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

Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

AsterixDB: A Scalable, Open Source BDMS

AsterixDB is a new, full-function BDMS (Big Data Management System) with a feature set that distinguishes it from other platforms in today's open source Big Data ecosystem. Its features make it well-suited to applications like web data warehousing, social data storage and analysis, and other use cases related to Big Data. AsterixDB has a flexible NoSQL style data model; a query language that supports a wide range of queries; a scalable runtime; partitioned, LSM-based data storage and indexing (including B+-tree, R-tree, and text indexes); support for external as well as natively stored data; a rich set of built-in types; support for fuzzy, spatial, and temporal types and queries; a built-in notion of data feeds for ingestion of data; and transaction support akin to that of a NoSQL store. Development of AsterixDB began in 2009 and led to a mid-2013 initial open source release. This paper is the first complete description of the resulting open source AsterixDB system. Covered herein are the system's data model, its query language, and its software architecture. Also included are a summary of the current status of the project and a first glimpse into how AsterixDB performs when compared to alternative technologies, including a parallel relational DBMS, a popular NoSQL store, and a popular Hadoop-based SQL data analytics platform, for things that both technologies can do. Also included is a brief description of some initial trials that the system has undergone and the lessons learned (and plans laid) based on those early "customer" engagements

The Family of MapReduce and Large Scale Data Processing Systems

In the last two decades, the continuous increase of computational power has produced an overwhelming flow of data which has called for a paradigm shift in the computing architecture and large scale data processing mechanisms. MapReduce is a simple and powerful programming model that enables easy development of scalable parallel applications to process vast amounts of data on large clusters of commodity machines. It isolates the application from the details of running a distributed program such as issues on data distribution, scheduling and fault tolerance. However, the original implementation of the MapReduce framework had some limitations that have been tackled by many research efforts in several followup works after its introduction. This article provides a comprehensive survey for a family of approaches and mechanisms of large scale data processing mechanisms that have been implemented based on the original idea of the MapReduce framework and are currently gaining a lot of momentum in both research and industrial communities. We also cover a set of introduced systems that have been implemented to provide declarative programming interfaces on top of the MapReduce framework. In addition, we review several large scale data processing systems that resemble some of the ideas of the MapReduce framework for different purposes and application scenarios. Finally, we discuss some of the future research directions for implementing the next generation of MapReduce-like solutions.Comment: arXiv admin note: text overlap with arXiv:1105.4252 by other author

Flattening an object algebra to provide performance

Algebraic transformation and optimization techniques have been the method of choice in relational query execution, but applying them in object-oriented (OO) DBMSs is difficult due to the complexity of OO query languages. This paper demonstrates that the problem can be simplified by mapping an OO data model to the binary relational model implemented by Monet, a state-of-the-art database kernel. We present a generic mapping scheme to flatten data models and study the case of straightforward OO model. We show how flattening enabled us to implement a query algebra, using only a very limited set of simple operations. The required primitives and query execution strategies are discussed, and their performance is evaluated on the 1-GByte TPC-D (Transaction-processing Performance Council's Benchmark D), showing that our divide-and-conquer approach yields excellent result