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awesome-TDA
A curated list of topological data analysis (TDA) resources and links.
https://github.com/FatemehTarashi/awesome-TDA
- Chunk
- Mapper
- brief summary
- PHrow
- Twist
- Vineyards
- Zigzag persistent homology
- Zigzag Persistent Cohomology
- A Short Course in Computational Geometry and Topology - Edelsbrunner, Herbert.
- Computational Homology (Applied Mathematical Sciences) - Kaczynski, Mischaikow, Mrozek.
- Computational Topology: An Introduction - Herbert Edelsbrunner, John L Harer.
- Computational Topology for Data Analysis - Tamal Krishna Dey, Yusu Wang.
- Elementary Applied Topology - Robert Ghrist.
- Fundamentals of Brain Network Analysis - Fundamentals of Brain Network Analysis.
- Geometric and Topological Inference - Boissonnat, Chazal, Yvinec.
- Persistence Theory: From Quiver Representations to Data Analysis - Steve Y Oudot.
- Topological and Statistical Methods for Complex Data: Tackling Large-Scale, High-Dimensional, and Multivariate Data Spaces - Bennett, Janine, Vivodtzev, Fabien, Pascucci, Valerio.
- Topological Based Machine Learning Methods - Alex Georges.
- Topological Data Analysis for Genomics and Evolution: Topology in Biology - Raul Rabadan, Andrew J Blumberg.
- Topological Data Analysis for Scientific Visualization - Tierny, Julien.
- Topological Methods for 3D Point Cloud Processing - William Joseph Beksi.
- Topology for Computing - AFRA J ZOMORODIAN.
- Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications
- Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications II
- Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications III
- Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications IV
- Topology-based Methods in Visualization - Hauser, Helwig, Hagen, Hans, Theisel, Holger (Eds.)
- A Fuzzy Clustering Algorithm for the Mode Seeking Framework - Bonis, Oudot.
- A topological data analysis based classification method for multiple measurements - Riihimäki, Chachólski, Theorell, Hillert, Ramanujam.
- A User's Guide to Topological Data Analysis - Elizabeth Munch.
- An introduction to Topological Data Analysis: fundamental and practical aspects for data scientists - Chazal, Michel.
- Barcodes: The Persistent Topology of Data - Robert Ghrist.
- Computing Persistent Homology (Discrete and Computational Geometry) - Zomorodian, Carlsson.
- Deep Learning with Topological Signatures - Hofer, Kwitt, Niethammer, Uhl.
- Designing machine learning workflows with an application to topological data analysis - Cawi, La Rosa, Nehorai.
- Introduction to the R package TDA - Fasy, Jisu Kim, Lecci, Clément Maria, Millman, Rouvreau.
- Homological Algebra and Data - Robert Ghrist.
- Large Scale computation of Means and Clusters for Persistence Diagrams using Optimal Transport - Lacombe, Cuturi, OUDOT.
- Sampling real algebraic varieties for topological data analysis - Dufresne, Edwards, Harrington, Hauenstein.
- Stratifying Multiparmeter Persistent Homology - Harriington, Otter, Schenck, Tillmann.
- Text Mining using Topological Data Analysis. An introduction - Carrazana, Chong.
- Topology and Data - Gunnar Carlsson.
- Topological Data Analysis - Larry Wasserman.
- Topological Data Analysis and Its Application to Time-Series Data Analysis - Umeda, Kaneko, Kikuchi.
- Topological Data Analysis and Machine Learning Theory - Carlsson , Jardine, Feichtner-Kozlov, Morozov.
- Topological Data Analysis for Object Data - Patrangenaru, Bubenik, Paige, Osborne .
- Two-Tier Mapper: a user-independent clustering method for global gene expression analysis based on topology - Jeitziner, Carrière, Rougemont, Oudot, Hess, Brisken.
- Why Topology for Machine Learning and Knowledge Extraction? - Massimo Ferri.
- Applied Algebraic Topology Seminars
- Computational Topology and Data Analysis - Course is not active, but the course notes are useful.
- Topological Data Analysis - Course is not active, but the course notes are useful.
- Topics in topology: Scientific and engineering applications of algebraic topology - 2013 lecture series.
- videos here - -->
- Ctl - (C++11 library) A set of generic tools for Building Neighborhood Graphs and Cellular Complexes, Computing (persistent) homology over finite fields, Parallel algorithms for homology. an be used with c++, Python, MATLAB and R.
- Knotter - Implementation of Mapper algorithm for TDA.
- RIVET - For the visualization and analysis of two-parameter persistent homology with [Python API](https://github.com/rivetTDA/rivet-python/).
- TdaToolbox - Some tools that may be applied to data science in general.
- TTk - Topological data analysis in scientific visualization. Can be used with C++, python.
- Dionysus - Computing persistent (co)homology, Implementation of the Persistent (co)homology computation, Vineyards, Zigzag persistent homology algorithms.
- PHAT - Persistent Homology Algorithm Toolbox.
- Topology ToolKit (TTK) - Efficient, generic and easy and Topological data analysis and visualization
- TDA - Some methods are provided for gridded data (images).
- Persistence
- JavaPlex - The JavaPlex library implements persistent homology and related techniques. It designed for ease of use from Matlab and java-based systems.
- Eirene.jl - For homological persistence.
- TDA.jl - This package provides Persistence Diagram & Barcode, Nerve, Mapper tools for topological data analysis.
- Clique Top - Doing topological analysis of symmetric matrices.
- GDA Public - Several fundamental tools by Geometric Data Analytics Inc. [geomdata](http://www.geomdata.com)
- Giotto TDA(GTDA) - A high-performance topological machine learning toolbox
- GUDHI - Geometry Understanding in Higher Dimensional with a Python interface.
- KeplerMapper - TDA Mapper algorithm for visualization of high-dimensional data. it can make use of Scikit-Learn API compatible cluster and scaling algorithms.
- Kohonen - Kohonen-style vector quantizers: Self-Organizing Map (SOM), Neural Gas, and Growing Neural Gas.
- Mapper Implementation - Topological Data Analysis for high dimensional dataset exploration.
- MoguTDA - Numerical calculation of algebraic topology in an application to topological data analysis: implicial complex, and the estimation of homology and Betti numbers.
- OpenTDA
- Persim - package for many tools used in analyzing Persistence Diagrams
- Python Mapper - Mapper algorithm implementation + graphical user interface.
- Qsv - Data structure visualizer.
- Ripser - lean persistent homology package.
- Scikit-TDA - For non-topologists.
- Giotto-TDA - A ``scikit-learn`` - compatible library for end-to-end topological machine learning including Mapper, persistent homology, vectorization methods for persistence diagrams, and preprocessing components for time series, graphs, images, and point clouds ([paper](https://openreview.net/forum?id=fjQtZJOCTXf)).
- ScTDA - It includes tools for the preprocessing, analysis, and exploration of single-cell RNA-seq data based on topological representations.
- Topology ToolKit (TTK) - Efficient, generic and easy and Topological data analysis and visualization
- TMAP - Population-scale microbiome data analysis.
- TDA - Some methods are provided for gridded data (images).
- TDAmapper - An R package for using discrete Morse theory to analyze a data set using the Mapper algorithm described in G. Singh, F. Memoli, G. Carlsson (2007).
- TDAstats - Computing persistent homology.
- Spark Mapper - Estimating a lower dimensional simplicial complex from a dataset.
- Spark TDA - Scalable topological data analysis package.
- List of Resources for Topological Data Analysis in Bioinformatics
- An algebraic topological method for multimodal brain networks comparisons
- Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey
- Functional Brain Network Topology Discriminates between Patients with Minimally Conscious State and Unresponsive Wakefulness Syndrome
- Graph theory methods: applications in brain networks
- Topological Methods in Brain Network Analysis
- Computing Homology
- Topological Data Analysis in Computer Vision
- Topological Data Analysis for Data Professionals
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- On Characterizing the Capacity of Neural Networks Using Algebraic Topology
- Using Topological Data Analysis to Understand the Behavior of Convolutional Neural Networks
- How TDA and Machine Learning Enhance Each Other
- Machine Learning Explanations with Topological Data Analysis
- Topological Methods for Machine Learning
- Topological Machine Learning
- A roadmap for the computation of persistent homology
- Practical Guide to Persistent Homology
- Python Tutorial on Topological Data Analysis
- Topological Data Analysis - A Python tutorial
- A Mathematician's Perspective on Topological Data Analysis and R
- A concrete application of Topological Data Analysis
- A Guide to Data Science from mathematics
- An Algebraic Geometry Perspective on Topological Data Analysis
- Topological Data Analysis - A Very Short Introduction
- Topological Data Analysis - UFL.
- Topological Data Analysis - IBM.
- Theory and applications of topological data analysis
- Conferences and workshops
- International Conference on Computational Topology and Topological Data Analysis
- Jan. 30 - Feb. 2 | The 4th POSTECH MINDS Workshop on Topological Data Analysis and Machine Learning | Korea
- Feb. 7 - Apr. 1 | self-study group for textbook: "Computational Topology for Data Analysis" | zoom
- Mar. 21 - Mar. 22 | Workshop on Topological Data Analysis | India
- Aug. 7 - Aug. 9 | the 4th annual Centre for Topological Data Analysis conference | Oxford, UK
- Oct. 13 - Oct. 18 | TopoInVis 2024 - Topological Data Analysis and Visualization | Florida, USA
Keywords
topological-data-analysis
8
tda
3
topology
3
data-science
2
persistent-homology
2
spark
2
visualization
2
homology
2
algebraic-topology
1
data-visualization
1
package
1
python
1
single-cell-rna-seq
1
cran
1
ggplot2
1
homology-calculations
1
homology-computation
1
joss
1
pipeline
1
r
1
r-package
1
r-packages
1
ripser
1
topology-visualization
1
apache-spark
1
machine-learning
1
ml
1
mllib
1