On An Improved Parallel Construction Of Suffix Arrays For Low Bandwidth Pc-Cluster.

An algorithm for the parallel construction of suffix arrays generation for any texts with larger alphabet size on distributed memory architecture is presente

Index structures for distributed text databases

The Web has became an obiquitous resource for distributed computing making it relevant to investigate new ways of providing efficient access to services available at dedicated sites. Efficiency is an ever-increasing demand which can be only satisfied with the development of parallel algorithms which are efficient in practice. This tutorial paper focuses on the design, analysis and implementation of parallel algorithms and data structures for widely-used text database applications on the Web. In particular we describe parallel algorithms for inverted files and suffix arrays structures that are suitable for implementing search engines. Algorithmic design is effected on top of the BSP model of parallel computing. This model ensures portability across diverse parallel architectures ranging from clusters to super-computers.Facultad de Informátic

Index structures for distributed text databases

The Web has became an obiquitous resource for distributed computing making it relevant to investigate new ways of providing efficient access to services available at dedicated sites. Efficiency is an ever-increasing demand which can be only satisfied with the development of parallel algorithms which are efficient in practice. This tutorial paper focuses on the design, analysis and implementation of parallel algorithms and data structures for widely-used text database applications on the Web. In particular we describe parallel algorithms for inverted files and suffix arrays structures that are suitable for implementing search engines. Algorithmic design is effected on top of the BSP model of parallel computing. This model ensures portability across diverse parallel architectures ranging from clusters to super-computers.Facultad de Informátic

Efficient estimation of evolutionary distances

The advent of high throughput sequencers has lead to a dramatic increase in the size of available genomic data. Standard methods, which have worked well for many years, are not suitable for the analysis of big data sets, due to their reliance on a time-consuming alignment step. In this thesis, a new alignment-free approach for phylogeny reconstruction is introduced. The corresponding program, andi, is orders of magnitude faster than classical approaches and also superior to comparable alignment-free methods. The central data structure in andi is the enhanced suffix array. It is used to find long exact matches between sequences. In this thesis, various approaches to the construction of enhanced suffix arrays, including novel ones, are evaluated with respect to performance. Additionally, a new parallel algorithm for the computation of suffix arrays is introduced

Parallel text index construction

In dieser Dissertation betrachten wir die parallele Konstruktion von Text-Indizes. Text-Indizes stellen Zusatzinformationen über Texte bereit, die Anfragen hinsichtlich dieser Texte beschleunigen können. Ein Beispiel hierfür sind Volltext-Indizes, welche für eine effiziente Phrasensuche genutzt werden, also etwa für die Frage, ob eine Phrase in einem Text vorkommt oder nicht. Diese Dissertation befasst sich hauptsächlich, aber nicht ausschließlich mit der parallelen Konstruktion von Text-Indizes im geteilten und verteilten Speicher. Im ersten Teil der Dissertation betrachten wir Wavelet-Trees. Dabei handelt es sich um kompakte Indizes, welche Rank- und Select-Anfragen von binären Alphabeten auf Alphabete beliebiger Größe verallgemeinern. Im zweiten Teil der Dissertation betrachten wir das Suffix-Array, den am besten erforschten Text-Index überhaupt. Das Suffix-Array enthält die Startpositionen aller lexikografisch sortierten Suffixe eines Textes, d.h., wir möchten alle Suffixe eines Textes sortieren. Oft wird das Suffix-Array um das Longest-Common-Prefix-Array (LCP-Array) erweitert. Das LCP-Array enthält die Länge der längsten gemeinsamen Präfixe zweier lexikografisch konsekutiven Suffixe. Abschließend nutzen wir verteilte Suffix- und LCP-Arrays, um den Distributed-Patricia-Trie zu konstruieren. Dieser erlaubt es uns, verschiedene Phrase-Anfragen effizienter zu beantworten, als wenn wir nur das Suffix-Array nutzen.The focus of this dissertation is the parallel construction of text indices. Text indices provide additional information about a text that allow to answer queries faster. Full-text indices for example are used to efficiently answer phrase queries, i.e., if and where a phrase occurs in a text. The research in this dissertation is focused on but not limited to parallel construction algorithms for text indices in both shared and distributed memory. In the first part, we look at wavelet trees: a compact index that generalizes rank and select queries from binary alphabets to alphabets of arbitrary size. In the second part of this dissertation, we consider the suffix array---one of the most researched text indices.The suffix array of a text contains the starting positions of the text's lexicographically sorted suffixes, i.e., we want to sort all its suffixes. Finally, we use the distributed suffix arrays (and LCP arrays) to compute distributed Patricia tries. This allows us to answer different phrase queries more efficiently than using only the suffix array

Scalable String and Suffix Sorting: Algorithms, Techniques, and Tools

This dissertation focuses on two fundamental sorting problems: string sorting and suffix sorting. The first part considers parallel string sorting on shared-memory multi-core machines, the second part external memory suffix sorting using the induced sorting principle, and the third part distributed external memory suffix sorting with a new distributed algorithmic big data framework named Thrill.Comment: 396 pages, dissertation, Karlsruher Instituts f\"ur Technologie (2018). arXiv admin note: text overlap with arXiv:1101.3448 by other author

Distributed Generation of Suffix Arrays: a Quicksort-Based Approach

An algorithm for the distributed computation of suffix arrays for large texts is presented. The parallelism model is that of a set of sequential tasks which execute in parallel and exchange messages between each other. The underlying architecture is that of a highbandwidth network of processors. In such a network, a remote memory access has a transfer time similar to the transfer time of magnetic disks (with no seek cost) which allows to use the aggregate memory distributed over the various processors as a giant cache for disks. Our algorithm takes advantage of this architectural feature to implement a quicksort-based distributed sorting procedure for building the suffix array. We show that such algorithm has computation complexity given by O(r log(n=r)+n=r log r log n) in the worst case and O(n=r log n) on average and communication complexity given by O(n=r log 2 r) in the worst case and O(n=r log r) on average, where n is the text size and r is the number of processors. This is ..