The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

/pdf/gapped-blast-and-psi-blast-a-new-generation-of-protein-2ybl67x5yx.pdf

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Reinforcement learning, one of the most active research areas in artificial intelligence, is a computational approach to learning whereby an agent tries to maximize the total amount of reward it receives when interacting with a complex, uncertain environment. In Reinforcement Learning, Richard Sutton and Andrew Barto provide a clear and simple account of the key ideas and algorithms of reinforcement learning. Their discussion ranges from the history of the field's intellectual foundations to the most recent developments and applications. The only necessary mathematical background is familiarity with elementary concepts of probability. The book is divided into three parts. Part I defines the reinforcement learning problem in terms of Markov decision processes. Part II provides basic solution methods: dynamic programming, Monte Carlo methods, and temporal-difference learning. Part III presents a unified view of the solution methods and incorporates artificial neural networks, eligibility traces, and planning; the two final chapters present case studies and consider the future of reinforcement learning.

/pdf/reinforcement-learning-an-introduction-rzxgej9p17.pdf

Reinforcement Learning: An Introduction

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

/pdf/data-mining-concepts-and-techniques-4dtvdfkvmi.pdf

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

https://www2.econ.iastate.edu/tesfatsi/DeepLearningInNeuralNetworksOverview.JSchmidhuber2015.pdf

Deep learning in neural networks

https://ftp.cs.wisc.edu/machine-learning/shavlik-group/towell.aij94.pdf

Knowledge-based artificial neural networks

A significant limitation of neural networks is that the representations they learn are usually incomprehensible to humans. We present a novel algorithm, TREPAN, for extracting comprehensible, symbolic representations from trained neural networks. Our algorithm uses queries to induce a decision tree that approximates the concept represented by a given network. Our experiments demonstrate that TREPAN is able to produce decision trees that maintain a high level of fidelity to their respective networks while being comprehensible and accurate. Unlike previous work in this area, our algorithm is general in its applicability and scales well to large networks and problems with high-dimensional input spaces.

/pdf/extracting-tree-structured-representations-of-trained-11oq131p3q.pdf

Extracting Tree-Structured Representations of Trained Networks

Neural networks, despite their empirically proven abilities, have been little used for the refinement of existing knowledge because this task requires a three-step process. First, knowledge must be inserted into a neural network. Second, the network must be refined. Third, the refined knowledge must be extracted from the network. We have previously described a method for the first step of this process. Standard neural learning techniques can accomplish the second step. In this article, we propose and empirically evaluate a method for the final, and possibly most difficult, step. Our method efficiently extracts symbolic rules from trained neural networks. The four major results of empirical tests of this method are that the extracted rules 1) closely reproduce the accuracy of the network from which they are extracteds 2) are superior to the rules produced by methods that directly refine symbolic ruless 3) are superior to those produced by previous techniques for extracting rules from trained neural networkss and 4) are “human comprehensible.” Thus, this method demonstrates that neural networks can be used to effectively refine symbolic knowledge. Moreover, the rule-extraction technique developed herein contributes to the understanding of how symbolic and connectionist approaches to artificial intelligence can be profitably integrated.

/pdf/extracting-refined-rules-from-knowledge-based-neural-1pa890jzi5.pdf

Extracting Refined Rules from Knowledge-Based Neural Networks

Standard algorithms for explanation-based learning require complete and correct knowledge bases. The KBANN system relaxes this constraint through the use of empirical learning methods to refine approximately correct knowledge. This knowledge is used to determine the structure of an artificial neural network and the weights on its links, thereby making the knowledge accessible for modification by neural learning. KBANN is evaluated by empirical tests in the domain of molecular biology. Networks created by KBANN are shown to be superior, in terms of their ability to correctly classify unseen examples, to randomly initialized neural networks, decision trees, "nearest neighbor" matching, and standard techniques reported in the biological literature. In addition, KBANN'S networks improve the initial knowledge in biologically interesting ways.

https://aaaipress.org/Papers/AAAI/1990/AAAI90-129.pdf

Refinement of approximate domain theories by knowledge-based neural networks

Neural-network ensembles have been shown to be very accurate classification techniques. Previous work has shown that an effective ensemble should consist of networks that are not only highly correct, but ones that make their errors on different parts of the input space as well. Most existing techniques, however, only indirectly address the problem of creating such a set of networks. In this paper we present a technique called ADDEMUP that uses genetic algorithms to directly search for an accurate and diverse set of trained networks. ADDEMUP works by first creating an initial population, then uses genetic operators to continually create new networks, keeping the set of networks that are as accurate as possible while disagreeing with each other as much as possible. Experiments on three DNA problems show that ADDEMUP is able to generate a set of trained networks that is more accurate than several existing approaches. Experiments also show that ADDEMUP is able to effectively incorporate prior knowledge, if available, to improve the quality of its ensemble.

/pdf/generating-accurate-and-diverse-members-of-a-neural-network-2xblobbtyw.pdf

Jude W. Shavlik

Papers

Knowledge-based artificial neural networks

Extracting Tree-Structured Representations of Trained Networks

Extracting Refined Rules from Knowledge-Based Neural Networks

Refinement of approximate domain theories by knowledge-based neural networks

Generating Accurate and Diverse Members of a Neural-Network Ensemble