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Register a new userComplete Inference of Causal Relations between Dynamical Systems
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Added by
Zsigmond Benk\\H{o}
Publication date
2018
fields
Biology
and research's language is
English
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From philosophers of ancient times to modern economists, biologists and other researchers are engaged in revealing causal relations. The most challenging problem is inferring the type of the causal relationship: whether it is uni- or bi-directional or only apparent - implied by a hidden common cause only. Modern technology provides us tools to record data from complex systems such as the ecosystem of our planet or the human brain, but understanding their functioning needs detection and distinction of causal relationships of the system components without interventions. Here we present a new method, which distinguishes and assigns probabilities to the presence of all the possible causal relations between two or more time series from dynamical systems. The new method is validated on synthetic datasets and applied to EEG (electroencephalographic) data recorded in epileptic patients. Given the universality of our method, it may find application in many fields of science.
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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, Patels Tau, Structural Equation Modelling, and Transfer Entropy. We finish with formulating some recommendations for the future directions in this area.
Understanding and even defining what constitutes animal interactions remains a challenging problem. Correlational tools may be inappropriate for detecting communication between a set of many agents exhibiting nonlinear behavior. A different approach is to define coordinated motions in terms of an information theoretic channel of direct causal information flow. In this work, we consider time series data obtained by an experimental protocol of optical tracking of the insect species Chironomus riparius. The data constitute reconstructed 3-D spatial trajectories of the insects flight trajectories and kinematics. We present an application of the optimal causation entropy (oCSE) principle to identify direct causal relationships or information channels among the insects. The collection of channels inferred by oCSE describes a network of information flow within the swarm. We find that information channels with a long spatial range are more common than expected under the assumption that causal information flows should be spatially localized. The tools developed herein are general and applicable to the inference and study of intercommunication networks in a wide variety of natural settings.
In this paper we present a new localization method SMS-LORETA (Simultaneous Multiple Sources- Low Resolution Brain Electromagnetic Tomography), capable to locate efficiently multiple simultaneous sources. The new method overcomes some of the drawbacks of sLORETA (standardized Low Resolution Brain Electromagnetic Tomography). The key idea of the new method is the iterative search for current dipoles, harnessing the low error single source localization performance of sLORETA. An evaluation of the new method by simulation has been enclosed.
In order to find effective treatments for Alzheimers disease (AD), we need to identify subjects at risk of AD as early as possible. To this end, recently developed disease progression models can be used to perform early diagnosis, as well as predict the subjects disease stages and future evolution. However, these models have not yet been applied to rare neurodegenerative diseases, are not suitable to understand the complex dynamics of biomarkers, work only on large multimodal datasets, and their predictive performance has not been objectively validated. In this work I developed novel models of disease progression and applied them to estimate the progression of Alzheimers disease and Posterior Cortical atrophy, a rare neurodegenerative syndrome causing visual deficits. My first contribution is a study on the progression of Posterior Cortical Atrophy, using models already developed: the Event-based Model (EBM) and the Differential Equation Model (DEM). My second contribution is the development of DIVE, a novel spatio-temporal model of disease progression that estimates fine-grained spatial patterns of pathology, potentially enabling us to understand complex disease mechanisms relating to pathology propagation along brain networks. My third contribution is the development of Disease Knowledge Transfer (DKT), a novel disease progression model that estimates the multimodal progression of rare neurodegenerative diseases from limited, unimodal datasets, by transferring information from larger, multimodal datasets of typical neurodegenerative diseases. My fourth contribution is the development of novel extensions for the EBM and the DEM, and the development of novel measures for performance evaluation of such models. My last contribution is the organization of the TADPOLE challenge, a competition which aims to identify algorithms and features that best predict the evolution of AD.
Neuroscientists are actively pursuing high-precision maps, or graphs, consisting of networks of neurons and connecting synapses in mammalian and non-mammalian brains. Such graphs, when coupled with physiological and behavioral data, are likely to facilitate greater understanding of how circuits in these networks give rise to complex information processing capabilities. Given that the automated or semi-automated methods required to achieve the acquisition of these graphs are still evolving, we develop a metric for measuring the performance of such methods by comparing their output with those generated by human annotators (ground truth data). Whereas classic metrics for comparing annotated neural tissue reconstructions generally do so at the voxel level, the metric proposed here measures the integrity of neurons based on the degree to which a collection of synaptic terminals belonging to a single neuron of the reconstruction can be matched to those of a single neuron in the ground truth data. The metric is largely insensitive to small errors in segmentation and more directly measures accuracy of the generated brain graph. It is our hope that use of the metric will facilitate the broader communitys efforts to improve upon existing methods for acquiring brain graphs. Herein we describe the metric in detail, provide demonstrative examples of the intuitive scores it generates, and apply it to a synthesized neural network with simulated reconstruction errors.
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