S. Inglis

Bio: S. Inglis is an academic researcher from University of Waikato. The author has contributed to research in topics: Image compression & Data compression. The author has an hindex of 10, co-authored 18 publications receiving 918 citations.

Using Model Trees for Classification

Abstract: Model trees, which are a type of decision tree with linear regression functions at the leaves, form the basis of a recent successful technique for predicting continuous numeric values. They can be applied to classification problems by employing a standard method of transforming a classification problem into a problem of function approximation. Surprisingly, using this simple transformation the model tree inducerM5 ′, based on Quinlan‘s M5, generates more accurate classifiers than the state-of-the-art decision tree learner C5.0, particularly when most of the attributes are numeric.

Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines

Abstract: To evaluate and compare the performance of variant calling methods and their confidence scores, comparisons between a test call set and a ?gold standard? need to be carried out. Unfortunately, these comparisons are not straightforward with the current Variant Call Files (VCF), which are the standard output of most variant calling algorithms for high-throughput sequencing data. Comparisons of VCFs are often confounded by the different representations of indels, MNPs, and combinations thereof with SNVs in complex regions of the genome, resulting in misleading results. A variant caller is inherently a classification method designed to score putative variants with confidence scores that could permit controlling the rate of false positives (FP) or false negatives (FN) for a given application. Receiver operator curves (ROC) and the area under the ROC (AUC) are efficient metrics to evaluate a test call set versus a gold standard. However, in the case of VCF data this also requires a special accounting to deal with discrepant representations. We developed a novel algorithm for comparing variant call sets that deals with complex call representation discrepancies and through a dynamic programing method that minimizes false positives and negatives globally across the entire call sets for accurate performance evaluation of VCFs.

Joint Variant and De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data

Abstract: The analysis of whole-genome or exome sequencing data from trios and pedigrees has been successfully applied to the identification of disease-causing mutations. However, most methods used to identify and genotype genetic variants from next-generation sequencing data ignore the relationships between samples, resulting in significant Mendelian errors, false positives and negatives. Here we present a Bayesian network framework that jointly analyzes data from all members of a pedigree simultaneously using Mendelian segregation priors, yet providing the ability to detect de novo mutations in offspring, and is scalable to large pedigrees. We evaluated our method by simulations and analysis of whole-genome sequencing (WGS) data from a 17-individual, 3-generation CEPH pedigree sequenced to 50× average depth. Compared with singleton calling, our family caller produced more high-quality variants and eliminated spurious calls as judged by common quality metrics such as Ti/Tv, Het/Hom ratios, and dbSNP/SNP a...

Jumble Java Byte Code to Measure the Effectiveness of Unit Tests

Abstract: Jumble is a byte code level mutation testing tool for Java which inter-operates with JUnit. It has been designed to operate in an industrial setting with large projects. Heuristics have been included to speed the checking of mutations, for example, noting which test fails for each mutation and running this first in subsequent mutation checks. Significant effort has been put into ensuring that it can test code which uses custom class loading and reflection. This requires careful attention to class path handling and coexistence with foreign class-loaders. Jumble is currently used on a continuous basis within an agile programming environment with approximately 370,000 lines of Java code under source control. This checks out project code every fifteen minutes and runs an incremental set of unit tests and mutation tests for modified classes. Jumble is being made available as open source.

Compression-based template matching

Abstract: Textual image compression is a method of both lossy and lossless image compression that is particularly effective for images containing repeated sub-images, notably pages of text. This paper addresses the problem of pattern comparison by using an information or compression based approach. Following Mohiuddin et al. ( 1984), the authors use the amount of uncertainty or entropy between marks as the criterion for the matching process. The entropy model they use is the context-based compression model proposed by Langdon and Rissanen (1981) and further developed by Moffat (1991). There are two principal issues to investigate when studying template matching methods: their susceptibility to different kinds of noise, and how they respond to errors in the initial registration. Because of the computation-intensive nature of the comparison operation, many schemes have been devised to pre-filter or screen the marks in advance to determine those that will surely fail the match. They present a novel method of screening which uses a quad-tree decomposition and finds local centroids at each tree level. >

Data Mining: Practical Machine Learning Tools and Techniques

Abstract: 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

A global reference for human genetic variation.

Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

Evolutionary algorithms for solving multi-objective problems

Abstract: List of Figures. List of Tables. Preface. Foreword. 1. Basic Concepts. 2. Evolutionary Algorithm MOP Approaches. 3. MOEA Test Suites. 4. MOEA Testing and Analysis. 5. MOEA Theory and Issues. 3. MOEA Theoretical Issues. 6. Applications. 7. MOEA Parallelization. 8. Multi-Criteria Decision Making. 9. Special Topics. 10. Epilog. Appendix A: MOEA Classification and Technique Analysis. Appendix B: MOPs in the Literature. Appendix C: Ptrue & PFtrue for Selected Numeric MOPs. Appendix D: Ptrue & PFtrue for Side-Constrained MOPs. Appendix E: MOEA Software Availability. Appendix F: MOEA-Related Information. Index. References.

Applied Predictive Modeling

Abstract: General Strategies.- Regression Models.- Classification Models.- Other Considerations.- Appendix.- References.- Indices.

Correlation-based Feature Selection for Machine Learning

Abstract: A central problem in machine learning is identifying a representative set of features from which to construct a classification model for a particular task. This thesis addresses the problem of feature selection for machine learning through a correlation based approach. The central hypothesis is that good feature sets contain features that are highly correlated with the class, yet uncorrelated with each other. A feature evaluation formula, based on ideas from test theory, provides an operational definition of this hypothesis. CFS (Correlation based Feature Selection) is an algorithm that couples this evaluation formula with an appropriate correlation measure and a heuristic search strategy. CFS was evaluated by experiments on artificial and natural datasets. Three machine learning algorithms were used: C4.5 (a decision tree learner), IB1 (an instance based learner), and naive Bayes. Experiments on artificial datasets showed that CFS quickly identifies and screens irrelevant, redundant, and noisy features, and identifies relevant features as long as their relevance does not strongly depend on other features. On natural domains, CFS typically eliminated well over half the features. In most cases, classification accuracy using the reduced feature set equaled or bettered accuracy using the complete feature set. Feature selection degraded machine learning performance in cases where some features were eliminated which were highly predictive of very small areas of the instance space. Further experiments compared CFS with a wrapper—a well known approach to feature selection that employs the target learning algorithm to evaluate feature sets. In many cases CFS gave comparable results to the wrapper, and in general, outperformed the wrapper on small datasets. CFS executes many times faster than the wrapper, which allows it to scale to larger datasets. Two methods of extending CFS to handle feature interaction are presented and experimentally evaluated. The first considers pairs of features and the second incorporates iii feature weights calculated by the RELIEF algorithm. Experiments on artificial domains showed that both methods were able to identify interacting features. On natural domains, the pairwise method gave more reliable results than using weights provided by RELIEF.