CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks

Zeeshan Gillani, Muhammad Sajid Hamid Akash, MD Matiur Rahaman, Ming Chen
2014 BMC Bioinformatics  
Predication of gene regularity network (GRN) from expression data is a challenging task. There are many methods that have been developed to address this challenge ranging from supervised to unsupervised methods. Most promising methods are based on support vector machine (SVM). There is a need for comprehensive analysis on prediction accuracy of supervised method SVM using different kernels on different biological experimental conditions and network size. Results: We developed a tool
more » ... based on SVM to compare different kernel methods for inference of GRN. Using CompareSVM, we investigated and evaluated different SVM kernel methods on simulated datasets of microarray of different sizes in detail. The results obtained from CompareSVM showed that accuracy of inference method depends upon the nature of experimental condition and size of the network. Conclusions: For network with nodes (<200) and average (over all sizes of networks), SVM Gaussian kernel outperform on knockout, knockdown, and multifactorial datasets compared to all the other inference methods. For network with large number of nodes (~500), choice of inference method depend upon nature of experimental condition. CompareSVM is available at http://bis.zju.edu.cn/CompareSVM/.
doi:10.1186/s12859-014-0395-x pmid:25433465 pmcid:PMC4260380 fatcat:dqsvssapurey5orvflghlmexdm