A New Approach to Pattern Matching in Degenerate DNA/RNA Sequences and Distributed Pattern Matching

In this paper, we consider the pattern matching problem in DNA and RNA sequences where either the pattern or the text can be degenerate, i.e., contain sets of characters. We present an asymptotically faster algorithm for the above problem that works in O(n log m) time, where n and m is the length of the text and the pattern respectively. We also suggest an efficient implementation of our algorithm, which works in linear time when the pattern size is small. Finally, we also describe how our approach can be used to solve the distributed pattern matching problem. The preliminary version of this paper appeared in [26].     

A Tutorial on Computational Cluster Analysis with Applications to Pattern Discovery in Microarray Data

Microarrays offer unprecedented possibilities for the so-called omic, e.g., genomic and proteomic, research. However, they are also quite challenging data to analyze. The aim of this paper is to provide a short tutorial on the most common approaches used for pattern discovery and cluster analysis as they are currently used for microarrays, in the hope to bring the attention of the Algorithmic Community on novel aspects of classification and data analysis that deserve attention and have potential for high reward. R. Giancarlo is partially supported by Italian MIUR grants PRIN “Metodi Combinatori ed Algoritmici per la Scoperta di Patterns in Biosequenze” and FIRB “Bioinformatica per la Genomica e la Proteomica” and Italy-Israel FIRB Project “Pattern Discovery Algorithms in Discrete Structures, with Applications to Bioinformatics”. D. Scaturro is supported by a MIUR Fellowship in the Italy-Israel FIRB Project “Pattern Discovery Algorithms in Discrete Structures, with Applications to Bioinformatics”.     

A General Tractable Density Concept for Graphs

In many applications it is an important algorithmic task to find a densest subgraph in an input graph. The complexity of this task depends on how density is defined. If density means the ratio of the number of edges and the number of vertices in the subgraph, then the algorithmic problem has long been known efficiently solvable. On the other hand, the task becomes NP-hard with closely related but somewhat modified concepts of density. To capture many possible tractable density concepts of interest in a common model, we define and analyze a general concept of density, called F-density. Here F is a family of graphs and we are looking for a subgraph of the input graph, such that this subgraph is the densest in terms of containing the highest number of graphs from F relative to the size of the subgraph. We show that for any fixed finite family F, a subgraph of maximum F-density can be found in polynomial time. As our main tool we develop an algorithm, that may be of independent interest, which can find an independent set of maximum independence ratio in a certain class of weighted graphs. The independence ratio is the weight of the independent set divided by the weight of its neighborhood. This work was supported in part by NSF grants ANI-0220001 and CCF-0634848.     

Parameterized Algorithms in Smooth 4-Regular Hamiltonian Graphs

Smooth 4-regular hamiltonian graphs are generalizations of cycle plus triangles graphs. It has been shown that both the independent set and 3-colorability problems are NP-Complete in this class of graphs. In this paper we show that these problems are fixed parameter tractable if we choose the number of inner cycles as parameter. The reseach has been supported by International Science Programme (ISP) of Sweden, under the project titled “The Eastern African Universities Mathematics Programme (EAUMP)”.     

From Lucid to TransLucid: Iteration, Dataflow, Intensional and Cartesian Programming

We present the development of the Lucid language from the Original Lucid of the mid-1970s to the TransLucid of today. Each successive version of the language has been a generalisation of previous languages, but with a further understanding of the problems at hand. The Original Lucid (1976), originally designed for purposes of formal verification, was used to formalise the iteration in while-loop programs. The pLucid language (1982) was used to describe dataflow networks. Indexical Lucid (1987) was introduced for intensional programming, in which the semantics of a variable was understood as a function from a universe of possible worlds to ordinary values. With TransLucid, and the use of contexts as firstclass values, programming can be understood in a Cartesian framework.      

Algorithms for Singleton Attractor Detection in Planar and Nonplanar AND/OR Boolean Networks

Singleton attractor (also called fixed point) detection is known to be NP-hard even for AND/OR Boolean networks (AND/OR BNs in short, i.e., BNs consisting of AND/OR nodes), where BN is a mathematical model of genetic networks and singleton attractors correspond to steady states. In our recent paper, we developed an O(1.787ⁿ) time algorithm for detecting a singleton attractor of a given AND/OR BN where n is the number of nodes. In this paper, we present an O(1.757ⁿ) time algorithm with which we succeeded in improving the above algorithm. We also show that this problem can be solved in time, which is less than O((1 + ∈)ⁿ) for any positive constant ∈, when a BN is planar. A preliminary version of this paper has appeared in Proc. 3rd International Conference on Algebraic Biology (AB2008) [27].     

Efficient Algorithms for Variants of Weighted Matching and Assignment Problems

Obtaining a matching in a graph satisfying a certain objective is an important class of graph problems. Matching algorithms have received attention for several decades. However, while there are efficient algorithms to obtain a maximum weight matching, not much is known about the maximum weight maximum cardinality, and maximum cardinality maximum weight matching problems for general graphs. Our contribution in this work is to show that for bounded weight input graphs one can obtain an algorithm for both maximum weight maximum cardinality (for real weights), and maximum cardinality maximum weight matching (for integer weights) by modifying the input and running the existing maximum weight matching algorithm. Also, given the current state of the art in maximum weight matching algorithms, we show that, for bounded weight input graphs, both maximum weight maximum cardinality, and maximum cardinality maximum weight matching have algorithms of similar complexities to that of maximum weight matching. Subsequently, we also obtain approximation algorithms for maximum weight maximum cardinality, and maximum cardinality maximum weight matching.      

From the Hele-Shaw Experiment to Integrable Systems: A Historical Overview

This paper is a historical overview of the development of the topic now commonly known as Laplacian Growth, from the original Hele-Shaw experiment to the modern treatment based on integrable systems. Supported by the grant of the Norwegian Research Council #177355/V30, and by the European Science Foundation Research Networking Programme HCAA.     

Hyperbolic Function Theory in the Clifford Algebra {\mathcal {C}}\ell_{n+1, 0}

The aim of this paper is to give the basic principles of hyperbolic function theory on the Clifford algebra . The structure of the theory is quite similar to the case of Clifford algebras with negative generators, but the proofs are not obvious. The (real) Clifford algebra is generated by unit vectors with positive squares e²_i = + 1. The hyperbolic Dirac operator is of the form where Q₀f is represented by the composition . If is a solution of H_kf = 0, then f is called k-hypergenic in Ω, where is an open set. We introduce some basic results of hyperbolic function theory and give some representation theorems on . Received: October, 2007. Accepted: February, 2008.     

Approximate Radical for Clusters: A Global Approach Using Gaussian Elimination or SVD

We introduce a matrix of traces, attached to a zero dimensional ideal . We show that the matrix of traces can be a useful tool in handling systems of polynomial equations with clustered roots. We present a method based on Dickson’s lemma to compute the “approximate radical” of in which has zero clusters: the approximate radical ideal has exactly one root in each cluster for sufficiently small clusters. Our method is “global” in the sense that it works simultaneously for all clusters: the problem is reduced to the computation of the numerical nullspace of the matrix of traces, a matrix efficiently computable from the generating polynomials of . To compute the numerical nullspace of the matrix of traces we propose to use Gaussian elimination with pivoting or singular value decomposition. We prove that if has k distinct zero clusters each of radius at most ɛ in the ∞-norm, then k steps of Gaussian elimination on the matrix of traces yields a submatrix with all entries asymptotically equal to ɛ². We also show that the (k + 1)-th singular value of the matrix of traces is proportional to ɛ². The resulting approximate radical has one root in each cluster with coordinates which are the arithmetic mean of the cluster, up to an error term asymptotically equal to ɛ². In the univariate case our method gives an alternative to known approximate square-free factorization algorithms which is simpler and its accuracy is better understood. This work was completed with the support of NSF grants CCR-0306406 and CCR-0347506 and OTKA grants T42481 and T42706 and NK63066.     

Carleson Measures via BMO

We obtain new characterizations of Carleson measures via uniform boundedness of BMO norms of certain mass functions associated with the given measure in a natural way. This research was performed during M. Stessin’s visit to Korea University. He thanks the Mathematics Department of Korea University and the “Brain Pool” program for their hospitality and support. The first two authors were supported by the Korea Research Foundation Grant funded by the Korean Government (KRF-2008-314-C00012).     

A note on the uniqueness of mild solutions to the Navier-Stokes equations

In this note, we will give another proof of the uniqueness of mild solutions to the Navier-Stokes equations in the class C([0,∞); by a simple application of Giga-Shor’s L ^p − L ^q (time-space) estimates, i.e., integral norms in the time variable. The proof relies on a method introduced by S. Monniaux [9] to prove the same result. Received: 11 June 2006     

Non-overlapping Common Substrings Allowing Mutations

This paper studies several combinatorial problems arising from finding the conserved genes of two genomes (i.e., the entire DNA of two species). The input is a collection of n maximal common substrings of the two genomes. The problem is to find, based on different criteria, a subset of such common substrings with maximum total length. The most basic criterion requires that the common substrings selected have the same ordering in the two genomes and they do not overlap among themselves in either genome. To capture mutations (transpositions and reversals) between the genomes, we do not insist the substrings selected to have the same ordering. Conceptually, we allow one ordering to go through some mutations to become the other ordering. If arbitrary mutations are allowed, the problem of finding a maximum-length, non-overlapping subset of substrings is found to be NP-hard. However, arbitrary mutations probably overmodel the problem and are likely to find more noise than conserved genes. We consider two criteria that attempt to model sparse and non-overlapping mutations. We show that both can be solved in polynomial time using dynamic programming.      

Dynamic Multi-level Overlay Graphs for Shortest Paths

Multi-level overlay graphs represent a speed-up technique for shortest paths computation which is based on a hierarchical decomposition of a weighted directed graph G. They have been shown to be experimentally efficient, especially when applied to timetable information. However, no theoretical result on the cost of constructing, maintaining and querying multi-level overlay graphs in a dynamic environment is known. In this paper, we show theoretical properties of multi-level overlay graphs that lead us to the definition of a new data structure for the computation and the maintenance of an overlay graph of G while weight decrease or weight increase operations are performed on G. Our solution is theoretically faster than the recomputation from scratch and allows queries that can be performed more efficiently than running Dijkstra’s shortest paths algorithm on G. This work was partially supported by the Future and Emerging Technologies Unit of EC (IST priority – 6th FP), under contract no. FP6-021235-2 (project ARRIVAL).     

Semi-local String Comparison: Algorithmic Techniques and Applications

Given two strings, the longest common subsequence (LCS) problem consists in computing the length of the longest string that is a subsequence of both input strings. Its generalisation, the all semi-local LCS problem, requires computing the LCS length for each string against all substrings of the other string, and for all prefixes of each string against all suffixes of the other string. We survey a number of algorithmic techniques related to the all semi-local LCS problem. We then present a number of algorithmic applications of these techniques, both existing and new. In particular, we obtain a new all semi-local LCS algorithm, with asymptotic running time matching (in the case of an unbounded alphabet) the fastest known global LCS algorithm by Masek and Paterson. We conclude that semi-local string comparison turns out to be a useful algorithmic plug-in, which unifies, and often improves on, a number of previous approaches to various substring- and subsequence-related problems. The author acknowledges the support of The University of Warwick’s DIMAP (the Centre for Discrete Mathematics and its Applications) during this work.     

Positive Elements and Automatic Continuity of Algebra Morphisms

We use positive elements of Hermitian algebras to give results on automatic continuity of algebra morphisms. Consequences and applications are also given.      

Scattering of an incident acoustic wave by an elastic sphere in a shallow water

The scattering of acoustic waves by an elastic sphere in a shallow ocean wave guide is investigated taking into account the shear waves which can exist in addition to compressional waves in scatterers of solid material. Expressions for the scattered waves are given. Numerical values for a quantity called the farfield form function for various depth are presented in graphical forms.      

Meromorphic Factorization Revisited and Application to Some Groups of Matrix Functions

Some properties and applications of meromorphic factorization of matrix functions are studied. It is shown that a meromorphic factorization of a matrix function G allows one to characterize the kernel of the Toeplitz operator with symbol G without actually having to previously obtain a Wiener–Hopf factorization. A method to turn a meromorphic factorization into a Wiener–Hopf one which avoids having to factorize a rational matrix that appears, in general, when each meromorphic factor is treated separately, is also presented. The results are applied to some classes of matrix functions for which the existence of a canonical factorization is studied and the factors of a Wiener–Hopf factorization are explicitly determined. Submitted: April 15, 2007. Revised: October 26, 2007. Accepted: December 12, 2007.     

A Math Query Language with an Expanded Set of Wildcards

Math search is a new area of research with many enabling technologies but also many challenges. Some of the enabling technologies include XML, XPath, XQuery, and MathML. Some of the challenges involve enabling search systems to recognize mathematical symbols and structures. Several math search projects have made considerable progress in meeting those challenges. One of the remaining challenges is the creation and implementation of a math query language that enables the general users to express their information needs intuitively yet precisely. This paper will present such a language and detail its features. The new math query language offers an alternative way to describe mathematical expressions that is more consistent and less ambiguous than conventional mathematical notation. In addition, the language goes beyond the Boolean and proximity query syntax found in standard text search systems. It defines a powerful set of wildcards that are deemed important for math search. These wildcards provide for more precise structural search and multi-levels of abstractions. Three new sets of wildcards and their implementation details will also be discussed.