/wn) algorithm of Wu and Manber, the O((k+2)(m−k)/wn) algorithm of Baeza-Yates and Navarro, and the O(m/wn) algorithm of Myers, where m is the pattern length, n is the text length, k is the error threshold and w is the computer word size. In this paper we discuss a uniform way of modifying each of these algorithms to permit also a fourth type of edit operation: transposing two adjacent characters in the pattern. This type of edit distance is also known as Damerau edit distance. In the end we also present an experimental comparison of the resulting algorithms.     

Uniform asymptotic expansions of the Pollaczek polynomials

Two uniform asymptotic expansions are obtained for the Pollaczek polynomials P_n(cosθ;a,b). One is for , , in terms of elementary functions and in descending powers of . The other is for , in terms of a special function closely related to the modified parabolic cylinder functions, in descending powers of n. This interval contains a turning point and all possible zeros of P_n(cosθ) in θ(0,π/2].     

Computing the Fréchet distance between piecewise smooth curves

We consider the Fréchet distance between two curves which are given as a sequence of m+n curved pieces. If these pieces are sufficiently well-behaved, we can compute the Fréchet distance in O(mnlog(mn)) time. The decision version of the problem can be solved in O(mn) time. The results are based on an analysis of the possible intersection patterns between circles and arcs of bounded curvature.     

A quadratic distance bound on sliding between crossing-free spanning trees

Let S be a set of n points in the plane and let be the set of all crossing-free spanning trees of S. We show that it is possible to transform any two trees in into each other by O(n²) local and constant-size edge slide operations. Previously no polynomial upper bound for this task was known, but in [O. Aichholzer, F. Aurenhammer, F. Hurtado, Sequences of spanning trees and a fixed tree theorem, Comput. Geom.: Theory Appl. 21 (1–2) (2002) 3–20] a bound of O(n²logn) operations was conjectured.     

Finding a length-constrained maximum-sum or maximum-density subtree and its application to logistics

We study the problem of finding a length-constrained maximum-density path in a tree with weight and length on each edge. This problem was proposed in [R.R. Lin, W.H. Kuo, K.M. Chao, Finding a length-constrained maximum-density path in a tree, Journal of Combinatorial Optimization 9 (2005) 147–156] and solved in O(nU) time when the edge lengths are positive integers, where n is the number of nodes in the tree and U is the length upper bound of the path. We present an algorithm that runs in O(nlog²n) time for the generalized case when the edge lengths are positive real numbers, which indicates an improvement when U=Ω(log²n). The complexity is reduced to O(nlogn) when edge lengths are uniform. In addition, we study the generalized problems of finding a length-constrained maximum-sum or maximum-density subtree in a given tree or graph, providing algorithmic and complexity results.     

Eigenvalues of association schemes of quadratic forms

The duality and primitivity of the association scheme Qua(n,q) of quadratic forms in n variables and the association scheme Sym(n,q) of symmetric bilinear forms in n variables over the finite field are discussed by Wang et al. [Association schemes of quadratic forms and symmetric bilinear forms, J. Algebraic Combin. 17 (2003) 149–161]. In this paper, eigenvalues of Qua(n,q) are computed, where q is a power of 2. As an application, two fusion schemes of Qua(n,q) are discussed and their dual schemes are constructed.     

An improved approximation algorithm for the asymmetric TSP with strengthened triangle inequality

We consider the asymmetric traveling salesperson problem with γ-parameterized triangle inequality for γ[1/2,1). That means, the edge weights fulfill w(u,v)γ(w(u,x)+w(x,v)) for all nodes u,v,x. Chandran and Ram [L.S. Chandran, L.S. Ram, Approximations for ATSP with parametrized triangle inequality, in: Proc. 19th Int. Symp. on Theoret. Aspects of Comput. Sci. (STACS), in: Lecture Notes in Comput. Sci., vol. 2285, Springer, Berlin, 2002, pp. 227–237] gave the first constant factor approximation algorithm with polynomial running time for this problem. They achieve performance ratio γ/(1−γ). We devise an approximation algorithm with performance ratio (1+γ)/(2−γ−γ³), which is better for γ[0.5437,1), that is, for the particularly interesting large values of γ.     

On relations between 1-lines of Adams–Novikov spectral sequences modulo invariant prime ideals

We have a ring homomorphism Θ from the cohomology of the extended Morava stabilizer group G_n with coefficients in F[w^±1] to the cohomology of G_n+1 with coefficients in the graded field F((u_n))[u^±1]. In this note we study the behavior of Θ on H¹. Then it is shown that Θ is injective on H¹ for n1 and for all primes p.