Identification of disease-causing genes using microarray data mining and gene ontology

Background: One of the best and most accurate methods for identifying disease-causing genes is monitoring gene expression values in different samples using microarray technology. One of the shortcomings of microarray data is that they provide a small quantity of samples with respect to the number of genes. This problem reduces the classification accuracy of the methods, so gene selection is essential to improve the predictive accuracy and to identify potential marker genes for a disease. Among numerous existing methods for gene selection, support vector machine-based recursive feature elimination (SVMRFE) has become one of the leading methods, but its performance can be reduced because of the small sample size, noisy data and the fact that the method does not remove redundant genes. Methods: We propose a novel framework for gene selection which uses the advantageous features of conventional methods and addresses their weaknesses. In fact, we have combined the Fisher method and SVMRFE to utilize the advantages of a filtering method as well as an embedded method. Furthermore, we have added a redundancy reduction stage to address the weakness of the Fisher method and SVMRFE. In addition to gene expression values, the proposed method uses Gene Ontology which is a reliable source of information on genes. The use of Gene Ontology can compensate, in part, for the limitations of microarrays, such as having a small number of samples and erroneous measurement results. Results: The proposed method has been applied to colon, Diffuse Large B-Cell Lymphoma (DLBCL) and prostate cancer datasets. The empirical results show that our method has improved classification performance in terms of accuracy, sensitivity and specificity. In addition, the study of the molecular function of selected genes strengthened the hypothesis that these genes are involved in the process of cancer growth. Conclusions: The proposed method addresses the weakness of conventional methods by adding a redundancy reduction stage and utilizing Gene Ontology information. It predicts marker genes for colon, DLBCL and prostate cancer with a high accuracy. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help in the search for a cure for cancers

SQL Injection Detection Using Machine Learning Techniques and Multiple Data Sources

SQL Injection continues to be one of the most damaging security exploits in terms of personal information exposure as well as monetary loss. Injection attacks are the number one vulnerability in the most recent OWASP Top 10 report, and the number of these attacks continues to increase. Traditional defense strategies often involve static, signature-based IDS (Intrusion Detection System) rules which are mostly effective only against previously observed attacks but not unknown, or zero-day, attacks. Much current research involves the use of machine learning techniques, which are able to detect unknown attacks, but depending on the algorithm can be costly in terms of performance. In addition, most current intrusion detection strategies involve collection of traffic coming into the web application either from a network device or from the web application host, while other strategies collect data from the database server logs. In this project, we are collecting traffic from two points: the web application host, and a Datiphy appliance node located between the webapp host and the associated MySQL database server. In our analysis of these two datasets, and another dataset that is correlated between the two, we have been able to demonstrate that accuracy obtained with the correlated dataset using algorithms such as rule-based and decision tree are nearly the same as those with a neural network algorithm, but with greatly improved performance

Sparse Matrix-based Random Projection for Classification

As a typical dimensionality reduction technique, random projection can be simply implemented with linear projection, while maintaining the pairwise distances of high-dimensional data with high probability. Considering this technique is mainly exploited for the task of classification, this paper is developed to study the construction of random matrix from the viewpoint of feature selection, rather than of traditional distance preservation. This yields a somewhat surprising theoretical result, that is, the sparse random matrix with exactly one nonzero element per column, can present better feature selection performance than other more dense matrices, if the projection dimension is sufficiently large (namely, not much smaller than the number of feature elements); otherwise, it will perform comparably to others. For random projection, this theoretical result implies considerable improvement on both complexity and performance, which is widely confirmed with the classification experiments on both synthetic data and real data