SummaryRecently, there has been increasing research to discover genomic biomarkers, haplotypes, and potentially other variables that together contribute to the development of diseases. Single Nucleotide Polymorphisms (SNPs) are the most common form of genomic variations and they can represent an individual's genetic variability in greatest detail. Genome-wide association studies (GWAS) of SNPs, high-dimensional case-control studies, are among the most promising approaches for identifying disease causing variants. METU-SNP software is a Java based integrated desktop application specifically designed for the prioritization of SNP biomarkers and the discovery of genes and pathways related to diseases via analysis of the GWAS case-control data. Outputs of METU-SNP can easily be utilized for the downstream biomarkers research to allow the prediction and the diagnosis of diseases and other personalized medical approaches. Here, we introduce and describe the system functionality and architecture of the METU-SNP. We believe that the METU-SNP will help researchers with the reliable identification of SNPs that are involved in the etiology of complex diseases, ultimately supporting the development of personalized medicine approaches and targeted drug discoveries.
The interplay of machine learning (ML) and optimization methods is an emerging field of artificial intelligence. Both ML and optimization are concerned with modeling of systems related to real-world problems. Parameter selection for classification models is an important task for ML algorithms. In statistical learning theory, cross-validation (CV) which is the most well-known model selection method can be very time consuming for large data sets. One of the recent model selection techniques developed for support vector machines (SVMs) is based on the observed test point margins. In this study, observed margin strategy is integrated into our novel infinite kernel learning (IKL) algorithm together with multi-local procedure (MLP) which is an optimization technique to find global solution. The experimental results show improvements in accuracy and speed when comparing with multiple kernel learning (MKL) and semi-infinite linear programming (SILP) with CV.
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