saturnscore 1.2.1

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.

Please notice that I developed the Saturn coefficient package originally in R, which is programming language I know better and is also where I was able to make more tests. I then ported this software package from R to Python, and here you can find the outcome. If you find anything that should be improved, please let me know.

Installation

You can execute the following command to install this package and its dependencies:

pip3 install numpy pandas scipy umap-learn scikit-learn saturnscore

Example

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

import numpy as np
import pandas as pd
import scipy
import umap.umap_ as umap
from saturnscore import Saturn_coefficient
from sklearn.preprocessing import StandardScaler

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)

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 something like Saturn coefficient = 0.1029461972317906 (this value might be slightly different because of the random component of UMAP).

Contact

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