Wasserstein Auto-Encoders of Merge Trees (and Persistence Diagrams) #1006
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
julien-tierny
requested changes
Feb 2, 2024
There was a problem hiding this comment.
hi mathieu,
thanks a lot for the PR.
here's a first batch of reviews (more to come).
in short:
- I believe the code should be compatible with the latest version of libtorch (at least version 2)
- there's a few occurrences where some minimal documentation should be included
- some re-wording here and there (especially change "geodesic" into "axis" and "geodesics" into "axes").
thanks for the fixes
core/vtk/ttkMergeTreeAutoencoderDecoding/ttkMergeTreeAutoencoderDecoding.cpp
Show resolved
Hide resolved
core/vtk/ttkMergeTreeAutoencoderDecoding/ttkMergeTreeAutoencoderDecoding.cpp
Show resolved
Hide resolved
core/vtk/ttkMergeTreeAutoencoder/ttkMergeTreeAutoencoderUtils.cpp
Outdated
Show resolved
Hide resolved
julien-tierny
requested changes
Feb 5, 2024
core/base/mergeTreeAutoencoderDecoding/MergeTreeAutoencoderDecoding.h
Outdated
Show resolved
Hide resolved
julien-tierny
approved these changes
Apr 23, 2024
julien-tierny
requested changes
Apr 23, 2024
There was a problem hiding this comment.
Hi @MatPont ,
thanks for the PR, I added a few more remarks (we can discuss them at our next meeting). Best,
julien-tierny
approved these changes
May 6, 2024
This reverts commit 1dbee0c.
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Outdated suggestions cannot be applied.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.
This PR adds the code corresponding to the following work:
Wasserstein Auto-Encoders of Merge Trees (and Persistence Diagrams)
Mathieu Pont, Julien Tierny
IEEE Transactions on Visualization and Computer Graphics, 2023
It adds 2 filters to TTK :
MergeTreeAutoencoderandMergeTreeAutoencoderDecoding.The first one,
MergeTreeAutoencoder, takes an ensemble of merge trees or persistence diagrams as input and compute a wasserstein auto-encoding minimizing the reconstruction error of the data.It outputs the processed input data (with some information attached to them, like correlation and so on), the origins of each basis, the vectors of each basis, the coefficients of the input for each layer (i.e. the coordinates of each input for each basis).
The second filter,
MergeTreeAutoencoderDecoding, is used to reconstruct merge trees (or persistence diagrams) given the model parameters, it can reconstruct the input and can construct other trees/diagrams like user-defined locations in the latent space.It takes as input the outputs of the previous filter (except the processed input data) and output an ensemble of merge trees (or persistence diagrams).
It also adds the Torch support to TTK.