A Primer on Causal Analysis

We provide a conceptual map to navigate causal analysis problems. Focusing on the case of discrete random variables, we consider the case of causal effect estimation from observational data. The presented approaches apply also to continuous variables, but the issue of estimation becomes more complex. We then introduce the four schools of thought for causal analysisComment: Parts of this document are copied verbatim from Finnian Lattimore's PhD thesis, ANU 201

Explaining Deep Learning Models using Causal Inference

Although deep learning models have been successfully applied to a variety of tasks, due to the millions of parameters, they are becoming increasingly opaque and complex. In order to establish trust for their widespread commercial use, it is important to formalize a principled framework to reason over these models. In this work, we use ideas from causal inference to describe a general framework to reason over CNN models. Specifically, we build a Structural Causal Model (SCM) as an abstraction over a specific aspect of the CNN. We also formulate a method to quantitatively rank the filters of a convolution layer according to their counterfactual importance. We illustrate our approach with popular CNN architectures such as LeNet5, VGG19, and ResNet32

Using Unsupervised Learning to Help Discover the Causal Graph

The software outlined in this paper, AitiaExplorer, is an exploratory causal analysis tool which uses unsupervised learning for feature selection in order to expedite causal discovery. In this paper the problem space of causality is briefly described and an overview of related research is provided. A problem statement and requirements for the software are outlined. The key requirements in the implementation, the key design decisions and the actual implementation of AitiaExplorer are discussed. Finally, this implementation is evaluated in terms of the problem statement and requirements outlined earlier. It is found that AitiaExplorer meets these requirements and is a useful exploratory causal analysis tool that automatically selects subsets of important features from a dataset and creates causal graph candidates for review based on these features. The software is available at https://github.com/corvideon/aitiaexplore

Genome-wide Causation Studies of Complex Diseases

Despite significant progress in dissecting the genetic architecture of complex diseases by genome-wide association studies (GWAS), the signals identified by association analysis may not have specific pathological relevance to diseases so that a large fraction of disease causing genetic variants is still hidden. Association is used to measure dependence between two variables or two sets of variables. Genome-wide association studies test association between a disease and SNPs (or other genetic variants) across the genome. Association analysis may detect superficial patterns between disease and genetic variants. Association signals provide limited information on the causal mechanism of diseases. The use of association analysis as a major analytical platform for genetic studies of complex diseases is a key issue that hampers discovery of the mechanism of diseases, calling into question the ability of GWAS to identify loci underlying diseases. It is time to move beyond association analysis toward techniques enabling the discovery of the underlying causal genetic strctures of complex diseases. To achieve this, we propose a concept of a genome-wide causation studies (GWCS) as an alternative to GWAS and develop additive noise models (ANMs) for genetic causation analysis. Type I error rates and power of the ANMs to test for causation are presented. We conduct GWCS of schizophrenia. Both simulation and real data analysis show that the proportion of the overlapped association and causation signals is small. Thus, we hope that our analysis will stimulate discussion of GWAS and GWCS.Comment: 61 pages, 5 figure