multipers 2.2.0__tar.gz → 2.2.1__tar.gz

{multipers-2.2.0/multipers.egg-info → multipers-2.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: multipers
-Version: 2.2.0
+Version: 2.2.1
 Summary: Multiparameter Topological Persistence for Machine Learning
 Author: Hannah Schreiber
 Author-email: David Loiseaux <david.lapous@proton.me>
@@ -46,7 +46,7 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: gudhi
+Requires-Dist: gudhi>=3.8
 Requires-Dist: tqdm
 Requires-Dist: scipy
 Requires-Dist: joblib
@@ -60,14 +60,14 @@ Requires-Dist: pot
 [![Build, test](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml/badge.svg)](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml)
 [![PyPI](https://img.shields.io/pypi/v/multipers?color=green)](https://pypi.org/project/multipers)
 [![Downloads](https://static.pepy.tech/badge/multipers)](https://pepy.tech/project/multipers)
-[Documentation](https://www-sop.inria.fr/members/David.Loiseaux/doc/multipers/index.html)
+[Documentation](https://davidlapous.github.io/multipers/index.html)
 <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 library](https://gudhi.inria.fr/).
 
 ## Multiparameter Persistence
-This library allows to compute several representation from "geometrical datasets", e.g., point clouds, images, graphs, that have multiple scales. A well known example is is the following one. 
+This library allows computing several representations from "geometrical datasets", e.g., point clouds, images, graphs, that have multiple scales. A well known example is the following one. 
 <br>
 Pick a point cloud that has diffuse noise, or on which the sampling measure has some interesting properties, e.g., in the following example the measure has three modes.
 <br>
@@ -76,13 +76,13 @@ This filtration $X$, indexed over a radius parameter $r$ and a codensity paramet
 
 $$ X_{r,s} = \bigcup_{x \in P, \, \mathrm{density}(x) \ge s} B(x,r) = \lbrace x\in \mathbb R^2 \mid \exists p \in P, \, \mathrm{density}(p) \ge s \text{ and } d(x,p) \le r \rbrace$$
 
-The green shape on the left represent the lifetime of the biggest annulus. On the right, each cycle appearing on the left gets a colored shape (the color is only a label) and the shape of this colored shape represents the lifetime of this cycle.
+The green shape on the left represents the lifetime of the biggest annulus. On the right, each cycle appearing on the left gets a colored shape (the color is only a label) and the shape of this colored shape represents the lifetime of this cycle.
 <br>
 In our case, the big green shape on the left corresponds to the largest green shape appearing on the right, recovering the structure of the annulus here.
 ![Alt text](docs/1.png)
 
 The **magic** part is that we never had to choose any parameter to remove the noise in this construction, but the annulus still naturally appears!
-<br>A more strinking example is the following one.
+<br>A more striking example is the following one.
 Using the same constructions, we can identify topological structure, and their size, in a parameter free approach, even though the majority of the sampling measure's mass is noise.
 <br> In this example, the lifetime shape associated to each cycle can be identified from 
  - Their radius : the smaller cycle will naturally live more this shape will appear on the "left" (smaller radius)
@@ -94,7 +94,7 @@ We also provide several other descriptors, as well as associated Machine Learnin
 ![alt text](docs/3.png)
 
 
-A non-exhaustive list of features can be found in the **Features** section, and in the [documentation](https://www-sop.inria.fr/members/David.Loiseaux/doc/multipers/index.html).
+A non-exhaustive list of features can be found in the **Features** section, and in the [documentation](https://davidlapous.github.io/multipers/index.html).
 ## Quick start
 
 
@@ -104,7 +104,7 @@ pip install multipers
 ```
 We recommend Windows user to use [WSL](https://learn.microsoft.com/en-us/windows/wsl/). 
 <br>
-A documentation and building instructions are available [here](https://www-sop.inria.fr/members/David.Loiseaux/doc/multipers/index.html).
+A documentation and building instructions are available [here](https://davidlapous.github.io/multipers/contributions.html).
 
 ## Features, and linked projects
 This library features a bunch of different functions and helpers. See below for a non-exhaustive list.
@@ -115,11 +115,11 @@ This library features a bunch of different functions and helpers. See below for
  - [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, SOCG20219]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
+ - [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.
- - [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 bi-filtrations.
+ - [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] [[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 to compute blazingly fast signed measures  convolutions (and more!) with custom kernels. 
+ - [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.
 

{multipers-2.2.0 → multipers-2.2.1}/README.md

@@ -2,14 +2,14 @@
 [![Build, test](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml/badge.svg)](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml)
 [![PyPI](https://img.shields.io/pypi/v/multipers?color=green)](https://pypi.org/project/multipers)
 [![Downloads](https://static.pepy.tech/badge/multipers)](https://pepy.tech/project/multipers)
-[Documentation](https://www-sop.inria.fr/members/David.Loiseaux/doc/multipers/index.html)
+[Documentation](https://davidlapous.github.io/multipers/index.html)
 <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 library](https://gudhi.inria.fr/).
 
 ## Multiparameter Persistence
-This library allows to compute several representation from "geometrical datasets", e.g., point clouds, images, graphs, that have multiple scales. A well known example is is the following one. 
+This library allows computing several representations from "geometrical datasets", e.g., point clouds, images, graphs, that have multiple scales. A well known example is the following one. 
 <br>
 Pick a point cloud that has diffuse noise, or on which the sampling measure has some interesting properties, e.g., in the following example the measure has three modes.
 <br>
@@ -18,13 +18,13 @@ This filtration $X$, indexed over a radius parameter $r$ and a codensity paramet
 
 $$ X_{r,s} = \bigcup_{x \in P, \, \mathrm{density}(x) \ge s} B(x,r) = \lbrace x\in \mathbb R^2 \mid \exists p \in P, \, \mathrm{density}(p) \ge s \text{ and } d(x,p) \le r \rbrace$$
 
-The green shape on the left represent the lifetime of the biggest annulus. On the right, each cycle appearing on the left gets a colored shape (the color is only a label) and the shape of this colored shape represents the lifetime of this cycle.
+The green shape on the left represents the lifetime of the biggest annulus. On the right, each cycle appearing on the left gets a colored shape (the color is only a label) and the shape of this colored shape represents the lifetime of this cycle.
 <br>
 In our case, the big green shape on the left corresponds to the largest green shape appearing on the right, recovering the structure of the annulus here.
 ![Alt text](docs/1.png)
 
 The **magic** part is that we never had to choose any parameter to remove the noise in this construction, but the annulus still naturally appears!
-<br>A more strinking example is the following one.
+<br>A more striking example is the following one.
 Using the same constructions, we can identify topological structure, and their size, in a parameter free approach, even though the majority of the sampling measure's mass is noise.
 <br> In this example, the lifetime shape associated to each cycle can be identified from 
  - Their radius : the smaller cycle will naturally live more this shape will appear on the "left" (smaller radius)
@@ -36,7 +36,7 @@ We also provide several other descriptors, as well as associated Machine Learnin
 ![alt text](docs/3.png)
 
 
-A non-exhaustive list of features can be found in the **Features** section, and in the [documentation](https://www-sop.inria.fr/members/David.Loiseaux/doc/multipers/index.html).
+A non-exhaustive list of features can be found in the **Features** section, and in the [documentation](https://davidlapous.github.io/multipers/index.html).
 ## Quick start
 
 
@@ -46,7 +46,7 @@ pip install multipers
 ```
 We recommend Windows user to use [WSL](https://learn.microsoft.com/en-us/windows/wsl/). 
 <br>
-A documentation and building instructions are available [here](https://www-sop.inria.fr/members/David.Loiseaux/doc/multipers/index.html).
+A documentation and building instructions are available [here](https://davidlapous.github.io/multipers/contributions.html).
 
 ## Features, and linked projects
 This library features a bunch of different functions and helpers. See below for a non-exhaustive list.
@@ -57,11 +57,11 @@ This library features a bunch of different functions and helpers. See below for
  - [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, SOCG20219]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
+ - [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.
- - [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 bi-filtrations.
+ - [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] [[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 to compute blazingly fast signed measures  convolutions (and more!) with custom kernels. 
+ - [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.