Universal Indexes for Highly Repetitive Document Collections

Indexing highly repetitive collections has become a relevant problem with the emergence of large repositories of versioned documents, among other applications. These collections may reach huge sizes, but are formed mostly of documents that are near-copies of others. Traditional techniques for indexing these collections fail to properly exploit their regularities in order to reduce space. We introduce new techniques for compressing inverted indexes that exploit this near-copy regularity. They are based on run-length, Lempel-Ziv, or grammar compression of the differential inverted lists, instead of the usual practice of gap-encoding them. We show that, in this highly repetitive setting, our compression methods significantly reduce the space obtained with classical techniques, at the price of moderate slowdowns. Moreover, our best methods are universal, that is, they do not need to know the versioning structure of the collection, nor that a clear versioning structure even exists. We also introduce compressed self-indexes in the comparison. These are designed for general strings (not only natural language texts) and represent the text collection plus the index structure (not an inverted index) in integrated form. We show that these techniques can compress much further, using a small fraction of the space required by our new inverted indexes. Yet, they are orders of magnitude slower.Comment: This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094

Document Retrieval on Repetitive Collections

Document retrieval aims at finding the most important documents where a pattern appears in a collection of strings. Traditional pattern-matching techniques yield brute-force document retrieval solutions, which has motivated the research on tailored indexes that offer near-optimal performance. However, an experimental study establishing which alternatives are actually better than brute force, and which perform best depending on the collection characteristics, has not been carried out. In this paper we address this shortcoming by exploring the relationship between the nature of the underlying collection and the performance of current methods. Via extensive experiments we show that established solutions are often beaten in practice by brute-force alternatives. We also design new methods that offer superior time/space trade-offs, particularly on repetitive collections.Comment: Accepted to ESA 2014. Implementation and experiments at http://www.cs.helsinki.fi/group/suds/rlcsa

Document retrieval on repetitive string collections

Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their repetitiveness, which can reduce their space usage by orders of magnitude. We study the problem of indexing repetitive string collections in order to perform efficient document retrieval operations on them. Document retrieval problems are routinely solved by search engines on large natural language collections, but the techniques are less developed on generic string collections. The case of repetitive string collections is even less understood, and there are very few existing solutions. We develop two novel ideas, interleaved LCPs and precomputed document lists, that yield highly compressed indexes solving the problem of document listing (find all the documents where a string appears), top-k document retrieval (find the k documents where a string appears most often), and document counting (count the number of documents where a string appears). We also show that a classical data structure supporting the latter query becomes highly compressible on repetitive data. Finally, we show how the tools we developed can be combined to solve ranked conjunctive and disjunctive multi-term queries under the simple model of relevance. We thoroughly evaluate the resulting techniques in various real-life repetitiveness scenarios, and recommend the best choices for each case.Peer reviewe

Versioned index data structures for time travel text search

In this work we develop a system for letting users search versioned documents – i.e.,\ncollections containing multiple versions for the same document – specifying their validity\nrange by means of time intervals. To this end, we decide to enhance the widely-used Terrier\nopen-source IR system by means of two strategies for index versioning: (i) the Baseline\nApproach (BA) and, (ii) the Mapping Approach (MA)ope

Document Listing on Repetitive Collections with Guaranteed Performance

We consider document listing on string collections, that is, finding in which strings a given pattern appears. In particular, we focus on repetitive collections: a collection of size N over alphabet [1,a] is composed of D copies of a string of size n, and s single-character edits are applied on the copies. We introduce the first document listing index with size O~(n + s), precisely O((n lg a + s lg^2 N) lg D) bits, and with useful worst-case time guarantees: Given a pattern of length m, the index reports the ndoc strings where it appears in time O(m^2 + m lg N (lg D + lg^e N) ndoc), for any constant e > 0

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

Grammar compressed sequences with rank/select support

An early partial version of this paper appeared in Proc. SPIRE 2014: G. Navarro, A. Ordóñez Grammar compressed sequences with rank/select support, Proc. 21st International Symposium on String Processing and Information Retrieval, LNCS, SPIRE, vol. 8799 (2014), pp. 31–44The final publication is available at Springer via http://dx.doi.org/10.1016/j.jda.2016.10.001[Abstract] Sequence representations supporting not only direct access to their symbols, but also rank/select operations, are a fundamental building block in many compressed data structures. Several recent applications need to represent highly repetitive sequences, and classical statistical compression proves ineffective. We introduce, instead, grammar-based representations for repetitive sequences, which use up to 6% of the space needed by statistically compressed representations, and support direct access and rank/select operations within tens of microseconds. We demonstrate the impact of our structures in text indexing applications.Chile. Fondo Nacional de Desarrollo Científico y Tecnológico; 140796Ministerio de Economía, Industria y Competitividad; 00645663/ITC-20133062Ministerio de Economía, Industria y Competitividad; TIN2009-14560-C03-02Ministerio de Economía, Industria y Competitividad; TIN2010-21246-C02-01Ministerio de Economía, Industria y Competitividad; TIN2013-46238-C4-3-RMinisterio de Economía, Industria y Competitividad; TIN2013-47090-C3-3-PMinisterio de Economía, Industria y Competitividad; AP2010-6038Xunta de Galicia; GRC2013/05

Multi-Version Search and Cache-Conscious Ranking Optimization

Organizations and companies archive many versions of digital data such as web pages, internal emails and so on. Such data is critical for internal investigation, regulatory compliance, and electronic discovery. It is estimated that electronic discovery market that leverages archival data will reach $9.9 billions globally in 2017. It is not uncommon for many businesses to retain archived collections for 10 to 15 years. How to archive these versioned data is worth to study and we are facing many challenges including 1) traditional index occupies too much space for versioned data, 2) traditional search is too slow on versioned data, and 3) how to guarantee high accuracy when improving efficiency in new architecture.In this dissertation, we take the opportunity of the fast development of information retrieval and tackle the problem by proposing a new multi-version search architecture with cache-conscious ranking optimization framework. Specifically, we will first discuss our new versioned search architecture. Then, we will talk about a cache-conscious online ranking algorithm to improve the online part. Finally, we will describe a framework to select best blocking methods and parameters for our algorithm to achieve best performance.Firstly, we present our new multi-version search architecture. We propose an approach that uses cluster-based retrieval to quickly narrow the search scope guided by version representatives at Phase 1 and develops a hybrid index structure with adaptive runtime data traversal to speed up Phase 2 search. The hybrid scheme exploits the advantages of forward index and inverted index based on the term characteristics to minimize the time in extracting positional and other feature information during runtime search. We compare several indexing and data traversal options with different time and space tradeoffs and describe evaluation results to demonstrate their effectiveness. The experiment results show that the proposed scheme can be up-to about 4x as fast as the previous work on solid state drives while retaining good relevance.Secondly, we talk about our 2D blocking algorithm to optimize the online ranking part of the system. Multi-tree ensemble models have been proven to be effective for document ranking. Using a large number of trees can improve accuracy, but it takes time to calculate ranking scores of matched documents. We investigate data traversal methods for fast score calculation with a large ensemble and propose a 2D blocking scheme for better cache utilization with simpler code structure compared to previous work. The experiments with several benchmarks show significant acceleration in score calculation without loss of ranking accuracy.Lastly, we describe a framework to fast select best blocking methods and parameters for our 2D blocking algorithm with the help of a full cache analysis. 2D blocking method is very helpful to improve online search efficiency. However, different traversal methods and blocking parameter settings can exhibit different cache and cost behavior depending on data and architectural characteristics. It is very time-consuming to conduct exhaustive search for performance comparison and optimum selection. We provide an analytic comparison of cache blocking methods on their data access performance for an approximation and propose a fast guided sampling scheme to select a traversal method and blocking parameters for effective use of memory hierarchy. The evaluation studies with three datasets show that within a reasonable amount of time, the proposed scheme can identify a highly competitive solution that significantly accelerates score calculation.In summary, we have proposed a new multi-version search architecture with cache-conscious ranking optimization for the online search part and a framework to help fast select best blocking methods and parameters with full cache analysis for the 2D blocking method. By proposing this new versioned search system, we can meet challenges from scalability, efficiency and accuracy in multi-version search, and we believe this work would be useful to future researchers in this direction