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

Current data structures for searching large string collections either fail to achieve minimum space or cause too many cache misses. In this paper we discuss some edge linearizations of the classic trie data structure that are simultaneously cache-friendly and compressed. We provide new insights on front coding [24], introduce other novel linearizations, and study how close their space occupancy is to the information-theoretic minimum. The moral is that they are not just heuristics. Our second contribution is a novel dictionary encoding scheme that builds upon such linearizations and achieves nearly optimal space, offers competitive I/O-search time, and is also conscious of the query distribution. Finally, we combine those data structures with cache-oblivious tries [2, 5] and obtain a succinct variant whose space is close to the information-theoretic minimum.

On searching compressed string collections cache-obliviously

In recent years, many theoretically I/O-efficient algorithms and data structures have been developed. The TPIE project at Duke University was started to investigate the practical importance of these theoretical results. The goal of this ongoing project is to provide a portable, extensible, flexible, and easy to use C++ programming environment for efficiently implementing I/O-algorithms and data structures. The TPIE library has been developed in two phases. The first phase focused on supporting algorithms with a sequential I/O pattern, while the recently developed second phase has focused on supporting on-line I/O-efficient data structures, which exhibit a more random I/O pattern. This paper describes the design and implementation of the second phase of TPIE.

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Implementing I/O-efficient Data Structures Using TPIE

We examine I/O-efficient data structures that provide indexing support for new data models. The database languages of these models include concepts from constraint programming (e.g., relational tuples are generalized to conjunctions of constraints) and from object-oriented programming (e.g., objects are organized in class hierarchies). Let $n$ be the size of the database, $c$ the number of classes, $B$ the secondary storage page size, and $t$ the size of the output of a query. Indexing by one attribute in the constraint data model (for a fairly general type of constraints) is equivalent to external dynamic interval management, which is a special case of external dynamic 2-dimensional range searching. We present a semi-dynamic data structure for this problem which has optimal worst-case space $O(n/B)$ pages and optimal query I/O time $O(\log_B n + t/B)$ and has $O(\log_B n + (\log^2_B n) / B)$ amortized insert I/O time. If the order of the insertions is random then the expected number of I/O operations needed to perform insertions is reduced to $O(\log_B n)$. Indexing by one attribute and by class name in an object-oriented model, where objects are organized as a forest hierarchy of classes, is also a special case of external dynamic 2-dimensional range searching. Based on this observation we first identify a simple algorithm with good worst-case performance for the class indexing problem. Using the forest structure of the class hierarchy and techniques from the constraint indexing problem, we improve its query I/O time from $O(\log_2 c \log_B n +t/B)$ to $O(\log_B n + t/B + \log_2 B)$.

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Indexing for Data Models with Constraints and Classes

Inverted indexes are the most fundamental and widely used data structures in information retrieval. For each unique word occurring in a document collection, the inverted index stores a list of the documents in which this word occurs. Compression techniques are often applied to further reduce the space requirement of these lists. However, the index has a shortcoming, in that only predefined pattern queries can be supported efficiently. In terms of string documents where word boundaries are undefined, if we have to index all the substrings of a given document, then the storage quickly becomes quadratic in the data size. Also, if we want to apply the same type of indexes for querying phrases or sequence of words, then the inverted index will end up storing redundant information. In this paper, we show the first set of inverted indexes which work naturally for strings as well as phrase searching. The central idea is to exclude document d in the inverted list of a string P if every occurrence of P in d is subsumed by another string of which P is a prefix. With this we show that our space utilization is close to the optimal. Techniques from succinct data structures are deployed to achieve compression while allowing fast access in terms of frequency and document id based retrieval. Compression and speed trade-offs are evaluated for different variants of the proposed index. For phrase searching, we show that our indexes compare favorably against a typical inverted index deploying position-wise intersections. We also show efficient top-k based retrieval under relevance metrics like frequency and tf-idf.

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Inverted indexes for phrases and strings

The World Wide Web is growing and changing at an astonishing rate. For the information in the web to be useful, web information systems such as search engines have to keep up with the growth and change of the web. In this paper we study how web documents change. In particular, we study two important characteristics of web document change that are directly related to keeping web information systems upto-date: the degree of the change and the clusteredness of the change. We analyze the evolution of web documents with respect to these two measures and discuss the implications for web information systems update.

Jeffrey Scott Vitter

Papers

On searching compressed string collections cache-obliviously

Implementing I/O-efficient Data Structures Using TPIE

Indexing for Data Models with Constraints and Classes

Inverted indexes for phrases and strings

Characterizing Web Document Change