[MRG] Add Swiss-Hole dataset and expand example #21482
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rth
reviewed
Oct 28, 2021
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Nice, thanks for the example update, the new figure looks great, for people lazy to click on the
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ogrisel
approved these changes
Oct 28, 2021
pujaltes
changed the title
ogrisel
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Oct 29, 2021
TomDLT
approved these changes
Nov 10, 2021
Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org>
Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org>
pull upstream from main to pass validation tests
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@TomDLT thanks for your detailed review. I've incorporated them to the PR. Let me know if there's anything else you need me to do. |
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Thanks @pujaltes ! |
glemaitre
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Nov 22, 2021
* added hole to swiss roll and expanded example * Fixed docstring for numpydoc validation * Changed error from original docstring. * Added test for swiss hole Codecov check was failing because there was no test for the addition of the swisshole. I simply expanded the original test to include it. * Formatting * Revert "Formatting" This reverts commit 727505b. * Revert "Added test for swiss hole" This reverts commit ae78864. * Added test for Swiss Hole * fixed test * added changelog * Set random state when creating the swiss roll in exampple. * Set random state when creating the swiss hole in exampple. * Changed test with reccommendation * Apply suggestions from code review of plots. Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org> * Apply grammar and naming suggestions from code review Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org> * Defined LLE and t-SNE acronyms at beginning * Linting Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org>
glemaitre
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Nov 29, 2021
* added hole to swiss roll and expanded example * Fixed docstring for numpydoc validation * Changed error from original docstring. * Added test for swiss hole Codecov check was failing because there was no test for the addition of the swisshole. I simply expanded the original test to include it. * Formatting * Revert "Formatting" This reverts commit 727505b. * Revert "Added test for swiss hole" This reverts commit ae78864. * Added test for Swiss Hole * fixed test * added changelog * Set random state when creating the swiss roll in exampple. * Set random state when creating the swiss hole in exampple. * Changed test with reccommendation * Apply suggestions from code review of plots. Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org> * Apply grammar and naming suggestions from code review Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org> * Defined LLE and t-SNE acronyms at beginning * Linting Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org>
samronsin
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Nov 30, 2021
* added hole to swiss roll and expanded example * Fixed docstring for numpydoc validation * Changed error from original docstring. * Added test for swiss hole Codecov check was failing because there was no test for the addition of the swisshole. I simply expanded the original test to include it. * Formatting * Revert "Formatting" This reverts commit 727505b. * Revert "Added test for swiss hole" This reverts commit ae78864. * Added test for Swiss Hole * fixed test * added changelog * Set random state when creating the swiss roll in exampple. * Set random state when creating the swiss hole in exampple. * Changed test with reccommendation * Apply suggestions from code review of plots. Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org> * Apply grammar and naming suggestions from code review Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org> * Defined LLE and t-SNE acronyms at beginning * Linting Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org>
mathijs02
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Dec 27, 2022
* added hole to swiss roll and expanded example * Fixed docstring for numpydoc validation * Changed error from original docstring. * Added test for swiss hole Codecov check was failing because there was no test for the addition of the swisshole. I simply expanded the original test to include it. * Formatting * Revert "Formatting" This reverts commit 727505b. * Revert "Added test for swiss hole" This reverts commit ae78864. * Added test for Swiss Hole * fixed test * added changelog * Set random state when creating the swiss roll in exampple. * Set random state when creating the swiss hole in exampple. * Changed test with reccommendation * Apply suggestions from code review of plots. Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org> * Apply grammar and naming suggestions from code review Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org> * Defined LLE and t-SNE acronyms at beginning * Linting Co-authored-by: Tom Dupré la Tour <tom.dupre-la-tour@m4x.org>
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Reference Issues/PRs
I had previously worked on this in #20950. As discussed with @ogrisel I also expanded and modernised the plot_swisroll example. However, after some errors by my part, I wasn't able to reconcile the conflicts with the main branch which is why I'm creating this new PR. I hope it doesn't seem spammy.
What does this implement/fix? Explain your changes.
This expands the swiss roll generator by adding the option to have a hole in the swiss roll. The swiss hole dataset appears in many articles (see [1] [2]) and is useful in studying the robustness of non-linear dimensionality reduction algorithms (NLDA) in preserving topological structures.
Furthermore, I expanded the plot_swissroll.py by adding a second part where I analyzed how NLDA's dealt with the hole. I also repreated all the analysis with t-sne to have a comparison to LLE.