On genetic programming representations and fitness functions for interpretable dimensionality reduction

Genetic and Evolutionary Computation Conference (GECCO), pp. 458–466

Abstract

Dimensionality reduction (DR) is an important technique for data exploration and knowledge discovery. However, most of the main DR methods are either linear (e.g., PCA), do not provide an explicit mapping between the original data and its lower-dimensional representation (e.g., MDS, t-SNE, isomap), or produce mappings that cannot be easily interpreted (e.g., kernel PCA, neural-based autoencoder). Recently genetic programming (GP) has been used to evolve interpretable DR mappings in the form of symbolic expressions. There exists a number of ways in which GP can be used to this end and no study exists that performs a comparison. In this paper, we fill this gap by comparing existing GP methods as well as devising new ones. We evaluate our methods on several benchmark datasets based on predictive accuracy and on how well the original features can be reconstructed using the lower-dimensional representation only. Finally we qualitatively assess the resulting expressions and their complexity. We find that various GP methods can be competitive with state-of-the-art DR algorithms and that they have the potential to produce interpretable DR mappings.

Authors 4

1. Thomas Uriot Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, Leiden, The Netherlands

2. Marco Virgolin

   Centrum Wiskunde & Informatica

   Affiliation as printed

   Centrum Wiskunde & Informatica, Amsterdam, The Netherlands

3. Tanja Alderliesten Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, Leiden, The Netherlands

4. Peter A. N. Bosman

   Centrum Wiskunde & Informatica

   Affiliation as printed

   Centrum Wiskunde & Informatica, Amsterdam, The Netherlands