Handling Massive N-Gram Datasets Efficiently

This paper deals with the two fundamental problems concerning the handling of large n-gram language models: indexing, that is compressing the n-gram strings and associated satellite data without compromising their retrieval speed; and estimation, that is computing the probability distribution of the strings from a large textual source. Regarding the problem of indexing, we describe compressed, exact and lossless data structures that achieve, at the same time, high space reductions and no time degradation with respect to state-of-the-art solutions and related software packages. In particular, we present a compressed trie data structure in which each word following a context of fixed length k, i.e., its preceding k words, is encoded as an integer whose value is proportional to the number of words that follow such context. Since the number of words following a given context is typically very small in natural languages, we lower the space of representation to compression levels that were never achieved before. Despite the significant savings in space, our technique introduces a negligible penalty at query time. Regarding the problem of estimation, we present a novel algorithm for estimating modified Kneser-Ney language models, that have emerged as the de-facto choice for language modeling in both academia and industry, thanks to their relatively low perplexity performance. Estimating such models from large textual sources poses the challenge of devising algorithms that make a parsimonious use of the disk. The state-of-the-art algorithm uses three sorting steps in external memory: we show an improved construction that requires only one sorting step thanks to exploiting the properties of the extracted n-gram strings. With an extensive experimental analysis performed on billions of n-grams, we show an average improvement of 4.5X on the total running time of the state-of-the-art approach.Comment: Published in ACM Transactions on Information Systems (TOIS), February 2019, Article No: 2

Data compression for sequencing data

Post-Sanger sequencing methods produce tons of data, and there is a general agreement that the challenge to store and process them must be addressed with data compression. In this review we first answer the question “why compression” in a quantitative manner. Then we also answer the questions “what” and “how”, by sketching the fundamental compression ideas, describing the main sequencing data types and formats, and comparing the specialized compression algorithms and tools. Finally, we go back to the question “why compression” and give other, perhaps surprising answers, demonstrating the pervasiveness of data compression techniques in computational biology

Multi-Stage Search Architectures for Streaming Documents

The web is becoming more dynamic due to the increasing engagement and contribution of Internet users in the age of social media. A more dynamic web presents new challenges for web search--an important application of Information Retrieval (IR). A stream of new documents constantly flows into the web at a high rate, adding to the old content. In many cases, documents quickly lose their relevance. In these time-sensitive environments, finding relevant content in response to user queries requires a real-time search service; immediate availability of content for search and a fast ranking, which requires an optimized search architecture. These aspects of today's web are at odds with how academic IR researchers have traditionally viewed the web, as a collection of static documents. Moreover, search architectures have received little attention in the IR literature. Therefore, academic IR research, for the most part, does not provide a mechanism to efficiently handle a high-velocity stream of documents, nor does it facilitate real-time ranking. This dissertation addresses the aforementioned shortcomings. We present an efficient mech- anism to index a stream of documents, thereby enabling immediate availability of content. Our indexer works entirely in main memory and provides a mechanism to control inverted list con- tiguity, thereby enabling faster retrieval. Additionally, we consider document ranking with a machine-learned model, dubbed "Learning to Rank" (LTR), and introduce a novel multi-stage search architecture that enables fast retrieval and allows for more design flexibility. The stages of our architecture include candidate generation (top k retrieval), feature extraction, and docu- ment re-ranking. We compare this architecture with a traditional monolithic architecture where candidate generation and feature extraction occur together. As we lay out our architecture, we present optimizations to each stage to facilitate low-latency ranking. These optimizations include a fast approximate top k retrieval algorithm, document vectors for feature extraction, architecture- conscious implementations of tree ensembles for LTR using predication and vectorization, and algorithms to train tree-based LTR models that are fast to evaluate. We also study the efficiency- effectiveness tradeoffs of these techniques, and empirically evaluate our end-to-end architecture on microblog document collections. We show that our techniques improve efficiency without degrading quality

A Case for Partitioned Bloom Filters

In a partitioned Bloom Filter the $m$ bit vector is split into $k$ disjoint $m/k$ sized parts, one per hash function. Contrary to hardware designs, where they prevail, software implementations mostly adopt standard Bloom filters, considering partitioned filters slightly worse, due to the slightly larger false positive rate (FPR). In this paper, by performing an in-depth analysis, first we show that the FPR advantage of standard Bloom filters is smaller than thought; more importantly, by studying the per-element FPR, we show that standard Bloom filters have weak spots in the domain: elements which will be tested as false positives much more frequently than expected. This is relevant in scenarios where an element is tested against many filters, e.g., in packet forwarding. Moreover, standard Bloom filters are prone to exhibit extremely weak spots if naive double hashing is used, something occurring in several, even mainstream, libraries. Partitioned Bloom filters exhibit a uniform distribution of the FPR over the domain and are robust to the naive use of double hashing, having no weak spots. Finally, by surveying several usages other than testing set membership, we point out the many advantages of having disjoint parts: they can be individually sampled, extracted, added or retired, leading to superior designs for, e.g., SIMD usage, size reduction, test of set disjointness, or duplicate detection in streams. Partitioned Bloom filters are better, and should replace the standard form, both in general purpose libraries and as the base for novel designs.Comment: 21 page

Efficient query processing for scalable web search

Search engines are exceptionally important tools for accessing information in today’s world. In satisfying the information needs of millions of users, the effectiveness (the quality of the search results) and the efficiency (the speed at which the results are returned to the users) of a search engine are two goals that form a natural trade-off, as techniques that improve the effectiveness of the search engine can also make it less efficient. Meanwhile, search engines continue to rapidly evolve, with larger indexes, more complex retrieval strategies and growing query volumes. Hence, there is a need for the development of efficient query processing infrastructures that make appropriate sacrifices in effectiveness in order to make gains in efficiency. This survey comprehensively reviews the foundations of search engines, from index layouts to basic term-at-a-time (TAAT) and document-at-a-time (DAAT) query processing strategies, while also providing the latest trends in the literature in efficient query processing, including the coherent and systematic reviews of techniques such as dynamic pruning and impact-sorted posting lists as well as their variants and optimisations. Our explanations of query processing strategies, for instance the WAND and BMW dynamic pruning algorithms, are presented with illustrative figures showing how the processing state changes as the algorithms progress. Moreover, acknowledging the recent trends in applying a cascading infrastructure within search systems, this survey describes techniques for efficiently integrating effective learned models, such as those obtained from learning-to-rank techniques. The survey also covers the selective application of query processing techniques, often achieved by predicting the response times of the search engine (known as query efficiency prediction), and making per-query tradeoffs between efficiency and effectiveness to ensure that the required retrieval speed targets can be met. Finally, the survey concludes with a summary of open directions in efficient search infrastructures, namely the use of signatures, real-time, energy-efficient and modern hardware and software architectures

Graph Processing in Main-Memory Column Stores

Evermore, novel and traditional business applications leverage the advantages of a graph data model, such as the offered schema flexibility and an explicit representation of relationships between entities. As a consequence, companies are confronted with the challenge of storing, manipulating, and querying terabytes of graph data for enterprise-critical applications. Although these business applications operate on graph-structured data, they still require direct access to the relational data and typically rely on an RDBMS to keep a single source of truth and access. Existing solutions performing graph operations on business-critical data either use a combination of SQL and application logic or employ a graph data management system. For the first approach, relying solely on SQL results in poor execution performance caused by the functional mismatch between typical graph operations and the relational algebra. To the worse, graph algorithms expose a tremendous variety in structure and functionality caused by their often domain-specific implementations and therefore can be hardly integrated into a database management system other than with custom coding. Since the majority of these enterprise-critical applications exclusively run on relational DBMSs, employing a specialized system for storing and processing graph data is typically not sensible. Besides the maintenance overhead for keeping the systems in sync, combining graph and relational operations is hard to realize as it requires data transfer across system boundaries. A basic ingredient of graph queries and algorithms are traversal operations and are a fundamental component of any database management system that aims at storing, manipulating, and querying graph data. Well-established graph traversal algorithms are standalone implementations relying on optimized data structures. The integration of graph traversals as an operator into a database management system requires a tight integration into the existing database environment and a development of new components, such as a graph topology-aware optimizer and accompanying graph statistics, graph-specific secondary index structures to speedup traversals, and an accompanying graph query language. In this thesis, we introduce and describe GRAPHITE, a hybrid graph-relational data management system. GRAPHITE is a performance-oriented graph data management system as part of an RDBMS allowing to seamlessly combine processing of graph data with relational data in the same system. We propose a columnar storage representation for graph data to leverage the already existing and mature data management and query processing infrastructure of relational database management systems. At the core of GRAPHITE we propose an execution engine solely based on set operations and graph traversals. Our design is driven by the observation that different graph topologies expose different algorithmic requirements to the design of a graph traversal operator. We derive two graph traversal implementations targeting the most common graph topologies and demonstrate how graph-specific statistics can be leveraged to select the optimal physical traversal operator. To accelerate graph traversals, we devise a set of graph-specific, updateable secondary index structures to improve the performance of vertex neighborhood expansion. Finally, we introduce a domain-specific language with an intuitive programming model to extend graph traversals with custom application logic at runtime. We use the LLVM compiler framework to generate efficient code that tightly integrates the user-specified application logic with our highly optimized built-in graph traversal operators. Our experimental evaluation shows that GRAPHITE can outperform native graph management systems by several orders of magnitude while providing all the features of an RDBMS, such as transaction support, backup and recovery, security and user management, effectively providing a promising alternative to specialized graph management systems that lack many of these features and require expensive data replication and maintenance processes

効率的で安全な集合間類似結合に関する研究

筑波大学 (University of Tsukuba)201

Indexing methods for web archives

There have been numerous efforts recently to digitize previously published content and preserving born-digital content leading to the widespread growth of large text reposi- tories. Web archives are such continuously growing text collections which contain ver- sions of documents spanning over long time periods. Web archives present many op- portunities for historical, cultural and political analyses. Consequently there is a grow- ing need for tools which can efficiently access and search them. In this work, we are interested in indexing methods for supporting text-search work- loads over web archives like time-travel queries and phrase queries. To this end we make the following contributions: • Time-travel queries are keyword queries with a temporal predicate, e.g., “mpii saarland” @ [06/2009], which return versions of documents in the past. We in- troduce a novel index organization strategy, called index sharding, for efficiently supporting time-travel queries without incurring additional index-size blowup. We also propose index-maintenance approaches which scale to such continuously growing collections. • We develop query-optimization techniques for time-travel queries called partition selection which maximizes recall at any given query-execution stage. • We propose indexing methods to support phrase queries, e.g., “to be or not to be that is the question”. We index multi-word sequences and devise novel query- optimization methods over the indexed sequences to efficiently answer phrase queries. We demonstrate the superior performance of our approaches over existing methods by extensive experimentation on real-world web archives.In der jüngsten Vergangenheit gab es zahlreiche Bemühungen zuvor veröffentlichte Inhalte zu digitalisieren und elektronisch erstellte Inhalte zu erhalten. Dies führte zu einem weit verbreitenden Anstieg großer Textdatenbestände. Webarchive sind eine solche Art konstant ansteigender Textdatensammlung. Sie enthalten mehrere Versionen von Dokumenten, welche sich über längere Zeiträume erstrecken. Darüber hinaus bieten sie viele Möglichkeiten für historische, kulturelle und politische Analysen. Infolgedessen gibt es einen wachsenden Bedarf an Werkzeugen, die eine effiziente Suche in Webarchiven und einen effizienten Zugriff auf die Daten erlauben. Der Fokus dieser Arbeit liegt auf Indexierungsverfahren, um die Arbeitslast von Textsuche auf Webarchiven zu unterstützen, wie zum Beispiel time-travel queries oder phrase queries. Zu diesem Zweck leisten wir folgende Beiträge: • Time-travel queries sind Suchwortanfragen mit einem temporalen Prädikat. Zum Beispiel liefert die Anfrage “mpii saarland” @ [06/2009] Versionen des Dokuments aus der Vergangenheit als Ergebnis. Zur effizienten Unterstützung solcher Anfragen ohne die Indexgröße aufzublasen, stellen wir eine neue Strategie zur Organisation von Indizes dar, so genanntes index sharding. Des Weiteren schlagen wir Wartungsverfahren für Indizes vor, die für solch konstant wachsende Datensätze skalieren. • WirentwickelnTechnikenzurAnfrageoptimierungvontime-travelqueries, nachstehend partition selection genannt. Diese maximieren den Recall in jeder Phase der Anfrageverarbeitung. • Wir stellen Indexierungsmethoden vor, die phrase queries unterstützen, z. B. “Sein oder Nichtsein, das ist hier die Frage”. Wir indexieren Sequenzen bestehend aus mehreren Wörtern und entwerfen neue Optimierungsverfahren für die indexierten Sequenzen, um phrase queries effizient zu beantworten. Die Performanz dieser Verfahren wird anhand von ausführlichen Experimenten auf realen Webarchiven demonstriert