-
Notifications
You must be signed in to change notification settings - Fork 205
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Adding a modified class for a GLM-HMM with different inputs/covariates for observation GLM and transition GLM #166
Open
Zeinab-Mohammadi
wants to merge
43
commits into
lindermanlab:master
Choose a base branch
from
Zeinab-Mohammadi:master
base: master
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
kjggy
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Hi Scott
Hope you are doing well. Thank you for providing this excellent package, and I extend my gratitude to everyone in your lab who collaborated on it.
I have included an HMM_TO class (TO stands for Transition and Observation) in which I considered working on a GLM-HMM with inputs of different sizes and different covariates for observation GLM and transition GLM. To use this class, I added two other modified classes: "InputDrivenTransitionsAlternativeFormulation" for transition and "InputDrivenObservationsDiffInputs" for observation. The results of employing this code for our analysis are detailed in our paper where we used an HMM with a multinomial GLM for transitions and a Bernoulli GLM for observations with various inputs. Please note that I added the HMM_TO class alongside the HMM class, without replacing it, to ensure that none of the other notebooks are affected.
Additionally, I have attached a notebook script titled "2c-Input-Driven-Transitions-and-Observations-GLM-HMM" that utilizes the mentioned code to implement GLM-HMM as a generative model. It simulates data and performs a recovery analysis to retrieve the generative parameters.
Once again, thank you for providing this great package for state space model inference. It was very useful in our analysis. I look forward to your valuable insights and feedback on this pull request.
Best,
Zeinab