A Research Platform for Artificial Neural Networks with Applications in Pediatric Epilepsy

This dissertation established a state-of-the-art programming tool for designing and training artificial neural networks (ANNs) and showed its applicability to brain research. The developed tool, called NeuralStudio, allows users without programming skills to conduct studies based on ANNs in a powerful and very user friendly interface. A series of unique features has been implemented in NeuralStudio, such as ROC analysis, cross-validation, network averaging, topology optimization, and optimization of the activation function’s slopes. It also included a Support Vector Machines module for comparison purposes. Once the tool was fully developed, it was applied to two studies in brain research. In the first study, the goal was to create and train an ANN to detect epileptic seizures from subdural EEG. This analysis involved extracting features from the spectral power in the gamma frequencies. In the second application, a unique method was devised to link EEG recordings to epileptic and non-epileptic subjects. The contribution of this method consisted of developing a descriptor matrix that can be used to represent any EEG file regarding its duration and the number of electrodes. The first study showed that the inter-electrode mean of the spectral power in the gamma frequencies and its duration above a specific threshold performs better than the other frequencies in seizure detection, exhibiting an accuracy of 95.90%, a sensitivity of 92.59%, and a specificity of 96.84%. The second study yielded that Hjorth’s parameter activity is sufficient to accurately relate EEG to epileptic and non-epileptic subjects. After testing, accuracy, sensitivity and specificity of the classifier were all above 0.9667. Statistical tests measured the superiority of activity at over 99.99 % certainty. It was demonstrated that 1) the spectral power in the gamma frequencies is highly effective in locating seizures from EEG and 2) activity can be used to link EEG recordings to epileptic and non-epileptic subjects. These two studies required high computational load and could be addressed thanks to NeuralStudio. From a medical perspective, both methods proved the merits of NeuralStudio in brain research applications. For its outstanding features, NeuralStudio has been recently awarded a patent (US patent No. 7502763).

Rigid and Non-rigid Point-based Medical Image Registration

The primary goal of this dissertation is to develop point-based rigid and non-rigid image registration methods that have better accuracy than existing methods. We first present point-based PoIRe, which provides the framework for point-based global rigid registrations. It allows a choice of different search strategies including (a) branch-and-bound, (b) probabilistic hill-climbing, and (c) a novel hybrid method that takes advantage of the best characteristics of the other two methods. We use a robust similarity measure that is insensitive to noise, which is often introduced during feature extraction. We show the robustness of PoIRe using it to register images obtained with an electronic portal imaging device (EPID), which have large amounts of scatter and low contrast. To evaluate PoIRe we used (a) simulated images and (b) images with fiducial markers; PoIRe was extensively tested with 2D EPID images and images generated by 3D Computer Tomography (CT) and Magnetic Resonance (MR) images. PoIRe was also evaluated using benchmark data sets from the blind retrospective evaluation project (RIRE). We show that PoIRe is better than existing methods such as Iterative Closest Point (ICP) and methods based on mutual information. We also present a novel point-based local non-rigid shape registration algorithm. We extend the robust similarity measure used in PoIRe to non-rigid registrations adapting it to a free form deformation (FFD) model and making it robust to local minima, which is a drawback common to existing non-rigid point-based methods. For non-rigid registrations we show that it performs better than existing methods and that is less sensitive to starting conditions. We test our non-rigid registration method using available benchmark data sets for shape registration. Finally, we also explore the extraction of features invariant to changes in perspective and illumination, and explore how they can help improve the accuracy of multi-modal registration. For multimodal registration of EPID-DRR images we present a method based on a local descriptor defined by a vector of complex responses to a circular Gabor filter.

An augmented reality pipeline to create scenes with coherent illumination using textured cuboids

Shadows and illumination play an important role when generating a realistic scene in computer graphics. Most of the Augmented Reality (AR) systems track markers placed in a real scene and retrieve their position and orientation to serve as a frame of reference for added computer generated content, thereby producing an augmented scene. Realistic depiction of augmented content with coherent visual cues is a desired goal in many AR applications. However, rendering an augmented scene with realistic illumination is a complex task. Many existent approaches rely on a non automated pre-processing phase to retrieve illumination parameters from the scene. Other techniques rely on specific markers that contain light probes to perform environment lighting estimation. This study aims at designing a method to create AR applications with coherent illumination and shadows, using a textured cuboid marker, that does not require a training phase to provide lighting information. Such marker may be easily found in common environments: most of product packaging satisfies such characteristics. Thus, we propose a way to estimate a directional light configuration using multiple texture tracking to render AR scenes in a realistic fashion. We also propose a novel feature descriptor that is used to perform multiple texture tracking. Our descriptor is an extension of the binary descriptor, named discrete descriptor, and outperforms current state-of-the-art methods in speed, while maintaining their accuracy.

Meating the social: sharing atiku-euiash in Sheshatshiu, Labrador

This work examines atiku-euiash (caribou meat) sharing practices in Sheshatshiu, Newfoundland and Labrador, and aims to elucidate an overarching question: how do sharing practices participate in the co-constitution of the Innu ‘social’? The ‘social’ is understood in this work as a descriptor that refers to the emergent properties of the Innu collective. The thesis is that sharing practices participate in the co-constitution of the Innu social and enact its boundaries. Inside these boundaries, atiku-euiash is more than simply a food resource: by realizing Innu values of generosity, respect and autonomy, sharing implicates the associations of human, animal, and animal masters that constitute the Innu world. Sharing is connected with the enskilment of the younger generations by their el-ders, and thus with the reproduction of Innu values through time. The ways of sharing are relevant because changes in such practices affect the constitution of the Innu social. Giv-en Euro-Canadian colonization, the Innu are in a fraught social space in which sharing is interrupted by colonization practices and values. Understanding sharing is necessary to develop policies that do not interrupt the reproduction of the Innu world This work uses several research methods: participant observation, sharing surveys, and interviews. It also uses network analysis as sharing practices leave traces of giving and receiving actions and these traces can be represented as a network of givers, receivers and circulating caribou meat. There are two main ways in which caribou is hunted and shared: household-based hunts and community-based hunts. The household-based hunts are organized by the hunters themselves, who are able and willing to hunt. Community-based hunts are completely organized and funded by the SIFN or the Innu Nation. In or-der to understand the differences in the distribution of the two hunt types, the categories of centrality and clustering are used to show how the flow of atiku-eiuash and its associ-ated realization of values and enskilment correlate with different degrees of centralization inside the sharing clusters.

Progettazione e implementazione di una applicazione didattica interattiva per il riconoscimento di oggetti basata sull'algoritmo SIFT

Nell'elaborato viene introdotto l'ambito della Computer Vision e come l'algoritmo SIFT si inserisce nel suo panorama. Viene inoltre descritto SIFT stesso, le varie fasi di cui si compone e un'applicazione al problema dell'object recognition. Infine viene presentata un'implementazione di SIFT in linguaggio Python creata per ottenere un'applicazione didattica interattiva e vengono mostrati esempi di questa applicazione.

Characterization of dynamic speckle sequences using principal component analysis and image descriptors

Speckle is being used as a characterization tool for the analysis of the dynamic of slow varying phenomena occurring in biological and industrial samples. The retrieved data takes the form of a sequence of speckle images. The analysis of these images should reveal the inner dynamic of the biological or physical process taking place in the sample. Very recently, it has been shown that principal component analysis is able to split the original data set in a collection of classes. These classes can be related with the dynamic of the observed phenomena. At the same time, statistical descriptors of biospeckle images have been used to retrieve information on the characteristics of the sample. These statistical descriptors can be calculated in almost real time and provide a fast monitoring of the sample. On the other hand, principal component analysis requires longer computation time but the results contain more information related with spatial-temporal pattern that can be identified with physical process. This contribution merges both descriptions and uses principal component analysis as a pre-processing tool to obtain a collection of filtered images where a simpler statistical descriptor can be calculated. The method has been applied to slow-varying biological and industrial processes

Spic'ing into Existence: Epitaph, Epithet, and the Ethnopoetic Imagination

Quién Es, Quién Somos? Spic’ing into Existence claims a four-fold close-reading: first, analysis of texts: from theoretical meditations to (prison) memoir and film. Second, a half dozen central figures appear, largely Latinx and black American. They cut across a score of registers, socio-economics, ideological reservations, but all are, as Carl Carlton sang, poetry in motion. Writers, poets, theologians, pathologists, artists, comedians, actors, students whose vocation is invocation, the inner surge of their calling. Third, the manuscript draws from a series of historical moments—from radical liberation of the late 60s, to contemporary student activism. Finally, this body of work is movement, in all its social, gestural, and kinesthetic viscera. From this last heading, we peel away layers of what I call the ethnopoet, the fascia undoing that reveals its bio-political anatomy, dressing its bare life with kinship speech. First, the social revolutions of the Civil Rights, Black Power, abolitionism, the Black Panthers and Young Lords, boycotts and jarring artistic performances. These events are superficial not in vain sense, but key epicenters of underground murmurings, the workings of a cunning assailant. She robs not lavish estates, but another day to breathe. Gesturally, as perhaps the interlocutor, lies this author, interspersing his own diatribes to conjure her presence. The final branch is admittedly the most intangible. Kinesthetically, we map the nimbleness, footwork lígera of what I call the ethnopoet. Ethnopoet is no mere aggregate of ethnicity and poetry, but like chemical reaction, the descriptor for its behavior under certain pressures, temperatures, and elements. Elusive and resisting confinement, and therefore definition, the ethnopoet is a shapeshifting figure of how racialized bodies [people of color] respond to hegemonic powers. She is, at bottom, however, a native translator, the plural-lensed subject whose loyalty is only to the imagination of a different world, one whose survival is not contingent upon her exploitation. The native translator’s constant re-calibrations of oppressive power apparatuses seem taxing at best, and near-impossible, at worst. To effectively navigate through these polarized loci, she must identify ideologies that in turn seek “affective liberatory sances” in relation to the dominant social order (43). In a kind of performative contradiction, she must marshall the knowledge necessary to “break with ideology” while speaking within it. Chicana Studies scholar, Chela Sandoval, describes this dual movement as “meta-ideologizing”: the appropriation of hegemonic ideological forms in order to transform them (82). Nuestros padres se subieron encima de La Bestia, y por eso somos pasageros a ese tren. Y ya, dentro su pansa, tenemos que ser vigilantes cuando plantamos las bombas. In Methodology of the Oppressed, Sandoval schematizes this oppositional consciousness around five principle categories: “equal rights,” “revolutionary,” “supremacist,” “separatist,” and “differential.” Taken by themselves, the first four modes appear mutually exclusive, incapable of occupying the same plane, until a fifth pillar emerges. Cinematographic in nature, differential consciousness, as Sandoval defines it, is “a kinetic motion that maneuvers, poetically transfigures, and orchestrates while demanding alienation, perversion, and reformation in both spectators and practitioners” (44). For Sandoval, then, differential consciousness is a methodology that privileges an incredible sense mobility, one reaching artistic sensibilities. Our fourth and final analytic of movement serves an apt example of this dual meaning. Lexically speaking, ‘movement’ may be regarded as a political mobilization of aggrieved populations (through sustained efforts), or the process of moving objects (people or otherwise) from one location to another. Praxis-wise, it is both action and ideal, content and form. Thus, an ethnic poetics must be regarded less as a series of stanzas, shortened lyric, or even arrangement of language, but as a lens through which peripheralized peoples kaleidecope ideological positions in an “original, eccentric, and queer sight” (43). Taking note of the advantages of postponing identifications, the thesis stands its ground on the term ethnopoet. Its abstraction is not dewey-eyed philosophy, but an anticipation of poetic justice, of what’s to come from callused hands. This thesis is divided into 7.5 chapters. The first maps out the ethnopoet’s cartographies of struggle. By revisiting that alleged Tío Tomas, Richard Rodriguez, we unearth the tensions that negatively, deny citizenship to one silo, but on the flipside, engender manifold ways of seeing, hearing, and moving . The second, through George Jackson’s prison memoirs, pans out from this ethnography of power, groping for an apparatus that feigns an impervious prestige: ‘the aesthetic regime of coercion.’ In half-way cut, the thesis sidesteps to spic into existence, formally announcing, through Aime Cesaire, myself, and Pedro Pietri, the poeticization of trauma. Such uplift denies New Age transcendence of self, but a rehearsal of our entrapment in these mortal envelopes. Thirdly, conscious of the bleeding ethnic body, we cut open the incipient corpse to observe her pathologist. Her native autopsies offer the ethnic body’s posthumous recognition, the ethnopoetics ability to speak for and through the dead. Chapter five examines prolific black artists—Beyonce and Kendrick Lamar—to elide the circumvention of their consumption via invoking radical black hi/her-stories, ones fragmenting the black body. Sixth, the paper compares the Black Power Salute of the 1968 Mexico City Olympics to Duke’s Mi Gente Boycott of their Latino Student Recruitment Weekend. Both wielded “silent gestures,” that shrewdly interfered with white noise of numbed negligence. Finally, ‘taking the mask off’ that are her functionalities, the CODA expounds on ethnopoet’s interiority, particularly after the rapid re-calibration of her politics. Through a rerun of El Chavo del Ocho, one of Mexican television’s most cherished shows, we tune into the heart-breaking indigence of barrio residents, only to marvel at the power of humor to, as Friday’s John Witherspoon put it, “fight another day.” This thesis is the tip of my tongue. Y por una vez, déjala que cante.

Statistical methods for polyhedral shape classification with incomplete data - application to cryo-electron tomographic images

A certain type of bacterial inclusion, known as a bacterial microcompartment, was recently identified and imaged through cryo-electron tomography. A reconstructed 3D object from single-axis limited angle tilt-series cryo-electron tomography contains missing regions and this problem is known as the missing wedge problem. Due to missing regions on the reconstructed images, analyzing their 3D structures is a challenging problem. The existing methods overcome this problem by aligning and averaging several similar shaped objects. These schemes work well if the objects are symmetric and several objects with almost similar shapes and sizes are available. Since the bacterial inclusions studied here are not symmetric, are deformed, and show a wide range of shapes and sizes, the existing approaches are not appropriate. This research develops new statistical methods for analyzing geometric properties, such as volume, symmetry, aspect ratio, polyhedral structures etc., of these bacterial inclusions in presence of missing data. These methods work with deformed and non-symmetric varied shaped objects and do not necessitate multiple objects for handling the missing wedge problem. The developed methods and contributions include: (a) an improved method for manual image segmentation, (b) a new approach to 'complete' the segmented and reconstructed incomplete 3D images, (c) a polyhedral structural distance model to predict the polyhedral shapes of these microstructures, (d) a new shape descriptor for polyhedral shapes, named as polyhedron profile statistic, and (e) the Bayes classifier, linear discriminant analysis and support vector machine based classifiers for supervised incomplete polyhedral shape classification. Finally, the predicted 3D shapes for these bacterial microstructures belong to the Johnson solids family, and these shapes along with their other geometric properties are important for better understanding of their chemical and biological characteristics.

The Hurst exponent as an indicator of the behaviour of a model monopile in an ocean wave testing basin

With the importance of renewable energy well-established worldwide, and targets of such energy quantified in many cases, there exists a considerable interest in the assessment of wind and wave devices. While the individual components of these devices are often relatively well understood and the aspects of energy generation well researched, there seems to be a gap in the understanding of these devices as a whole and especially in the field of their dynamic responses under operational conditions. The mathematical modelling and estimation of their dynamic responses are more evolved but research directed towards testing of these devices still requires significant attention. Model-free indicators of the dynamic responses of these devices are important since it reflects the as-deployed behaviour of the devices when the exposure conditions are scaled reasonably correctly, along with the structural dimensions. This paper demonstrates how the Hurst exponent of the dynamic responses of a monopile exposed to different exposure conditions in an ocean wave basin can be used as a model-free indicator of various responses. The scaled model is exposed to Froude scaled waves and tested under different exposure conditions. The analysis and interpretation is carried out in a model-free and output-only environment, with only some preliminary ideas regarding the input of the system. The analysis indicates how the Hurst exponent can be an interesting descriptor to compare and contrast various scenarios of dynamic response conditions.

Ant abundance and occurrence along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2013)

This data set contains measurements of ant abundance (number of individuals attracted to baits) and ant occurrence (binary data) measured in the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown in the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, or 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Ants where sampled in 80 plots of the Main Experiment using baited traps end of July/ beginning of August 2013. Sampling took place 36 days after the end of a major flooding of the field site that lasted for several weeks (see DOI flood descriptor). In each plot two petri dishes were set on the ground, one received ~10g of Tuna the other ~10g of Honey. After 30min the occurrence (presence = 1 / absence = 0) and abundance (number) of ants at the two baits was recorded. Given is, per plot, the sum of ants attracted to the two different baits.

Automatic Identification of Large Fragments in a Pile of Broken Rock Using a Time-of-Flight Camera

This paper presents a solution to part of the problem of making robotic or semi-robotic digging equipment less dependant on human supervision. A method is described for identifying rocks of a certain size that may affect digging efficiency or require special handling. The process involves three main steps. First, by using range and intensity data from a time-of-flight (TOF) camera, a feature descriptor is used to rank points and separate regions surrounding high scoring points. This allows a wide range of rocks to be recognized because features can represent a whole or just part of a rock. Second, these points are filtered to extract only points thought to belong to the large object. Finally, a check is carried out to verify that the resultant point cloud actually represents a rock. Results are presented from field testing on piles of fragmented rock. Note to Practitioners—This paper presents an algorithm to identify large boulders in a pile of broken rock as a step towards an autonomous mining dig planner. In mining, piles of broken rock can contain large fragments that may need to be specially handled. To assess rock piles for excavation, we make use of a TOF camera that does not rely on external lighting to generate a point cloud of the rock pile. We then segment large boulders from its surface by using a novel feature descriptor and distinguish between real and false boulder candidates. Preliminary field experiments show promising results with the algorithm performing nearly as well as human test subjects.

Dynamic Distance-Based Shape Features for Gait Recognition

We propose a novel skeleton-based approach to gait recognition using our Skeleton Variance Image. The core of our approach consists of employing the screened Poisson equation to construct a family of smooth distance functions associated with a given shape. The screened Poisson distance function approximation nicely absorbs and is relatively stable to shape boundary perturbations which allows us to define a rough shape skeleton. We demonstrate how our Skeleton Variance Image is a powerful gait cycle descriptor leading to a significant improvement over the existing state of the art gait recognition rate.

Catalyst screening: Refinement of the origin of the volcano curve and its implication in heterogeneous catalysis

Understanding the overall catalytic activity trend for rational catalyst design is one of the core goals in heterogeneous catalysis. In the past two decades, the development of density functional theory (DFT) and surface kinetics make it feasible to theoretically evaluate and predict the catalytic activity variation of catalysts within a descriptor-based framework. Thereinto, the concept of the volcano curve, which reveals the general activity trend, usually constitutes the basic foundation of catalyst screening. However, although it is a widely accepted concept in heterogeneous catalysis, its origin lacks a clear physical picture and definite interpretation. Herein, starting with a brief review of the development of the catalyst screening framework, we use a two-step kinetic model to refine and clarify the origin of the volcano curve with a full analytical analysis by integrating the surface kinetics and the results of first-principles calculations. It is mathematically demonstrated that the volcano curve is an essential property in catalysis, which results from the self-poisoning effect accompanying the catalytic adsorption process. Specifically, when adsorption is strong, it is the rapid decrease of surface free sites rather than the augmentation of energy barriers that inhibits the overall reaction rate and results in the volcano curve. Some interesting points and implications in assisting catalyst screening are also discussed based on the kinetic derivation. Moreover, recent applications of the volcano curve for catalyst design in two important photoelectrocatalytic processes (the hydrogen evolution reaction and dye-sensitized solar cells) are also briefly discussed.

Plane detection from monocular image sequences

AIRES, Kelson R. T. ; ARAÚJO, Hélder J. ; MEDEIROS, Adelardo A. D. . Plane Detection from Monocular Image Sequences. In: VISUALIZATION, IMAGING AND IMAGE PROCESSING, 2008, Palma de Mallorca, Spain. Proceedings..., Palma de Mallorca: VIIP, 2008

Plane Detection Using Affine Homography

AIRES, Kelson R. T.; ARAÚJO, Hélder J.; MEDEIROS, Adelardo A. D. Plane Detection Using Affine Homography. In: CONGRESSO BRASILEIRO DE AUTOMÁTICA, 2008, Juiz de Fora, MG: Anais... do CBA 2008.