Gene regulatory network - Clock and Flip-flop

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Submitted ⁨⁨1⁩ ⁨year⁩ ago⁩ by ⁨sixfold@lemmy.sdf.org⁩ to ⁨[deleted]⁩

https://diode.zone/w/8rSmur1cVZahiBVgkfuxid

I’m working on a program to edit and simulate gene regulatory networks using recurrent neural networks as a model. Here’s a demo.

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appel@whiskers.bim.boats ⁨1⁩ ⁨year⁩ ago
This is pretty cool, but is there a reason to use NN rather than differential equations? Seems like it might be more computationally expensive.

Are you using some kind of declarative language to define the networks? Not sure if a standard for that exists yet. There are the standard symbols for genetic circuits though.

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- sixfold@lemmy.sdf.org ⁨1⁩ ⁨year⁩ ago
  Well, it is technically differential equations, but with weighted inputs like a NN. Here’s the equations
  
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  for each node (gene/morphogen) i. f(x) is the sigmoid function, k1 is the maximum rate of expression, k2 is the degradation rate, b is the bias. wij is the weight for an edge from j to i.
  
  What are the standard symbols for genetic circuits?
  
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