multipers 2.4.0b1__cp312-cp312-macosx_11_0_arm64.whl

multipers/vector_interface.pxd

@@ -0,0 +1,46 @@
+
+from libcpp.utility cimport pair
+from libc.stdint cimport intptr_t, uint16_t, uint32_t, int32_t, int64_t
+from libcpp.vector cimport vector
+from libcpp cimport bool, float
+
+cdef extern from "config.hpp":
+  cdef cppclass aida_config "aida::AIDA_config":
+    bool sort 
+    bool exhaustive 
+    bool brute_force 
+    bool sort_output 
+    bool compare_both 
+    bool exhaustive_test 
+    bool progress 
+    bool save_base_change 
+    bool turn_off_hom_optimisation 
+    bool show_info 
+    bool compare_hom 
+    bool supress_col_sweep 
+    bool alpha_hom 
+
+
+cdef extern from "aida_interface.hpp":
+
+  cdef cppclass multipers_interface_input "aida::multipers_interface_input<int>":
+    multipers_interface_input(const vector[pair[double,double]]&, const vector[pair[double,double]]&, const vector[vector[int]]&) except + nogil
+    multipers_interface_input() except + nogil
+    vector[pair[double,double]] col_degrees
+    vector[pair[double,double]] row_degrees
+    vector[vector[int]] matrix
+
+  cdef cppclass multipers_interface_output "aida::multipers_interface_output<int>":
+    multipers_interface_output() except + nogil
+    vector[multipers_interface_input] summands
+    # vector[pair[double,double]] col_degrees
+    # vector[pair[double,double]] row_degrees
+    # vector[vector[int]] matrix
+
+  cdef cppclass AIDA_functor "aida::AIDA_functor":
+    AIDA_functor() except + nogil
+    multipers_interface_output multipers_interface(multipers_interface_input&) except + nogil
+    aida_config config
+
+
+

multipers-2.4.0b1.dist-info/METADATA

@@ -0,0 +1,131 @@
+Metadata-Version: 2.4
+Name: multipers
+Version: 2.4.0b1
+Summary: Multiparameter Topological Persistence for Machine Learning
+Author-email: David Loiseaux <david.lapous@proton.me>, Hannah Schreiber <hannah.schreiber@inria.fr>
+Maintainer-email: David Loiseaux <david.lapous@proton.me>
+License-Expression: MIT
+Project-URL: source, https://github.com/DavidLapous/multipers
+Project-URL: download, https://pypi.org/project/multipers/#files
+Project-URL: tracker, https://github.com/DavidLapous/multipers/issues
+Project-URL: release notes, https://github.com/DavidLapous/multipers/releases
+Keywords: TDA,Persistence,Multiparameter,sklearn,autodiff
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: gudhi>=3.8
+Requires-Dist: tqdm
+Requires-Dist: scipy
+Requires-Dist: joblib
+Requires-Dist: matplotlib
+Requires-Dist: scikit-learn
+Requires-Dist: filtration-domination
+Requires-Dist: pykeops
+Requires-Dist: pot
+Dynamic: license-file
+
+# multipers : Multiparameter Persistence for Machine Learning
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06773/status.svg)](https://doi.org/10.21105/joss.06773) [![Documentation](https://img.shields.io/badge/Documentation-website-blue)](https://davidlapous.github.io/multipers) [![Build, test](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml/badge.svg)](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml)
+<br>
+Scikit-style PyTorch-autodiff multiparameter persistent homology python library. 
+This library aims to provide easy to use and performant strategies for applied multiparameter topology.
+<br> Meant to be integrated in the [Gudhi](https://gudhi.inria.fr/) library.
+
+## Compiled packages
+| Source | Version | Downloads | Platforms | 
+| --- | --- | --- | --- | 
+| [![Conda Recipe](https://img.shields.io/badge/conda-recipe-green.svg)](https://github.com/conda-forge/multipers-feedstock)| [![Conda Version](https://img.shields.io/conda/vn/conda-forge/multipers.svg)](https://anaconda.org/conda-forge/multipers) |  [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/multipers.svg)](https://anaconda.org/conda-forge/multipers) |[![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/multipers.svg)](https://anaconda.org/conda-forge/multipers) | 
+| [![pip Recipe](https://img.shields.io/badge/pip-package-green.svg)](https:///pypi.org/project/multipers) | [![PyPI](https://img.shields.io/pypi/v/multipers?color=green)](https://pypi.org/project/multipers) | [![ pip downloads](https://static.pepy.tech/badge/multipers)](https://pepy.tech/project/multipers) | | 
+
+
+
+## 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](https://davidlapous.github.io/multipers/index.html). 
+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](https://learn.microsoft.com/en-us/windows/wsl/).
+<br>
+A documentation and building instructions are available
+[here](https://davidlapous.github.io/multipers/compilation.html).
+
+
+## Features, and linked projects
+This library features a bunch of different functions and helpers. See below for a non-exhaustive list.
+<br>Filled box refers to implemented or interfaced code.
+ - [x] [[Multiparameter Module Approximation, JACT]](https://doi.org/10.1007/s41468-025-00222-y) 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]](https://proceedings.neurips.cc/paper_files/paper/2023/hash/d75c474bc01735929a1fab5d0de3b189-Abstract-Conference.html) 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]](https://proceedings.neurips.cc/paper_files/paper/2023/hash/702b67152ec4435795f681865b67999c-Abstract-Conference.html) 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]](https://proceedings.mlr.press/v235/scoccola24a.html) 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]](https://jmlr.org/papers/v21/19-054.html) A vectorization technic for multiparameter persistence modules.
+ - [x] [[Filtration-Domination in Bifiltered Graphs, ALENEX2023]](https://doi.org/10.1137/1.9781611977561.ch3) 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]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
+ - [x] [[Computing Minimal Presentations and Bigraded Betti Numbers of 2-Parameter Persistent Homology, JAAG]](https://doi.org/10.1137/20M1388425) Minimal presentation of multiparameter persistence modules, using [mpfree](https://bitbucket.org/mkerber/mpfree/src/master/). Hilbert, Rank Decomposition Signed Measures, and MMA decompositions can be computed using the mpfree backend.
+ - [ ] [WIP] [[Decomposing Multiparameter Persistence Modules, SoCG2025]](https://doi.org/10.4230/LIPIcs.SoCG.2025.41) Using the [AIDA](https://github.com/JanJend/AIDA) and [Persistence-Algebra](https://github.com/JanJend/Persistence-Algebra/) libraries.
+ - [x] [[Delaunay Bifiltrations of Functions on Point Clouds, SODA2024]](https://epubs.siam.org/doi/10.1137/1.9781611977912.173) Provides an alternative to function rips bifiltrations, using Delaunay complexes. Very good alternative to Rips-Density like bifiltrations.
+ - [x] [[Delaunay Core Bifiltration]](https://arxiv.org/abs/2405.01214) Bifiltration for point clouds, taking into account the density. Similar to Rips-Density. 
+ - [x] [[Rivet]](https://github.com/rivetTDA/rivet) Interactive two parameter persistence
+ - [x] [[Kernel Operations on the GPU, with Autodiff, without Memory Overflows, JMLR]](http://jmlr.org/papers/v22/20-275.html) 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]](https://arxiv.org/abs/2206.08818) 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]](https://doi.org/10.4230/LIPIcs.SoCG.2023.15) 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](https://davidlapous.github.io/),<br>
+[Hannah Schreiber](https://github.com/hschreiber) (Persistence backend code),<br>
+[Luis Scoccola](https://luisscoccola.com/) 
+(Möbius inversion in python, degree-rips using [persistable](https://github.com/LuisScoccola/persistable) and [RIVET](https://github.com/rivetTDA/rivet/)),<br>
+[Mathieu Carrière](https://www-sop.inria.fr/members/Mathieu.Carriere/) (Sliced Wasserstein),<br>
+[Odin Hoff Gardå](https://odinhg.github.io/) (Delaunay Core bifiltration).<br>
+Jan Jendrysiak (Module Decomposition).<br>
+
+## 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.<br>
+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.

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multipers-2.4.0b1.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2023 David Loiseaux
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

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