Boyer-Moore strategy to efficient approximate string matching

International audienceWe propose a simple but e cient algorithm for searching all occurrences of a pattern or a class of patterns (length m) in a text (length n) with at most k mismatches. This algorithm relies on the Shift-Add algorithm of Baeza-Yates and Gonnet [6], which involves representing by a bit number the current state of the search and uses the ability of programming languages to handle bit words. State representation should not, therefore, exceeds the word size w, that is, m(⌈log2(k+1)⌉+1 )≤w. This algorithm consists in a preprocessing step and a searching step. It is linear and performs 3n operations during the searching step. Notions of shift and character skip found in the Boyer-Moore (BM) [9] approach, are introduced in this algorithm. Provided that the considered alphabet is large enough (compared to the Pattern length), the average number of operations performed by our algorithm during the searching step becomes n(2+(k+4)/(m-k))

An approximate search engine for structure

As the size of structural databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute-value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. In this dissertation, efficient search techniques are presented for retrieving trees from a database that are similar to a given query tree. Rooted ordered labeled trees, rooted unordered labeled trees and free trees are considered. Ordered labeled trees are trees in which each node has a label and the left-to-right order among siblings matters. Unordered labeled trees are trees in which the parent-child relationship is significant, but the order among siblings is unimportant. Free trees (unrooted unordered trees) are acyclic graphs. These trees find many applications in bioinformatics, Web log analysis, phyloinformatics, XML processing, etc. Two types of similarity measures are investigated: (i) counting the mismatching paths in the query tree and a data tree, and (ii) measuring the topological relationship between the trees. The proposed approaches include storing the paths of trees in a suffix array, employing hashing techniques to speed up retrieval, and counting the number of up-down operations to move a token from one node to another node in a tree. Various filters for accelerating a search, different strategies for parallelizing these search algorithms and applications of these algorithms to XML and phylogenetic data management are discussed. The proposed techniques have been implemented into a phylogenetic search engine which is fully operational and is available on the World Wide Web. Experimental results on comparing the similarity measures with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate the effectiveness of the search engine. Future work includes extending the techniques to other structural data, as well as developing new filters and algorithms for speeding up searching and mining in complex structures

Parallel machine architecture and compiler design facilities

The objective is to provide an integrated simulation environment for studying and evaluating various issues in designing parallel systems, including machine architectures, parallelizing compiler techniques, and parallel algorithms. The status of Delta project (which objective is to provide a facility to allow rapid prototyping of parallelized compilers that can target toward different machine architectures) is summarized. Included are the surveys of the program manipulation tools developed, the environmental software supporting Delta, and the compiler research projects in which Delta has played a role

On-line Chinese character recognition.

by Jian-Zhuang Liu.Thesis (Ph.D.)--Chinese University of Hong Kong, 1997.Includes bibliographical references (p. 183-196).Microfiche. Ann Arbor, Mich.: UMI, 1998. 3 microfiches ; 11 x 15 cm

Data structures and algorithms for approximate string matching Zvi Galil, Raffaele Giancarlo

This paper surveys techniques for designing efficient sequential and parallel approximate string matching algorithms. Special attention is given to the methods for the construction of data structures that efficiently support primitive operations needed in approximate string matching

Phoneme-based Video Indexing Using Phonetic Disparity Search

This dissertation presents and evaluates a method to the video indexing problem by investigating a categorization method that transcribes audio content through Automatic Speech Recognition (ASR) combined with Dynamic Contextualization (DC), Phonetic Disparity Search (PDS) and Metaphone indexation. The suggested approach applies genome pattern matching algorithms with computational summarization to build a database infrastructure that provides an indexed summary of the original audio content. PDS complements the contextual phoneme indexing approach by optimizing topic seek performance and accuracy in large video content structures. A prototype was established to translate news broadcast video into text and phonemes automatically by using ASR utterance conversions. Each phonetic utterance extraction was then categorized, converted to Metaphones, and stored in a repository with contextual topical information attached and indexed for posterior search analysis. Following the original design strategy, a custom parallel interface was built to measure the capabilities of dissimilar phonetic queries and provide an interface for result analysis. The postulated solution provides evidence of a superior topic matching when compared to traditional word and phoneme search methods. Experimental results demonstrate that PDS can be 3.7% better than the same phoneme query, Metaphone search proved to be 154.6% better than the same phoneme seek and 68.1 % better than the equivalent word search

VisualGREP : a systematic method to compare and retrieve video sequences

In this paper, we consider the problem of similarity between video sequences. Three basic questions are raised and (partially) answered. Firstly, at what temporal duration can video sequences be compared? The frame, shot, scene and video levels are identified. Secondly, given some image or video feature, what are the requirements on its distance measure and how can it be "easily" transformed into the visual similarity desired by the inquirer? Thirdly, how can video sequences be compared at different levels? A general approach based on either a set or sequence representation with variable degrees of aggregation is proposed and applied recursively over the different levels of temporal resolution: It allows the inquirer to fully control the importance of temporal ordering and duration. The general approach is illustrated by introducing and discussing some of the many possible image and video features. Promising experimental results are presented

A Similarity Matrix for Irish Traditional Dance Music

It is estimated that there are between seven and ten thousand Irish traditional dance tunes in existence. As Irish musicians travelled the world they carried their repertoire in their memories and rarely recorded these pieces in writing. When the music was passed down from generation to generation by ear the names of these pieces of music and the melodies themselves were forgotten or changed over time. This has led to problems for musicians and archivists when identifying the names of traditional Irish tunes. Almost all of this music is now available in ABC notation from online collections. An ABC file is a text file containing a transcription of one or more melodies, the tune title, musical key, time signature and other relevant details. The principal aim of this project is to define a process by which Irish music can be compared using string distance algorithms. An online survey will then be conducted to assess if human participants agree with the computer comparisons. Improvements will then be made to the string distance algorithms by considering music theory. Two other methods of assessing musical similarity, Breandán Breathnach‟s Melodic Indexing System and Parsons Code will be computerised and integrated into a Combined Ranking System (CRS). An hypothesis will be formed based on the results and experiences of creating this system. This hypothesis will be tested on humans and if successful, used to achieve the final aim of the project, to construct a similarity matrix