Disentangling causal webs in the brain using functional Magnetic Resonance Imaging: A review of current approaches

In the past two decades, functional Magnetic Resonance Imaging has been used to relate neuronal network activity to cognitive processing and behaviour. Recently this approach has been augmented by algorithms that allow us to infer causal links between component populations of neuronal networks. Multiple inference procedures have been proposed to approach this research question but so far, each method has limitations when it comes to establishing whole-brain connectivity patterns. In this work, we discuss eight ways to infer causality in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality, Likelihood Ratios, LiNGAM, Patel's Tau, Structural Equation Modelling, and Transfer Entropy. We finish with formulating some recommendations for the future directions in this area

Discriminative conditional restricted Boltzmann machine for discrete choice and latent variable modelling

Conventional methods of estimating latent behaviour generally use attitudinal questions which are subjective and these survey questions may not always be available. We hypothesize that an alternative approach can be used for latent variable estimation through an undirected graphical models. For instance, non-parametric artificial neural networks. In this study, we explore the use of generative non-parametric modelling methods to estimate latent variables from prior choice distribution without the conventional use of measurement indicators. A restricted Boltzmann machine is used to represent latent behaviour factors by analyzing the relationship information between the observed choices and explanatory variables. The algorithm is adapted for latent behaviour analysis in discrete choice scenario and we use a graphical approach to evaluate and understand the semantic meaning from estimated parameter vector values. We illustrate our methodology on a financial instrument choice dataset and perform statistical analysis on parameter sensitivity and stability. Our findings show that through non-parametric statistical tests, we can extract useful latent information on the behaviour of latent constructs through machine learning methods and present strong and significant influence on the choice process. Furthermore, our modelling framework shows robustness in input variability through sampling and validation

Inferring causal relations from multivariate time series : a fast method for large-scale gene expression data

Various multivariate time series analysis techniques have been developed with the aim of inferring causal relations between time series. Previously, these techniques have proved their effectiveness on economic and neurophysiological data, which normally consist of hundreds of samples. However, in their applications to gene regulatory inference, the small sample size of gene expression time series poses an obstacle. In this paper, we describe some of the most commonly used multivariate inference techniques and show the potential challenge related to gene expression analysis. In response, we propose a directed partial correlation (DPC) algorithm as an efficient and effective solution to causal/regulatory relations inference on small sample gene expression data. Comparative evaluations on the existing techniques and the proposed method are presented. To draw reliable conclusions, a comprehensive benchmarking on data sets of various setups is essential. Three experiments are designed to assess these methods in a coherent manner. Detailed analysis of experimental results not only reveals good accuracy of the proposed DPC method in large-scale prediction, but also gives much insight into all methods under evaluation