Toc #394
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Toc #394
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Signed-off-by: ammedmar <anibal@medina-mardones.com>
Signed-off-by: ammedmar <anibal@medina-mardones.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
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Signed-off-by: ammedmar <ammedmar@gmail.com>
Signed-off-by: ammedmar <ammedmar@gmail.com>
wreise
reviewed
Apr 9, 2020
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Thanks!
I have two additional comments/questions:
- I see the same table of content (organisation/layout-wise) as the one currently online. I don't think this is the desired effect, is it?
- I have a problem with references. I didn't notice that, but already in docs for 0.2.0, the label appears as, f.ex.
[equation:bla]in the html. IMO, this should not be addressed (not explicitly, at least) in this PR, and a solution can be found by milking pandoc a bit better.
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| \paragraph{\\ References:} \cite{chazal2014stochastic} | ||
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| \subsection*{Heat vectorizations} \label{heat_vectorization} |
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Similarly to some other descriptions of representations, we do not say what really is the vector representation ("the coordinate i,j is equal to... ") - we only say more or less what it corresponds to.
For heat kernel, it's how it's done in the paper as well, i think (since you compute pairwise-evaluations).
In persistence images, a pixel is the integral of the smooth surface, as in Def.2.
While i am not saying that it is important to mention the distinction (especially since we do not call it persistence image anyway atm), just pointing out there is one.
What do you think?
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I think that if we write a persistence image entry we could explain this. How to go from vectorization into an infinite dimensional space into R^n. I.e. Persistence images are a composition of the symmetric vectorization and an average discreteization.
Signed-off-by: ammedmar <ammedmar@gmail.com>
ulupo
suggested changes
Apr 14, 2020
Signed-off-by: ammedmar <ammedmar@gmail.com>
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Signed-off-by: ammedmar <ammedmar@gmail.com>
ulupo
suggested changes
Apr 14, 2020
ulupo
suggested changes
Apr 14, 2020
Signed-off-by: ammedmar <ammedmar@gmail.com>
ulupo
suggested changes
Apr 14, 2020
Signed-off-by: ammedmar <ammedmar@gmail.com>
ulupo
approved these changes
Apr 17, 2020
ulupo
reviewed
Apr 17, 2020
| \end{align} | ||
| where $\Omega = \{(x_1, x_2) \in \mathbb R^2\ |\ x_1 \leq x_2\}$, then solving the same equation after precomposing the data of \eqref{equation: heat equation} with the change of coordinates $(x_1, x_2) \mapsto (x_2, x_1)$, and defining the image of $D$ to be the difference between these two solutions at the chosen time $t$. | ||
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| Similarly, the \textit{rotation heat vectorization} is defined by sending $D$ to the solution, evaluated at time $t$, of the equation obtained by precomposing the data of \eqref{equation: heat equation} with the change of coordinates $(x_1, x_2) \mapsto (x_1, x_2-x_1)$. |
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I note that there is a tension here between using "persistence image" in the library, and "rotation heat vectorization" here. Not asking for a change here as it is beyond the scope for this PR.
ulupo
reviewed
Apr 17, 2020
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| Considering the points in a persistence diagram as the support of Dirac deltas one can construct, for any $t > 0$, | ||
| %\hyperref[vectorization_amplitude_and_kernel]{vectorization} | ||
| two vectorizations of the set of persistence diagrams to the set of continuous real-valued function on the first quadrant $\mathbb{R}^2_{>0}$. The \textit{symmetry heat vectorization} is constructed for every persistence diagram $D$ by solving the heat equation |
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I thought we had settled for "antisymmetric" over "symmetric" in #348 (comment). Maybe that discussion got superseded?
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* Fix issue with docstring example and document reshaping of 1D outputs (#396) * Toc (#394) * Update P landscapes Signed-off-by: ammedmar <anibal@medina-mardones.com> * Add distances, inner products and kernels glossary entry Signed-off-by: ammedmar <anibal@medina-mardones.com> * Remake vectorization changes Signed-off-by: ammedmar <ammedmar@gmail.com> * Change [] for \lbrack \rbrack Signed-off-by: ammedmar <ammedmar@gmail.com> * Update after W's comments Signed-off-by: ammedmar <ammedmar@gmail.com> * Update after W's comments Signed-off-by: ammedmar <ammedmar@gmail.com> * Update afte W's second comments Signed-off-by: ammedmar <ammedmar@gmail.com> * Update after Umbe's comments Signed-off-by: ammedmar <ammedmar@gmail.com> * Update after Umbe's second comments Signed-off-by: ammedmar <ammedmar@gmail.com> * Update after Umbe's third comments Signed-off-by: ammedmar <ammedmar@gmail.com> * Update after Umbe's 4th comments Signed-off-by: ammedmar <ammedmar@gmail.com> * Remove concept k-skeleton Signed-off-by: ammedmar <ammedmar@gmail.com> * Add table of content Signed-off-by: ammedmar <ammedmar@gmail.com> * Add Lp & lp. Update landscape Signed-off-by: ammedmar <ammedmar@gmail.com> * Update TOC indentation Signed-off-by: ammedmar <ammedmar@gmail.com> * Add heat vectorizations entry Signed-off-by: ammedmar <ammedmar@gmail.com> * Update indentation of TOC Signed-off-by: ammedmar <ammedmar@gmail.com> * Fix extra spacing in bibliography Signed-off-by: ammedmar <ammedmar@gmail.com> * Update bibliography hack for caps Signed-off-by: ammedmar <ammedmar@gmail.com> * After Umbe's Comments Signed-off-by: ammedmar <ammedmar@gmail.com> * Update after issue #398 Signed-off-by: ammedmar <ammedmar@gmail.com> * Update after Umbe's comments Signed-off-by: ammedmar <ammedmar@gmail.com> * Update after Umbe's 2nd comments Signed-off-by: ammedmar <ammedmar@gmail.com> Co-authored-by: ammedmar <anibal@medina-mardones.com> * Speedup windows pipeline (#402) * Improve boost location for azure pipeline on windows The boost version installed in the pipeline is now used Signed-off-by: julian <julian.burellaperez@heig-vd.ch> Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com> * Make bindings public (#395) * Make bindings public Signed-off-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com> * Fix pipeline on Mac (#407) * Refresh ccache * Enforce CXX standard to 14 on each module * Change variable name to comply with E741 Signed-off-by: julian <julian.burellaperez@heig-vd.ch> Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com> * Mapper visualisation refactor: fix bugs, add summary statistics in hovertext, improve opacity, remove matplotlib dependency, add node_scale kwarg, add clone_pipeline kwarg to interactive plots,restructure/rename plotly_kwargs, improve code (#406) * Refactor of `mapper/visualisation.py` and `mapper/utils/visualisation.py` - Removal of color scaling - More modularity - Variable and function name changes - Remove matplotlib functions used for hoverlabel background color - Remove cmin and cmax - Change return signature of some functions * Add test-output.xml to .gitignore * Replace "text" key in plot_options["node_trace"] with "hovertext" * Improve width and opacity of nodes and edges * Display summary statistics in hovertext with significant figure rounding via new n_sig_figs kwarg * Rename plotly_kwargs to plotly_params * Remove matplotlib installation requirement * Fix mapper notebook * Add small comment on use of matplotlib in voids_on_the_plane * Place matplotlib in examples requirement in setup.py * Improve docstring of make_mapper_pipeline * Improve examples for make_mapper_pipeline and create one for plot_static_mapper_graph * Hide set_node_sizeref, add node_scale kwarg, add clone_pipeline kwarg to plot_interactive_mapper_graph - Update docstrings - Update quickstart notebook * Add helper function for colorscale-based interpolations, improve use of plotly_params Static and interactive plots display the expect hoverlabel colors in 3D, or white if things go wrong. Thanks to @lewtun for pointing out that this was needed. * Improve docstrings * Hide visualization module in mapper/utils * Add pip install matplotlib to notebook tests in manylinux job (#410) * Fix mapper docstring issues following #406 (#411) * Fix issues with mapper docs following #406 * Create giotto-tda version 0.2.2 (#413) * Turn CODE_OWNERS and CODE_AUTHORS into an rst file * Bump version number to 0.2.2 * Add release notes for v0.2.2 Co-authored-by: Anibal M. Medina-Mardones <ammedmar@gmail.com> Co-authored-by: ammedmar <anibal@medina-mardones.com> Co-authored-by: REDS institute <reds-heig@users.noreply.github.com> Co-authored-by: Guillaume Tauzin <guillaumetauzin.ut@gmail.com>
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Reference issues/PRs
Fixes #356 and #398 . See also #343 and following the discussion in #348
Description
After including a Table of content and restructuring the document by including an section titled "Analysis". We add lp norm, Lp norm and heat vectorization entries.