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Although there is software available to "fit" networks to measured data and to translate Boolean models into simple ODE systems [ 3, 5, 6], there is no simple software available for the step-by-step analysis and visualisation of Boolean simulations on network graphs with simultaneous state space visualization.
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An evolved and fit network is not necessarily the sum of its optimal sub-modules.
To find the best fit network among the modules, a generalized PSO method, including basic PSO and neural network pruning technique, is used to determine RNN structure and its parameters.
The conventional approach for applying NNs to a classification problem is to specify a network architecture, select which variables (SNPs) are included as inputs to the network, and fit network weights using a gradient-descent based approach such as backpropagation (BP) [ 33].
In other words, the fittest networks maintaining a sharp distribution around the peak dominate only when Vip>Vg is satisfied.
The state space of the fittest networks resulting from selection for attractor size and attractor number are shown in Fig. 9. Selecting on these particular properties resulted in some very atypical networks.
These populations are a heterogeneous mix of architectures, weights, and input variables which undergo mating, crossover, and recombination to ultimately identify an optimum NN solution, simultaneously finding influential SNPs and fitting networks weights.
It's clear that comparing the well fitted network properties mentioned above is not sufficient to identify the best-fitting model.
The fittest network with F̅≈0 chooses such orbits having no turning points within the noise range from the original orbit.
We tested this by subjecting the fittest network from each simulation to a number of trials (10,000) in a noisy environment.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com