Biology

2626 readers

18 users here now

This is a general community to discuss of all things related to biology!

For a more specific community about asking questions to biologists, you can also visit:

/c/askbiologists@lemmy.world

founded 3 years ago

MODERATORS

Sal@mander.xyz

Gene regulatory network - Clock and Flip-flop (diode.zone)

submitted 2 years ago by sixfold@lemmy.sdf.org to c/biology@mander.xyz

2 comments fedilink hide all child comments

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

you are viewing a single comment's thread
view the rest of the comments

[–] appel@whiskers.bim.boats 4 points 2 years ago (1 children)

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.

[–] sixfold@lemmy.sdf.org 1 points 2 years ago* (last edited 2 years ago)

Well, it is technically differential equations, but with weighted inputs like a NN. Here's the equations

for each node (gene/morphogen) i. zi is the concentration of morphogen i, zj is that of j. 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.

This is just written in python, so the network is defined by a matrix with each number representing the weight between two of the edges. I ignore the edge if it's weight is zero.

What are the standard symbols for genetic circuits?

edit: sorry it's impossible to see the equations if you have a black background.