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Nice work! Just a small comment on this part:

Second limitation : During training Mathematica is not keeping track of the statistics of the intermediate values (input and output of layers).

[...]

So, to get those statistics I am just applying each layer of the trained network one after another and keeping track of the input / output

This can be done with more ease using the NetPort[All] evaluation property:

NetChain[{Sin, Cos, Log}][{1, 2, 3}, NetPort[All]]

<|NetPort[{1, "Output"}] -> {0.841471, 0.909297, 0.14112}, 
 NetPort[{2, "Output"}] -> {0.666367, 0.6143, 0.990059}, 
 NetPort[{3, "Output"}] -> {-0.405915, -0.487271, -0.00999066}|>

The original notebook is no more working with Version 12.0 of Mathematica. Here is an updated one which is working.

But I still have an issue : the last Manipulate is auto-updating in version 12 and I don't understand why. It was not the case with version 11.3.

Attachments:

NeuralNetworkCMSISNN.nb