Detection of pathologies in retina digital images an empirical mode decomposition approach

Accurate automatic detection of pathologies in retina digital images offers a promising approach in clinicalapplications. This thesis employs the discrete wavelet transform (DWT) and empirical mode decomposition (EMD) to extract six statistical textural features from retina digital images. The statistical features are the mean, standard deviation, smoothness, third moment, uniformity, and entropy. The purpose is to classify normal and abnormal images. Five different pathologies are considered. They are Artery sheath (Coat’s disease), blot hemorrhage, retinal degeneration (circinates), age-related macular degeneration (drusens), and diabetic retinopathy (microaneurysms and exudates). Four classifiers are employed; including support vector machines (SVM), quadratic discriminant analysis (QDA), k-nearest neighbor algorithm (k-NN), and probabilistic neural networks (PNN). For each experiment, ten random folds are generated to perform cross-validation tests. In order to assess the performance of the classifiers, the average and standard deviation of the correct recognition rate, sensitivity and specificity are computed for each simulation. The experimental results highlight two main conclusions. First, they show the outstanding performance of EMD over DWT with all classifiers. Second, they demonstrate the superiority of the SVM classifier over QDA, k-NN, and PNN. Finally, principal component analysis (PCA) was employed to reduce the number of features in hope to improve the accuracy of classifiers. We find that there is no general and significant improvement of the performance, however. In sum, the EMD-SVM system provides a promising approach for the detection of pathologies in digital retina

A study of information-theoretic metaheuristics applied to functional neuroimaging datasets

This dissertation presents a new metaheuristic related to a two-dimensional ensemble empirical mode decomposition (2DEEMD). It is based on Green’s functions and is called Green’s Function in Tension - Bidimensional Empirical Mode Decomposition (GiT-BEMD). It is employed for decomposing and extracting hidden information of images. A natural image (face image) as well as images with artificial textures have been used to test and validate the proposed approach. Images are selected to demonstrate efficiency and performance of the GiT-BEMD algorithm in extracting textures on various spatial scales from the different images. In addition, a comparison of the performance of the new algorithm GiT-BEMD with a canonical BEEMD is discussed. Then, GiT-BEMD as well as canonical bidimensional EEMD (BEEMD) are applied to an fMRI study of a contour integration task. Thus, it explores the potential of employing GiT-BEMD to extract such textures, so-called bidimensional intrinsic mode functions (BIMFs), of functional biomedical images. Because of the enormous computational load and the artifacts accompanying the extracted textures when using a canonical BEEMD, GiT-BEMD is developed to cope with such challenges. It is seen that the computational cost is decreased dramatically, and the quality of the extracted textures is enhanced considerably. Consequently, GiT-BEMD achieves a higher quality of the estimated BIMFs as can be seen from a direct comparison of the results obtained with different variants of BEEMD and GiT-BEMD. Moreover, results generated by 2DBEEMD, especially in case of GiT-BEMD, distinctly show a superior precision in spatial localization of activity blobs when compared with a canonical general linear model (GLM) analysis employing statistical parametric mapping (SPM). Furthermore, to identify most informative textures, i.e. BIMFs, a support vector machine (SVM) as well as a random forest (RF) classifier is employed. Classification performance demonstrates the potential of the extracted BIMFs in supporting decision making of the classifier. With GiT-BEMD, the classification performance improved significantly which might also be a consequence of a clearer structure for these modes compared to the ones obtained with canonical BEEMD. Altogether, there is strong believe that the newly proposed metaheuristic GiT-BEMD offers a highly competitive alternative to existing BEMD algorithms and represents a promising technique for blindly decomposing images and extracting textures thereof which may be used for further analysis

Time resolved functional brain networks : a novel method and developmental perspective

Functional neuroimaging has helped elucidating the complexity of brain function in ever more detail during the last 30 years. In this time the concepts used to understand how the brain works has also developed from a focus on regional activation to a network based whole brain perspective (Deco et al., 2015). The understanding that the brain is not just merely responding to external demands but is itself a co-creator of its perceived reality is now the default perspective (Buzsáki and Fernández-Ruiz, 2019). This means that the brain is never resting and its intrinsic architecture is the basis for any task related modulation (Cole et al., 2014). As often in science, understanding and technological advances go hand in hand. For the advancement of the functional neuroimaging field during the last decade, methods that are able to track, capture and model time resolved connectivity changes has been essential (Lurie et al., 2020). This development is an ongoing process. Part of the work presented in this thesis is a small contribution to this collective endeavor. The first theme in the thesis is time resolved connectivity of functional brain networks. This theme is present in Study I which presents a novel method for analysis of time resolved connectivity using BOLD fMRI data. With this method, subnetworks in the brain are defined dynamically. It allows for connectivity changes to be tracked from time point to time point while respecting the temporal ordering of the data. It also provides relational properties in terms of differences in phase coherence between simultaneously integrated networks and their gradual change. The method can be used see how whole brain connectivity configurations recure in quasi-cyclic patterns. Finally, the method is able to estimate flexibility and modularity of individual brain areas. The method is applied in Study III in order to understand how premature birth effects flexibility and modularity of intrinsic functional brain networks. Beyond the purely scientific endeavor to understand how the brain creates cognition, consciousness, perception and supports motor function, neuroimaging research has also been helpful in elucidating normal brain development and neurodevelopmental disorders. The second theme in this thesis is brain development in extremely preterm born children at school age. This theme is the focus of Study II & III. Study II investigates the prevalence of discrete white matter abnormalities at school age in children born extremely preterm and the relationship to neuro-motor outcome. The prevalence of white matter abnormalities was high but there was no relationship to an unfavorable outcome. Also, a longitudinal association to neonatal white matter injury was seen. While discrete white matter abnormalities were not correlated to quantitative measures of white matter volume and white matter integrity, neonatal white matter injury was associated with lower volume and integrity at age 8- 11 years. Moreover, neonatal white matter injury was associated with lower processing speed at 12 years. The third and final study investigated flexibility and modularity as well as lateralization of intrinsic networks in children born extremely preterm at age 8-11 years. No significant differences in either flexibility or modularity was seen for any intrinsic network after correcting for multiple comparisons. However, at the level of individual brain areas, preterm children showed decreased flexibility in both the basal ganglia and thalamus. Also, children born extremely preterm had a decreased level of lateralization in most networks

Engineering Approaches for Improving Cortical Interfacing and Algorithms for the Evaluation of Treatment Resistant Epilepsy

abstract: Epilepsy is a group of disorders that cause seizures in approximately 2.2 million people in the United States. Over 30% of these patients have epilepsies that do not respond to treatment with anti-epileptic drugs. For this population, focal resection surgery could offer long-term seizure freedom. Surgery candidates undergo a myriad of tests and monitoring to determine where and when seizures occur. The “gold standard” method for focus identification involves the placement of electrocorticography (ECoG) grids in the sub-dural space, followed by continual monitoring and visual inspection of the patient’s cortical activity. This process, however, is highly subjective and uses dated technology. Multiple studies were performed to investigate how the evaluation process could benefit from an algorithmic adjust using current ECoG technology, and how the use of new microECoG technology could further improve the process. Computational algorithms can quickly and objectively find signal characteristics that may not be detectable with visual inspection, but many assume the data are stationary and/or linear, which biological data are not. An empirical mode decomposition (EMD) based algorithm was developed to detect potential seizures and tested on data collected from eight patients undergoing monitoring for focal resection surgery. EMD does not require linearity or stationarity and is data driven. The results suggest that a biological data driven algorithm could serve as a useful tool to objectively identify changes in cortical activity associated with seizures. Next, the use of microECoG technology was investigated. Though both ECoG and microECoG grids are composed of electrodes resting on the surface of the cortex, changing the diameter of the electrodes creates non-trivial changes in the physics of the electrode-tissue interface that need to be accounted for. Experimenting with different recording configurations showed that proper grounding, referencing, and amplification are critical to obtain high quality neural signals from microECoG grids. Finally, the relationship between data collected from the cortical surface with micro and macro electrodes was studied. Simultaneous recordings of the two electrode types showed differences in power spectra that suggest the inclusion of activity, possibly from deep structures, by macroelectrodes that is not accessible by microelectrodes.Dissertation/ThesisDoctoral Dissertation Bioengineering 201

River landform dynamics detection and responses to morphology change in the rivers of North Luzon, the Philippines

River morphology detection has been improved considerably with the application of remote sensing and developments in computer science. However, applications that extract landforms within the active river channel remain limited, and there is a lack of studies from tropical regions. This thesis developed and then applied a workflow employing Sentinel-2 imagery for seasonal and annual river landform classification. Image downscaling approaches were investigated, and the performance of object-based image segmentation was assessed. The area to point regression kriging (ATPRK) approach was chosen to downscale coarser 20 m resolution Sentinel-2 bands to finer 10 m resolution bands. All features were set or processed at 10 m resolution before applying support vector machine (SVM) classification. To improve machine learning classification accuracy, Sentinel-2 acquisitions across one year, which incorporates multiple seasons, should be used. For rivers with different hydrological or geology settings, the thesis considered collecting river specific ground truth data to build a training model to avoid underfitting of models from other hydrological/geological settings. Applying the workflow, three landforms (water, unvegetated bars and vegetated bars) were classified within the active channel of the Bislak, Laoag, Abra and Cagayan Rivers, north Luzon, the Philippines, between 2016 to 2021, respectively. The spatial-temporal river landform datasets enabled the quantitative analysis of the river morphology changes. Water and unvegetated bars showed clear seasonal dynamics in all four rivers, whilst vegetated bars only showed seasonality in the rivers located in the northwest Luzon (the Bislak, Laoag and Abra Rivers). This thesis employed correlated coefficients to investigate the longitudinal correlation between river landforms and active width. It was found that vegetated bar areas always have strong significant correlations (≥0.67) with the active widths in all four rivers, whilst correlation coefficients between vegetated bar areas and active widths in the wet season are higher than that in the dry season. Ensemble empirical mode decomposition (EEMD) was applied to detect landform periodicity; this method indicated that water and vegetated bars commonly showed synchronised fluctuations with precipitation, while unvegetated bars had an anti-phase oscillation with precipitation. In the case of EEMD, deviations from periodic consistency in river pattern may reflect the influence of extreme events and/or human disturbance. Coefficient of variation (COV) was then used to evaluate the stability of the landforms; results suggested that the interplay of faults, elevation, confinement and tributary locations impacted landform stability. Finally, tributary inflow impacts on the mainstem river were investigated for eight tributaries of the lowland Cagayan River, also on Luzon Island. Longitudinal variations in channel morphology and stability, and temporal changes in landform frequency, using Simpson’s diversity index and COV, showed downstream widening associated with tributaries that was controlled by water discharge, with a secondary sediment flux effect. Overall, this thesis provided a novel example of combining remote sensing and GIS science, computing science, statistical science, and river morphology science to study the earth surface processes synthetically and quantitatively within river active channels in the tropical north Luzon, the Philippines. This work demonstrated how the fusion of techniques from these disciplines can be used to detect and analyse river landform changes, with potential applications for river management and restoration

Low-latency, query-driven analytics over voluminous multidimensional, spatiotemporal datasets

2017 Summer.Includes bibliographical references.Ubiquitous data collection from sources such as remote sensing equipment, networked observational devices, location-based services, and sales tracking has led to the accumulation of voluminous datasets; IDC projects that by 2020 we will generate 40 zettabytes of data per year, while Gartner and ABI estimate 20-35 billion new devices will be connected to the Internet in the same time frame. The storage and processing requirements of these datasets far exceed the capabilities of modern computing hardware, which has led to the development of distributed storage frameworks that can scale out by assimilating more computing resources as necessary. While challenging in its own right, storing and managing voluminous datasets is only the precursor to a broader field of study: extracting knowledge, insights, and relationships from the underlying datasets. The basic building block of this knowledge discovery process is analytic queries, encompassing both query instrumentation and evaluation. This dissertation is centered around query-driven exploratory and predictive analytics over voluminous, multidimensional datasets. Both of these types of analysis represent a higher-level abstraction over classical query models; rather than indexing every discrete value for subsequent retrieval, our framework autonomously learns the relationships and interactions between dimensions in the dataset (including time series and geospatial aspects), and makes the information readily available to users. This functionality includes statistical synopses, correlation analysis, hypothesis testing, probabilistic structures, and predictive models that not only enable the discovery of nuanced relationships between dimensions, but also allow future events and trends to be predicted. This requires specialized data structures and partitioning algorithms, along with adaptive reductions in the search space and management of the inherent trade-off between timeliness and accuracy. The algorithms presented in this dissertation were evaluated empirically on real-world geospatial time-series datasets in a production environment, and are broadly applicable across other storage frameworks

Object Detection and Classification based on Hierarchical Semantic Features and Deep Neural Networks

The abilities of feature learning, semantic understanding, cognitive reasoning, and model generalization are the consistent pursuit for current deep learning-based computer vision tasks. A variety of network structures and algorithms have been proposed to learn effective features, extract contextual and semantic information, deduct the relationships between objects and scenes, and achieve robust and generalized model.Nevertheless, these challenges are still not well addressed. One issue lies in the inefficient feature learning and propagation, static single-dimension semantic memorizing, leading to the difficulty of handling challenging situations, such as small objects, occlusion, illumination, etc. The other issue is the robustness and generalization, especially when the data source has diversified feature distribution. The study aims to explore classification and detection models based on hierarchical semantic features ("transverse semantic" and "longitudinal semantic"), network architectures, and regularization algorithm, so that the above issues could be improved or solved. (1) A detector model is proposed to make full use of "transverse semantic", the semantic information in space scene, which emphasizes on the effectiveness of deep features produced in high-level layers for better detection of small and occluded objects. (2) We also explore the anchor-based detector algorithm and propose the location-aware reasoning (LAAR), where both the location and classification confidences is considered for the bounding box quality criterion, so that the bestqualified boxes can be picked up in Non-Maximum Suppression (NMS). (3) A semantic clustering-based deduction learning is proposed, which explores the "longitudinal semantic", realizing the high-level clustering in the semantic space, enabling the model to deduce the relations among various classes so as better classification performance is expected. (4) We propose the near-orthogonality regularization by introducing an implicit self-regularization to push the mean and variance of filter angles in a network towards 90◦ and 0◦ simultaneously, revealing it helps stabilize the training process, speed up convergence and improve robustness. (5) Inspired by the research that self attention networks possess a strong inductive bias which leads to the loss of feature expression power, the transformer architecture with mitigatory attention mechanism is proposed and applied with the state-of-the-art detectors, verifying the superiority of detection enhancement