Modelling neuronal behaviour with time series regression: Recurrent Neural Networks on synthetic C. elegans data

Gonçalo Leote Cardoso Mestre, Ruxandra Barbulescu, Arlindo L. Oliveira, L. Miguel Silveira

Keywords: Data-driven models, RNNs, LSTMs, GRUs, C. Elegans, Time series regression, black-box

Abstract:

Given the inner complexity of the human nervous system, insight into the dynamics of brain activity can be gained from understanding smaller and simpler organisms, such as the nematode C. elegans. The behavioural and structural biology of these organisms is well-known, making them prime candidates for benchmarking modelling and simulation techniques. In these complex neuronal collections, classical white-box modelling techniques based on intrinsic structural or behavioural information are either unable to capture the profound nonlinearities of the neuronal response to different stimuli or generate extremely complex models, which are computationally intractable. In this paper we investigate whether it is possible to generate lower complexity black-box models that can capture the system dynamics with low error using only measured or simulated input-output information. We show how the nervous system of C. elegans can be modelled and simulated with data-driven models using different neural network architectures. Specifically, we target the use of state of the art recurrent neural networks architectures such as LSTMs and GRUs and compare these architectures in terms of their properties and their RMSE, as well as the complexity of the resulting models.
We show that GRU models with a hidden layer size of 4 units are able to accurately reproduce the system's response to very different stimuli.