awesome-TDA
A curated list of topological data analysis (TDA) resources and links.
https://github.com/FatemehTarashi/awesome-TDA
Last synced: 22 days ago
JSON representation
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Theory
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Algorithms
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Books
- 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.)
- Elementary Applied Topology - Robert Ghrist.
- Computational Homology (Applied Mathematical Sciences) - Kaczynski, Mischaikow, Mrozek.
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Articles
- A Fuzzy Clustering Algorithm for the Mode Seeking Framework - Bonis, Oudot.
- 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.
- 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 .
- Why Topology for Machine Learning and Knowledge Extraction? - Massimo Ferri.
- Barcodes: The Persistent Topology of Data - Robert Ghrist.
- Homological Algebra and Data - Robert Ghrist.
- Stratifying Multiparmeter Persistent Homology - Harriington, Otter, Schenck, Tillmann.
- A topological data analysis based classification method for multiple measurements - Riihimäki, Chachólski, Theorell, Hillert, Ramanujam.
- Introduction to the R package TDA - Fasy, Jisu Kim, Lecci, Clément Maria, Millman, Rouvreau.
- Two-Tier Mapper: a user-independent clustering method for global gene expression analysis based on topology - Jeitziner, Carrière, Rougemont, Oudot, Hess, Brisken.
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Courses
- Applied Algebraic Topology Seminars
- 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 - -->
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Tools
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Courses
- TTk - Topological data analysis in scientific visualization. Can be used with C++, python.
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Frameworks and Libs
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C++
- Dionysus - Computing persistent (co)homology, Implementation of the Persistent (co)homology computation, Vineyards, Zigzag persistent homology algorithms.
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Haskell
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Python
- Giotto TDA(GTDA) - A high-performance topological machine learning toolbox
- GUDHI - Geometry Understanding in Higher Dimensional with a Python interface.
- Persim - package for many tools used in analyzing Persistence Diagrams
- Python Mapper - Mapper algorithm implementation + graphical user interface.
- Ripser - lean persistent homology package.
- Scikit-TDA - For non-topologists.
- TMAP - Population-scale microbiome data analysis.
- Topology ToolKit (TTK) - Efficient, generic and easy and Topological data analysis and visualization
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R
- TDA - Tools for the statistical analysis of persistent homology and for density clustering.
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Useful Links
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Bioinformatics
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Brain Network Analysis
- 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
- Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey
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Computing Homology
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Computer Vision
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Data Professionals
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Deep Learning
- 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
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
- Applied Topological Data Analysis to Deep Learning? Hands-on Arrhythmia Classification!
- From Topological Data Analysis to Deep Learning: No Pain No Gain
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Machine Learning
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Persistent Homology
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Use Python
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Use R
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Theory and applications of TDA
- 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
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
- A concrete application of Topological Data Analysis
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Event
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Theory and applications of TDA
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2024
- 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
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