Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Predicting worker disagreement for more effective crowd labeling

Crowdsourcing is a popular mechanism used for labeling tasks to produce large corpora for training. However, producing a reliable crowd labeled training corpus is challenging and resource consuming. Research on crowdsourcing has shown that label quality is much affected by worker engagement and expertise. In this study, we postulate that label quality can also be affected by inherent ambiguity of the documents to be labeled. Such ambiguities are not known in advance, of course, but, once encountered by the workers, they lead to disagreement in the labeling – a disagreement that cannot be resolved by employing more workers. To deal with this problem, we propose a crowd labeling framework: we train a disagreement predictor on a small seed of documents, and then use this predictor to decide which documents of the complete corpus should be labeled and which should be checked for document-inherent ambiguities before assigning (and potentially wasting) worker effort on them. We report on the findings of the experiments we conducted on crowdsourcing a Twitter corpus for sentiment classification

Knee Joint Angle Measuring Portable Embedded System based on Inertial Measurement Units for Gait Analysis

Inside clinical research, gait analysis is a fundamental part of the functional evaluation of the human body's movement. Its evaluation has been carried out through different methods and tools, which allow early diagnosis of diseases, and monitoring and assessing the effectiveness of therapeutic plans applied to patients for rehabilitation. The observational method is one of the most used in specialized centers in Colombia; however, to avoid any possible errors associated with the subjectivity observation, technological tools that provide quantitative data can support this method. This paper deals with the methodological process for developing a computational tool and hardware device for the analysis of gait, specifically on articular kinematics of the knee.  This work develops a prototype based on the fusion of inertial measurement units (IMU) data as an alternative for the attenuation of errors associated with each of these technologies. A videogrammetry technique measured the same human gait patterns to validate the proposed system, in terms of accuracy and repeatability of the recorded data. Results showed that the developed prototype successfully captured the knee-joint angles of the flexion-extension motions with high consistency and accuracy in with the measurements obtained from the videogrammetry technique. Statistical analysis (ICC and RMSE) exhibited a high correlation between the two systems for the measures of the joint angles. These results suggest the possibility of using an IMU-based prototype in realistic scenarios for accurately tracking a patient’s knee-joint kinematics during a human gait

Deep Learning Techniques for Music Generation -- A Survey

This paper is a survey and an analysis of different ways of using deep learning (deep artificial neural networks) to generate musical content. We propose a methodology based on five dimensions for our analysis: Objective - What musical content is to be generated? Examples are: melody, polyphony, accompaniment or counterpoint. - For what destination and for what use? To be performed by a human(s) (in the case of a musical score), or by a machine (in the case of an audio file). Representation - What are the concepts to be manipulated? Examples are: waveform, spectrogram, note, chord, meter and beat. - What format is to be used? Examples are: MIDI, piano roll or text. - How will the representation be encoded? Examples are: scalar, one-hot or many-hot. Architecture - What type(s) of deep neural network is (are) to be used? Examples are: feedforward network, recurrent network, autoencoder or generative adversarial networks. Challenge - What are the limitations and open challenges? Examples are: variability, interactivity and creativity. Strategy - How do we model and control the process of generation? Examples are: single-step feedforward, iterative feedforward, sampling or input manipulation. For each dimension, we conduct a comparative analysis of various models and techniques and we propose some tentative multidimensional typology. This typology is bottom-up, based on the analysis of many existing deep-learning based systems for music generation selected from the relevant literature. These systems are described and are used to exemplify the various choices of objective, representation, architecture, challenge and strategy. The last section includes some discussion and some prospects.Comment: 209 pages. This paper is a simplified version of the book: J.-P. Briot, G. Hadjeres and F.-D. Pachet, Deep Learning Techniques for Music Generation, Computational Synthesis and Creative Systems, Springer, 201

Doctor of Philosophy

dissertationFunctional magnetic resonance imaging (fMRI) measures the change of oxygen consumption level in the blood vessels of the human brain, hence indirectly detecting the neuronal activity. Resting-state fMRI (rs-fMRI) is used to identify the intrinsic functional patterns of the brain when there is no external stimulus. Accurate estimation of intrinsic activity is important for understanding the functional organization and dynamics of the brain, as well as differences in the functional networks of patients with mental disorders. This dissertation aims to robustly estimate the functional connectivities and networks of the human brain using rs-fMRI data of multiple subjects. We use Markov random field (MRF), an undirected graphical model to represent the statistical dependency among the functional network variables. Graphical models describe multivariate probability distributions that can be factorized and represented by a graph. By defining the nodes and the edges along with their weights according to our assumptions, we build soft constraints into the graph structure as prior information. We explore various approximate optimization methods including variational Bayesian, graph cuts, and Markov chain Monte Carlo sampling (MCMC). We develop the random field models to solve three related problems. In the first problem, the goal is to detect the pairwise connectivity between gray matter voxels in a rs-fMRI dataset of the single subject. We define a six-dimensional graph to represent our prior information that two voxels are more likely to be connected if their spatial neighbors are connected. The posterior mean of the connectivity variables are estimated by variational inference, also known as mean field theory in statistical physics. The proposed method proves to outperform the standard spatial smoothing and is able to detect finer patterns of brain activity. Our second work aims to identify multiple functional systems. We define a Potts model, a special case of MRF, on the network label variables, and define von Mises-Fisher distribution on the normalized fMRI signal. The inference is significantly more difficult than the binary classification in the previous problem. We use MCMC to draw samples from the posterior distribution of network labels. In the third application, we extend the graphical model to the multiple subject scenario. By building a graph including the network labels of both a group map and the subject label maps, we define a hierarchical model that has richer structure than the flat single-subject model, and captures the shared patterns as well as the variation among the subjects. All three solutions are data-driven Bayesian methods, which estimate model parameters from the data. The experiments show that by the regularization of MRF, the functional network maps we estimate are more accurate and more consistent across multiple sessions

An Overview of DNA Microarray Grid Alignment and Foreground Separation Approaches

This paper overviews DNA microarray grid alignment and foreground separation approaches. Microarray grid alignment and foreground separation are the basic processing steps of DNA microarray images that affect the quality of gene expression information, and hence impact our confidence in any data-derived biological conclusions. Thus, understanding microarray data processing steps becomes critical for performing optimal microarray data analysis. In the past, the grid alignment and foreground separation steps have not been covered extensively in the survey literature. We present several classifications of existing algorithms, and describe the fundamental principles of these algorithms. Challenges related to automation and reliability of processed image data are outlined at the end of this overview paper.</p

Fetal cardiac cine magnetic resonance imaging in utero.

Fast magnetic resonance imaging (MRI) led to the emergence of 'cine MRI' techniques, which enable the visualization of the beating heart and the assessment of cardiac morphology and dynamics. However, established cine MRI methods are not suitable for fetal heart imaging in utero, where anatomical structures are considerably smaller and recording an electrocardiogram signal for synchronizing MRI data acquisition is difficult. Here we present a framework to overcome these challenges. We use methods for image acquisition and reconstruction that robustly produce images with sufficient spatial and temporal resolution to detect the heart contractions of the fetus, enabling a retrospective gating of the images and thus the generation of images of the beating heart. To underline the potential of our approach, we acquired in utero images in six pregnant patients and compared these with their echocardiograms. We found good agreement in terms of diameter and area measurements, and low inter- and intra- observer variability. These results establish MRI as a reliable modality for fetal cardiac imaging, with a substantial potential for prenatal evaluation of congenital heart defects