Jacob Schreiber

`self.edges` should give you the transition matrix. `self.distributions` will give you a list of distribution objects, each of which will have their own parameters. See the distributions documentation for more...

Thanks for contributing this! Understandable about the test suite. At some point this will be merged back into the broader Kundaje-lab suite of tools and hopefully someone there will be...

Hi @MuhammedHasan. Thanks for taking the time to re-organize this. When I said breaking the PR into smaller chunks what I meant is breaking it into smaller PRs that can...

Hi That's not really within my expertise, but you can implement Bayesian Networks and Factor Graphs using pomegranate and they're pretty fast and will run on a GPU. Let me...

Without seeing the output or an example it's difficult to know exactly what is going on, but it is possible that some of the "patterns" learned by modisco are not...

Thanks for pointing out this issue. I don't think we have time to consider changes like this right now. Potentially after the next set of ENCODE papers comes out there...

Sorry for the delay and thanks for pointing this out. Would you mind posting a minimal reproducing script? I've been having some trouble reproducing the issue, but I also didn't...