Applications of brain imaging methods in driving behaviour research

Applications of neuroimaging methods have substantially contributed to the scientific understanding of human factors during driving by providing a deeper insight into the neuro-cognitive aspects of driver brain. This has been achieved by conducting simulated (and occasionally, field) driving experiments while collecting driver brain signals of certain types. Here, this sector of studies is comprehensively reviewed at both macro and micro scales. Different themes of neuroimaging driving behaviour research are identified and the findings within each theme are synthesised. The surveyed literature has reported on applications of four major brain imaging methods. These include Functional Magnetic Resonance Imaging (fMRI), Electroencephalography (EEG), Functional Near-Infrared Spectroscopy (fNIRS) and Magnetoencephalography (MEG), with the first two being the most common methods in this domain. While collecting driver fMRI signal has been particularly instrumental in studying neural correlates of intoxicated driving (e.g. alcohol or cannabis) or distracted driving, the EEG method has been predominantly utilised in relation to the efforts aiming at development of automatic fatigue/drowsiness detection systems, a topic to which the literature on neuro-ergonomics of driving particularly has shown a spike of interest within the last few years. The survey also reveals that topics such as driver brain activity in semi-automated settings or the brain activity of drivers with brain injuries or chronic neurological conditions have by contrast been investigated to a very limited extent. Further, potential topics in relation to driving behaviour are identified that could benefit from the adoption of neuroimaging methods in future studies

NiftyNet: a deep-learning platform for medical imaging

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.Comment: Wenqi Li and Eli Gibson contributed equally to this work. M. Jorge Cardoso and Tom Vercauteren contributed equally to this work. 26 pages, 6 figures; Update includes additional applications, updated author list and formatting for journal submissio

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Deep Active Inference for Autonomous Robot Navigation

Active inference is a theory that underpins the way biological agent's perceive and act in the real world. At its core, active inference is based on the principle that the brain is an approximate Bayesian inference engine, building an internal generative model to drive agents towards minimal surprise. Although this theory has shown interesting results with grounding in cognitive neuroscience, its application remains limited to simulations with small, predefined sensor and state spaces. In this paper, we leverage recent advances in deep learning to build more complex generative models that can work without a predefined states space. State representations are learned end-to-end from real-world, high-dimensional sensory data such as camera frames. We also show that these generative models can be used to engage in active inference. To the best of our knowledge this is the first application of deep active inference for a real-world robot navigation task.Comment: workshop paper at BAICS at ICLR 202

Deep Interpretability Methods for Neuroimaging

Brain dynamics are highly complex and yet hold the key to understanding brain function and dysfunction. The dynamics captured by resting-state functional magnetic resonance imaging data are noisy, high-dimensional, and not readily interpretable. The typical approach of reducing this data to low-dimensional features and focusing on the most predictive features comes with strong assumptions and can miss essential aspects of the underlying dynamics. In contrast, introspection of discriminatively trained deep learning models may uncover disorder-relevant elements of the signal at the level of individual time points and spatial locations. Nevertheless, the difficulty of reliable training on high-dimensional but small-sample datasets and the unclear relevance of the resulting predictive markers prevent the widespread use of deep learning in functional neuroimaging. In this dissertation, we address these challenges by proposing a deep learning framework to learn from high-dimensional dynamical data while maintaining stable, ecologically valid interpretations. The developed model is pre-trainable and alleviates the need to collect an enormous amount of neuroimaging samples to achieve optimal training. We also provide a quantitative validation module, Retain and Retrain (RAR), that can objectively verify the higher predictability of the dynamics learned by the model. Results successfully demonstrate that the proposed framework enables learning the fMRI dynamics directly from small data and capturing compact, stable interpretations of features predictive of function and dysfunction. We also comprehensively reviewed deep interpretability literature in the neuroimaging domain. Our analysis reveals the ongoing trend of interpretability practices in neuroimaging studies and identifies the gaps that should be addressed for effective human-machine collaboration in this domain. This dissertation also proposed a post hoc interpretability method, Geometrically Guided Integrated Gradients (GGIG), that leverages geometric properties of the functional space as learned by a deep learning model. With extensive experiments and quantitative validation on MNIST and ImageNet datasets, we demonstrate that GGIG outperforms integrated gradients (IG), which is considered to be a popular interpretability method in the literature. As GGIG is able to identify the contours of the discriminative regions in the input space, GGIG may be useful in various medical imaging tasks where fine-grained localization as an explanation is beneficial