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Reservoir computing methods for functional identification of biological networks
BMC Neuroscience volume 10, Article number: P293 (2009)
The complexity of biological neural networks (BNN) necessitates automated methods for investigating their stimulus-response and structure-dynamics relations. In the present work, we aim at building a functionally equivalent network to a reference BNN. The response signal of the BNN to various input streams is regarded as a characterization of its function. Therefore, we train an artificial system that imitates the input-output relation of the reference BNN under the applied stimulus range. In other words, we take a system identification approach for biological neural networks. Generic network models with fixed random connectivity, recurrent dynamics and fading memory, reservoirs, were shown to have a strong separation property on various input streams. Equipped with additional simple readout units, such systems have been successfully applied to several nonlinear modeling and engineering tasks .
Here we take a reservoir computing approach for functional identification of simulated random BNNs and neuronal cell cultures . More specifically, we utilize an Echo State Network (ESN) of leaky integrator (non-spiking) neurons with sigmoid activation functions to identify a BNN. We propose algorithms to adapt the ESN parameters for modeling the relations between continuous input streams and multi-unit recordings in BNNs. Our findings indicate that the trained ESNs can imitate the response signal of a reference biological network for several tasks. For instance, we trained an ESN to estimate the instantaneous firing rate (conditional intensity) of a randomly selected neuron in a simulated BNN. Receiver Operating Characteristic (ROC) curve analysis showed that the ESN can estimate the conditional intensity of this selected neuron (see Figure 1).
Jaeger H: The "echo state" approach to analysing and training recurrent neural networks. GMD Report 148. 2001, GMD – German National Research Institute for Computer Science
Marom S, Shahaf G: Development, learning and memory in large random networks of cortical neurons: Lessons beyond anatomy. Q Rev Biophys. 2002, 35: 63-87.
This work was supported by the German BMBF (BCCN Freiburg, 01GQ0420) and the European Community (NEURO no 12788).
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Gürelu, T., Rotter, S. & Egert, U. Reservoir computing methods for functional identification of biological networks. BMC Neurosci 10, P293 (2009). https://doi.org/10.1186/1471-2202-10-S1-P293
- Input Stream
- Functional Identification
- Conditional Intensity
- Sigmoid Activation Function
- Echo State Network