Online quantization algorithm for gudhi by tlacombe · Pull Request #536 · GUDHI/gudhi-devel

tlacombe · 2021-10-15T10:15:52Z

Provide a quantization algorithm to "summarize" a collection of persistence diagrams.

(At least) One thing that may be discussed :

I put the code in the python/gudhi/wasserstein/ repo, because it is of a "Wasserstein metric" flavor (we minimize something in terms of Wasserstein distance between persistence diagrams). However, it does not rely on POT as other functions in this repo do ; we actually never need to explicitly compute a Wasserstein distance/matching explicitly. Perhaps would it belong directly to the gudhi/ repo ?

Also TODO :

Check for quantization.py : is the copyright correct?

src/python/doc/wasserstein_distance_user.rst

biblio/bibliography.bib

src/python/doc/wasserstein_distance_user.rst

src/python/gudhi/wasserstein/quantization.py

src/python/doc/wasserstein_distance_user.rst

Co-authored-by: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>

…evel into quantization_v2

tlacombe · 2021-12-01T10:56:06Z

Corrected.
Any thought on if this code belong to the /wasserstein module? From a theoretical perspective, the goal is to solve some minimization with respect to the Wasserstein distance between persistence diagrams (so it makes sense to put it there), but from a practical perspective (code), it does not rely on pot contrarily to other functions in the /wasserstein module (because we can solve our optimization problem without explicitly computing such distances/matchings).
My feeling is that it can stay there, doing gudhi.wasserstein.quantization makes clear that we are quantizing something with respect to the Wasserstein distance ; but I am open to discussion of course.

mglisse

I guess keeping it in wasserstein/ is ok.

src/python/doc/wasserstein_distance_user.rst

mglisse · 2022-01-15T12:13:53Z

src/python/doc/wasserstein_distance_user.rst

+different tori with some additional noise.
+Starting from an initial codebook ``c0``, centroids are iteratively updated as new diagrams are provided.
+As we use the standard metrics between persistence diagrams (denoted here by :math:`\mathrm{OT}_2`), points in the
+diagrams that are close to the diagonal do not interfere in the codebook update process.


So it is the same as having an implicit point on the diagonal in the codebook?

More precisely, having a point in the codebook that represents "all the points on the diagonal" (or, formally, looking at the quotient space where you identify the points on the diagonal).

src/python/doc/wasserstein_distance_user.rst

src/python/gudhi/wasserstein/quantization.py

Co-authored-by: Marc Glisse <marc.glisse@inria.fr>

tlacombe · 2022-05-18T09:18:20Z

I just realized that I never managed to do the last requested modifications (my local build was broken for some reason at that time).
I finally did it.
As I'm working on a new machine, I hope I managed correctly the fork/branching/etc.

PS : and one day later I realize that I forgot to post this comment... 😴

mglisse

The algorithm is presented as on online algorithm. So it should be normal to give it some data, look at the codebook at that point, pass it more data, look at the updated codebook, etc. The init parameter could be used towards that goal, but the number of diagrams (or batches) already processed is forgotten, and indeed t (the learning rate) is reset to 0 at every call.

mglisse · 2022-06-20T19:17:10Z

src/python/doc/wasserstein_distance_user.rst

+(the two loops generating the tori).
+
+.. figure::
+     ./img/quantiz.gif


On the one hand, the GIF is cool. On the other hand, I have trouble reading the doc with that thing moving on my screen...

mglisse · 2022-06-20T19:30:09Z

src/python/gudhi/wasserstein/quantization.py

+    if withdiag:
+        a = np.argmin(M[:-1, :], axis=1)
+    else:
+        a = np.argmin(M[:-1, :-1], axis=1)


It feels a bit strange to call _build_dist_matrix, whose main difference with cdist is that it adds the diagonal, just to drop the diagonal immediately... But I don't think it really matters.

mglisse · 2022-06-20T19:32:12Z

src/python/gudhi/wasserstein/quantization.py

+        X_batch = np.concatenate(list_of_non_empty_diags)
+        return X_batch
+    else:
+        return np.array([])


It is sometimes useful to force the shape of empty arrays, to (0,2) for instance. I don't know if that's the case here.

mglisse · 2022-06-20T19:34:40Z

src/python/gudhi/wasserstein/quantization.py

+    :param internal_p: Ground metric to assess centroid affectation. Default is ``2.``.
+    :type internal_p: ``float``
+
+    :returns: The final codebook obtained after going through the all pdiagset.


:rtype: kx2 numpy array?

mglisse · 2022-06-20T19:36:12Z

src/python/gudhi/wasserstein/quantization.py

+
+def _init_c(pdiagset, k, internal_p=2):
+    """
+    A naive heuristic to initialize a codebook: we take the k points with largest distances to the diagonal


What if the first diagram has fewer than k points?

mglisse · 2022-06-20T19:40:25Z

src/python/gudhi/wasserstein/quantization.py

+    :param batch_size: Size of batches used during the online exploration of the ``pdiagset``.
+                        Default is ``1``.


As a user, should I stick to the default value of 1? If I already have all the diagrams, I may think that I don't need an online algorithm, which is for when data appears progressively, and consider using one huge batch under the impression that it disables the "online" stuff and gets the best result.

mglisse · 2022-06-20T19:48:18Z

src/python/gudhi/wasserstein/quantization.py

+                    # stochastic-gradient-descent like approach (decreasing learning rate).
+                    c_current[j] = c_current[j] - grad / (t + 1)
+        else:
+            raise NotImplemented('Order = %s is not available yet. Only order=2. is valid' %order)


I think you could error out earlier (or not provide this option at all and just say that it is W2).

tlacombe added 2 commits October 15, 2021 11:59

online quantization algorithm for gudhi

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added header to quantization.py with Université Gustave Eiffel copyright

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tlacombe and others added 7 commits November 10, 2021 16:26

Update biblio/bibliography.bib

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Co-authored-by: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>

Update src/python/gudhi/wasserstein/quantization.py

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Co-authored-by: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>

Adding "Since GUDHI 3.5" in the file.

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Co-authored-by: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>

Merge remote-tracking branch 'upstream/master' into quantization_v2

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updated wasserstein/__init__.py

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Merge branch 'quantization_v2' of https://github.com/tlacombe/gudhi-d…

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…evel into quantization_v2

changed tutorials : one tutorial per section, at the end of the section

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updated date in copyright

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mglisse reviewed Jan 15, 2022

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tlacombe and others added 8 commits January 16, 2022 22:48

Update src/python/doc/wasserstein_distance_user.rst

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Co-authored-by: Marc Glisse <marc.glisse@inria.fr>

Update src/python/doc/wasserstein_distance_user.rst

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Co-authored-by: Marc Glisse <marc.glisse@inria.fr>

added _utils.py file in gudhi/wasserstein with some global functions.

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changed standard distances to Wasserstein distances

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refactor following the creation of _utils.py

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update quantization including final remarks...

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changed how funcs from _utils are imported.

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changed how funcs from _utils are imported bis.

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mglisse reviewed Jun 20, 2022

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mglisse marked this pull request as draft July 8, 2023 19:08

		:param batch_size: Size of batches used during the online exploration of the ``pdiagset``.
		Default is ``1``.

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