A Parallel Computational Approach for String Matching- A Novel Structure with Omega Model

In r e cent day2019;s parallel string matching problem catch the attention of so many researchers because of the importance in different applications like IRS, Genome sequence, data cleaning etc.,. While it is very easily stated and many of the simple algorithms perform very well in practice, numerous works have been published on the subject and research is still very active. In this paper we propose a omega parallel computing model for parallel string matching. The algorithm is designed to work on omega model pa rallel architecture where text is divided for parallel processing and special searching at division point is required for consistent and complete searching. This algorithm reduces the number of comparisons and parallelization improves the time efficiency. Experimental results show that, on a multi - processor system, the omega model implementation of the proposed parallel string matching algorithm can reduce string matching time

Compressed Full-Text Indexes for Highly Repetitive Collections

This thesis studies problems related to compressed full-text indexes. A full-text index is a data structure for indexing textual (sequence) data, so that the occurrences of any query string in the data can be found efficiently. While most full-text indexes require much more space than the sequences they index, recent compressed indexes have overcome this limitation. These compressed indexes combine a compressed representation of the index with some extra information that allows decompressing any part of the data efficiently. This way, they provide similar functionality as the uncompressed indexes, while using only slightly more space than the compressed data. The efficiency of data compression is usually measured in terms of entropy. While entropy-based estimates predict the compressed size of most texts accurately, they fail with highly repetitive collections of texts. Examples of such collections include different versions of a document and the genomes of a number of individuals from the same population. While the entropy of a highly repetitive collection is usually similar to that of a text of the same kind, the collection can often be compressed much better than the entropy-based estimate. Most compressed full-text indexes are based on the Burrows-Wheeler transform (BWT). Originally intended for data compression, the BWT has deep connections with full-text indexes such as the suffix tree and the suffix array. With some additional information, these indexes can be simulated with the Burrows-Wheeler transform. The first contribution of this thesis is the first BWT-based index that can compress highly repetitive collections efficiently. Compressed indexes allow us to handle much larger data sets than the corresponding uncompressed indexes. To take full advantage of this, we need algorithms for constructing the compressed index directly, instead of first constructing an uncompressed index and then compressing it. The second contribution of this thesis is an algorithm for merging the BWT-based indexes of two text collections. By using this algorithm, we can derive better space-efficient construction algorithms for BWT-based indexes. The basic BWT-based indexes provide similar functionality as the suffix array. With some additional structures, the functionality can be extended to that of the suffix tree. One of the structures is an array storing the lengths of the longest common prefixes of lexicographically adjacent suffixes of the text. The third contribution of this thesis is a space-efficient algorithm for constructing this array, and a new compressed representation of the array. In the case of individual genomes, the highly repetitive collection can be considered a sample from a larger collection. This collection consists of a reference sequence and a set of possible differences from the reference, so that each sequence contains a subset of the differences. The fourth contribution of this thesis is a BWT-based index that extrapolates the larger collection from the sample and indexes it.Tässä väitöskirjassa käsitellään tiivistettyjä kokotekstihakemistoja tekstimuotoisille aineistoille. Kokotekstihakemistot ovat tietorakenteita, jotka mahdollistavat mielivaltaisten hahmojen esiintymien löytämisen tekstistä tehokkaasti. Perinteiset kokotekstihakemistot, kuten loppuosapuut ja -taulukot, vievät moninkertaisesti tilaa itse aineistoon nähden. Viime aikoina on kuitenkin kehitetty tiivistettyjä hakemistorakenteita, jotka tarjoavat vastaavan toiminnallisuuden alkuperäistä tekstiä pienemmässä tilassa. Tämä on mahdollistanut aikaisempaa suurempien aineistojen käsittelyn. Tekstin tiivistyvyyttä mitataan yleensä suhteessa sen entropiaan. Vaikka entropiaan perustuvat arviot ovat useimmilla aineistoilla varsin tarkkoja, aliarvioivat ne vahvasti toisteisien aineistojen tiivistyvyyttä. Esimerkkejä tällaisista aineistoista ovat kokoelmat saman populaation yksilöiden genomeita tai saman dokumentin eri versioita. Siinä missä tällaisen kokoelman entropia suhteessa aineiston kokoon on vastaava kuin yksittäisellä samaa tyyppiä olevalla tekstillä, tiivistyy kokoelma yleensä huomattavasti paremmin kuin entropian perusteella voisi odottaa. Useimmat tiivistetyt kokotekstihakemistot perustuvat Burrows-Wheeler-muunnokseen (BWT), joka kehitettiin alun perin tekstimuotoisten aineistojen tiivistämiseen. Pian kuitenkin havaittiin, että koska BWT muistuttaa rakenteeltaan loppuosapuuta ja -taulukkoa, voidaan sitä käyttää niissä tehtävien hakujen simulointiin. Tässä väitöskirjassa esitetään ensimmäinen BWT-pohjainen kokotekstihakemisto, joka pystyy tiivistämään vahvasti toisteiset aineistot tehokkaasti. Tiivistettyjen tietorakenteiden käyttö mahdollistaa suurempien aineistoiden käsittelemisen kuin tavallisia tietorakenteita käytettäessä. Tämä etu kuitenkin menetetään, jos tiivistetty tietorakenne muodostetaan luomalla ensin vastaava tavallinen tietorakenne ja tiivistämällä se. Tässä väitöskirjassa esitetään aikaisempaa vähemmän muistia käyttäviä algoritmeja BWT-pohjaisten kokotekstihakemistojen muodostamiseen. Kokoelma yksilöiden genomeita voidaan käsittää otokseksi suuremmasta kokoelmasta, joka koostuu populaation kaikkien yksilöiden sekä niiden hypoteettisten jälkeläisten genomeista. Tällainen kokoelma voidaan esittää äärellisenä automaattina, joka muodostuu referenssigenomista ja yksilöiden genomeissa esiintyvistä poikkeamista referenssistä. Tässä väitöskirjassa esitetään BWT-pohjaisten kokotekstihakemistojen yleistys, joka mahdollistaa tällaisten automaattien indeksoinnin

Efficient compression of large repetitive strings

When is comes to managing large volumes of data, general-purpose compressors such as gzip are ubiquitous. They are fast, practical and available on every modern platform from standard desktops to mobile devices. These tools exploit local redundancy in a text using a fixed-size sliding window. This window is usually very small relative to the text, however, in principle it can be as large as available memory. The window acts as a dictionary. Compression is achieved by replacing substrings with pointers to previous occurrences found in the dictionary. This type of algorithm becomes problematic when dealing with collections that are larger than physical memory, as it fails to capture any non-local redundancy, that is, repetition that occurs outside of its search window. With rapid growth in the already enormous amount of data we store and process there is a pressing need for improving compression effectiveness, reducing both storage requirements and decompression costs. However, many systems still use general-purpose compression tools on large highly repetitive data collections. In this thesis we focus on addressing this issue. We explore compression in a variety of domains where large volumes of data need to be stored and accessed, and general-purpose compression tools are cannon. First we discuss our work on web corpus compression, then we discuss the implementation of a practical index for repetitive texts that gives strong theoretical bounds in terms of size and access, and finally, we discuss our work on compression of high-throughput sequencing reads. We show that in all cases, our new methods improve on current techniques in both run-time and compression effectiveness, and provide important functionality such as fast decoding and random access

Advances in Character Recognition

This book presents advances in character recognition, and it consists of 12 chapters that cover wide range of topics on different aspects of character recognition. Hopefully, this book will serve as a reference source for academic research, for professionals working in the character recognition field and for all interested in the subject

A novel approach to handwritten character recognition

A number of new techniques and approaches for off-line handwritten character recognition are presented which individually make significant advancements in the field. First. an outline-based vectorization algorithm is described which gives improved accuracy in producing vector representations of the pen strokes used to draw characters. Later. Vectorization and other types of preprocessing are criticized and an approach to recognition is suggested which avoids separate preprocessing stages by incorporating them into later stages. Apart from the increased speed of this approach. it allows more effective alteration of the character images since more is known about them at the later stages. It also allows the possibility of alterations being corrected if they are initially detrimental to recognition. A new feature measurement. the Radial Distance/Sector Area feature. is presented which is highly robust. tolerant to noise. distortion and style variation. and gives high accuracy results when used for training and testing in a statistical or neural classifier. A very powerful classifier is therefore obtained for recognizing correctly segmented characters. The segmentation task is explored in a simple system of integrated over-segmentation. Character classification and approximate dictionary checking. This can be extended to a full system for handprinted word recognition. In addition to the advancements made by these methods. a powerful new approach to handwritten character recognition is proposed as a direction for future research. This proposal combines the ideas and techniques developed in this thesis in a hierarchical network of classifier modules to achieve context-sensitive. off-line recognition of handwritten text. A new type of "intelligent" feedback is used to direct the search to contextually sensible classifications. A powerful adaptive segmentation system is proposed which. when used as the bottom layer in the hierarchical network. allows initially incorrect segmentations to be adjusted according to the hypotheses of the higher level context modules