lmcinnes/umap

Uniform Manifold Approximation and Projection

Language: Python - Size: 90.4 MB - Last synced at: 1 day ago - Pushed at: 13 days ago - Stars: 7,933 - Forks: 848

giotto-ai/giotto-tda

A high-performance topological machine learning toolbox in Python

Language: Python - Size: 58.4 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 925 - Forks: 187

scikit-tda/kepler-mapper

Kepler Mapper: A flexible Python implementation of the Mapper algorithm.

Language: Python - Size: 47.1 MB - Last synced at: 4 days ago - Pushed at: 27 days ago - Stars: 642 - Forks: 183

scikit-tda/scikit-tda

Topological Data Analysis for Python🐍

Language: Python - Size: 18.2 MB - Last synced at: 2 months ago - Pushed at: about 1 year ago - Stars: 548 - Forks: 54

topology-tool-kit/ttk

TTK - Topological Data Analysis and Visualization - Source Code

Language: C++ - Size: 62.3 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 451 - Forks: 130

scikit-tda/ripser.py

A Lean Persistent Homology Library for Python

Language: C++ - Size: 20.2 MB - Last synced at: 4 days ago - Pushed at: 13 days ago - Stars: 306 - Forks: 62

Ripser/ripser

Ripser: efficient computation of Vietoris–Rips persistence barcodes

Language: C++ - Size: 4.53 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 293 - Forks: 69

pyt-team/TopoModelX

Topological Deep Learning

Language: Jupyter Notebook - Size: 13.5 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 292 - Forks: 101

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: 48.8 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 287 - Forks: 73

erdogant/findpeaks

The detection of peaks and valleys in a 1d-vector or 2d-array (image)

Language: Jupyter Notebook - Size: 65.3 MB - Last synced at: 2 days ago - Pushed at: 8 days ago - Stars: 266 - Forks: 37

pyt-team/TopoNetX

Computing on Topological Domains

Language: Jupyter Notebook - Size: 5.95 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 236 - Forks: 44

FatemehTarashi/awesome-tda

A curated list of topological data analysis (TDA) resources and links.

Size: 197 KB - Last synced at: 8 days ago - Pushed at: 12 months ago - Stars: 206 - Forks: 26

aidos-lab/pytorch-topological

A topological machine learning framework based on PyTorch

Language: Python - Size: 396 KB - Last synced at: 6 days ago - Pushed at: 2 months ago - Stars: 185 - Forks: 29

stephenhky/PyTDA

Topological Data Analysis in Python

Language: Python - Size: 18.6 KB - Last synced at: about 2 months ago - Pushed at: over 6 years ago - Stars: 171 - Forks: 34

dillondaudert/UMAP.jl

Uniform Manifold Approximation and Projection (UMAP) implementation in Julia

Language: Julia - Size: 4.63 MB - Last synced at: 25 days ago - Pushed at: about 2 months ago - Stars: 135 - Forks: 17

stephenhky/MoguTDA

Topological Data Analysis in Python: Simplicial Complex

Language: Python - Size: 162 KB - Last synced at: 13 days ago - Pushed at: about 1 month ago - Stars: 123 - Forks: 27

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 at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 117 - Forks: 28

hyungkwonko/umato

Uniform Manifold Approximation with Two-phase Optimization (IEEE VIS 2022 short)

Language: Jupyter Notebook - Size: 190 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 111 - Forks: 13

LAIT-CVLab/TopPR

NeurIPS 2023 - TopP&R: Robust Support Estimation Approach for Evaluating Fidelity and Diversity in Generative Models Official Code

Language: Python - Size: 84.9 MB - Last synced at: 16 days ago - Pushed at: about 1 year ago - Stars: 103 - Forks: 4

Pseudomanifold/Aleph

A library for exploring persistent homology

Language: C++ - Size: 1.7 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 100 - Forks: 16

rivetTDA/rivet

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

Language: C++ - Size: 4.53 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 78 - Forks: 26

hanssmail/quantQ

The repository for the Machine Learning and Big Data with kdb+/q book by Novotny et al.

Language: q - Size: 247 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 75 - Forks: 44

mtsch/Ripserer.jl

Flexible and efficient persistent homology computation.

Language: Julia - Size: 233 MB - Last synced at: 4 days ago - Pushed at: 17 days ago - Stars: 74 - Forks: 8

multinetlab-amsterdam/network_TDA_tutorial

This repository is dedicated for the tutorial on network and topological neuroscience.

Language: HTML - Size: 201 MB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 70 - Forks: 25

stefaniaebli/simplicial_neural_networks

Simplicial neural networks (SNNs), a generalization of graph neural networks to data that live on a class of topological spaces called simplicial complexes.

Language: Jupyter Notebook - Size: 2.41 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 65 - Forks: 7

ksanjeevan/mapper-tda

Mapper implementation (Topological Data Analysis) in Python

Language: Python - Size: 1.19 MB - Last synced at: 4 months ago - Pushed at: about 7 years ago - Stars: 65 - Forks: 10

BorgwardtLab/P-WL

A Persistent Weisfeiler–Lehman Procedure for Graph Classification

Language: Python - Size: 163 MB - Last synced at: about 2 months ago - Pushed at: about 4 years ago - Stars: 61 - Forks: 17

c-hofer/torchph

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

Language: Jupyter Notebook - Size: 7.33 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 60 - Forks: 10

CamaraLab/scTDA

An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data

Language: Python - Size: 3.47 MB - Last synced at: 14 days ago - Pushed at: about 7 years ago - Stars: 52 - Forks: 21

giotto-ai/giotto-ph

High performance implementation of Vietoris-Rips persistence.

Language: C++ - Size: 35.2 MB - Last synced at: 17 days ago - Pushed at: over 1 year ago - Stars: 51 - Forks: 13

braindynamicslab/dyneusr

Dynamical Neuroimaging Spatiotemporal Representations (DyNeuSR)

Language: Python - Size: 24.3 MB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 49 - Forks: 16

ognis1205/spark-tda

SparkTDA is a package for Apache Spark providing Topological Data Analysis Functionalities.

Language: Scala - Size: 31.4 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 47 - Forks: 5

scikit-tda/DREiMac

Dimensionality Reduction with Eilenberg-MacLane Coordinates

Language: Python - Size: 29.8 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 42 - Forks: 14

aidos-lab/TARDIS

TARDIS: Topological Algorithms for Robust DIscovery of Singularities

Language: Python - Size: 6.44 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 42 - Forks: 4

LuisScoccola/persistable

density-based clustering for exploratory data analysis based on multi-parameter persistence

Language: Python - Size: 11.3 MB - Last synced at: 4 days ago - Pushed at: about 2 months ago - Stars: 41 - Forks: 2

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 at: 1 day ago - Pushed at: almost 4 years ago - Stars: 41 - Forks: 9

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 at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 40 - Forks: 8

wildart/TDA.jl

A Julia package for topological data analysis

Language: Julia - Size: 20.5 KB - Last synced at: 3 months ago - Pushed at: over 4 years ago - Stars: 39 - Forks: 5

pierrebaudot/infotopopy

computes most of information functions (joint entropy, conditional, mutual information, total correlation information distance) and deep information networks

Language: Python - Size: 33.3 MB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 38 - Forks: 8

scikit-tda/tadasets

Synthetic data sets apt for Topological Data Analysis

Language: Python - Size: 6.11 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 36 - Forks: 7

openantz/antz

ANTz immersive 3D data visualization engine

Language: C - Size: 68.7 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 36 - Forks: 13

HuXiaoling/awesome-topology-driven-image-analysis

awesome-topology-driven-deep-image-analysis

Size: 77.1 KB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 34 - Forks: 2

TeaspoonTDA/teaspoon

Topological Signal Processing in Python

Language: Jupyter Notebook - Size: 168 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 33 - Forks: 11

DavidLapous/multipers

Python library for multipersistence

Language: C++ - Size: 59.7 MB - Last synced at: 1 day ago - Pushed at: 4 days ago - Stars: 32 - Forks: 7

GPZ-Bioinfo/tmap

topological data analysis of population-scale microbiomes

Language: Python - Size: 11.4 MB - Last synced at: 20 days ago - Pushed at: over 2 years ago - Stars: 31 - Forks: 12

rodrgo/OpenPH

Parallel reduction of boundary matrices for Persistent Homology with CUDA

Language: Cuda - Size: 276 KB - Last synced at: 1 day ago - Pushed at: about 4 years ago - Stars: 31 - Forks: 5

shehper/AC-Solver

A long-horizon, sparse-reward math environment for reinforcement learning. Official code repo for "What makes Math problems hard for reinforcement learning: A case study".

Language: Jupyter Notebook - Size: 1.29 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 30 - Forks: 6

gd-vae/gd-vae

Geometric Dynamic Variational Autoencoders (GD-VAEs) for learning embedding maps for nonlinear dynamics into general latent spaces. This includes methods for standard latent spaces or manifold latent spaces with specified geometry and topology. The manifold latent spaces can be based on analytic expressions or general point cloud representations.

Language: TeX - Size: 29.7 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 29 - Forks: 1

Ebanflo42/Persistence

A topological data analysis library for Haskell

Language: Haskell - Size: 1.68 MB - Last synced at: 28 days ago - Pushed at: over 4 years ago - Stars: 29 - Forks: 3

scikit-tda/pervect

Vectorization of persistence diagrams and approximate Wasserstein distance

Language: Jupyter Notebook - Size: 4.04 MB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 27 - Forks: 0

anirudhsom/PI-Net

Python code to directly compute persistence images (PIs) from data (time-series or images) using deep learning.

Language: Jupyter Notebook - Size: 91.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 26 - Forks: 5

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 at: about 2 months ago - Pushed at: almost 5 years ago - Stars: 24 - Forks: 4

lordgrilo/AML-days-TDA-tutorial

Language: Jupyter Notebook - Size: 339 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 24 - Forks: 22

tdaverse/ggtda

ggplot2 extension to visualize persistent homology

Language: R - Size: 45.4 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 23 - Forks: 6

WoComtoQC/wocomtoqc.github.io Fork of In2Py/In2Py.github.io

Code for the website of the Workshop on 'Workshop on Computational Topology & Quantum Computing' (WoComToQC).

Language: SCSS - Size: 6.72 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 23 - Forks: 2

tda-in-ml/tda-in-ml.github.io

Code for the website of the NeurIPS 2020 workshop on 'Topological Data Analysis and Beyond'

Language: TeX - Size: 41.6 MB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 23 - Forks: 4

shervinazadi/topoGenesis

Python Package for Generative Systems and Sciences

Language: Python - Size: 9.36 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 21 - Forks: 1

cakcora/CoinWorks

Language: Python - Size: 18 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 20 - Forks: 21

ndcroos/awesome-topological-data-analysis

A collection of topological data analysis links, frameworks, libraries and software. Inspired by awesome projects line.

Size: 26.4 KB - Last synced at: 18 days ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 4

Pseudomanifold/pyper

Python-based persistent homology algorithms

Language: Python - Size: 83 KB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 19 - Forks: 2

BorgwardtLab/filtration_curves

Code for the KDD 2021 paper 'Filtration Curves for Graph Representation'

Language: Python - Size: 1.14 MB - Last synced at: 2 days ago - Pushed at: about 2 years ago - Stars: 18 - Forks: 9

aidos-lab/dect-evaluation

Differentiable Euler Characteristic Transform

Language: Python - Size: 21 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 17 - Forks: 0

peekxc/simplextree

R package for simplifying general computation on simplicial complexes

Language: C++ - Size: 3.35 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 17 - Forks: 2

TheMesocarp/koho

Full spectrum sheaf neural network over arbitrary CW complexes.

Language: Rust - Size: 105 KB - Last synced at: 25 days ago - Pushed at: 2 months ago - Stars: 16 - Forks: 4

anirudhsom/Perturbed-Topological-Signature

Matlab and Python code to compute perturbed topological signatures (PTS), an efficient topological representation that lies on the Grassmann manifold.

Language: Python - Size: 9.22 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 16 - Forks: 4

ryanholbrook/critical-transitions 📦

Detecting critical transitions in financial networks with topological data analysis.

Language: Jupyter Notebook - Size: 266 KB - Last synced at: 7 days ago - Pushed at: over 6 years ago - Stars: 16 - Forks: 6

OnDraganov/chromatic-tda

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

Language: Jupyter Notebook - Size: 4.7 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 15 - Forks: 2

lucasimi/tda-mapper-python

A simple and efficient Python implementation of Mapper algorithm for Topological Data Analysis

Language: Python - Size: 9.29 MB - Last synced at: 3 days ago - Pushed at: about 2 months ago - Stars: 15 - Forks: 6

giotto-ai/molecule_bond_prediction

Predict scalar coupling in molecules

Language: Python - Size: 5.68 MB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 15 - Forks: 5

patnicolas/geometriclearning

Classes and methods for Geometric Deep Learning to support Substack, LinkedIn newsletters and tutorials

Language: Python - Size: 141 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 14 - Forks: 4

AdaUchendu/AwesomeTDA4NLP

Topological Data Analysis (TDA) for Natural Language Processing (NLP) Applications

Language: Jupyter Notebook - Size: 1.12 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 14 - Forks: 0

aidos-lab/curvature-filtrations

SCOTT: Synthesizing Curvature Operations and Topological Tools

Language: Python - Size: 1.05 MB - Last synced at: 16 days ago - Pushed at: 2 months ago - Stars: 14 - Forks: 3

paul-english/spark-mapper

Spark based implementation of the Topological Mapper algorithm

Language: Scala - Size: 708 KB - Last synced at: over 1 year ago - Pushed at: over 8 years ago - Stars: 14 - Forks: 5

aidos-lab/DONUT

DONUT: Database of Original and Non-Theoretical Applications of Topology

Language: TeX - Size: 1.12 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 13 - Forks: 1

giotto-ai/pyflagser

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

Language: Python - Size: 975 KB - Last synced at: 12 days ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 15

trneedham/gromov-wasserstein-statistics

Statistics on the space of asymmetric networks via Gromov-Wasserstein distance

Language: Jupyter Notebook - Size: 4.24 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 13 - Forks: 4

jh-chung1/GNN_ElasticModulus_Prediction

Application of Graph Neural Networks to predict material properties from their microstructures.

Language: Jupyter Notebook - Size: 4.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 12 - Forks: 2

dashtiali/vectorisation-app

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

Language: Python - Size: 512 KB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 12 - Forks: 3

aidos-lab/neural-k-forms

Simplicial Representation Learning with Neural k-Forms

Language: Jupyter Notebook - Size: 323 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 5

trneedham/Decorated-Merge-Trees

Tools for generating and comparing Decorated Merge Trees, enriched persistence-based topological data descriptors.

Language: Jupyter Notebook - Size: 894 KB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 12 - Forks: 1

markolalovic/tda-digits

Topological features applied to the digits dataset

Language: Python - Size: 9.51 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 1

tdaverse/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: 115 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 10 - Forks: 6

psweens/Vascular-TDA

Software to analyse the topology of vascular networks.

Language: Python - Size: 5.33 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 10 - Forks: 0

Cimagroup/vectorization-maps

Language: Python - Size: 300 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 2

AdrienC21/CCSD

Combinatorial Complex Score-based Diffusion model using stochastic differential equations

Language: Python - Size: 65.6 MB - Last synced at: 3 days ago - Pushed at: almost 2 years ago - Stars: 10 - Forks: 1

stefaniaebli/dmt-signal-processing

Signal compression and reconstruction on complexes preserving topological features via Discrete Morse Theory

Language: Jupyter Notebook - Size: 12.2 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 1

CamaraLab/RayleighSelection

An R package for feature selection in topological spaces.

Language: R - Size: 326 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 10 - Forks: 3

NREL/tda-ps

Topological Data Analysis for Power System Contingencies

Language: Jupyter Notebook - Size: 291 MB - Last synced at: 1 day ago - Pushed at: almost 5 years ago - Stars: 10 - Forks: 7

Javihaus/Explainable-Deep-Neural-Networks

Explainable Deep Neural Networks

Language: Jupyter Notebook - Size: 788 KB - Last synced at: 27 days ago - Pushed at: 28 days ago - Stars: 9 - Forks: 1

irishryoon/Dowker_persistence

Code for computing Dowker persistence diagrams

Language: Jupyter Notebook - Size: 2.47 MB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 1

davidmiheev/GalaxyWitness

Package for topological data analysis of the big data. It is attempt to study distribution of galaxies in the universe via TDA

Language: Python - Size: 20.9 MB - Last synced at: 14 days ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 2

lcrawlab/SINATRA

A statistical framework for feature selection and association mapping with 3D shapes

Language: R - Size: 547 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 4

mtsch/Ripser.jl

Simple Ripser wrapper in Julia

Language: Julia - Size: 12.2 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 8 - Forks: 0

mvlier/topapprox

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

Language: Jupyter Notebook - Size: 24.9 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 7 - Forks: 0

peekxc/simplextree-py

Python bindings to Simplex Tree data structure (w/ C++)

Language: C++ - Size: 2.29 MB - Last synced at: about 2 months ago - Pushed at: 9 months ago - Stars: 7 - Forks: 1

HiddenBeginner/hiddenbeginner.github.io

데이터사이언스 기술 블로그

Language: HTML - Size: 34.7 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 1

vadimlebovici/eulearning

Eulearning: Euler characteristic tools for topological data analysis

Language: Python - Size: 3.71 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0

peekxc/Mapper 📦

R package for computing the Mapper construction from Topological Data Analysis

Language: R - Size: 64.6 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 5

JonasTriki/masters-thesis-ml 📦

Repository for my master's thesis in machine learning at UiB

Language: Jupyter Notebook - Size: 144 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 2

tsuno0829/som.github.io

Visualization of Unsupervised Kernel Regression(UKR) & Self-Organizing Map(SOM) in artificial dataset using Javascript(under development)

Size: 175 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 0