multipers
multipers: Multiparameter Persistence for Machine Learning - Published in JOSS (2024)
Science Score: 100.0%
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Published in Journal of Open Source Software
Keywords
Scientific Fields
Repository
Python library for multipersistence
Basic Info
- Host: GitHub
- Owner: DavidLapous
- License: mit
- Language: C++
- Default Branch: main
- Homepage: https://davidlapous.github.io/multipers/
- Size: 59.7 MB
Statistics
- Stars: 31
- Watchers: 1
- Forks: 7
- Open Issues: 12
- Releases: 21
Topics
Metadata Files
README.md
multipers : Multiparameter Persistence for Machine Learning
Scikit-style PyTorch-autodiff multiparameter persistent homology python library.
This library aims to provide easy to use and performant strategies for applied multiparameter topology.
Meant to be integrated in the Gudhi library.
Compiled packages
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Quick start
This library allows computing several representations from "geometrical datasets", e.g., point clouds, images, graphs, that have multiple scales. We provide some nice pictures in the documentation. A non-exhaustive list of features can be found in the Features section.
This library is available on pip and conda-forge for (reasonably up to date) Linux, macOS and Windows, via
sh
pip install multipers
or
sh
conda install multipers -c conda-forge
Pre-releases are available via
sh
pip install --pre multipers
These release usually contain small bugfixes or unstable new features.
Windows support is experimental, and some core dependencies are not available on Windows.
We hence recommend Windows user to use WSL.
A documentation and building instructions are available
here.
Features, and linked projects
This library features a bunch of different functions and helpers. See below for a non-exhaustive list.
Filled box refers to implemented or interfaced code.
- [x] [Multiparameter Module Approximation] provides the multiparameter simplicial structure, as well as technics for approximating modules, via interval-decomposable modules. It is also very useful for visualization.
- [x] [Stable Vectorization of Multiparameter Persistent Homology using Signed Barcodes as Measures, NeurIPS2023] provides fast representations of multiparameter persistence modules, by using their signed barcodes decompositions encoded into signed measures. Implemented decompositions : Euler surfaces, Hilbert function, rank invariant (i.e. rectangles). It also provides representation technics for Machine Learning, i.e., Sliced Wasserstein kernels, and Vectorizations.
- [x] [A Framework for Fast and Stable Representations of Multiparameter Persistent Homology Decompositions, NeurIPS2023] Provides a vectorization framework for interval decomposable modules, for Machine Learning. Currently implemented as an extension of MMA.
- [x] [Differentiability and Optimization of Multiparameter Persistent Homology, ICML2024] An approach to compute a (clarke) gradient for any reasonable multiparameter persistent invariant. Currently, any multipers computation is auto-differentiable using this strategy, provided that the input are pytorch gradient capable tensor.
- [x] [Multiparameter Persistence Landscapes, JMLR] A vectorization technic for multiparameter persistence modules.
- [x] [Filtration-Domination in Bifiltered Graphs, ALENEX2023] Allows for 2-parameter edge collapses for 1-critical clique complexes. Very useful to speed up, e.g., Rips-Codensity bifiltrations.
- [x] [Chunk Reduction for Multi-Parameter Persistent Homology, SOCG2019] Multi-filtration preprocessing algorithm for homology computations.
- [x] [Computing Minimal Presentations and Bigraded Betti Numbers of 2-Parameter Persistent Homology, JAAG] Minimal presentation of multiparameter persistence modules, using mpfree. Hilbert, Rank Decomposition Signed Measures, and MMA decompositions can be computed using the mpfree backend.
- [x] [Delaunay Bifiltrations of Functions on Point Clouds, SODA2024] Provides an alternative to function rips bifiltrations, using Delaunay complexes. Very good alternative to Rips-Density like bifiltrations.
- [x] [Delaunay Core Bifiltration] Bifiltration for point clouds, taking into account the density. Similar to Rips-Density.
- [x] [Rivet] Interactive two parameter persistence
- [x] [Kernel Operations on the GPU, with Autodiff, without Memory Overflows, JMLR] Although not linked, at first glance, to persistence in any way, this library allows computing blazingly fast signed measures convolutions (and more!) with custom kernels.
- [ ] [Backend only] [Projected distances for multi-parameter persistence modules] Provides a strategy to estimate the convolution distance between multiparameter persistence module using projected barcodes. Implementation is a WIP.
- [ ] [Partial, and experimental] [Efficient Two-Parameter Persistence Computation via Cohomology, SoCG2023] Minimal presentations for 2-parameter persistence algorithm.
If I missed something, or you want to add something, feel free to open an issue.
Authors
David Loiseaux,
Hannah Schreiber (Persistence backend code),
Luis Scoccola
(Möbius inversion in python, degree-rips using persistable and RIVET),
Mathieu Carrière (Sliced Wasserstein),
Odin Hoff Gardå (Delaunay Core bifiltration).
Citation
Please cite this library when using it in scientific publications;
you can use the following journal bibtex entry
bib
@article{multipers,
title = {Multipers: {{Multiparameter Persistence}} for {{Machine Learning}}},
shorttitle = {Multipers},
author = {Loiseaux, David and Schreiber, Hannah},
year = {2024},
month = nov,
journal = {Journal of Open Source Software},
volume = {9},
number = {103},
pages = {6773},
issn = {2475-9066},
doi = {10.21105/joss.06773},
langid = {english},
}
Contributions
Feel free to contribute, report a bug on a pipeline, or ask for documentation by opening an issue.
In particular, if you have a nice example or application that is not taken care in the documentation (see the ./docs/notebooks/ folder), please contact me to add it there.
Owner
- Name: David Loiseaux
- Login: DavidLapous
- Kind: user
- Company: Inria Sophia Antipolis
- Website: https://www-sop.inria.fr/members/David.Loiseaux/
- Repositories: 3
- Profile: https://github.com/DavidLapous
JOSS Publication
multipers: Multiparameter Persistence for Machine Learning
Authors
Centre Inria d'Université Côte d'Azur, France
Centre Inria d'Université Côte d'Azur, France
Editor
Rocco Meli
Tags
machine learning topological data analysisCitation (CITATION.cff)
cff-version: "1.2.0"
authors:
- family-names: Loiseaux
given-names: David
- family-names: Schreiber
given-names: Hannah
doi: 10.5281/zenodo.14042221
message: If you use this software, please cite our article in the
Journal of Open Source Software.
preferred-citation:
authors:
- family-names: Loiseaux
given-names: David
- family-names: Schreiber
given-names: Hannah
date-published: 2024-11-13
doi: 10.21105/joss.06773
issn: 2475-9066
issue: 103
journal: Journal of Open Source Software
publisher:
name: Open Journals
start: 6773
title: "multipers: Multiparameter Persistence for Machine Learning"
type: article
url: "https://joss.theoj.org/papers/10.21105/joss.06773"
volume: 9
title: "multipers: Multiparameter Persistence for Machine Learning"
GitHub Events
Total
- Create event: 8
- Commit comment event: 1
- Issues event: 13
- Release event: 6
- Watch event: 19
- Issue comment event: 25
- Push event: 274
- Pull request review comment event: 5
- Pull request review event: 18
- Pull request event: 15
- Fork event: 4
Last Year
- Create event: 8
- Commit comment event: 1
- Issues event: 13
- Release event: 6
- Watch event: 19
- Issue comment event: 25
- Push event: 274
- Pull request review comment event: 5
- Pull request review event: 18
- Pull request event: 15
- Fork event: 4
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| David Loiseaux | d****x@i****r | 802 |
| hschreiber | h****k@g****m | 26 |
| Odin Hoff Gardå | o****a@p****e | 25 |
| Vincent Rouvreau | v****u@i****r | 2 |
| Rocco Meli | r****i@b****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 28
- Total pull requests: 26
- Average time to close issues: 8 months
- Average time to close pull requests: 1 day
- Total issue authors: 8
- Total pull request authors: 5
- Average comments per issue: 0.61
- Average comments per pull request: 1.23
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 15
- Pull requests: 26
- Average time to close issues: about 1 month
- Average time to close pull requests: 1 day
- Issue authors: 6
- Pull request authors: 5
- Average comments per issue: 1.07
- Average comments per pull request: 1.23
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- DavidLapous (19)
- peekxc (3)
- lar-sal (1)
- hailuu684 (1)
- yossibokorbleile (1)
- jmou19 (1)
- EnricoMariaFerrari (1)
- odinhg (1)
Pull Request Authors
- hschreiber (19)
- VincentRouvreau (2)
- odinhg (2)
- RMeli (2)
- Copilot (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 3,630 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 37
- Total maintainers: 1
pypi.org: multipers
Multiparameter Topological Persistence for Machine Learning
- Documentation: https://multipers.readthedocs.io/
- License: mit
-
Latest release: 2.3.4
published 5 months ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v4 composite
- actions/download-artifact v3 composite
- actions/setup-python v4 composite
- actions/upload-artifact v3 composite
- boost
- boost-cpp
- cgal-cpp
- cmake
- cxx-compiler
- cycler
- cython
- gudhi
- joblib
- llvm-openmp
- matplotlib
- mdanalysis
- networkx
- numpy
- pandas
- plotly
- pot
- pybind11
- pytest
- python
- pytorch
- scikit-learn
- scipy
- setuptools
- shapely
- sympy
- tbb
- tbb-devel
- tqdm
- typing