Finding gene network topologies for given biological function with recurrent neural network

Jingxiang Shen, Feng Liu, Yuhai Tu and Chao Tang ()
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Jingxiang Shen: Center for Quantitative Biology, Peking University
Feng Liu: Center for Quantitative Biology, Peking University
Yuhai Tu: IBM T. J. Watson Research Center, Yorktown Heights
Chao Tang: Center for Quantitative Biology, Peking University

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: Abstract Searching for possible biochemical networks that perform a certain function is a challenge in systems biology. For simple functions and small networks, this can be achieved through an exhaustive search of the network topology space. However, it is difficult to scale this approach up to larger networks and more complex functions. Here we tackle this problem by training a recurrent neural network (RNN) to perform the desired function. By developing a systematic perturbative method to interrogate the successfully trained RNNs, we are able to distill the underlying regulatory network among the biological elements (genes, proteins, etc.). Furthermore, we show several cases where the regulation networks found by RNN can achieve the desired biological function when its edges are expressed by more realistic response functions, such as the Hill-function. This method can be used to link topology and function by helping uncover the regulation logic and network topology for complex tasks.

Date: 2021
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DOI: 10.1038/s41467-021-23420-5

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