Distributed suffix trees

We present a new variant of the suffix tree called a distributed suffix tree (DST) which allows for much larger databases of strings to be handled efficiently. The method is based on a new linear time construction algorithm for subtrees of a suffix tree. The new data structure tackles the memory bottleneck problem by constructing these subtrees independently and in parallel. It is designed for distributed memory parallel computing environments (e.g., Beowulf clusters). The central advantage is that standard operations of biological importance on suffix trees are shown to be easily translatable to this new data structure. While none of these operations on the DST require inter-process communication, many have optimal expected parallel running times.     

Three problems about simple polygons

We give three related algorithmic results concerning a simple polygon P:

1. Improving a series of previous work, we show how to find a largest pair of disjoint congruent disks inside P in linear expected time.

2. As a subroutine for the above result, we show how to find the convex hull of any given subset of the vertices of P in linear worst-case time.

3. More generally, we show how to compute a triangulation of any given subset of the vertices or edges of P in almost linear time.

Voronoi drawings of trees

We study the problem of characterizing sets of points whose Voronoi diagrams are trees and if so, what are the combinatorial properties of these trees. The second part of the problem can be naturally turned into the following graph drawing question: Given a tree T, can one represent T so that the resulting drawing is a Voronoi diagram of some set of points? We investigate the problem both in the Euclidean and in the Manhattan metric. The major contributions of this paper are as follows.

• We characterize those trees that can be drawn as Voronoi diagrams in the Euclidean metric.

• We characterize those sets of points whose Voronoi diagrams are trees in the Manhattan metric.

• We show that the maximum vertex degree of any tree that can be drawn as a Manhattan Voronoi diagram is at most five and prove that this bound is tight.

• We characterize those binary trees that can be drawn as Manhattan Voronoi diagrams.

The suffix binary search tree and suffix AVL tree

Suffix trees and suffix arrays are classical data structures that are used to represent the set of suffixes of a given string, and thereby facilitate the efficient solution of various string processing problems—in particular on-line string searching. Here we investigate the potential of suitably adapted binary search trees as competitors in this context. The suffix binary search tree (SBST) and its balanced counterpart, the suffix AVL-tree, are conceptually simple, relatively easy to implement, and offer time and space efficiency to rival suffix trees and suffix arrays, with distinct advantages in some circumstances—for instance in cases where only a subset of the suffixes need be represented.

Construction of a suffix BST for an n-long string can be achieved in O(nh) time, where h is the height of the tree. In the case of a suffix AVL-tree this will be O(nlogn) in the worst case. Searching for an m-long substring requires O(m+l) time, where l is the length of the search path. In the suffix AVL-tree this is O(m+logn) in the worst case. The space requirements are linear in n, generally intermediate between those for a suffix tree and a suffix array.

Empirical evidence, illustrating the competitiveness of suffix BSTs, is presented.     

A note on convergence in Banach spaces of cotype p

Let B be a separable Banach space. The following is one of the results proved in this paper. The Banach space B is of cotype p if and only if

1. d_n, n 1, has no subsequence converging in probability, and

2. ∑_{n 1}|a_n|^p < ∞ whenever ∑_{n 1}a_nd_n converges almost surely are equivalent for every sequence d_n, n 1, of symmetric independent random elements taking values in B.

Space efficient linear time construction of suffix arrays

We present a linear time algorithm to sort all the suffixes of a string over a large alphabet of integers. The sorted order of suffixes of a string is also called suffix array, a data structure introduced by Manber and Myers that has numerous applications in pattern matching, string processing, and computational biology. Though the suffix tree of a string can be constructed in linear time and the sorted order of suffixes derived from it, a direct algorithm for suffix sorting is of great interest due to the space requirements of suffix trees. Our result is one of the first linear time suffix array construction algorithms, which improve upon the previously known O(nlogn) time direct algorithms for suffix sorting. It can also be used to derive a different linear time construction algorithm for suffix trees. Apart from being simple and applicable for alphabets not necessarily of fixed size, this method of constructing suffix trees is more space efficient.     

Reverse engineering of compact suffix trees and links: A novel algorithm

Invented in the 1970s, the Suffix Tree (ST) is a data structure that indexes all substrings of a text in linear space. Although more space demanding than other indexes, the ST remains likely an inspiring index because it represents substrings in a hierarchical tree structure. Along time, STs have acquired a central position in text algorithmics with myriad of algorithms and applications to for instance motif discovery, biological sequence comparison, or text compression. It is well known that different words can lead to the same suffix tree structure with different labels. Moreover, the properties of STs prevent all tree structures from being STs. Even the suffix links, which play a key role in efficient construction algorithms and many applications, are not sufficient to discriminate the suffix trees of distinct words. The question of recognising which trees can be STs has been raised and termed Reverse Engineering on STs. For the case where a tree is given with potential suffix links, a seminal work provides a linear time solution only for binary alphabets. Here, we also investigate the Reverse Engineering problem on ST with links and exhibit a novel approach and algorithm. Hopefully, this new suffix tree characterisation makes up a valuable step towards a better understanding of suffix tree combinatorics.     

Stable rank boundary principle

Let K denote a compact subset of the complex plane . We present correct proof that the stable rank of A(K) is one. Hereby, A (K) is the algebra of all continuous functions on K which are analytic in the interior of K.

Let G denote a plane domain whose boundary consists of finitely many closed, nonintersecting Jordan curves. We show that for a fixed function of gεC( ), g≠0, the following assertions are equivalent:

Every unimodular element (f, g) is reducible to the principal component exp(C( )).

The zero set Z_g is polynomially convex, i.e., its complement Z_g is connected.

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.     

Convolution integral equations with Gegenbauer function kernel

In this paper we develop a concise and transparent approach for solving Mellin convolution equations where the convolutor is the product of an algebraic function and a Gegenbauer function. Our method is primarily based on

1. the use of fractional integral/differential operators;

2. a formula for Gegenbauer functions which is a fractional extension of the Rodrigues formula for Gegenbauer polynomials (see Theorem 3);

3. an intertwining relation concerning fractional integral/differential operators (see Theorem 1), which in the integer case reads (d/dx)²ⁿ⁺¹ = (x⁻¹ d/dx)ⁿx²ⁿ⁺¹(x⁻¹ d/dx)ⁿ⁺¹.

Thus we cover most of the known results on this type of integral equations and obtain considerable extensions. As a special illustration we present the Gegenbauer transform pair associated to the Radon transformation.     

Replacing suffix trees with enhanced suffix arrays

The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome this obstacle. We will show how every algorithm that uses a suffix tree as data structure can systematically be replaced with an algorithm that uses an enhanced suffix array and solves the same problem in the same time complexity. The generic name enhanced suffix array stands for data structures consisting of the suffix array and additional tables. Our new algorithms are not only more space efficient than previous ones, but they are also faster and easier to implement.     

On a problem concerning ordered colourings

Let G be a connected graph with v(G) 2 vertices and independence number (G). G is critical if for any edge e of G:

1. (i) (G − e) > (G), if e is not a cut edge of G, and

2. (ii) v(G_i) − (G_i) < v(G) − (G), I = 1, 2, if e is a cut edge and G₁, G₂ are the two components of G − e.

Recently, Katchalski et al. (1995) conjectured that: if G is a connected critical graph, then with equality possible if and only if G is a tree. In this paper we establish this conjecture.     

Dynamic extended suffix arrays

The suffix tree data structure has been intensively described, studied and used in the eighties and nineties, its linear-time construction counterbalancing his space-consuming requirements. An equivalent data structure, the suffix array, has been described by Manber and Myers in 1990. This space-economical structure has been neglected during more than a decade, its construction being too slow. Since 2003, several linear-time suffix array construction algorithms have been proposed, and this structure has slowly replaced the suffix tree in many string processing problems. All these constructions are building the suffix array from the text, and any edit operation on the text leads to the construction of a brand new suffix array. In this article, we are presenting an algorithm that modifies the suffix array and the Longest Common Prefix (LCP) array when the text is edited (insertion, substitution or deletion of a letter or a factor). This algorithm is based on a recent four-stage algorithm developed for dynamic Burrows–Wheeler Transforms (BWT). For minimizing the space complexity, we are sampling the Suffix Array, a technique used in BWT-based compressed indexes. We furthermore explain how this technique can be adapted for maintaining a sample of the Extended Suffix Array, containing a sample of the Suffix Array, a sample of the Inverse Suffix Array and the whole LCP array. Our practical experiments show that it operates very well in practice, being quicker than the fastest suffix array construction algorithm.     

Parallel lightweight wavelet tree,suffix array and FM-index construction

We present parallel lightweight algorithms to construct wavelet trees, rank and select structures, and suffix arrays in a shared-memory setting. The work and depth of our first parallel wavelet tree algorithm match those of the best existing parallel algorithm while requiring asymptotically less memory and our second algorithm achieves the same asymptotic bounds for small alphabet sizes. Our experiments show that they are both faster and more memory-efficient than existing parallel algorithms. We also present an experimental evaluation of the parallel construction of rank and select structures, which are used in wavelet trees. Next, we design the first parallel suffix array algorithm based on induced copying. Our induced copying requires linear work and polylogarithmic depth for constant alphabets sizes. When combined with a parallel prefix doubling algorithm, it is more efficient in practice both in terms of running time and memory usage compared to existing parallel implementations. As an application, we combine our algorithms to build the FM-index in parallel.     

A theory of heating of Voigt solids and fluids by external energy sources and flame theory

The purpose of this paper is to develop

1. a theory of laser stimulated vaporization of droplets,

2. a theory of internal heating resulting from vibration waves in linearly responding elastic material, and

3. flame theory.

There are applications to sending information through clouds on laser beams and to the control of temperature in ultrasonic welding, and improvement of the design of aircraft engines and the processes used for the destruction of toxic chemicals.

We develop a theory of thermal excursions resulting from ultrasonic welding in 3 and 7 dimensions, and interpret it as an elastic interaction with damping in a Voigt solid. It is hypothesized that with good control of temperature, one could achieve strong and uniform welds by this process and greatly reduce the cost of manufacturing aircraft, and other aluminum structures. We consider equations describing the conservation of mass, momentum, and energy coupled by an equation of state, and consider general mass, momentum, and energy transfer relationships in a compressible body subjected to external stimuli. For the Voigt solid theory, a linear elastic theory with damping forces, we show how some simple local time averaging gives us a dovetailed system consisting of the elastic wave equations whose solution provides the source term for an otherwise uncoupled heat equation. For the more general theory of droplet vaporization, we illustrate a general nonlinear energy equation which includes a radiation energy conductivity term. We get a class of exact solutions for a nonlinear flame front boundary value problem.     

Continuous bottleneck tree partitioning problems

We study continuous partitioning problems on tree network spaces whose edges and nodes are points in Euclidean spaces. A continuous partition of this space into p connected components is a collection of p subtrees, such that no pair of them intersect at more than one point, and their union is the tree space. An edge-partition is a continuous partition defined by selecting p−1 cut points along the edges of the underlying tree, which is assumed to have n nodes. These cut points induce a partition into p subtrees (connected components). The objective is to minimize (maximize) the maximum (minimum) “size” of the components (the min–max (max–min) problem). When the size is the length of a subtree, the min–max and the max–min partitioning problems are NP-hard. We present O(n² log(min(p,n))) algorithms for the edge-partitioning versions of the problem. When the size is the diameter, the min–max problems coincide with the continuous p-center problem. We describe O(n log³ n) and O(n log² n) algorithms for the max–min partitioning and edge-partitioning problems, respectively, where the size is the diameter of a component.     

Biased random walks on directed trees

Summary. We define directed rooted labeled and unlabeled trees and find measures on the space of directed rooted unlabeled trees which are invariant with respect to transition probabilities corresponding to a biased random walk on a directed rooted labeled tree. We use these to calculate the speed of a biased random walk on directed rooted labeled trees. The results are mainly applied to directed trees with recurrent subtrees, where the random walker cannot escape. Received: 12 March 1997/ In revised form: 11 December 1997     

Dynamic Enumeration of All Mixed Cells

The polyhedral homotopy method, which has been known as a powerful numerical method for computing all isolated zeros of a polynomial system, requires all mixed cells of the support of the system to construct a family of homotopy functions. The mixed cells are reformulated in terms of a linear inequality system with an additional combinatorial condition. An enumeration tree is constructed among a family of linear inequality systems induced from it such that every mixed cell corresponds to a unique feasible leaf node, and the depth-first search is applied to the enumeration tree for finding all the feasible leaf nodes. How to construct such an enumeration tree is crucial in computational efficiency. This paper proposes a dynamic construction of an enumeration tree, which branches each parent node into its child nodes so that the number of feasible child nodes is expected to be small; hence we can prune many subtrees which do not contain any mixed cell. Numerical results exhibit that the proposed dynamic construction of an enumeration tree works very efficiently for large scale polynomial systems; for example, it generated all mixed cells of the cyclic-15 problem for the first time in less than 16 hours.     

Finding the maximum suffix with fewer comparisons

It is shown how to compute the lexicographically maximum suffix of a string of n?2 characters over a totally ordered alphabet using at most (4/3)n−5/3 three-way character comparisons. The best previous bound, which has stood unchallenged for more than 25 years, is (3/2)n−O(1) comparisons. We also prove an interesting property of an algorithm for computing the maximum suffix both with respect to a total order < and with respect to its inverse order >.     

Two linear transformations each tridiagonal with respect to an eigenbasis of the other

Let denote a field, and let V denote a vector space over with finite positive dimension. We consider a pair of linear transformations A:V→V and A^*:V→V satisfying both conditions below:

1. [(i)] There exists a basis for V with respect to which the matrix representing A is diagonal and the matrix representing A^* is irreducible tridiagonal.

2. [(ii)] There exists a basis for V with respect to which the matrix representing A^* is diagonal and the matrix representing A is irreducible tridiagonal.

We call such a pair a Leonard pair on V. Refining this notion a bit, we introduce the concept of a Leonard system. We give a complete classification of Leonard systems. Integral to our proof is the following result. We show that for any Leonard pair A,A^* on V, there exists a sequence of scalars β,γ,γ^*,,^* taken from such that both

where [r,s] means rs−sr. The sequence is uniquely determined by the Leonard pair if the dimension of V is at least 4. We conclude by showing how Leonard systems correspond to q-Racah and related polynomials from the Askey scheme.