Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.

Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ~10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package.

Availability: http://maq.sourceforge.net 

Contact: [email protected]

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Fast and accurate short read alignment with Burrows–Wheeler transform

The increasing volume of data in modern business and science calls for more complex and sophisticated tools. Although advances in data mining technology have made extensive data collection much easier, it's still always evolving and there is a constant need for new techniques and tools that can help us transform this data into useful information and knowledge. Since the previous edition's publication, great advances have been made in the field of data mining. Not only does the third of edition of Data Mining: Concepts and Techniques continue the tradition of equipping you with an understanding and application of the theory and practice of discovering patterns hidden in large data sets, it also focuses on new, important topics in the field: data warehouses and data cube technology, mining stream, mining social networks, and mining spatial, multimedia and other complex data. Each chapter is a stand-alone guide to a critical topic, presenting proven algorithms and sound implementations ready to be used directly or with strategic modification against live data. This is the resource you need if you want to apply today's most powerful data mining techniques to meet real business challenges. * Presents dozens of algorithms and implementation examples, all in pseudo-code and suitable for use in real-world, large-scale data mining projects. * Addresses advanced topics such as mining object-relational databases, spatial databases, multimedia databases, time-series databases, text databases, the World Wide Web, and applications in several fields. *Provides a comprehensive, practical look at the concepts and techniques you need to get the most out of real business data

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Data Mining: Concepts and Techniques

Data Mining: Practical Machine Learning Tools and Techniques offers a thorough grounding in machine learning concepts as well as practical advice on applying machine learning tools and techniques in real-world data mining situations. This highly anticipated third edition of the most acclaimed work on data mining and machine learning will teach you everything you need to know about preparing inputs, interpreting outputs, evaluating results, and the algorithmic methods at the heart of successful data mining. Thorough updates reflect the technical changes and modernizations that have taken place in the field since the last edition, including new material on Data Transformations, Ensemble Learning, Massive Data Sets, Multi-instance Learning, plus a new version of the popular Weka machine learning software developed by the authors. Witten, Frank, and Hall include both tried-and-true techniques of today as well as methods at the leading edge of contemporary research. *Provides a thorough grounding in machine learning concepts as well as practical advice on applying the tools and techniques to your data mining projects *Offers concrete tips and techniques for performance improvement that work by transforming the input or output in machine learning methods *Includes downloadable Weka software toolkit, a collection of machine learning algorithms for data mining tasks-in an updated, interactive interface. Algorithms in toolkit cover: data pre-processing, classification, regression, clustering, association rules, visualization

Data Mining: Practical Machine Learning Tools and Techniques

More than twelve years have elapsed since the first public release of WEKA. In that time, the software has been rewritten entirely from scratch, evolved substantially and now accompanies a text on data mining [35]. These days, WEKA enjoys widespread acceptance in both academia and business, has an active community, and has been downloaded more than 1.4 million times since being placed on Source-Forge in April 2000. This paper provides an introduction to the WEKA workbench, reviews the history of the project, and, in light of the recent 3.6 stable release, briefly discusses what has been added since the last stable version (Weka 3.4) released in 2003.

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The WEKA data mining software: an update

Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

Given an array A[1...n] of n distinct elements from the set {1, 2, ..., n} a range maximum query RMQ(a, b) returns the highest element in A[a...b] along with its position. In this paper, we study a generalization of this classical problem called Categorical Range Maxima Query (CRMQ) problem, in which each element A[i] in the array has an associated category (color) given by C[i] ∈ [σ]. A query then asks to report each distinct color c appearing in C[a...b] along with the highest element (and its position) in A[a...b] with color c. Let pc denote the position of the highest element in A[a...b] with color c. We investigate two variants of this problem: a threshold version and a top-k version. In threshold version, we only need to output the colors with A[pc] more than the input threshold τ, whereas top-k variant asks for k colors with the highest A[pc] values. In the word RAM model, we achieve linear space structure along with O(k) query time, that can report colors in sorted order of A[•]. In external memory, we present a data structure that answers queries in optimal O(1+k/B) I/O's using almost-linear O(n log* n) space, as well as a linear space data structure with O(log* n + k/B) query I/Os. Here k represents the output size, log* n is the iterated logarithm of n and B is the block size. CRMQ has applications to document retrieval and categorical range reporting -- giving a one-shot framework to obtain improved results in both these problems. Our results for CRMQ not only improve the existing best known results for three-sided categorical range reporting but also overcome the hurdle of maintaining color uniqueness in the output set.

Categorical range maxima queries

In this paper we describe a fast algorithm that creates a wavelet tree for a sequence of symbols. We show that a wavelet tree can be constructed in $O(n\lceil{\frac{\log \sigma}{\sqrt{\log n}}}\rceil)$ time where n is the number of symbols and σ is the alphabet size.

Fast Construction of Wavelet Trees

Query optimization is an integral part of relational database management systems. One important task in query optimization is selectivity estimation, that is, given a query P, one needs to estimate the fraction of records in the database that satisfy P. Almost all previous work dealt with the estimation of numeric selectivity, i.e., the query contains only numeric variables. The general problem of estimating alphanumeric selectivity is much more difficult and has attracted attention only very recently, and the focus has been on the special case when only one column is involved. The authors consider the more general case when there are two correlated alphanumeric columns. They develop efficient algorithms to build storage structures that can fit in a database catalog. Results from extensive experiments to test the algorithms, on the basis of error analysis and space requirements, are given to guide DBMS implementors.

Selectivity estimation in the presence of alphanumeric correlations

Parallel independent disks can enhance the performance of external memory (EM) algorithms, but the programming task is often difficult. In this paper we develop randomized variants of distribution sort for use with parallel independent disks. We propose a simple variant called randomized cycling distribution sort (RCD) and prove that it has optimal expected I/O complexity. The analysis uses a novel reduction to a model with significantly fewer probabilistic interdependencies. Experimental evidence is provided to support its practicality. Other simple variants are also examined experimentally and appear to offer similar advantages to RCD. Based upon ideas in RCD we propose general techniques that transparently simulate algorithms developed for the unrealistic multihead disk model so that they can be run on the realistic parallel disk model. The simulation is optimal for two important classes of algorithms; the class of multipass algorithms, which make a complete pass through their data before accessing any element a second time, and the algorithms based upon the well-known distribution paradigm of EM computation.

Jeffrey Scott Vitter

Papers

Categorical range maxima queries

Fast Construction of Wavelet Trees

Selectivity estimation in the presence of alphanumeric correlations

Distribution sort with randomized cycle

Efficient memory access in large-scale computation (invited paper)