Search results for "Block matrix"
showing 10 items of 11 documents
PINCoC: a Co-Clustering based Method to Analyze Protein-Protein Interaction Networks
2007
Anovel technique to search for functionalmodules in a protein-protein interaction network is presented. The network is represented by the adjacency matrix associated with the undirected graph modelling it. The algorithm introduces the concept of quality of a sub-matrix of the adjacency matrix, and applies a greedy search technique for finding local optimal solutions made of dense submatrices containing the maximum number of ones. An initial random solution, constituted by a single protein, is evolved to search for a locally optimal solution by adding/removing connected proteins that best contribute to improve the quality function. Experimental evaluations carried out on Saccaromyces Cerevis…
O(n 2 log n) Time On-Line Construction of Two-Dimensional Suffix Trees
2005
The two-dimensional suffix tree of an n × n square matrix A is a compacted trie that represents all square submatrices of Ai¾?[9]. For the off-line case, i.e., A is given in advance to the algorithm, it is known how to build it in optimal time, for any type of alphabet sizei¾?[9,15]. Motivated by applications in Image Compressioni¾?[18], Giancarlo and Guaianai¾?[12] considered the on-line version of the two-dimensional suffix tree and presented an On2log2n-time algorithm, which we refer to as GG. That algorithm is a non-trivial generalization of Ukkonen's on-line algorithm for standard suffix trees [19]. The main contribution in this paper is an Olog n factor improvement in the time complex…
A new mathematical tool for an exact treatment of open quantum system dynamics
2005
A new method to obtain an operatorial exact solution of a wide class of Markovian master equations is presented. Its key point is the existence of a constant of motion partitioning the Hilbert space into finite-dimensional subspaces. The consequent possibility of representing the reduced density operator as a block diagonal matrix is shown. Each “block operator” evolves under the action of a non-unitary operator explicitly derived. Our mathematical approach is illustrated applying it to simple physical systems.
Multi-Dimensional Pattern Matching with Dimensional Wildcards: Data Structures and Optimal On-Line Search Algorithms
1997
We introduce a new multidimensional pattern matching problem that is a natural generalization of string matching, a well studied problem1. The motivation for its algorithmic study is mainly theoretical. LetA1:n1,?,1:nd be a text matrix withN=n1?ndentries andB1:m1,?,1:mr be a pattern matrix withM=m1?mrentries, whered?r?1 (the matrix entries are taken from an ordered alphabet ?). We study the problem of checking whether somer-dimensional submatrix ofAis equal toB(i.e., adecisionquery).Acan be preprocessed andBis given on-line. We define a new data structure for preprocessingAand propose CRCW-PRAM algorithms that build it inO(logN) time withN2/nmaxprocessors, wherenmax=max(n1,?,nd), such that …
Versatile Direct and Transpose Matrix Multiplication with Chained Operations: An Optimized Architecture Using Circulant Matrices
2016
With growing demands in real-time control, classification or prediction, algorithms become more complex while low power and small size devices are required. Matrix multiplication (direct or transpose) is common for such computation algorithms. In numerous algorithms, it is also required to perform matrix multiplication repeatedly, where the result of a multiplication is further multiplied again. This work describes a versatile computation procedure and architecture: one of the matrices is stored in internal memory in its circulant form, then, a sequence of direct or transpose multiplications can be performed without timing penalty. The architecture proposes a RAM-ALU block for each matrix c…
On the Construction of Classes of Suffix Trees for Square Matrices: Algorithms and Applications
1996
AbstractWe provide a uniform framework for the study of index data structures for a two-dimensional matrixTEXT[1:n, 1:n] whose entries are drawn from an ordered alphabetΣ. An index forTEXTcan be informally seen as the two-dimensional analog of the suffix tree for a string. It allows on-line searches and statistics to be performed onTEXTby representing compactly theΘ(n3) square submatrices ofTEXTin optimalO(n2) space. We identify 4n−1families of indices forTEXT, each containing ∏ni=1(2i−1)! isomorphic data structures. We also develop techniques leading to a single algorithm that efficiently builds any index in any family inO(n2logn) time andO(n2) space. Such an algorithm improves in various …
A branch and bound algorithm for the matrix bandwidth minimization
2008
In this article, we first review previous exact approaches as well as theoretical contributions for the problem of reducing the bandwidth of a matrix. This problem consists of finding a permutation of the rows and columns of a given matrix which keeps the non-zero elements in a band that is as close as possible to the main diagonal. This NP-complete problem can also be formulated as a labeling of vertices on a graph, where edges are the non-zero elements of the corresponding symmetrical matrix. We propose a new branch and bound algorithm and new expressions for known lower bounds for this problem. Empirical results with a collection of previously reported instances indicate that the propose…
What is the Best Method of Matrix Adjustment? A Formal Answer by a Return to the World of Vectors
2003
The principle of matrix adjustment methods consists into finding what is the matrix which is the closest to an initial matrix but with respect of the column and row sum totals of a second matrix. In order to help deciding which matrix-adjustment method is the better, the article returns to the simpler problem of vector adjustment then back to matrices. The information-lost minimization (biproportional methods and RAS) leads to a multiplicative form and generalize the linear model. On the other hand, the distance minimization which leads to an additive form tends to distort the data by giving a result asymptotically independent to the initial matrix. The result allows concluding non-ambiguou…
Order optimal preconditioners for fully implicit Runge-Kutta schemes applied to the bidomain equations
2010
The partial differential equation part of the bidomain equations is discretized in time with fully implicit Runge–Kutta methods, and the resulting block systems are preconditioned with a block diagonal preconditioner. By studying the time-stepping operator in the proper Sobolev spaces, we show that the preconditioned systems have bounded condition numbers given that the Runge–Kutta scheme is A-stable and irreducible with an invertible coefficient matrix. A new proof of order optimality of the preconditioners for the one-leg discretization in time of the bidomain equations is also presented. The theoretical results are verified by numerical experiments. Additionally, the concept of weakly po…
High selective H-plane TE dual mode cavity filter design by using nonresonating nodes
2013
The design of H-plane TE dual mode cavity filters using models containing nonresonating nodes is presented. From the models a coupling matrix is derived and decomposed into submatrices, each representing a subcircuit. The optimization and cascading of subcircuits represents a good starting point for the global optimization. © 2014 Wiley Periodicals, Inc. Microwave Opt Technol Lett 56:161–166, 2014