saturnscore 1.0.5

Saturn coefficient to assess the results of an UMAP dimensionality reduction

Saturn score

Summary

A Python package that computes the Saturn coefficient of a matrix to assess the quality of its UMAP dimensionality reduction.

Installation

You can run the following command to install this package:

pip3 install saturnscore

Example

You can run the following Python code to test your package installation:

import numpy as np import pandas as pd import random import scipy import umap.umap_ as umap from saturnscore import Saturn_coefficient

# Test Example
if __name__ == "__main__":
    random.seed(0)
    np.random.seed(0)  # Set random seed for reproducibility
    input_data = np.random.randn(120, 200)  # Generate random matrix X1

    these_n_neighbors = 20
    this_min_dist = 0.01
    these_n_components = 2
    this_metric = 'euclidean'
    this_random_state = 42
    this_n_jobs = 1
    this_n_epochs = 200

    print("these_n_neighbors = ", these_n_neighbors)
    print("this_min_dist = ", this_min_dist)
    print("these_n_components = ", these_n_components)
    print("this_metric = ", this_metric)

    umap_verbose = False
    fit = umap.UMAP(n_neighbors=these_n_neighbors,
        min_dist=this_min_dist,
        n_components=these_n_components,
        metric=this_metric,
        n_jobs=this_n_jobs,
        random_state=this_random_state,
        n_epochs = this_n_epochs,
        verbose=umap_verbose)

    if(umap_verbose == True):
        pprint.pp(fit.get_params())
    umap_output_layout = fit.fit_transform(input_data)

    result = Saturn_coefficient.SaturnCoefficient(input_data, umap_output_layout)
    print(f" Saturn coefficient =  ", result)

The final command should print Saturn coefficient = 0.11817430122179944

Contact

The SaturnScore package was developed by Davide Chicco. Questions should be addressed to davidechicco(AT)davidechicco.it