MassJoin: A mapreduce-based method for scalable string similarity joins

Abstract—String similarity join is an essential operation in data integration. The era of big data calls for scalable algorithms to support large-scale string similarity joins. In this paper, we study scalable string similarity joins using MapReduce. We propose a MapReduce-based framework, called MASSJOIN, which supports both set-based similarity functions and character-based similarity functions. We extend the existing partition-based signature scheme to support set-based similarity functions. We utilize the signatures to generate key-value pairs. To reduce the transmission cost, we merge key-value pairs to significantly reduce the number of key-value pairs, from cubic to linear com-plexity, while not sacrificing the pruning power. To improve the performance, we incorporate “light-weight ” filter units into the key-value pairs which can be utilized to prune large number of dissimilar pairs without significantly increasing the transmission cost. Experimental results on real-world datasets show that our method significantly outperformed state-of-the-art approaches. I

Scalable Model-Based Management of Correlated Dimensional Time Series in ModelarDB+

To monitor critical infrastructure, high quality sensors sampled at a high frequency are increasingly used. However, as they produce huge amounts of data, only simple aggregates are stored. This removes outliers and fluctuations that could indicate problems. As a remedy, we present a model-based approach for managing time series with dimensions that exploits correlation in and among time series. Specifically, we propose compressing groups of correlated time series using an extensible set of model types within a user-defined error bound (possibly zero). We name this new category of model-based compression methods for time series Multi-Model Group Compression (MMGC). We present the first MMGC method GOLEMM and extend model types to compress time series groups. We propose primitives for users to effectively define groups for differently sized data sets, and based on these, an automated grouping method using only the time series dimensions. We propose algorithms for executing simple and multi-dimensional aggregate queries on models. Last, we implement our methods in the Time Series Management System (TSMS) ModelarDB (ModelarDB+). Our evaluation shows that compared to widely used formats, ModelarDB+ provides up to 13.7 times faster ingestion due to high compression, 113 times better compression due to the adaptivity of GOLEMM, 630 times faster aggregates by using models, and close to linear scalability. It is also extensible and supports online query processing.Comment: 12 Pages, 28 Figures, and 1 Tabl

Nephele: genotyping via complete composition vectors and MapReduce

<p>Abstract</p> <p>Background</p> <p>Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences.</p> <p>Results</p> <p>Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on traditional hardware. Nephele can use the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. We were able to generate a neighbour-joined tree of over 10,000 16S samples in less than 2 hours.</p> <p>Conclusions</p> <p>We conclude that using Nephele can substantially decrease the processing time required for generating genotype trees of tens to hundreds of organisms at genome scale sequence coverage.</p

Efficient processing of similarity queries with applications

Today, a myriad of data sources, from the Internet to business operations to scientific instruments, produce large and different types of data. Many application scenarios, e.g., marketing analysis, sensor networks, and medical and biological applications, call for identifying and processing similarities in big data. As a result, it is imperative to develop new similarity query processing approaches and systems that scale from low dimensional data to high dimensional data, from single machine to clusters of hundreds of machines, and from disk-based to memory-based processing. This dissertation introduces and studies several similarity-aware query operators, analyzes and optimizes their performance. The first contribution of this dissertation is an SQL-based Similarity Group-by operator (SGB, for short) that extends the semantics of the standard SQL Group-by operator to group data with similar but not necessarily equal values. We realize these SGB operators by extending the Standard SQL Group-by and introduce two new SGB operators for multi-dimensional data. We implement and test the new SGB operators and their algorithms inside an open-source centralized database server (PostgreSQL). In the second contribution of this dissertation, we study how to efficiently process Hamming-distance-based similarity queries (Hamming-distance select and Hamming-distance join) that are crucial to many applications. We introduce a new index, termed the HA-Index, that speeds up distance comparisons and eliminates redundancies when performing the two flavors of Hamming distance range queries (namely, the selects and joins). In the third and last contribution of this dissertation, we develop a system for similarity query processing and optimization in an in-memory and distributed setup for big spatial data. We propose a query scheduler and a distributed query optimizer that use a new cost model to optimize the cost of similarity query processing in this in-memory distributed setup. The scheduler and query optimizer generates query execution plans that minimize the effect of query skew. The query scheduler employs new spatial indexing techniques based on bloom filters to forward queries to the appropriate local sites. The proposed query processing and optimization techniques are prototyped inside Spark, a distributed main-memory computation system

PASS-JOIN: A Partition-based Method for Similarity Joins

As an essential operation in data cleaning, the similarity join has attracted considerable attention from the database community. In this paper, we study string similarity joins with edit-distance constraints, which find similar string pairs from two large sets of strings whose edit distance is within a given threshold. Existing algorithms are efficient either for short strings or for long strings, and there is no algorithm that can efficiently and adaptively support both short strings and long strings. To address this problem, we propose a partition-based method called Pass-Join. Pass-Join partitions a string into a set of segments and creates inverted indices for the segments. Then for each string, Pass-Join selects some of its substrings and uses the selected substrings to find candidate pairs using the inverted indices. We devise efficient techniques to select the substrings and prove that our method can minimize the number of selected substrings. We develop novel pruning techniques to efficiently verify the candidate pairs. Experimental results show that our algorithms are efficient for both short strings and long strings, and outperform state-of-the-art methods on real datasets.Comment: VLDB201

A comparison of statistical machine learning methods in heartbeat detection and classification

In health care, patients with heart problems require quick responsiveness in a clinical setting or in the operating theatre. Towards that end, automated classification of heartbeats is vital as some heartbeat irregularities are time consuming to detect. Therefore, analysis of electro-cardiogram (ECG) signals is an active area of research. The methods proposed in the literature depend on the structure of a heartbeat cycle. In this paper, we use interval and amplitude based features together with a few samples from the ECG signal as a feature vector. We studied a variety of classification algorithms focused especially on a type of arrhythmia known as the ventricular ectopic fibrillation (VEB). We compare the performance of the classifiers against algorithms proposed in the literature and make recommendations regarding features, sampling rate, and choice of the classifier to apply in a real-time clinical setting. The extensive study is based on the MIT-BIH arrhythmia database. Our main contribution is the evaluation of existing classifiers over a range sampling rates, recommendation of a detection methodology to employ in a practical setting, and extend the notion of a mixture of experts to a larger class of algorithms