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

Machine Learning for Human Activity Detection in Smart Homes

Recognizing human activities in domestic environments from audio and active power consumption sensors is a challenging task since on the one hand, environmental sound signals are multi-source, heterogeneous, and varying in time and on the other hand, the active power consumption varies significantly for similar type electrical appliances. Many systems have been proposed to process environmental sound signals for event detection in ambient assisted living applications. Typically, these systems use feature extraction, selection, and classification. However, despite major advances, several important questions remain unanswered, especially in real-world settings. A part of this thesis contributes to the body of knowledge in the field by addressing the following problems for ambient sounds recorded in various real-world kitchen environments: 1) which features, and which classifiers are most suitable in the presence of background noise? 2) what is the effect of signal duration on recognition accuracy? 3) how do the SNR and the distance between the microphone and the audio source affect the recognition accuracy in an environment in which the system was not trained? We show that for systems that use traditional classifiers, it is beneficial to combine gammatone frequency cepstral coefficients and discrete wavelet transform coefficients and to use a gradient boosting classifier. For systems based on deep learning, we consider 1D and 2D CNN using mel-spectrogram energies and mel-spectrograms images, as inputs, respectively and show that the 2D CNN outperforms the 1D CNN. We obtained competitive classification results for two such systems and validated the performance of our algorithms on public datasets (Google Brain/TensorFlow Speech Recognition Challenge and the 2017 Detection and Classification of Acoustic Scenes and Events Challenge). Regarding the problem of the energy-based human activity recognition in a household environment, machine learning techniques to infer the state of household appliances from their energy consumption data are applied and rule-based scenarios that exploit these states to detect human activity are used. Since most activities within a house are related with the operation of an electrical appliance, this unimodal approach has a significant advantage using inexpensive smart plugs and smart meters for each appliance. This part of the thesis proposes the use of unobtrusive and easy-install tools (smart plugs) for data collection and a decision engine that combines energy signal classification using dominant classifiers (compared in advanced with grid search) and a probabilistic measure for appliance usage. It helps preserving the privacy of the resident, since all the activities are stored in a local database. DNNs received great research interest in the field of computer vision. In this thesis we adapted different architectures for the problem of human activity recognition. We analyze the quality of the extracted features, and more specifically how model architectures and parameters affect the ability of the automatically extracted features from DNNs to separate activity classes in the final feature space. Additionally, the architectures that we applied for our main problem were also applied to text classification in which we consider the input text as an image and apply 2D CNNs to learn the local and global semantics of the sentences from the variations of the visual patterns of words. This work helps as a first step of creating a dialogue agent that would not require any natural language preprocessing. Finally, since in many domestic environments human speech is present with other environmental sounds, we developed a Convolutional Recurrent Neural Network, to separate the sound sources and applied novel post-processing filters, in order to have an end-to-end noise robust system. Our algorithm ranked first in the Apollo-11 Fearless Steps Challenge.Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 676157, project ACROSSIN

Cell Nuclear Morphology Analysis Using 3D Shape Modeling, Machine Learning and Visual Analytics

Quantitative analysis of morphological changes in a cell nucleus is important for the understanding of nuclear architecture and its relationship with cell differentiation, development, proliferation, and disease. Changes in the nuclear form are associated with reorganization of chromatin architecture related to altered functional properties such as gene regulation and expression. Understanding these processes through quantitative analysis of morphological changes is important not only for investigating nuclear organization, but also has clinical implications, for example, in detection and treatment of pathological conditions such as cancer. While efforts have been made to characterize nuclear shapes in two or pseudo-three dimensions, several studies have demonstrated that three dimensional (3D) representations provide better nuclear shape description, in part due to the high variability of nuclear morphologies. 3D shape descriptors that permit robust morphological analysis and facilitate human interpretation are still under active investigation. A few methods have been proposed to classify nuclear morphologies in 3D, however, there is a lack of publicly available 3D data for the evaluation and comparison of such algorithms. There is a compelling need for robust 3D nuclear morphometric techniques to carry out population-wide analyses. In this work, we address a number of these existing limitations. First, we present a largest publicly available, to-date, 3D microscopy imaging dataset for cell nuclear morphology analysis and classification. We provide a detailed description of the image analysis protocol, from segmentation to baseline evaluation of a number of popular classification algorithms using 2D and 3D voxel-based morphometric measures. We proposed a specific cross-validation scheme that accounts for possible batch effects in data. Second, we propose a new technique that combines mathematical modeling, machine learning, and interpretation of morphometric characteristics of cell nuclei and nucleoli in 3D. Employing robust and smooth surface reconstruction methods to accurately approximate 3D object boundary enables the establishment of homologies between different biological shapes. Then, we compute geometric morphological measures characterizing the form of cell nuclei and nucleoli. We combine these methods into a highly parallel computational pipeline workflow for automated morphological analysis of thousands of nuclei and nucleoli in 3D. We also describe the use of visual analytics and deep learning techniques for the analysis of nuclear morphology data. Third, we evaluate proposed methods for 3D surface morphometric analysis of our data. We improved the performance of morphological classification between epithelial vs mesenchymal human prostate cancer cells compared to the previously reported results due to the more accurate shape representation and the use of combined nuclear and nucleolar morphometry. We confirmed previously reported relevant morphological characteristics, and also reported new features that can provide insight in the underlying biological mechanisms of pathology of prostate cancer. We also assessed nuclear morphology changes associated with chromatin remodeling in drug-induced cellular reprogramming. We computed temporal trajectories reflecting morphological differences in astroglial cell sub-populations administered with 2 different treatments vs controls. We described specific changes in nuclear morphology that are characteristic of chromatin re-organization under each treatment, which previously has been only tentatively hypothesized in literature. Our approach demonstrated high classification performance on each of 3 different cell lines and reported the most salient morphometric characteristics. We conclude with the discussion of the potential impact of method development in nuclear morphology analysis on clinical decision-making and fundamental investigation of 3D nuclear architecture. We consider some open problems and future trends in this field.PHDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/147598/1/akalinin_1.pd

Deep Learning in Medical Image Analysis

The accelerating power of deep learning in diagnosing diseases will empower physicians and speed up decision making in clinical environments. Applications of modern medical instruments and digitalization of medical care have generated enormous amounts of medical images in recent years. In this big data arena, new deep learning methods and computational models for efficient data processing, analysis, and modeling of the generated data are crucially important for clinical applications and understanding the underlying biological process. This book presents and highlights novel algorithms, architectures, techniques, and applications of deep learning for medical image analysis

Brain Network Connectivity in Anaesthesia and Disorders of Consciousness

Until recently, understanding the nature of consciousness was considered a philosophical pursuit. However, technological developments in brain imaging have allowed the study of consciousness as a natural, neurobiological phenomenon. The neurobiology of consciousness has been studied using cognitive and behavioural testing in healthy volunteers and by examining how brain function and connectivity is altered in various clinical settings. The focus of this thesis is to use two of these clinical settings, pharmacologically-induced sedation and disorders of consciousness (DOC), as experimental models for measuring changes in connectivity patterns associated with alterations in consciousness. Experiment 1 presents a method for improving functional magnetic resonance imaging (fMRI) data pre-processing to measure brain network connectivity more accurately. This pre-processing method is then applied to the analyses in the remainder of the thesis. Experiment 2 focuses on a fMRI dataset in which healthy volunteers were administered propofol, an anaesthetic drug known to act on inhibitory GABAergic interneurons. Using a novel multimodal analysis, changes in functional brain network connectivity in default mode, salience, and frontoparietal control networks were found to correlate with the cortical distribution of parvalbumin-expressing GABAergic interneurons. Using the same dataset, Experiment 3 identified a relationship between structural and functional networks in connections between default mode and salience networks. Similar results have been reported in non-human primate models, however, this is the first study to find network-specific structure-function relationships during sedation in humans. These findings informed the remainder of the thesis, which focused on developing network-based machine learning methods for examining brain connectivity in patients with DOC. Experiment 4 developed and validated a graph convolutional neural network (GCNN) classifier using fMRI data and functional connectivity from healthy volunteers performing a volitional mental imagery task. Experiment 5 applied the GCNN to patients with DOC and found frontoparietal control network connectivity measured at rest to be most important in classifying patients capable of performing the mental imagery task. Taken together, these results contribute to the improvement of brain network analysis techniques, the understanding of the neurobiology of propofol-induced sedation, and the development of machine learning algorithms to identify DOC patients with preserved covert volitional capacity. This work demonstrates the utility of clinical models in deepening our understanding of the neurobiology of consciousness

Computational Imaging for Phase Retrieval and Biomedical Applications

In conventional imaging, optimizing hardware is prioritized to enhance image quality directly. Digital signal processing is viewed as supplementary. Computational imaging intentionally distorts images through modulation schemes in illumination or sensing. Then its reconstruction algorithms extract desired object information from raw data afterwards. Co-designing hardware and algorithms reduces demands on hardware and achieves the same or even better image quality. Algorithm design is at the heart of computational imaging, with model-based inverse problem or data-driven deep learning methods as approaches. This thesis presents research work from both perspectives, with a primary focus on the phase retrieval issue in computational microscopy and the application of deep learning techniques to address biomedical imaging challenges. The first half of the thesis begins with Fourier ptychography, which was employed to overcome chromatic aberration problems in multispectral imaging. Then, we proposed a novel computational coherent imaging modality based on Kramers-Kronig relations, aiming to replace Fourier ptychography as a non-iterative method. While this approach showed promise, it lacks certain essential characteristics of the original Fourier ptychography. To address this limitation, we introduced two additional algorithms to form a whole package scheme. Through comprehensive evaluation, we demonstrated that the combined scheme outperforms Fourier ptychography in achieving high-resolution, large field-of-view, aberration-free coherent imaging. The second half of the thesis shifts focus to deep-learning-based methods. In one project, we optimized the scanning strategy and image processing pipeline of an epifluorescence microscope to address focus issues. Additionally, we leveraged deep-learning-based object detection models to automate cell analysis tasks. In another project, we predicted the polarity status of mouse embryos from bright field images using adapted deep learning models. These findings highlight the capability of computational imaging to automate labor-intensive processes, and even outperform humans in challenging tasks.</p

Nonlinear Model Reduction of Stochastic Microdynamics

This thesis presents a nonlinear model reduction procedure for stochastic microdynamics models that possess mesoscale separation between fast and slow dynamics. Model reduction procedures typically reduce the dimension of deterministic dynamical systems through linear projection operators which offer limited compression capabilities for nonlinear systems. On the other hand, deep neural networks provide a class of nonlinear transformations for regression that can approximate arbitrarily complex functions. The approach developed in this thesis attempts to carry out nonlinear model reduction of stochastic models using deep neural networks to approximate a transformation onto reduced coordinates taken to be the parameters of the network. The stochasticity of the microdynamics is inherited by the reduced, mesoscale model by viewing the parameters as stochastic processes. Moderate time scale separation suggests that non-Gaussian behavior must be considered in contrast with the convergence to Gaussian noise in the limit of infinite timescale separation provided by homogenization theory. This thesis considers several approaches for modeling the stochastic processes concluding with an information geometric strategy for estimating probability distribution functions. The procedure is applied to protein folding within molecular dynamics simulations, a widely used technique to model large collections of atoms which interact through nonlinear forces and are driven by a stochastic heat bath. Protein folding occurs on a larger, mesoscale with respect to the timescale of numerical integration.Doctor of Philosoph

Recent Studies of Rodent Ultrasonic Vocalizations and Their Use in Experimental Models

This book includes articles written by over 80 specialists from many countries that demonstrate the biological functions of ultrasonic vocalizations and how they are used in studies of vocal expression of emotional states and in numerous animal models of neuropsychiatric diseases and disorders. Results of investigations of emissions of ultrasonic vocalizations are useful in studies of emotional disturbances, affective disorders, autism spectrum disorders, addiction, developmental abnormalities, and many other pathologies

Safety and Reliability - Safe Societies in a Changing World

The contributions cover a wide range of methodologies and application areas for safety and reliability that contribute to safe societies in a changing world. These methodologies and applications include: - foundations of risk and reliability assessment and management - mathematical methods in reliability and safety - risk assessment - risk management - system reliability - uncertainty analysis - digitalization and big data - prognostics and system health management - occupational safety - accident and incident modeling - maintenance modeling and applications - simulation for safety and reliability analysis - dynamic risk and barrier management - organizational factors and safety culture - human factors and human reliability - resilience engineering - structural reliability - natural hazards - security - economic analysis in risk managemen