Anselm Blumer

Bio: Anselm Blumer is an academic researcher from Tufts University. The author has contributed to research in topics: Deterministic finite automaton & Directed acyclic word graph. The author has an hindex of 12, co-authored 21 publications receiving 3166 citations. Previous affiliations of Anselm Blumer include University of California, Santa Cruz & University of Denver.

Learnability and the Vapnik-Chervonenkis dimension

Abstract: Valiant's learnability model is extended to learning classes of concepts defined by regions in Euclidean space En. The methods in this paper lead to a unified treatment of some of Valiant's results, along with previous results on distribution-free convergence of certain pattern recognition algorithms. It is shown that the essential condition for distribution-free learnability is finiteness of the Vapnik-Chervonenkis dimension, a simple combinatorial parameter of the class of concepts to be learned. Using this parameter, the complexity and closure properties of learnable classes are analyzed, and the necessary and sufficient conditions are provided for feasible learnability.

Complete inverted files for efficient text retrieval and analysis

Abstract: Given a finite set of texts S = {w1, … , wk} over some fixed finite alphabet S, a complete inverted file for S is an abstract data type that provides the functions find(w), which returns the longest prefix of w that occurs (as a subword of a word) in S; freq(w), which returns the number of times w occurs in S; and locations(w), which returns the set of positions where w occurs in S. A data structure that implements a complete inverted file for S that occupies linear space and can be built in linear time, using the uniform-cost RAM model, is given. Using this data structure, the time for each of the above query functions is optimal. To accomplish this, techniques from the theory of finite automata and the work on suffix trees are used to build a deterministic finite automaton that recognizes the set of all subwords of the set S. This automaton is then annotated with additional information and compacted to facilitate the desired query functions. The result is a data structure that is smaller and more flexible than the suffix tree.

An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality

Abstract: Motivation: Modularity analysis is a powerful tool for studying the design of biological networks, offering potential clues for relating the biochemical function(s) of a network with the 'wiring' of its components. Relatively little work has been done to examine whether the modularity of a network depends on the physiological perturbations that influence its biochemical state. Here, we present a novel modularity analysis algorithm based on edge-betweenness centrality, which facilitates the use of directional information and measurable biochemical data. Contact: kyongbum.lee@tufts.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Fast and accurate short read alignment with Burrows–Wheeler transform

Abstract: 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]

Deep Learning

Abstract: Deep learning is a form of machine learning that enables computers to learn from experience and understand the world in terms of a hierarchy of concepts. Because the computer gathers knowledge from experience, there is no need for a human computer operator to formally specify all the knowledge that the computer needs. The hierarchy of concepts allows the computer to learn complicated concepts by building them out of simpler ones; a graph of these hierarchies would be many layers deep. This book introduces a broad range of topics in deep learning. The text offers mathematical and conceptual background, covering relevant concepts in linear algebra, probability theory and information theory, numerical computation, and machine learning. It describes deep learning techniques used by practitioners in industry, including deep feedforward networks, regularization, optimization algorithms, convolutional networks, sequence modeling, and practical methodology; and it surveys such applications as natural language processing, speech recognition, computer vision, online recommendation systems, bioinformatics, and videogames. Finally, the book offers research perspectives, covering such theoretical topics as linear factor models, autoencoders, representation learning, structured probabilistic models, Monte Carlo methods, the partition function, approximate inference, and deep generative models. Deep Learning can be used by undergraduate or graduate students planning careers in either industry or research, and by software engineers who want to begin using deep learning in their products or platforms. A website offers supplementary material for both readers and instructors.

Neural networks for pattern recognition

Abstract: From the Publisher: This is the first comprehensive treatment of feed-forward neural networks from the perspective of statistical pattern recognition. After introducing the basic concepts, the book examines techniques for modelling probability density functions and the properties and merits of the multi-layer perceptron and radial basis function network models. Also covered are various forms of error functions, principal algorithms for error function minimalization, learning and generalization in neural networks, and Bayesian techniques and their applications. Designed as a text, with over 100 exercises, this fully up-to-date work will benefit anyone involved in the fields of neural computation and pattern recognition.

Machine learning

Abstract: 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.).

Approximation by superpositions of a sigmoidal function

Abstract: In this paper we demonstrate that finite linear combinations of compositions of a fixed, univariate function and a set of affine functionals can uniformly approximate any continuous function ofn real variables with support in the unit hypercube; only mild conditions are imposed on the univariate function. Our results settle an open question about representability in the class of single hidden layer neural networks. In particular, we show that arbitrary decision regions can be arbitrarily well approximated by continuous feedforward neural networks with only a single internal, hidden layer and any continuous sigmoidal nonlinearity. The paper discusses approximation properties of other possible types of nonlinearities that might be implemented by artificial neural networks.