A multiprocessor parallel approach to bit-parallel approximate string matching

The purpose of this project is to present with empirical results that a parallel design with the use of multiple processors can be successfully applied along with bit-parallel approximate string matching algorithms to solve practical bioinformatics problems. It will demonstrate that nearly optimal speedup can be achieved with a cluster of between two and eight workstations using MPI (Message Passing Interface), directly decreasing the total latency required to perform a string matching problem

On the first k moments of the random count of a pattern in a multi-states sequence generated by a Markov source

In this paper, we develop an explicit formula allowing to compute the first k moments of the random count of a pattern in a multi-states sequence generated by a Markov source. We derive efficient algorithms allowing to deal both with low or high complexity patterns and either homogeneous or heterogenous Markov models. We then apply these results to the distribution of DNA patterns in genomic sequences where we show that moment-based developments (namely: Edgeworth's expansion and Gram-Charlier type B series) allow to improve the reliability of common asymptotic approximations like Gaussian or Poisson approximations

A sheaf-theoretic approach to pattern matching and related problems

AbstractWe present a general theory of pattern matching by adopting an extensional, geometric view of patterns. Representing the geometry of the pattern via a Grothendieck topology, the extension of the matching relation for a constant target and varying pattern forms a sheaf. We derive a generalized version of the Knuth-Morris-Pratt string-matching algorithm by gradually converting this extensional description into an intensional description, i.e., an algorithm. The generality of this approach is illustrated by briefly considering other applications: Earley's algorithm for parsing, Waltz filtering for scene analysis, matching modulo commutativity, and the n-queens problem

Algorithms for Stable Matching and Clustering in a Grid

We study a discrete version of a geometric stable marriage problem originally proposed in a continuous setting by Hoffman, Holroyd, and Peres, in which points in the plane are stably matched to cluster centers, as prioritized by their distances, so that each cluster center is apportioned a set of points of equal area. We show that, for a discretization of the problem to an $n\times n$ grid of pixels with $k$ centers, the problem can be solved in time $O(n^2 \log^5 n)$, and we experiment with two slower but more practical algorithms and a hybrid method that switches from one of these algorithms to the other to gain greater efficiency than either algorithm alone. We also show how to combine geometric stable matchings with a $k$-means clustering algorithm, so as to provide a geometric political-districting algorithm that views distance in economic terms, and we experiment with weighted versions of stable $k$-means in order to improve the connectivity of the resulting clusters.Comment: 23 pages, 12 figures. To appear (without the appendices) at the 18th International Workshop on Combinatorial Image Analysis, June 19-21, 2017, Plovdiv, Bulgari

Distances and Isomorphism between Networks and the Stability of Network Invariants

We develop the theoretical foundations of a network distance that has recently been applied to various subfields of topological data analysis, namely persistent homology and hierarchical clustering. While this network distance has previously appeared in the context of finite networks, we extend the setting to that of compact networks. The main challenge in this new setting is the lack of an easy notion of sampling from compact networks; we solve this problem in the process of obtaining our results. The generality of our setting means that we automatically establish results for exotic objects such as directed metric spaces and Finsler manifolds. We identify readily computable network invariants and establish their quantitative stability under this network distance. We also discuss the computational complexity involved in precisely computing this distance, and develop easily-computable lower bounds by using the identified invariants. By constructing a wide range of explicit examples, we show that these lower bounds are effective in distinguishing between networks. Finally, we provide a simple algorithm that computes a lower bound on the distance between two networks in polynomial time and illustrate our metric and invariant constructions on a database of random networks and a database of simulated hippocampal networks

Pattern matching : a sheaf-theoretic approach

A general theory of pattern matching is presented by adopting an extensional, geometric view of patterns. The extension of the matching relation consists of the occurrences of all possible patterns in a particular target. The geometry of the pattern describes the structure of the pattern and the spatial relationships among parts of the pattern. The extension and the geometry, when combined, produce a structure called a sheaf. Sheaf theory is a well developed branch of mathematics which studies the global consequences of locally defined properties. For pattern matching, an occurrence of a pattern, a global property of the pattern, is obtained by gluing together occurrences of parts of the pattern, which are locally defined properties.A sheaf-theoretic view of pattern rnatching provides a uniforrn treatrnent of pattern matching on any kind of data structure-strings, trees, graphs, hypergraphs, and so on. Such a parametric description is achieved by using the language of category theory, a highly abstract description of commonly occurring structures and relationships in mathematics.A generalized version of the Knuth-Morris-Pratt pattern matching algorithm is derived by gradually converting the extensional description of pattern rnatching as a sheaf into an intensional description. The algorithm results from a synergy of four very general program synthesis/transformation techniques: (1) Divide and conquer: exploit the sheaf condition; assemble a full match by gluing together partial matches; (2) Finite differencing: collect and update partial matches incrementally while traversing the target; (3) Backtracking: instead of saving all partial matches, save just one; when this partial match cannot be extended, fail back to another; (4) Partial evaluation: precompute pattern-based (and therefore constant) computations.The derivation is carried out in a general frarnework using Grothendieck topologies. By appropriately instantiating the underlying data structures and topologies, the sarne scheme results in matching algorithms for patterns with variables and with multiple patterns. Slight variations of the derivation result in Earley's algorithm for context-free parsing, and Waltz filtering, a relaxation algorithm for providing 3-D interpretations to 2-D irnages.Other applications of a geometric view of patterns are briefly considered: rewrites, parallel algorithms, induction and computability