Identification of Interaction Patterns and Classification with Applications to Microarray Data

Emerging patterns represent a class of interaction structures which has been recently proposed as a tool in data mining. In this paper, a new and more general definition refering to underlying probabilities is proposed. The defined interaction patterns carry information about the relevance of combinations of variables for distinguishing between classes. Since they are formally quite similar to the leaves of a classification tree, we propose a fast and simple method which is based on the CART algorithm to find the corresponding empirical patterns in data sets. In simulations, it can be shown that the method is quite effective in identifying patterns. In addition, the detected patterns can be used to define new variables for classification. Thus, we propose a simple scheme to use the patterns to improve the performance of classification procedures. The method may also be seen as a scheme to improve the performance of CARTs concerning the identification of interaction patterns as well as the accuracy of prediction

Mining learning preferences in web-based instruction: Holists vs. Serialists

Web-based instruction programs are used by learners with diverse knowledge, skills and needs. These differences determine their preferences for the design of Web-based instruction programs and ultimately influence learners' success in using them. Cognitive style has been found to significantly affect learners' preferences of web-based instruction programs. However, the majority of previous studies focus on Field Dependence/Independence. Pask's Holist/Serialist dimension has conceptual links with Field Dependence/Independence but it is left mostly unstudied. Therefore, this study focuses on identifying how this dimension of cognitive style affects learner preferences of Web-based instruction programs. A data mining approach is used to illustrate the difference in preferences between Holists and Serialists. The findings show that there are clear differences in regard to content presentation and navigation support. A set of design features were then produced to help designers incorporate cognitive styles into the development of Web-based instruction programs to ensure that they can accommodate learners' different preferences.This work is partially funded by National Science Council, Taiwan, ROC (NSC 98-2511-S-008-012- MY3; NSC 99- 2511-S-008 -003 -MY2; NSC 99-2631-S-008-001)

Multiple testing for SNP-SNP interactions

Most genetic diseases are complex, i.e. associated to combinations of SNPs rather than individual SNPs. In the last few years, this topic has often been addressed in terms of SNP-SNP interaction patterns given as expressions linked by logical operators. Methods for multiple testing in high-dimensional settings can be applied when many SNPs are considered simultaneously. However, another less well-known multiple testing problem arises within a fixed subset of SNPs when the logic expression is chosen optimally. In this article, we propose a general asymptotic approach for deriving the distribution of the maximally selected chi-square statistic in various situations. We show how this result can be used for testing logic expressions - in particular SNP-SNP interaction patterns - while controlling for multiple comparisons. Simulations show that our method provides multiple testing adjustment when the logic expression is chosen such as to maximize the statistic. Its benefit is demonstrated through an application to a real dataset from a large population-based study considering allergy and asthma in KORA. An implementation of our method is available from the Comprehensive R Archive Network (CRAN) as R package 'SNPmaxsel'

A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model

<p>Abstract</p> <p>Background</p> <p>Bioactivity profiling using high-throughput <it>in vitro </it>assays can reduce the cost and time required for toxicological screening of environmental chemicals and can also reduce the need for animal testing. Several public efforts are aimed at discovering patterns or classifiers in high-dimensional bioactivity space that predict tissue, organ or whole animal toxicological endpoints. Supervised machine learning is a powerful approach to discover combinatorial relationships in complex <it>in vitro/in vivo </it>datasets. We present a novel model to simulate complex chemical-toxicology data sets and use this model to evaluate the relative performance of different machine learning (ML) methods.</p> <p>Results</p> <p>The classification performance of Artificial Neural Networks (ANN), K-Nearest Neighbors (KNN), Linear Discriminant Analysis (LDA), Naïve Bayes (NB), Recursive Partitioning and Regression Trees (RPART), and Support Vector Machines (SVM) in the presence and absence of filter-based feature selection was analyzed using K-way cross-validation testing and independent validation on simulated <it>in vitro </it>assay data sets with varying levels of model complexity, number of irrelevant features and measurement noise. While the prediction accuracy of all ML methods decreased as non-causal (irrelevant) features were added, some ML methods performed better than others. In the limit of using a large number of features, ANN and SVM were always in the top performing set of methods while RPART and KNN (k = 5) were always in the poorest performing set. The addition of measurement noise and irrelevant features decreased the classification accuracy of all ML methods, with LDA suffering the greatest performance degradation. LDA performance is especially sensitive to the use of feature selection. Filter-based feature selection generally improved performance, most strikingly for LDA.</p> <p>Conclusion</p> <p>We have developed a novel simulation model to evaluate machine learning methods for the analysis of data sets in which in vitro bioassay data is being used to predict in vivo chemical toxicology. From our analysis, we can recommend that several ML methods, most notably SVM and ANN, are good candidates for use in real world applications in this area.</p

Rank discriminants for predicting phenotypes from RNA expression

Statistical methods for analyzing large-scale biomolecular data are commonplace in computational biology. A notable example is phenotype prediction from gene expression data, for instance, detecting human cancers, differentiating subtypes and predicting clinical outcomes. Still, clinical applications remain scarce. One reason is that the complexity of the decision rules that emerge from standard statistical learning impedes biological understanding, in particular, any mechanistic interpretation. Here we explore decision rules for binary classification utilizing only the ordering of expression among several genes; the basic building blocks are then two-gene expression comparisons. The simplest example, just one comparison, is the TSP classifier, which has appeared in a variety of cancer-related discovery studies. Decision rules based on multiple comparisons can better accommodate class heterogeneity, and thereby increase accuracy, and might provide a link with biological mechanism. We consider a general framework ("rank-in-context") for designing discriminant functions, including a data-driven selection of the number and identity of the genes in the support ("context"). We then specialize to two examples: voting among several pairs and comparing the median expression in two groups of genes. Comprehensive experiments assess accuracy relative to other, more complex, methods, and reinforce earlier observations that simple classifiers are competitive.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS738 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Dimension reduction and Classification with High-Dimensional Microarray Data

Usual microarray data sets include only a handful of observations, but several thousands of predictor variables. Transforming the high-dimensional predictor space to make classification (for instance cancer diagnosis) possible is a major challenge. This thesis deals with various dimension reduction approaches which can handle such data. Chapter 2 gives an introduction into classification with microarray data as well as an overview of a few specific problems such as variable selection and comparison of classification methods. In Chapter 3, I discuss a particular class of interaction structures in the classification framework: "emerging patterns". I propose a new and more general definition referring to underlying probabilities and present a new simple method which is based on the CART algorithm to find the corresponding empirical patterns in concrete data sets. In addition, the detected patterns can be used to define new variables for classification. Thus, I propose a simple scheme to use the patterns to improve the performance of classification procedures. I implemented the search algorithm as well as the classification procedure in the language R. Some of these programs are publicly available from my homepage. Chapter 4 deals with classical linear dimension reduction methods. In the context of binary classification with continuous predictors, I prove two properties concerning the connections between Partial Least Squares (PLS) dimension reduction, between-group PCA and between linear discriminant analysis and between-group PCA. PLS dimension reduction for classification is examined thoroughly in Chapter 5. The classification procedure consisting of PLS dimension reduction and linear discriminant analysis on the new components is compared favorably with some of the best state-of-the-art classification methods using nine real microarray cancer data sets. Moreover, I apply a boosting algorithm to this classification method, which is a novel approach. In addition, I suggest a simple procedure to choose the number of PLS components. At last, I examine the connection between PLS dimension reduction and variable selection and prove a property concerning the equivalence between a common univariate selection criterion and a variable selection approach based on the first PLS component

The importance of data classification using machine learning methods in microarray data

The detection of genetic mutations has attracted global attention. several methods have proposed to detect diseases such as cancers and tumours. One of them is microarrays, which is a type of representation for gene expression that is helpful in diagnosis. To unleash the full potential of microarrays, machine-learning algorithms and gene selection methods can be implemented to facilitate processing on microarrays and to overcome other potential challenges. One of these challenges involves high dimensional data that are redundant, irrelevant, and noisy. To alleviate this problem, this representation should be simplified. For example, the feature selection process can be implemented by reducing the number of features adopted in clustering and classification. A subset of genes can be selected from a pool of gene expression data recorded on DNA micro-arrays. This paper reviews existing classification techniques and gene selection methods. The effectiveness of emerging techniques, such as the swarm intelligence technique in feature selection and classification in microarrays, are reported as well. These emerging techniques can be used in detecting cancer. The swarm intelligence technique can be combined with other statistical methods for attaining better results

KTDA: emerging patterns based data analysis system

Emerging patterns are kind of relationships discovered in databases containing a decision attribute. They represent contrast characteristics of individual decision classes. This form of knowledge can be useful for experts and has been successfully employed in a field of classification. In this paper we present the KTDA system. It enables discovering emerging patterns and applies them to classification purposes. The system has capabilities of identifying improper data by making use of data credibility analysis, a new approach to assessment data typicality