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Inferring gene regulatory networks with nonlinear models via exploiting sparsity

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4 Author(s)
Noor, A. ; Dept. of ECE, Texas A&M Univ., College Station, TX, USA ; Serpedin, E. ; Nounou, M. ; Nounou, H.

This paper considers the problem of inferring gene regulatory networks using time series data. A nonlinear model is assumed for the gene expression profiles, whereas the microarray data follows a linear Gaussian model. A particle filter based approach is proposed to estimate the gene expression profiles and the parameters are estimated online using Kalman filter. In order to capture the inherent sparsity of the gene networks, LASSO based least square optimization is performed. The performance of the proposed algorithm is compared with the extended Kalman filter (EKF) algorithm using Mean Square Error (MSE) as the fidelity criterion. The simulations are performed using the synthetic as well as real data and the proposed algorithm is observed to outperform the EKF in the scenarios considered.

Published in:

Acoustics, Speech and Signal Processing (ICASSP), 2012 IEEE International Conference on

Date of Conference:

25-30 March 2012