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

Unsupervised Manifold Learning using High-order Morphological Brain Networks derived from T1-w MRI for Autism Diagnosis

Brain disorders, such as Autism Spectrum Disorder (ASD), alter brain functional (from fMRI) and structural (from diffusion MRI) connectivities at multiple levels and in varying degrees. While unraveling such alterations have been the focus of a large number of studies, morphological brain connectivity has been out of the research scope. In particular, shape-to-shape relationships across brain regions of interest (ROIs) were rarely investigated. As such, the use of networks based on morphological brain data in neurological disorder diagnosis, while leveraging the advent of machine learning, could complement our knowledge on brain wiring alterations in unprecedented ways. In this paper, we use conventional T1-weighted MRI to define morphological brain networks (MBNs), each quantifying shape relationship between different cortical regions for a specific cortical attribute at both low-order and high-order levels. While typical brain connectomes investigate the relationship between two ROIs, we propose high-order MBN which better captures brain complex interactions by modeling the morphological relationship between pairs of ROIs. For ASD identification, we present a connectomic manifold learning framework, which learns multiple kernels to estimate a similarity measure between ASD and normal controls (NC) connectional features, to perform dimensionality reduction for clustering ASD and NC subjects. We benchmark our ASD identification method against both supervised and unsupervised state-of-the-art methods, while depicting the most discriminative high- and low-order relationships between morphological regions in the left and right hemispheres

Data-driven detection of multi-messenger transients

The primary challenge in the study of explosive astrophysical transients is their detection and characterisation using multiple messengers. For this purpose, we have developed a new data-driven discovery framework, based on deep learning. We demonstrate its use for searches involving neutrinos, optical supernovae, and gamma rays. We show that we can match or substantially improve upon the performance of state-of-the-art techniques, while significantly minimising the dependence on modelling and on instrument characterisation. Particularly, our approach is intended for near- and real-time analyses, which are essential for effective follow-up of detections. Our algorithm is designed to combine a range of instruments and types of input data, representing different messengers, physical regimes, and temporal scales. The methodology is optimised for agnostic searches of unexpected phenomena, and has the potential to substantially enhance their discovery prospects.Comment: 16 page

Unsupervised detection of regions of interest using iterative link analysis

This paper proposes a fast and scalable alternating optimization technique to detect regions of interest (ROIs) in cluttered Web images without labels. The proposed approach discovers highly probable regions of object instances by iteratively repeating the following two functions: (1) choose the exemplar set (i.e. a small number of highly ranked reference ROIs) across the dataset and (2) refine the ROIs of each image with respect to the exemplar set. These two subproblems are formulated as ranking in two different similarity networks of ROI hypotheses by link analysis. The experiments with the PASCAL 06 dataset show that our unsupervised localization performance is better than one of state-of-the-art techniques and comparable to supervised methods. Also, we test the scalability of our approach with five objects in Flickr dataset consisting of more than 200K images

Domain-general Stroop Performance and Hemispheric Asymmetries: A Resting-state EEG Study

The ability to suppress irrelevant information while executing a task or interference resistance is a function of pFC that is critical for successful goal-directed human behavior. In the study of interference resistance and, more generally, executive functions, two key questions are still open: Does pFC contribute to cognitive control abilities through lateralized but domain-general mechanisms or through hemispheric specialization of domain-specific processes? And what are the underlying causes of interindividual differences in executive control performance? To shed light on these issues, here we employed an interindividual difference approach to investigate whether participants' hemispheric asymmetry in resting-state electrophysiological brain dynamics may reflect their variability in domain-general interference resistance. We recorded participants' resting-state electroencephalographic activity and performed spectral power analyses on the estimated cortical source activity. To measure participants' lateralized brain dynamics at rest, we computed the right-left hemispheric asymmetry score for the \u3b2/\u3b1 power ratio. To measure their domain-general interference resistance ability, verbal and spatial Stroop tasks were used. Robust correlations followed by intersection analyses showed that participants with stronger resting-state-related left-lateralized activity in different pFC regions, namely the mid-posterior superior frontal gyrus, middle and posterior middle frontal gyrus, and inferior frontal junction, were more able to inhibit irrelevant information in both domains. The present results confirm and extend previous findings showing that neurophysiological difference factors may explain interindividual differences in executive functioning. They also provide support for the hypothesis of a left pFC hemispheric specialization for domain-independent phasic cognitive control processes mediating Stroop performance

Tissue Phenomics for prognostic biomarker discovery in low- and intermediate-risk prostate cancer

Tissue Phenomics is the discipline of mining tissue images to identify patterns that are related to clinical outcome providing potential prognostic and predictive value. This involves the discovery process from assay development, image analysis, and data mining to the final interpretation and validation of the findings. Importantly, this process is not linear but allows backward steps and optimization loops over multiple sub-processes. We provide a detailed description of the Tissue Phenomics methodology while exemplifying each step on the application of prostate cancer recurrence prediction. In particular, we automatically identified tissue-based biomarkers having significant prognostic value for low-and intermediate-risk prostate cancer patients (Gleason scores 6-7b) after radical prostatectomy. We found that promising phenes were related to CD8(+) and CD68(+) cells in the microenvironment of cancerous glands in combination with the local micro-vascularization. Recurrence prediction based on the selected phenes yielded accuracies up to 83% thereby clearly outperforming prediction based on the Gleason score. Moreover, we compared different machine learning algorithms to combine the most relevant phenes resulting in increased accuracies of 88% for tumor progression prediction. These findings will be of potential use for future prognostic tests for prostate cancer patients and provide a proof-of-principle of the Tissue Phenomics approach