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arXiv · 1509.03221

Recurrent Neural Network Based Modeling of Gene Regulatory Network Using Bat Algorithm

Sudip Mandal·Goutam Saha·Rajat K. Pal
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Abstract

Correct inference of genetic regulations inside a cell is one of the greatest challenges in post genomic era for the biologist and researchers. Several intelligent techniques and models were already proposed to identify the regulatory relations among genes from the biological database like time series microarray data. Recurrent Neural Network (RNN) is one of the most popular and simple approach to model the dynamics as well as to infer correct dependencies among genes. In this paper, Bat Algorithm (BA) is applied to optimize the model parameters of RNN model of Gene Regulatory Network (GRN). Initially the proposed method is tested against small artificial network without any noise and the efficiency is observed in term of number of iteration, number of population and BA optimization parameters. The model is also validated in presence of different level of random noise for the small artificial network and that proved its ability to infer the correct inferences in presence of noise like real world dataset. In the next phase of this research, BA based RNN is applied to real world benchmark time series microarray dataset of E. coli. The results prove that it can able to identify the maximum number of true positive regulation but also include some false positive regulations. Therefore, BA is very suitable for identifying biological plausible GRN with the help RNN model.

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Sudip Mandal, Goutam Saha, Rajat K. Pal. 2015-08-21. Recurrent Neural Network Based Modeling of Gene Regulatory Network Using Bat Algorithm. https://arxiv.org/abs/1509.03221

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