Any Matlab procedure to compute Peristence Diagram in a dimension higher than 3? I have the Topological Data Analysis module but the procedures go just up to dim-3

I have the Topological Data Analysis module (Matlab) but the procedures go just up to dim-3

Answer 1

[Aditya]

Hi tanya ,

Currently, MATLAB’s Topological Data Analysis (TDA) module only supports computation of persistence diagrams up to dimension 3. If you need to compute persistence diagrams in higher dimensions, you will need to use an external library such as GUDHI or Ripser, which support arbitrary homology dimensions. You can interface these Python libraries with MATLAB using the built-in Python integration. Below is an example of how you might use GUDHI from MATLAB to compute persistence diagrams in higher dimensions:

% Make sure Python and GUDHI are installed and recognized by MATLAB
pyenv('Version', '/usr/bin/python3'); % Adjust the path to your Python installation

% Example data: a point cloud as a MATLAB NxD matrix
X = rand(100, 5); % 100 points in 5D

% Convert MATLAB array to Python list of lists
py_points = py.list(num2cell(X, 2));

% Create Rips complex and simplex tree in GUDHI (up to dimension 5)
rips_complex = py.gudhi.RipsComplex('points', py_points, 'max_edge_length', 2.0);
simplex_tree = rips_complex.create_simplex_tree('max_dimension', int32(5));

% Compute persistence diagram
diag = simplex_tree.persistence();

% Extract and display the persistence pairs (as a Python list of tuples)
pairs = simplex_tree.persistence_pairs();
disp(pairs)