A Succinct Four Russians Speedup for Edit Distance Computation and One-against-many Banded Alignment

The classical Four Russians speedup for computing edit distance (a.k.a. Levenshtein distance), due to Masek and Paterson [Masek and Paterson, 1980], involves partitioning the dynamic programming table into k-by-k square blocks and generating a lookup table in O(psi^{2k} k^2 |Sigma|^{2k}) time and O(psi^{2k} k |Sigma|^{2k}) space for block size k, where psi depends on the cost function (for unit costs psi = 3) and |Sigma| is the size of the alphabet. We show that the O(psi^{2k} k^2) and O(psi^{2k} k) factors can be improved to O(k^2 lg{k}) time and O(k^2) space. Thus, we improve the time and space complexity of that aspect compared to Masek and Paterson [Masek and Paterson, 1980] and remove the dependence on psi. We further show that for certain problems the O(|Sigma|^{2k}) factor can also be reduced. Using this technique, we show a new algorithm for the fundamental problem of one-against-many banded alignment. In particular, comparing one string of length m to n other strings of length m with maximum distance d can be performed in O(n m + m d^2 lg{d} + n d^3) time. When d is reasonably small, this approaches or meets the current best theoretic result of O(nm + n d^2) achieved by using the best known pairwise algorithm running in O(m + d^2) time [Myers, 1986][Ukkonen, 1985] while potentially being more practical. It also improves on the standard practical approach which requires O(n m d) time to iteratively run an O(md) time pairwise banded alignment algorithm. Regarding pairwise comparison, we extend the classic result of Masek and Paterson [Masek and Paterson, 1980] which computes the edit distance between two strings in O(m^2/log{m}) time to remove the dependence on psi even when edits have arbitrary costs from a penalty matrix. Crochemore, Landau, and Ziv-Ukelson [Crochemore, 2003] achieved a similar result, also allowing for unrestricted scoring matrices, but with variable-sized blocks. In practical applications of the Four Russians speedup wherein space efficiency is important and smaller block sizes k are used (notably k < |Sigma|), Kim, Na, Park, and Sim [Kim et al., 2016] showed how to remove the dependence on the alphabet size for the unit cost version, generating a lookup table in O(3^{2k} (2k)! k^2) time and O(3^{2k} (2k)! k) space. Combining their work with our result yields an improvement to O((2k)! k^2 lg{k}) time and O((2k)! k^2) space

Evaluating Matrix Functions by Resummations on Graphs: the Method of Path-Sums

We introduce the method of path-sums which is a tool for exactly evaluating a function of a discrete matrix with possibly non-commuting entries, based on the closed-form resummation of infinite families of terms in the corresponding Taylor series. If the matrix is finite, our approach yields the exact result in a finite number of steps. We achieve this by combining a mapping between matrix powers and walks on a weighted directed graph with a universal graph-theoretic result on the structure of such walks. We present path-sum expressions for a matrix raised to a complex power, the matrix exponential, matrix inverse, and matrix logarithm. We show that the quasideterminants of a matrix can be naturally formulated in terms of a path-sum, and present examples of the application of the path-sum method. We show that obtaining the inversion height of a matrix inverse and of quasideterminants is an NP-complete problem.Comment: 23 pages, light version submitted to SIAM Journal on Matrix Analysis and Applications (SIMAX). A separate paper with the graph theoretic results is available at: arXiv:1202.5523v1. Results for matrices over division rings will be published separately as wel

Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions

Effective network grid synthesis and optimization for high performance very large scale integration system design

制度:新 ; 文部省報告番号:甲2642号 ; 学位の種類:博士(工学) ; 授与年月日:2008/3/15 ; 早大学位記番号:新480

Systolic Array Implementations With Reduced Compute Time.

The goal of the research is the establishment of a formal methodology to develop computational structures more suitable for the changing nature of real-time signal processing and control applications. A major effort is devoted to the following question: Given a systolic array designed to execute a particular algorithm, what other algorithms can be executed on the same array? One approach for answering this question is based on a general model of array operations using graph-theoretic techniques. As a result, a systematic procedure is introduced that models array operations as a function of the compute cycle. As a consequence of the analysis, the dissertation develops the concept of fast algorithm realizations. This concept characterizes specific realizations that can be evaluated in a reduced number of cycles. It restricts the operations to remain in the same class but with reduced execution time. The concept takes advantage of the data dependencies of the algorithm at hand. This feature allows the modification of existing structures by reordering the input data. Applications of the principle allows optimum time band and triangular matrix product on arrays designed for dense matrices. A second approach for analyzing the families of algorithms implementable in an array, is based on the concept of array time constrained operation. The principle uses the number of compute cycle as an additional degree of freedom to expand the class of transformations generated by a single array. A mathematical approach, based on concepts from multilinear algebra, is introduced to model the recursive transformations implemented in linear arrays at each compute cycle. The proposed representation is general enough to encompass a large class of signal processing and control applications. A complete analytical model of the linear maps implementable by the array at each compute cycle is developed. The proposed methodology results in arrays that are more adaptable to the changing nature of operations. Lessons learned from analyzing existing arrays are used to design smart arrays for special algorithm realizations. Applications of the methodology include the design of flexible time structures and the ability to decompose a full size array into subarrays implementing smaller size problems