ncfs 0.1.2

Python implementation of Neighborhood Component Feature Selection (NCFS)

Neigbhorhood Component Feature Selection

This is a Python implementation of Neighborhood Component Feature Selection, originally introduced in Yang et al. 2012. NCFS is an embedded feature selection method that learns feature weights by maximizing prediction accuracy in a leave-one-out KNN classifier.

Installation

The package can be with pip using the following command:

pip install ncfs

Example

from NCFS import NCFS

X, y = NCFS.toy_dataset()
feature_select = NCFS.NCFS()
feature_select.fit(X, y)
print(sum(feature_select.coef_ > 1))

Tests

To compare results to the original paper run the following command python tests/generate_results.py

To perform unit tests ensuring accurate distance calculations, run: python tests/test_distances.py

Comparison with Original Results

Distance metric

The original paper uses the Manhattan distance when calculating distances between samples/features. While this implementation defaults to using this distance, weights comparable with published results were only found using the euclidean distance. However, while exact weights differed between distance metrics, the selected features did not. Unfortunately, the original paper did not link to the code used, and I've been unable to find a public implementation of the aglorithm.

Numerical stability

NCFS uses the original kernel function when calculating probabilities; however, with a large number of features, distance values can easily approach a large enough value such that the negative exponent rounds to zero. This leads to division by zero issues, and fitting fails. To get around this, small pseudocounts are added to distances when a division by zero would otherwise occur. To keep distances small, features should be scaled between 0 and 1 (enforced by NCFS).