A balanced iterative random forest for gene selection from microarray data

Background: The wealth of gene expression values being generated by high throughput microarray technologies leads to complex high dimensional datasets. Moreover, many cohorts have the problem of imbalanced classes where the number of patients belonging

Exploiting the accumulated evidence for gene selection in microarray gene expression data

Machine Learning methods have of late made signicant efforts to solving multidisciplinary problems in the field of cancer classification using microarray gene expression data. Feature subset selection methods can play an important role in the modeling process, since these tasks are characterized by a large number of features and a few observations, making the modeling a non-trivial undertaking. In this particular scenario, it is extremely important to select genes by taking into account the possible interactions with other gene subsets. This paper shows that, by accumulating the evidence in favour (or against) each gene along the search process, the obtained gene subsets may constitute better solutions, either in terms of predictive accuracy or gene size, or in both. The proposed technique is extremely simple and applicable at a negligible overhead in cost.Postprint (published version

A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data

Background: Feature selection techniques are critical to the analysis of high dimensional datasets. This is especially true in gene selection from microarray data which are commonly with extremely high feature-to-sample ratio. In addition to the essential objectives such as to reduce data noise, to reduce data redundancy, to improve sample classification accuracy, and to improve model generalization property, feature selection also helps biologists to focus on the selected genes to further validate their biological hypotheses.Results: In this paper we describe an improved hybrid system for gene selection. It is based on a recently proposed genetic ensemble (GE) system. To enhance the generalization property of the selected genes or gene subsets and to overcome the overfitting problem of the GE system, we devised a mapping strategy to fuse the goodness information of each gene provided by multiple filtering algorithms. This information is then used for initialization and mutation operation of the genetic ensemble system.Conclusion: We used four benchmark microarray datasets (including both binary-class and multi-class classification problems) for concept proving and model evaluation. The experimental results indicate that the proposed multi-filter enhanced genetic ensemble (MF-GE) system is able to improve sample classification accuracy, generate more compact gene subset, and converge to the selection results more quickly. The MF-GE system is very flexible as various combinations of multiple filters and classifiers can be incorporated based on the data characteristics and the user preferences. <br /

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)