A framework based on Gaussian mixture models and Kalman filters for the segmentation and tracking of anomalous events in shipboard video

Anomalous indications in monitoring equipment on board U.S. Navy vessels must be handled in a timely manner to prevent catastrophic system failure. The development of sensor data analysis techniques to assist a ship\u27s crew in monitoring machinery and summon required ship-to-shore assistance is of considerable benefit to the Navy. In addition, the Navy has a large interest in the development of distance support technology in its ongoing efforts to reduce manning on ships. In this thesis, algorithms have been developed for the detection of anomalous events that can be identified from the analysis of monochromatic stationary ship surveillance video streams. The specific anomalies that we have focused on are the presence and growth of smoke and fire events inside the frames of the video stream. The algorithm consists of the following steps. First, a foreground segmentation algorithm based on adaptive Gaussian mixture models is employed to detect the presence of motion in a scene. The algorithm is adapted to emphasize gray-level characteristics related to smoke and fire events in the frame. Next, shape discriminant features in the foreground are enhanced using morphological operations. Following this step, the anomalous indication is tracked between frames using Kalman filtering. Finally, gray level shape and motion features corresponding to the anomaly are subjected to principal component analysis and classified using a multilayer perceptron neural network. The algorithm is exercised on 68 video streams that include the presence of anomalous events (such as fire and smoke) and benign/nuisance events (such as humans walking the field of view). Initial results show that the algorithm is successful in detecting anomalies in video streams, and is suitable for application in shipboard environments

Methods for Analysing Endothelial Cell Shape and Behaviour in Relation to the Focal Nature of Atherosclerosis

The aim of this thesis is to develop automated methods for the analysis of the spatial patterns, and the functional behaviour of endothelial cells, viewed under microscopy, with applications to the understanding of atherosclerosis. Initially, a radial search approach to segmentation was attempted in order to trace the cell and nuclei boundaries using a maximum likelihood algorithm; it was found inadequate to detect the weak cell boundaries present in the available data. A parametric cell shape model was then introduced to fit an equivalent ellipse to the cell boundary by matching phase-invariant orientation fields of the image and a candidate cell shape. This approach succeeded on good quality images, but failed on images with weak cell boundaries. Finally, a support vector machines based method, relying on a rich set of visual features, and a small but high quality training dataset, was found to work well on large numbers of cells even in the presence of strong intensity variations and imaging noise. Using the segmentation results, several standard shear-stress dependent parameters of cell morphology were studied, and evidence for similar behaviour in some cell shape parameters was obtained in in-vivo cells and their nuclei. Nuclear and cell orientations around immature and mature aortas were broadly similar, suggesting that the pattern of flow direction near the wall stayed approximately constant with age. The relation was less strong for the cell and nuclear length-to-width ratios. Two novel shape analysis approaches were attempted to find other properties of cell shape which could be used to annotate or characterise patterns, since a wide variability in cell and nuclear shapes was observed which did not appear to fit the standard parameterisations. Although no firm conclusions can yet be drawn, the work lays the foundation for future studies of cell morphology. To draw inferences about patterns in the functional response of cells to flow, which may play a role in the progression of disease, single-cell analysis was performed using calcium sensitive florescence probes. Calcium transient rates were found to change with flow, but more importantly, local patterns of synchronisation in multi-cellular groups were discernable and appear to change with flow. The patterns suggest a new functional mechanism in flow-mediation of cell-cell calcium signalling

Modeling and Analysis of Neural Spike Trains

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Text Similarity Between Concepts Extracted from Source Code and Documentation

Context: Constant evolution in software systems often results in its documentation losing sync with the content of the source code. The traceability research field has often helped in the past with the aim to recover links between code and documentation, when the two fell out of sync. Objective: The aim of this paper is to compare the concepts contained within the source code of a system with those extracted from its documentation, in order to detect how similar these two sets are. If vastly different, the difference between the two sets might indicate a considerable ageing of the documentation, and a need to update it. Methods: In this paper we reduce the source code of 50 software systems to a set of key terms, each containing the concepts of one of the systems sampled. At the same time, we reduce the documentation of each system to another set of key terms. We then use four different approaches for set comparison to detect how the sets are similar. Results: Using the well known Jaccard index as the benchmark for the comparisons, we have discovered that the cosine distance has excellent comparative powers, and depending on the pre-training of the machine learning model. In particular, the SpaCy and the FastText embeddings offer up to 80% and 90% similarity scores. Conclusion: For most of the sampled systems, the source code and the documentation tend to contain very similar concepts. Given the accuracy for one pre-trained model (e.g., FastText), it becomes also evident that a few systems show a measurable drift between the concepts contained in the documentation and in the source code.</p

A Statistical Approach to the Alignment of fMRI Data

Multi-subject functional Magnetic Resonance Image studies are critical. The anatomical and functional structure varies across subjects, so the image alignment is necessary. We define a probabilistic model to describe functional alignment. Imposing a prior distribution, as the matrix Fisher Von Mises distribution, of the orthogonal transformation parameter, the anatomical information is embedded in the estimation of the parameters, i.e., penalizing the combination of spatially distant voxels. Real applications show an improvement in the classification and interpretability of the results compared to various functional alignment methods

A comparison of the CAR and DAGAR spatial random effects models with an application to diabetics rate estimation in Belgium

When hierarchically modelling an epidemiological phenomenon on a finite collection of sites in space, one must always take a latent spatial effect into account in order to capture the correlation structure that links the phenomenon to the territory. In this work, we compare two autoregressive spatial models that can be used for this purpose: the classical CAR model and the more recent DAGAR model. Differently from the former, the latter has a desirable property: its ρ parameter can be naturally interpreted as the average neighbor pair correlation and, in addition, this parameter can be directly estimated when the effect is modelled using a DAGAR rather than a CAR structure. As an application, we model the diabetics rate in Belgium in 2014 and show the adequacy of these models in predicting the response variable when no covariates are available

Multimedia

The nowadays ubiquitous and effortless digital data capture and processing capabilities offered by the majority of devices, lead to an unprecedented penetration of multimedia content in our everyday life. To make the most of this phenomenon, the rapidly increasing volume and usage of digitised content requires constant re-evaluation and adaptation of multimedia methodologies, in order to meet the relentless change of requirements from both the user and system perspectives. Advances in Multimedia provides readers with an overview of the ever-growing field of multimedia by bringing together various research studies and surveys from different subfields that point out such important aspects. Some of the main topics that this book deals with include: multimedia management in peer-to-peer structures & wireless networks, security characteristics in multimedia, semantic gap bridging for multimedia content and novel multimedia applications

Machine Learning Methods with Noisy, Incomplete or Small Datasets

In many machine learning applications, available datasets are sometimes incomplete, noisy or affected by artifacts. In supervised scenarios, it could happen that label information has low quality, which might include unbalanced training sets, noisy labels and other problems. Moreover, in practice, it is very common that available data samples are not enough to derive useful supervised or unsupervised classifiers. All these issues are commonly referred to as the low-quality data problem. This book collects novel contributions on machine learning methods for low-quality datasets, to contribute to the dissemination of new ideas to solve this challenging problem, and to provide clear examples of application in real scenarios

The Molecular Biophysics of Evolutionary and Physiological Adaptation

Central to any definition of Life is the ability to sense changes in one’s environment and respond in kind. Adaptive phenomena can be found across the biological scales ranging from the nanosecond-scale conformational changes of proteins, to temporary rewiring of metabolic networks, to the 3.5 billion years of evolution that produced the enormous biodiversity we see today. This thesis presents a body of work which attempts to examine the overlap between these three scales of adaptation through the quantitative lens of statistical physics. Namely, we examine how molecular, physiological, and evolutionary adaptation governs a feature common to all life – the regulation of gene expression. We begin by examining the phenomenon of molecular adaptation in the context of allostery, specifically in the context of allosteric transcriptional repressors. Using simple tools of quasi-equilibrium thermodynamics, we derive and experimentally dissect a quantitative model of how such a repressor adapts to different concentrations of an extracellular inducer molecule, modulating the repressors activity and thereby gene expression. While the model is relatively simple, it is remarkably powerful in its ability to draw concrete, quantitative predictions about not only the level of gene expression at a given concentration of inducer, but details of how the repressor responds to changes in the inducer concentration. With a few lines of simple mathematics, we are able to use this model to derive a state variable of the simple repression motif which we term the free energy of the regulatory architecture. This permits us to collapse nearly 500 distinct measurements of the level of gene expression onto a master curve defined by this free energy. We leverage this feature of the model and use data collapse as a method to identify the effects of mutation, a strong evolutionary force responsible for much of the genetic diversity in bacteria. In Chapter 3, we examine how mutations within the allosteric repressor itself can be mapped to changes in the free energy. The precise value of these free energy shifts and their dependence on the inducer concentration reveal different classes of mutations with one class affecting only the DNA-repressor interaction and another class governing the allosteric nature of the repressor. We test these pen-and-paper predictions experimentally and illustrate that given sufficient knowledge of how single mutants behave, the complete phenotypic response of pairwise double mutants can be predicted with quantitative accuracy. With this framework in hand, we turn to exploring how changes in the physiological state of the cell influence the molecular biophysics of the regulatory architecture. We hypothesize that changes in the source of carbon in the growth medium or changes in the growth temperature can be accounted for by the existing model without any additional parameters. We experimentally show that the parameter values determined in one physiological state are inherited when the available carbon source is verified, but changes in the growth temperature require some additional considerations. Chapter 4 as a whole reveals that, while there remains work to be done both theoretically and experimentally when it comes to temperature variation, thermodynamic models can remain powerful tools to draw predictions of gene expression in different physiological contexts. Finally, in Chapter 5, we explore physiological adaptation and cellular decision making where it counts – in the survival of cells to environmental insults. We turn our focus beyond transcriptional regulation and consider the relationship between osmotic shocks, the abundance of mechanosensitive channels, and cellular survival with single cell resolution. Using a combination of quantitative microscopy and tricks of statistical inference, we infer how the probability of a cell surviving an osmotic shock scales as a function of the cell’s number of mechanosensitive channels.</p