Learn Topological Data Analysis for Machine Learning with Me

I'll be sharing my resources and notebooks used to learn TDA. I'm specifically interested in the use of TDA for ML models using medical data such as images and waveforms. For this project, I'm using electrohysterograph data collected from pregnant women for a study of preterm birth.

Introductory Videos by Shaw Talebi

• Topological Data Analysis (TDA) | An introduction - https://www.youtube.com/watch?v=fpL5fMmJHqk
• Persistent Homology - https://youtu.be/5ezFcy9CIWE

• Mapper - https://youtu.be/NlMrvCYlOOQ

Introductory Article by Gary Koplik

• Persistent Homology: A Non-Mathy Introduction with Examples - https://towardsdatascience.com/persistent-homology-with-examples-1974d4b9c3d0

Lectures by Bastian Grossenbacher-Rieck

• Topological Data Analysis for Machine Learning I: Algebraic Topology - https://www.youtube.com/watch?v=gVq_xXnwV-4
• Topological Data Analysis for Machine Learning Lecture II: Computational Topology - https://www.youtube.com/watch?v=UKXIyC7l16g
• Topological Data Analysis for Machine Learning III: Topological Descriptors & How to Use Them - https://www.youtube.com/watch?v=7i1kabhl5IU
• Topological Data Analysis for Machine Learning IV: Recent Advances in Topological Machine Learning - https://www.youtube.com/watch?v=-SqbDUiutu8

Textbook by Tamal Krishna Dey and Yusu Wang

• Computational Topology for Data Analysis - https://maa.org/press/maa-reviews/computational-topology-for-data-analysis

Dataset from Franc Jager et al

• Term-Preterm EHG DataSet with Tocogram - https://physionet.org/content/tpehgt/1.0.0/
• Jager F, Libenšek S, Geršak K (2018) Characterization and automatic classification of preterm and term uterine records. PLoS ONE 13(8): e0202125. https://doi.org/10.1371/journal.pone.0202125.
• Goldberger, A., Amaral, L., Glass, L., Hausdorff, J., Ivanov, P. C., Mark, R., Mietus, J.E., Moody, G.B., Peng, C.K., & Stanley, H. E. (2000). PhysioBank, PhysioToolkit, and PhysioNet: Components of a new research resource for complex physiologic signals. Circulation [Online]. 101 (23), pp. e215–e220.

Set up a Virtual Environment in Python

https://www.geeksforgeeks.org/create-virtual-environment-using-venv-python/

Get a Virtual Machine

I needed power, much more power, so I turned to Google Cloud and their free trial.

• Set up the Virtual Machine: Running Jupyter Notebook on Google Cloud Platform in 15 min, Amulya Aankul, https://towardsdatascience.com/running-jupyter-notebook-in-google-cloud-platform-in-15-min-61e16da34d52
• Set up Anaconda and Transfer Files: How to set up Anaconda under Google Cloud VM and transfer files on Windows, Raymond Chu, https://medium.com/google-cloud/set-up-anaconda-under-google-cloud-vm-on-windows-f71fc1064bd7