GUDHI/gudhi-devel

The GUDHI library is a generic open source C++ library, with a Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding.

Language: C++ - Size: 45.5 MB - Last synced: about 18 hours ago - Pushed: about 18 hours ago - Stars: 243 - Forks: 65

irishryoon/Dowker_persistence

Code for computing Dowker persistence diagrams

Language: Jupyter Notebook - Size: 2.47 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 7 - Forks: 1

CarloCarlo25/Alphabet-Sign-Language-Recognition

This will serve as the repository of the Special Problem

Language: Jupyter Notebook - Size: 1.14 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

marrlab/SHAPR_torch

SHAPR: Code for "Capturing Shape Information with Multi-Scale Topological Loss Terms for 3D Reconstruction"

Language: Python - Size: 11.1 MB - Last synced: 4 days ago - Pushed: 8 months ago - Stars: 32 - Forks: 10

nihell/pyDowker

Dowker complexes with custom relations for 1- and 2-parameter persistence

Language: Python - Size: 2.81 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0

mtsch/Ripserer.jl

Flexible and efficient persistent homology computation.

Language: Julia - Size: 233 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 61 - Forks: 6

DavidLapous/multipers

Multiparameter Persistence for Machine Learning

Language: C++ - Size: 21.4 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 10 - Forks: 0

nebneuron/Simplicial.jl

A package for various computations with simplicial complexes, combinatorial codes, directed complexes and their filtrations.

Language: C++ - Size: 5.62 MB - Last synced: 1 day ago - Pushed: over 1 year ago - Stars: 27 - Forks: 9

mtsch/PersistenceDiagrams.jl

Persistence Diagrams in Julia

Language: Julia - Size: 1.6 MB - Last synced: 1 day ago - Pushed: 7 months ago - Stars: 13 - Forks: 3

shizuo-kaji/TutorialTopologicalDataAnalysis

Tutorial on Topological Data Analysis

Language: Jupyter Notebook - Size: 56.2 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 16 - Forks: 3

OnDraganov/chromatic-tda

Tool to compute six-packs of persistence diagrams for chromatic point clouds [packaged on PyPI]

Language: Jupyter Notebook - Size: 1.91 MB - Last synced: about 13 hours ago - Pushed: about 1 month ago - Stars: 10 - Forks: 0

tdaverse/ggtda

ggplot2 extension to visualize persistent homology

Language: R - Size: 45.4 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 19 - Forks: 5

rrrlw/TDAstats

R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.

Language: R - Size: 949 KB - Last synced: 23 days ago - Pushed: over 2 years ago - Stars: 37 - Forks: 8

aidos-lab/SHAPR_torch Fork of marrlab/SHAPR_torch

SHAPR: Code for "Capturing Shape Information with Multi-Scale Topological Loss Terms for 3D Reconstruction"

Language: Python - Size: 10.6 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

aidos-lab/py-oineus

Python bindings for `oineus`

Language: Python - Size: 6.84 KB - Last synced: about 1 month ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

appliedtopology/tda4j

TDA library for the JVM

Language: Scala - Size: 21.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0

shizuo-kaji/CubicalRipser_3dim Fork of CubicalRipser/CubicalRipser_3dim

Persistent homology calculation for 1D (scalar time series), 2D (image), and 3D (voxel) arrays

Language: C++ - Size: 21.5 MB - Last synced: 28 days ago - Pushed: 2 months ago - Stars: 39 - Forks: 5

giotto-ai/pyflagser

Python bindings and API for the flagser C++ library (https://github.com/luetge/flagser).

Language: Python - Size: 931 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 12 - Forks: 13

mvlier/topapprox

Package for computing topological approximation using Persistent Homology in various settings.

Language: Jupyter Notebook - Size: 2.94 MB - Last synced: 22 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

aleskunder/topology_loop_caller

Chromatin loop caller using Topological Data Analysis based on Hi-C data

Language: Python - Size: 625 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 3 - Forks: 1

mhw32/persistent-homology

Statistically Quantifying Difference in the Observable Universe under Warm and Cold Dark Matter Assumptions

Language: Jupyter Notebook - Size: 339 MB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

BorgwardtLab/TOGL

Topological Graph Neural Networks (ICLR 2022)

Language: Python - Size: 1.61 MB - Last synced: 3 months ago - Pushed: about 2 years ago - Stars: 98 - Forks: 18

Ripser/ripser

Ripser: efficient computation of Vietoris–Rips persistence barcodes

Language: C++ - Size: 4.53 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 293 - Forks: 69

scikit-tda/ripser.py

A Lean Persistent Homology Library for Python

Language: C++ - Size: 19.9 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 251 - Forks: 56

corybrunson/plt

R interface & extension to an adapted Persistence Landscapes Toolbox

Language: R - Size: 9.61 MB - Last synced: 2 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

oleg-kachan/diagram2vec

Vector Representations of Persistence Diagrams

Language: Python - Size: 4.88 KB - Last synced: about 10 hours ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 2

rodrgo/OpenPH

Parallel reduction of boundary matrices for Persistent Homology with CUDA

Language: Cuda - Size: 276 KB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 25 - Forks: 5

rivetTDA/rivet

RIVET is a tool for Topological Data Analysis, in particular two-parameter persistent homology.

Language: C++ - Size: 4.53 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 67 - Forks: 24

rrrlw/ripserr

R package porting Ripser-based persistent homology calculation engines from C++ via Rcpp. Currently ports Ripser (Vietoris-Rips complex) and Cubical Ripser (cubical complex).

Language: C++ - Size: 114 MB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 7 - Forks: 5

tomchaplin/lophat

Lockfree Persistent Homology Algorithm Toolkit

Language: Rust - Size: 153 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 1

jrocks/persistent_homology

Persistent Homology Library

Language: C++ - Size: 27.5 MB - Last synced: 5 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

DavidLapous/multipers-signed-measure 📦

Scikit-style multiparameter persistent homology, using signed measure and their representation for machine learning.

Language: Jupyter Notebook - Size: 4.97 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 5 - Forks: 0

BorgwardtLab/P-WL

A Persistent Weisfeiler–Lehman Procedure for Graph Classification

Language: Python - Size: 163 MB - Last synced: 3 months ago - Pushed: about 3 years ago - Stars: 58 - Forks: 15

dashtiali/vectorisation-app

This web app can be used to compute and visualize featurized PH barcodes.

Language: Python - Size: 510 KB - Last synced: 5 months ago - Pushed: 6 months ago - Stars: 10 - Forks: 1

mehdimerbah/TDA-PPIN

This is a repository for a study on applying Topological Data Analysis techniques, specifically Persistent Homology on Protein-Protein Interaction data to predict functional protein complexes.

Language: Jupyter Notebook - Size: 28.2 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

corybrunson/plt-topdown

R interface to & implementation of the Persistence Landscapes Toolbox

Language: C++ - Size: 7.83 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

aidos-lab/TEQUAL

Topological Equivalency classes for Understanding Autoencoder Latent Spaces

Language: Python - Size: 411 KB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

eOnofri04/AlphaStructures.jl

AlphaStructures.jl - Theory and Practice of Alpha Shapes for Julia

Language: Julia - Size: 34.7 MB - Last synced: 6 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

s-clausen/cecher

Cecher: efficient computation of Čech persistence barcodes

Language: C++ - Size: 1.19 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 1

mtsch/Ripser.jl

Simple Ripser wrapper in Julia

Language: Julia - Size: 12.2 MB - Last synced: 6 months ago - Pushed: about 4 years ago - Stars: 8 - Forks: 0

aidos-lab/EmbedEQ

Determining hyperparameter equivalency classes for dimensionality reduction algorithms based on the topology of the embedding space.

Language: Python - Size: 664 KB - Last synced: about 1 month ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

ammedmar/stability

Steenrod barcodes of Vietoris-Rips complexes

Language: TeX - Size: 40 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

salimandre/unsupervised-image-segmentation-persistent-homology

Unsupervised image segmentation by applying topological data analysis techniques.

Language: Python - Size: 5.34 MB - Last synced: 8 months ago - Pushed: over 4 years ago - Stars: 22 - Forks: 1

scikit-tda/pervect

Vectorization of persistence diagrams and approximate Wasserstein distance

Language: Jupyter Notebook - Size: 4.04 MB - Last synced: 11 days ago - Pushed: over 4 years ago - Stars: 26 - Forks: 0

BorgwardtLab/topological-autoencoders 📦

Code for the paper "Topological Autoencoders" by Michael Moor, Max Horn, Bastian Rieck, and Karsten Borgwardt.

Language: Python - Size: 50.5 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 117 - Forks: 28

ansonb/Knowledge_Persistence

Code of the Knowledge Persistence (KP) method proposed in WWW'23 paper

Language: Python - Size: 4.61 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 2 - Forks: 0

upunaprosk/la-tda

Official code for EACL Workshop paper Can BERT eat RuCoLA? Topological Data Analysis to Explain

Language: Jupyter Notebook - Size: 7.36 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 0

Pseudomanifold/Aleph

A library for exploring persistent homology

Language: C++ - Size: 1.7 MB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 95 - Forks: 17

shizuo-kaji/HomologyCNN

Homology assisted CNN for image classification

Language: Python - Size: 31.8 MB - Last synced: 9 months ago - Pushed: about 4 years ago - Stars: 15 - Forks: 2

olivergafvert/topcat

Topcat - a library for multiparameter persistence

Language: Jupyter Notebook - Size: 777 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 4 - Forks: 0

SiyangJ/Topological-Data-Analysis

TDA starting from Summer 2018

Language: Java - Size: 172 MB - Last synced: 10 months ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 1

Pseudomanifold/pyper

Python-based persistent homology algorithms

Language: Python - Size: 83 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 15 - Forks: 1

eashwarsoma/TDA-benchmark

Code supporting "Comparing R packages for calculation of persistent homology" manuscript

Language: R - Size: 26.9 MB - Last synced: 11 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

BorgwardtLab/Topf

Topological peak filtering

Language: Python - Size: 89.8 KB - Last synced: 12 months ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1

BorgwardtLab/Neural-Persistence

Code for the paper 'Neural Persistence: A Complexity Measure for Deep Neural Networks Using Algebraic Topology'

Language: Python - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 24 - Forks: 6

Vidhish-Trivedi/Topology-Project

This project was made as part of the course: Basic Computational Topology (SM402) at IIIT-Bangalore

Language: Python - Size: 4.34 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

c-hofer/torchph

The essence of my research, distilled for reusability. Enjoy 🥃!

Language: Jupyter Notebook - Size: 7.33 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 47 - Forks: 10

UDATG/analogous_bars

Code for the persistent extension and analogous bars methods of comparing persistence barcodes of clique complexes using a cross-dissimilarity measure.

Language: Jupyter Notebook - Size: 10.9 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

jakipatryk/spark-persistent-homology

(WIP) Library for persistent homology computations in Apache Spark.

Language: Scala - Size: 272 KB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

markolalovic/tda-digits

Topological features applied to the digits data set

Language: Python - Size: 9.15 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 9 - Forks: 1

BorgwardtLab/fMRI_Cubical_Persistence

Code of our NeurIPS 2020 publication 'Uncovering the Topology of Time-Varying fMRI Data using Cubical Persistence'

Language: Python - Size: 202 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 13 - Forks: 3

scikit-tda/cechmate

Custom filtration constructors for Python

Language: Python - Size: 890 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 15 - Forks: 11

nhchristianson/Math-text-semantic-networks

Python code for construction and analysis of semantic networks from text.

Language: Jupyter Notebook - Size: 28.2 MB - Last synced: over 1 year ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 0

Pseudomanifold/enchiridion-tda

An enchiridion for instructing mortals in the hidden arts of topological data analysis

Language: Python - Size: 191 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 5 - Forks: 1

ammedmar/funct_top

Persistent homology for functionals

Language: TeX - Size: 608 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

gjkoplik/pers-hom-examples

A placeholder repo to hold widgets for my Towards Data Science persistent homology medium article.

Language: HTML - Size: 16.1 MB - Last synced: 5 months ago - Pushed: over 4 years ago - Stars: 5 - Forks: 1

Tyler-Hecht/GEMS-TDA

Topological Data Analysis for Parameter Estimation of Noisy Biexponential Decay (UD GEMS research project)

Language: Python - Size: 11.2 MB - Last synced: over 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

Steenroder/steenroder

Computation of persistence Steenrod barcodes

Language: Jupyter Notebook - Size: 83.7 MB - Last synced: 4 days ago - Pushed: about 2 years ago - Stars: 6 - Forks: 0

kiranvad/ComputationalTopology

This is primarily a set of examples for computational topological studies.

Language: Python - Size: 655 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 1

laplcebeltrami/orderstat

Topological data analysis of brain networks through order statistics

Language: MATLAB - Size: 13 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

mitxael/SSHIVA

CHoleR: a C++ Tool for the Analysis of Persistent Homology on Undirected Weighted Graphs [C++, CLI/CLR, JNI, WPF, C#]

Language: C++ - Size: 9.32 MB - Last synced: over 1 year ago - Pushed: over 4 years ago - Stars: 2 - Forks: 1

Pseudomanifold/TML

Experiments in topological machine learning

Language: Python - Size: 9.46 MB - Last synced: over 1 year ago - Pushed: over 2 years ago - Stars: 6 - Forks: 1

rrrlw/visual-tda

R code associated with preprint proposing flat persistence diagram for better visualization of persistent homology.

Language: R - Size: 8.79 KB - Last synced: over 1 year ago - Pushed: over 4 years ago - Stars: 4 - Forks: 3

arksch/fuzzy-eureka

Approximating Persistent Homology for Geometric Insights

Language: Jupyter Notebook - Size: 3.65 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

trneedham/IntroductionToTopologicalDataAnalysis

Language: Jupyter Notebook - Size: 6.05 MB - Last synced: over 1 year ago - Pushed: about 5 years ago - Stars: 5 - Forks: 1

ArGintum/PersistenceHomology

A small but developing tool for fast computation of Persistence Diagrams of Flag Filtrations.

Language: C++ - Size: 1.72 MB - Last synced: 11 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

asier-gutierrez/nn-evolution

Neural Network Learning monitoring without a validation set based on Persistent Homology.

Language: Python - Size: 58.6 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

izzortsi/hr-graphs-ph

geometric graphs based on a Hertzsprung–Russell diagram and their corresponding persistent homology graph families

Language: Jupyter Notebook - Size: 78.4 MB - Last synced: over 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

lorinanthony/Tropix

Code to Compute Tropical Sufficient Statistics for Persistent Homology

Language: C++ - Size: 765 KB - Last synced: over 1 year ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 3

toggled/PHComputation

A Pure Python Library for use in Topological Data Analysis

Language: Python - Size: 11.7 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

kowshikthopalli/my-TDA

auxiliary scripts TDA - matlab and R

Language: Matlab - Size: 10.7 KB - Last synced: over 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

xoltar/rivet Fork of rivetTDA/rivet

RIVET is a tool for Topological Data Analysis, in particular the interactive visualization of two-parameter persistent homology.

Language: C++ - Size: 3.98 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0