TopoMap #987
Merged
TopoMap #987
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
…algorithm. It computes a 2D embedding of points whose distance matrix is given as input. The embedding is computed so that the distances of a minimum spanning tree compute with Kruskal's algorithm are preserved. This commits includes a separate vtk module for this algorithm.
the TopoMap module to compute the embedding of the input points, given as coordinates or given their distance matrix.
… for the vtk layer, indicating for each point the time it was embedded in 2D.
…er can now choose between this one and Kruskal (the legacy one).
atalon-lip6
force-pushed
the
topomap-clean
branch
4 times, most recently
from
b657258 to
1358c43
Compare
julien-tierny
requested changes
Nov 20, 2023
There was a problem hiding this comment.
hi @atalon-lip6,
thanks a lot for the PR.
here's a first batch of comments (more to come soon).
thanks for addressing them!
cheers,
julien-tierny
requested changes
Nov 24, 2023
atalon-lip6
force-pushed
the
topomap-clean
branch
from
b642dc3 to
b9a4fb5
Compare
atalon-lip6
force-pushed
the
topomap-clean
branch
5 times, most recently
from
5a9b502 to
a2ee32b
Compare
…ted by the object).
atalon-lip6
force-pushed
the
topomap-clean
branch
from
a2ee32b to
e62db22
Compare
|
alright, looks good. thanks! |
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Outdated suggestions cannot be applied.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 introduces the Topological Mapper (TopoMap) method for DimensionReduction. TopoMap projects high-dimension points into 2D by computing and using a Minimum Spanning Tree (MST) on the high dimension points. We project the points so as to preserve the costs of the eges of the spanning tree.
It can use either Boost or Qhull for building the MST, but for now some bugs have been reported in peticular cases with Boost. A fix has been identified, yet not merged into Boost::Geometry for now.
This method was studied in the following paper: "Topomap: A 0-dimensional homology preserving projection of high-dimensional data" by Harish Doraiswamy, Julien Tierny, Paulo J. S. Silva, Luis Gustavo Nonato, and Claudio Silva, in
Proc. of IEEE VIS 2020. IEEE Transactions on Visualization and Computer Graphics 27(2): 561-571, 2020.