search

StochSS / GillesPy2

Modeling toolkit for biochemical simulation
http://gillespy2.readthedocs.io/
GNU General Public License v3.0
72 stars 32 forks source link

gillespy2 & pytorch #444

Closed ignorant96 closed 2 years ago

ignorant96 commented 4 years ago

I want to combine gillespy2 with torch to train the parameters of the model, but I failed. I find parameters without changing.So I want to know if gillespy2 can combine with pytorch. Thank You!

briandrawert commented 4 years ago

I am not sure about pytorch, but if you are looking to infer model parameter I would strongly suggest Sciope: https://github.com/StochSS/sciope as it is designed specifically for this and works well with GillesPy2.

rmjiang7 commented 4 years ago

I second the usage of sciope for parameter estimation. GillesPy2's implementation doesn't use any of PyTorch's data structures so most of PyTorch's features won't work. In addition, the types of models that GillesPy2 is used for typically have intractable likelihoods/gradients, so the optimization methods in PyTorch won't really be too useful - sciope is built for those type of situations.

ignorant96 commented 4 years ago

I second the usage of sciope for parameter estimation. GillesPy2's implementation doesn't use any of PyTorch's data structures so most of PyTorch's features won't work. In addition, the types of models that GillesPy2 is used for typically have intractable likelihoods/gradients, so the optimization methods in PyTorch won't really be too useful - sciope is built for those type of situations.

Thank you so much.I will try sciope.

ignorant96 commented 4 years ago

I am not sure about pytorch, but if you are looking to infer model parameter I would strongly suggest Sciope: https://github.com/StochSS/sciope as it is designed specifically for this and works well with GillesPy2.

Thank you so much! I will try it!