I'm trying to build a neural network between protein sequence and its drug fingerprint. My input size is 20000. The output size is 881. The sample size is 610.
Can I process this huge neural network? But how? And in which tool?
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Yes, it should be no problem.
When you decide to use a CNN, you have to make sure that this makes sense. Another answer mentioned using
3x3 convolutions -- which I would recommend against. For that to work, you would need to turn your vector into a rectangular array, and you would be implying a structure that isn't there.
Use one-dimensional convolutions instead.
It sure is possible, imagine a CNN can handle way bigger number of inputs. An image with size of
512x512 has already
262144 input nodes when re-arranged to a one-row vector. The trick sicne 2012/2014 is to use Convolutions, and deep ones, so stacking a lot of
3x3 Convolutions for example. Its way less sensitive than a fully-connected Dense network and needs a siginificant amount of less parameters. For more check this out,
chapter 9 : Ian-Goodfellow, Deep Learning