In most gene expression data, the number of training samples is very small compared to the large number of genes involved in the experiments. However, among the large amount of genes, only a small fraction is effective for performing a certain task. Furthermore, a small subset of genes is desirable in developing gene expression based diagnostic tools for delivering reliable and understandable results. With the gene selection results, the cost of biological experiment and decision can be greatly reduced by analyzing only the marker genes. An important application of gene expression data in functional genomics is to classify samples according to their gene expression profiles. Feature selection (FS) is a process which attempts to select more informative features. It is one of the important steps in knowledge discovery. Conventional supervised FS methods evaluate various feature subsets using an evaluation function or metric to select only those features which are related to the decision classes of the data under consideration. This paper studies a feature selection method based on rough set theory. Further K-Means, Fuzzy C-Means (FCM) algorithm have implemented for the reduced feature set without considering class labels. Then the obtained results are compared with the original class labels. Back Propagation Network (BPN) has also been used for classification. Then the performance of K-Means, FCM, and BPN are analyzed through the confusion matrix. It is found that the BPN is performing well comparatively.

Mammography is the most effective and available tool for breast cancer screening. However, the low positive predictive value of breast biopsy resulting from mammogram interpretation leads to approximately 70% unnecessary biopsies with benign outcomes. Data mining algorithms could be used to help physicians in their decisions to perform a breast biopsy on a suspicious lesion seen in a mammogram image or to perform a short term follow-up examination instead. In this research paper data mining classification algorithms; Decision Tree (DT), Artificial Neural Network (ANN), and Support Vector Machine (SVM) are analyzed on mammographic masses data set. The purpose of this study is to increase the ability of physicians to determine the severity (benign or malignant) of a mammographic mass lesion from BI-RADS attributes and the patient,s age. The whole data set is divided for training the models and test them by the ratio of 70:30% respectively and the performances of classification algorithms are compared through three statistical measures; sensitivity, specificity, and classification accuracy. Accuracy of DT, ANN and SVM are 78.12%, 80.56% and 81.25% of test samples respectively. Our analysis shows that out of these three classification models SVM predicts severity of breast cancer with least error rate and highest accuracy.

In many applications, one has side information, e.g., labels that are provided in a semi-supervised manner, about a specific target region of a large data set, and one wants to perform machine learning and data analysis tasks "nearby" that prespecified target region. For example, one might be interested in the clustering structure of a data graph near a prespecified "seed set" of nodes, or one might be interested in finding partitions in an image that are near a prespecified "ground truth" set of pixels. Locally-biased problems of this sort are particularly challenging for popular eigenvector-based machine learning and data analysis tools. At root, the reason is that eigenvectors are inherently global quantities, thus limiting the applicability of eigenvector-based methods in situations where one is interested in very local properties of the data. In this paper, we address this issue by providing a methodology to construct semi-supervised eigenvectors of a graph Laplacian, and we illustrate how these locally-biased eigenvectors can be used to perform locally-biased machine learning. These semi-supervised eigenvectors capture successively-orthogonalized directions of maximum variance, conditioned on being well-correlated with an input seed set of nodes that is assumed to be provided in a semi-supervised manner. We show that these semi-supervised eigenvectors can be computed quickly as the solution to a system of linear equations; and we also describe several variants of our basic method that have improved scaling properties. We provide several empirical examples demonstrating how these semi-supervised eigenvectors can be used to perform locally-biased learning; and we discuss the relationship between our results and recent machine learning algorithms that use global eigenvectors of the graph Laplacian.

The change of two orders of magnitude in the 'new DCF' of NIST's SRE'10, relative to the 'old DCF' evaluation criterion, posed a difficult challenge for participants and evaluator alike. Initially, participants were at a loss as to how to calibrate their systems, while the evaluator underestimated the required number of evaluation trials. After the fact, it is now obvious that both calibration and evaluation require very large sets of trials. This poses the challenges of (i) how to decide what number of trials is enough, and (ii) how to process such large data sets with reasonable memory and CPU requirements. After SRE'10, at the BOSARIS Workshop, we built solutions to these problems into the freely available BOSARIS Toolkit. This paper explains the principles and algorithms behind this toolkit. The main contributions of the toolkit are: 1. The Normalized Bayes Error-Rate Plot, which analyses likelihood- ratio calibration over a wide range of DCF operating points. These plots also help in judging the adequacy of the sizes of calibration and evaluation databases. 2. Efficient algorithms to compute DCF and minDCF for large score files, over the range of operating points required by these plots. 3. A new score file format, which facilitates working with very large trial lists. 4. A faster logistic regression optimizer for fusion and calibration. 5. A principled way to define EER (equal error rate), which is of practical interest when the absolute error count is small.

We introduce a new approach to variable selection, called Predictive Correlation Screening, for predictor design. Predictive Correlation Screening (PCS) implements false positive control on the selected variables, is well suited to small sample sizes, and is scalable to high dimensions. We establish asymptotic bounds for Familywise Error Rate (FWER), and resultant mean square error of a linear predictor on the selected variables. We apply Predictive Correlation Screening to the following two-stage predictor design problem. An experimenter wants to learn a multivariate predictor of gene expressions based on successive biological samples assayed on mRNA arrays. She assays the whole genome on a few samples and from these assays she selects a small number of variables using Predictive Correlation Screening. To reduce assay cost, she subsequently assays only the selected variables on the remaining samples, to learn the predictor coefficients. We show superiority of Predictive Correlation Screening relative to LASSO and correlation learning (sometimes popularly referred to in the literature as marginal regression or simple thresholding) in terms of performance and computational complexity.

In machine learning, the choice of a learning algorithm that is suitable for the application domain is critical. The performance metric used to compare different algorithms must also reflect the concerns of users in the application domain under consideration. In this work, we propose a novel probability-based performance metric called Relevance Score for evaluating supervised learning algorithms. We evaluate the proposed metric through empirical analysis on a dataset gathered from an intelligent lighting pilot installation. In comparison to the commonly used Classification Accuracy metric, the Relevance Score proves to be more appropriate for a certain class of applications.

We present a new classification method for quasar identification in the EROS-2 and MACHO datasets based on a boosted version of Random Forest classifier. We use a set of variability features including parameters of a continuous auto regressive model. We prove that continuous auto regressive parameters are very important discriminators in the classification process. We create two training sets (one for EROS-2 and one for MACHO datasets) using known quasars found in the LMC. Our model's accuracy in both EROS-2 and MACHO training sets is about 90% precision and 86% recall, improving the state of the art models accuracy in quasar detection. We apply the model on the complete, including 28 million objects, EROS-2 and MACHO LMC datasets, finding 1160 and 2551 candidates respectively. To further validate our list of candidates, we crossmatched our list with a previous 663 known strong candidates, getting 74% of matches for MACHO and 40% in EROS-2. The main difference on matching level is because EROS-2 is a slightly shallower survey which translates to significantly lower signal-to-noise ratio lightcurves.

Many data sets contain rich information about objects, as well as pairwise relations between them. For instance, in networks of websites, scientific papers, and other documents, each node has content consisting of a collection of words, as well as hyperlinks or citations to other nodes. In order to perform inference on such data sets, and make predictions and recommendations, it is useful to have models that are able to capture the processes which generate the text at each node and the links between them. In this paper, we combine classic ideas in topic modeling with a variant of the mixed-membership block model recently developed in the statistical physics community. The resulting model has the advantage that its parameters, including the mixture of topics of each document and the resulting overlapping communities, can be inferred with a simple and scalable expectation-maximization algorithm. We test our model on three data sets, performing unsupervised topic classification and link prediction. For both tasks, our model outperforms several existing state-of-the-art methods, achieving higher accuracy with significantly less computation, analyzing a data set with 1.3 million words and 44 thousand links in a few minutes.

This paper reports work in progress on an explanation facility for Bayesian conditioning aimed at improving user acceptance of probability-based decision support systems. Design of the facility, which appears to be reasonably domain-independent, is based on an information processing model that accounts both for biased and normative behavior in reasoning about conditional evidence. Preliminary results indicate that the facility is both acceptable to naive users and effective in improving understanding of Bayesian conditioning.

Associative classification is a recent and rewarding technique which integrates association rule mining and classification to a model for prediction and achieves maximum accuracy. Associative classifiers are especially fit to applications where maximum accuracy is desired to a model for prediction. There are many domains such as medical where the maximum accuracy of the model is desired. Heart disease is a single largest cause of death in developed countries and one of the main contributors to disease burden in developing countries. Mortality data from the registrar general of India shows that heart disease are a major cause of death in India, and in Andhra Pradesh coronary heart disease cause about 30%of deaths in rural areas. Hence there is a need to develop a decision support system for predicting heart disease of a patient. In this paper we propose efficient associative classification algorithm using genetic approach for heart disease prediction. The main motivation for using genetic algorithm in the discovery of high level prediction rules is that the discovered rules are highly comprehensible, having high predictive accuracy and of high interestingness values. Experimental Results show that most of the classifier rules help in the best prediction of heart disease which even helps doctors in their diagnosis decisions.