Nonparametric causal discovery with applications to cancer bioinformatics

Abstract

Many natural phenomena are intrinsically causal. The discovery of the cause-effect relationships implicit in these processes can help us to understand and describe them more effectively, which boils down to causal discovery about the data and variables that describe them. However, causal discovery is not an easy task. Current methods for this are extremely complex and costly, and their usefulness is strongly compromised in contexts with large amounts of data or where the nature of the variables involved is unknown. As an alternative, this paper presents an original methodology for causal discovery, built on essential aspects of the main theories of causality, in particular probabilistic causality, with many meeting points with the inferential approach of regularity theories and others. Based on this methodology, a non-parametric algorithm is developed for the discovery of causal relationships between binary variables associated to data sets, and the modeling in graphs of the causal networks they describe. This algorithm is applied to gene expression data sets in normal and cancerous prostate tissues, with the aim of discovering cause-effect relationships between gene dysregulations leading to carcinogenesis. The gene characterizations constructed from the causal relationships discovered are compared with another study based on principal component analysis (PCA) on the same data, with satisfactory results.