Improved Fuzzy Cognitive Maps for Gene Regulatory Networks Inference based on time series data.

Abstract

Microarray data provide lots of information regarding gene expression levels. Due to the large amount of such data, their analysis requires sufficient computational methods for identifying and analyzing gene regulation networks; however, researchers in this field are faced with numerous challenges such as consideration for too many genes and at the same time, the limited number of samples and their noisy nature of the data. In this paper, a hybrid method base on fuzzy cognitive map and compressed sensing is used to identify interactions between genes. For this purpose, in inference of the gene regulation network, the Ensemble Kalman filtered compressed sensing is used to learn the fuzzy cognitive map. Using the Ensemble Kalman filter and compressed sensing, the fuzzy cognitive map will be robust against noise. The proposed algorithm is evaluated using several metrics and compared with several well know methods such as LASSOFCM, KFRegular, CMI2NI. The experimental results show that the proposed method outperforms methods proposed in recent years in terms of SSmean, Data Error and accuracy.