error in Isomap function

I was trying to run the Isomap function on my dataset (32 rows and 1632 columns).

function [Y, R, E] = Isomap(D, n_fcn, n_size, options);

what should be the n_fcn and n_size?

Do I need to do any preprocessing?

Answer 1

[Pratyush Swain]

Hi Pritom,

I guess you are referring to this file exchange function: https://www.mathworks.com/matlabcentral/fileexchange/62449-isomap-d-n_fcn-n_size-options

The Isomap algorithm builds a neighborhood to understand which points are "close" to each other in your high-dimensional data.

1. 'n_fcn' is the neighborhood selection method. It can be 'k' (for k nearest neighbor) or 'epsilon' (connects to all points within distance epsilon)
2. 'n_size' is the the value chosen for your neighborhood method 'n_fcn'. If n_fcn = 'k', then n_size should be integer (like 2,5,etc.) or if n_fcn = 'epsilon', then n_size should be distance threshold (0.5,1,etc.)

Isomap works on D(Distance Matrix), a NxN matrix which contains pairwise distance between data points and hence cannot directly work on your raw data. You can perform a preprocessing similar to as follows:

% Data Size: 32 data points with each 1632 features %

% Compute a 32x32 distance matrix %

% Calculates euclidean distance by default, but other distance metrics can be specified %
D = pdist2(data, data);   

% Can also conider normalizing the data %

D = normalize(D,2) % Nomalizes each row

% Now you can pass D to Isomap: example usage with k=5 neighbors %
[Y, R, E] = Isomap(D, 'k', 5); 

For more information on the functions used above, please refer to

1. https://www.mathworks.com/help/stats/pdist2.html
2. https://www.mathworks.com/help/matlab/ref/double.normalize.html

Hope this helps.