Indexing Highly Repetitive String Collections

Two decades ago, a breakthrough in indexing string collections made it possible to represent them within their compressed space while at the same time offering indexed search functionalities. As this new technology permeated through applications like bioinformatics, the string collections experienced a growth that outperforms Moore's Law and challenges our ability of handling them even in compressed form. It turns out, fortunately, that many of these rapidly growing string collections are highly repetitive, so that their information content is orders of magnitude lower than their plain size. The statistical compression methods used for classical collections, however, are blind to this repetitiveness, and therefore a new set of techniques has been developed in order to properly exploit it. The resulting indexes form a new generation of data structures able to handle the huge repetitive string collections that we are facing. In this survey we cover the algorithmic developments that have led to these data structures. We describe the distinct compression paradigms that have been used to exploit repetitiveness, the fundamental algorithmic ideas that form the base of all the existing indexes, and the various structures that have been proposed, comparing them both in theoretical and practical aspects. We conclude with the current challenges in this fascinating field

Compressed Text Indexes:From Theory to Practice!

A compressed full-text self-index represents a text in a compressed form and still answers queries efficiently. This technology represents a breakthrough over the text indexing techniques of the previous decade, whose indexes required several times the size of the text. Although it is relatively new, this technology has matured up to a point where theoretical research is giving way to practical developments. Nonetheless this requires significant programming skills, a deep engineering effort, and a strong algorithmic background to dig into the research results. To date only isolated implementations and focused comparisons of compressed indexes have been reported, and they missed a common API, which prevented their re-use or deployment within other applications. The goal of this paper is to fill this gap. First, we present the existing implementations of compressed indexes from a practitioner's point of view. Second, we introduce the Pizza&Chili site, which offers tuned implementations and a standardized API for the most successful compressed full-text self-indexes, together with effective testbeds and scripts for their automatic validation and test. Third, we show the results of our extensive experiments on these codes with the aim of demonstrating the practical relevance of this novel and exciting technology

Toward Entity-Aware Search

As the Web has evolved into a data-rich repository, with the standard "page view," current search engines are becoming increasingly inadequate for a wide range of query tasks. While we often search for various data "entities" (e.g., phone number, paper PDF, date), today's engines only take us indirectly to pages. In my Ph.D. study, we focus on a novel type of Web search that is aware of data entities inside pages, a significant departure from traditional document retrieval. We study the various essential aspects of supporting entity-aware Web search. To begin with, we tackle the core challenge of ranking entities, by distilling its underlying conceptual model Impression Model and developing a probabilistic ranking framework, EntityRank, that is able to seamlessly integrate both local and global information in ranking. We also report a prototype system built to show the initial promise of the proposal. Then, we aim at distilling and abstracting the essential computation requirements of entity search. From the dual views of reasoning--entity as input and entity as output, we propose a dual-inversion framework, with two indexing and partition schemes, towards efficient and scalable query processing. Further, to recognize more entity instances, we study the problem of entity synonym discovery through mining query log data. The results we obtained so far have shown clear promise of entity-aware search, in its usefulness, effectiveness, efficiency and scalability

Building a Text Collection for Urdu Information Retrieval

Urdu is a widely spoken language in the Indian subcontinent with over 300 million speakers worldwide. However, linguistic advancements in Urdu are rare compared to those in other European and Asian languages. Therefore, by following Text Retrieval Conference standards, we attempted to construct an extensive text collection of 85 304 documents from diverse categories covering over 52 topics with relevance judgment sets at 100 pool depth. We also present several applications to demonstrate the effectiveness of our collection. Although this collection is primarily intended for text retrieval, it can also be used for named entity recognition, text summarization, and other linguistic applications with suitable modifications. Ours is the most extensive existing collection for the Urdu language, and it will be freely available for future research and academic education

Adaptive text mining: Inferring structure from sequences

Text mining is about inferring structure from sequences representing natural language text, and may be defined as the process of analyzing text to extract information that is useful for particular purposes. Although hand-crafted heuristics are a common practical approach for extracting information from text, a general, and generalizable, approach requires adaptive techniques. This paper studies the way in which the adaptive techniques used in text compression can be applied to text mining. It develops several examples: extraction of hierarchical phrase structures from text, identification of keyphrases in documents, locating proper names and quantities of interest in a piece of text, text categorization, word segmentation, acronym extraction, and structure recognition. We conclude that compression forms a sound unifying principle that allows many text mining problems to be tacked adaptively

Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot

<p>Abstract</p> <p>Background</p> <p>In the context of the BioCreative competition, where training data were very sparse, we investigated two complementary tasks: 1) given a Swiss-Prot triplet, containing a protein, a GO (Gene Ontology) term and a relevant article, extraction of a short passage that justifies the GO category assignement; 2) given a Swiss-Prot pair, containing a protein and a relevant article, automatic assignement of a set of categories.</p> <p>Methods</p> <p>Sentence is the basic retrieval unit. Our classifier computes a distance between each sentence and the GO category provided with the Swiss-Prot entry. The Text Categorizer computes a distance between each GO term and the text of the article. Evaluations are reported both based on annotator judgements as established by the competition and based on mean average precision measures computed using a curated sample of Swiss-Prot.</p> <p>Results</p> <p>Our system achieved the best recall and precision combination both for passage retrieval and text categorization as evaluated by official evaluators. However, text categorization results were far below those in other data-poor text categorization experiments The top proposed term is relevant in less that 20% of cases, while categorization with other biomedical controlled vocabulary, such as the Medical Subject Headings, we achieved more than 90% precision. We also observe that the scoring methods used in our experiments, based on the retrieval status value of our engines, exhibits effective confidence estimation capabilities.</p> <p>Conclusion</p> <p>From a comparative perspective, the combination of retrieval and natural language processing methods we designed, achieved very competitive performances. Largely data-independent, our systems were no less effective that data-intensive approaches. These results suggests that the overall strategy could benefit a large class of information extraction tasks, especially when training data are missing. However, from a user perspective, results were disappointing. Further investigations are needed to design applicable end-user text mining tools for biologists.</p

Foundation, Implementation and Evaluation of the MorphoSaurus System: Subword Indexing, Lexical Learning and Word Sense Disambiguation for Medical Cross-Language Information Retrieval

Im medizinischen Alltag, zu welchem viel Dokumentations- und Recherchearbeit gehört, ist mittlerweile der überwiegende Teil textuell kodierter Information elektronisch verfügbar. Hiermit kommt der Entwicklung leistungsfähiger Methoden zur effizienten Recherche eine vorrangige Bedeutung zu. Bewertet man die Nützlichkeit gängiger Textretrievalsysteme aus dem Blickwinkel der medizinischen Fachsprache, dann mangelt es ihnen an morphologischer Funktionalität (Flexion, Derivation und Komposition), lexikalisch-semantischer Funktionalität und der Fähigkeit zu einer sprachübergreifenden Analyse großer Dokumentenbestände. In der vorliegenden Promotionsschrift werden die theoretischen Grundlagen des MorphoSaurus-Systems (ein Akronym für Morphem-Thesaurus) behandelt. Dessen methodischer Kern stellt ein um Morpheme der medizinischen Fach- und Laiensprache gruppierter Thesaurus dar, dessen Einträge mittels semantischer Relationen sprachübergreifend verknüpft sind. Darauf aufbauend wird ein Verfahren vorgestellt, welches (komplexe) Wörter in Morpheme segmentiert, die durch sprachunabhängige, konzeptklassenartige Symbole ersetzt werden. Die resultierende Repräsentation ist die Basis für das sprachübergreifende, morphemorientierte Textretrieval. Neben der Kerntechnologie wird eine Methode zur automatischen Akquise von Lexikoneinträgen vorgestellt, wodurch bestehende Morphemlexika um weitere Sprachen ergänzt werden. Die Berücksichtigung sprachübergreifender Phänomene führt im Anschluss zu einem neuartigen Verfahren zur Auflösung von semantischen Ambiguitäten. Die Leistungsfähigkeit des morphemorientierten Textretrievals wird im Rahmen umfangreicher, standardisierter Evaluationen empirisch getestet und gängigen Herangehensweisen gegenübergestellt

Text Data Mining: Theory and Methods

This paper provides the reader with a very brief introduction to some of the theory and methods of text data mining. The intent of this article is to introduce the reader to some of the current methodologies that are employed within this discipline area while at the same time making the reader aware of some of the interesting challenges that remain to be solved within the area. Finally, the articles serves as a very rudimentary tutorial on some of techniques while also providing the reader with a list of references for additional study.Comment: Published in at http://dx.doi.org/10.1214/07-SS016 the Statistics Surveys (http://www.i-journals.org/ss/) by the Institute of Mathematical Statistics (http://www.imstat.org