Geometric data understanding : deriving case specific features

There exists a tradition using precise geometric modeling, where uncertainties in data can be considered noise. Another tradition relies on statistical nature of vast quantity of data, where geometric regularity is intrinsic to data and statistical models usually grasp this level only indirectly. This work focuses on point cloud data of natural resources and the silhouette recognition from video input as two real world examples of problems having geometric content which is intangible at the raw data presentation. This content could be discovered and modeled to some degree by such machine learning (ML) approaches like deep learning, but either a direct coverage of geometry in samples or addition of special geometry invariant layer is necessary. Geometric content is central when there is a need for direct observations of spatial variables, or one needs to gain a mapping to a geometrically consistent data representation, where e.g. outliers or noise can be easily discerned. In this thesis we consider transformation of original input data to a geometric feature space in two example problems. The first example is curvature of surfaces, which has met renewed interest since the introduction of ubiquitous point cloud data and the maturation of the discrete differential geometry. Curvature spectra can characterize a spatial sample rather well, and provide useful features for ML purposes. The second example involves projective methods used to video stereo-signal analysis in swimming analytics. The aim is to find meaningful local geometric representations for feature generation, which also facilitate additional analysis based on geometric understanding of the model. The features are associated directly to some geometric quantity, and this makes it easier to express the geometric constraints in a natural way, as shown in the thesis. Also, the visualization and further feature generation is much easier. Third, the approach provides sound baseline methods to more traditional ML approaches, e.g. neural network methods. Fourth, most of the ML methods can utilize the geometric features presented in this work as additional features.Geometriassa käytetään perinteisesti tarkkoja malleja, jolloin datassa esiintyvät epätarkkuudet edustavat melua. Toisessa perinteessä nojataan suuren datamäärän tilastolliseen luonteeseen, jolloin geometrinen säännönmukaisuus on datan sisäsyntyinen ominaisuus, joka hahmotetaan tilastollisilla malleilla ainoastaan epäsuorasti. Tämä työ keskittyy kahteen esimerkkiin: luonnonvaroja kuvaaviin pistepilviin ja videohahmontunnistukseen. Nämä ovat todellisia ongelmia, joissa geometrinen sisältö on tavoittamattomissa raakadatan tasolla. Tämä sisältö voitaisiin jossain määrin löytää ja mallintaa koneoppimisen keinoin, esim. syväoppimisen avulla, mutta joko geometria pitää kattaa suoraan näytteistämällä tai tarvitaan neuronien lisäkerros geometrisia invariansseja varten. Geometrinen sisältö on keskeinen, kun tarvitaan suoraa avaruudellisten suureiden havainnointia, tai kun tarvitaan kuvaus geometrisesti yhtenäiseen dataesitykseen, jossa poikkeavat näytteet tai melu voidaan helposti erottaa. Tässä työssä tarkastellaan datan muuntamista geometriseen piirreavaruuteen kahden esimerkkiohjelman suhteen. Ensimmäinen esimerkki on pintakaarevuus, joka on uudelleen virinneen kiinnostuksen kohde kaikkialle saatavissa olevan datan ja diskreetin geometrian kypsymisen takia. Kaarevuusspektrit voivat luonnehtia avaruudellista kohdetta melko hyvin ja tarjota koneoppimisessa hyödyllisiä piirteitä. Toinen esimerkki koskee projektiivisia menetelmiä käytettäessä stereovideosignaalia uinnin analytiikkaan. Tavoite on löytää merkityksellisiä paikallisen geometrian esityksiä, jotka samalla mahdollistavat muun geometrian ymmärrykseen perustuvan analyysin. Piirteet liittyvät suoraan johonkin geometriseen suureeseen, ja tämä helpottaa luonnollisella tavalla geometristen rajoitteiden käsittelyä, kuten väitöstyössä osoitetaan. Myös visualisointi ja lisäpiirteiden luonti muuttuu helpommaksi. Kolmanneksi, lähestymistapa suo selkeän vertailumenetelmän perinteisemmille koneoppimisen lähestymistavoille, esim. hermoverkkomenetelmille. Neljänneksi, useimmat koneoppimismenetelmät voivat hyödyntää tässä työssä esitettyjä geometrisia piirteitä lisäämällä ne muiden piirteiden joukkoon

Accurate multigrid solution of the Euler equations on unstructured and adaptive meshes

A method for accurately solving inviscid compressible flow in the subcritical and supercritical regimes about complex configurations is presented. The method is based on the use of unstructured triangular meshes in two dimensions, and special emphasis is placed on the accuracy and efficiency of the solutions. High accuracy is achieved by careful scaling of the artificial dissipation terms, and by reformulating the inner and outer boundary conditions for both the convective and dissipative operators. An adaptive grid refinement strategy is presented which enhances the solution accuracy for complex flows. When coupled with an unstructured multigrid algorithm, this method is shown to produce an efficient solver for flows about arbitrary configurations

Application and assessment of time-domain DGM for intake acoustics using 3D linearized Euler equations

Fan noise is one of the major sources of aircraft noise. This can be modelled by means of frequency and time domain CAA methods. Frequency domain methods based on the convected Helmholtz equation are widely used for noise propagation and radiation from turbofan intakes. However, these methods are unsuited to deal easily with turbofan exhaust noise and presently unable to solve large 3D (three-dimensional) problems at high frequencies. In this thesis the application of time-domain Discontinuous Galerkin Methods (DGM) for solving linearized Euler equations is investigated. The research is focused on large 3D problems with arbitrary mean flows. A commercially available DGM code, Actran DGM, is used.An automatic procedure has been developed to perform the DGM simulations for axisymmetric and 3D intake problems by providing simple control of all the parameters (flow, geometry, liners). Moreover, a new method for integrating source predictions obtained from CFD calculations for the fan stage of a turbofan engine with the DGM code to predict tonal noise radiation in the far field has been proposed, implemented and validated.The DGM is validated and benchmarked for intake and exhaust problems against analytical solutions and other numerical methods. The principal properties of the DGM are assessed, best practice is defined, and important issues which relate to the accuracy and stability of the liner model are identified. The accuracy and efficiency of the CFD/CAA coupling are investigated and results obtained are compared to rig test data.The influence of the 3D intake shapes and the mean flow distortion on the sound field is investigated for static rig and flight conditions by using the DGM approach. Moreover, it is shown that the mean flow distortion can have a significant effect on the sound attenuation by a liner

High frequency homogenisation for elastic lattices

A complete methodology, based on a two-scale asymptotic approach, that enables the homogenisation of elastic lattices at non-zero frequencies is developed. Elastic lattices are distinguished from scalar lattices in that two or more types of coupled waves exist, even at low frequencies. Such a theory enables the determination of effective material properties at both low and high frequencies. The theoretical framework is developed for the propagation of waves through lattices of arbitrary geometry and dimension. The asymptotic approach provides a method through which the dispersive properties of lattices at frequencies near standing waves can be described; the theory accurately describes both the dispersion curves and the response of the lattice near the edges of the Brillouin zone. The leading order solution is expressed as a product between the standing wave solution and long-scale envelope functions that are eigensolutions of the homogenised partial differential equation. The general theory is supplemented by a pair of illustrative examples for two archetypal classes of two-dimensional elastic lattices. The efficiency of the asymptotic approach in accurately describing several interesting phenomena is demonstrated, including dynamic anisotropy and Dirac cones.Comment: 24 pages, 7 figure

Shape analysis and description based on the isometric invariances of topological skeletonization

ilustracionesIn this dissertation, we explore the problem of how to describe the shape of an object in 2D and 3D with a set of features that are invariant to isometric transformations. We focus to based our approach on the well-known Medial Axis Transform and its topological properties. We aim to study two problems. The first is how to find a shape representation of a segmented object that exhibits rotation, translation, and reflection invariance. The second problem is how to build a machine learning pipeline that uses the isometric invariance of the shape representation to do both classification and retrieval. Our proposed solution demonstrates competitive results compared to state-of-the-art approaches. We based our shape representation on the medial axis transform (MAT), sometimes called the topological skeleton. Accepted and well-studied properties of the medial axis include: homotopy preservation, rotation invariance, mediality, one pixel thickness, and the ability to fully reconstruct the object. These properties make the MAT a suitable input to create shape features; however, several problems arise because not all skeletonization methods satisfy all the above-mentioned properties at the same time. In general, skeletons based on thinning approaches preserve topology but are noise sensitive and do not allow a proper reconstruction. They are also not invariant to rotations. Voronoi skeletons also preserve topology and are rotation invariant, but do not have information about the thickness of the object, making reconstruction impossible. The Voronoi skeleton is an approximation of the real skeleton. The denser the sampling of the boundary, the better the approximation; however, a denser sampling makes the Voronoi diagram more computationally expensive. In contrast, distance transform methods allow the reconstruction of the original object by providing the distance from every pixel in the skeleton to the boundary. Moreover, they exhibit an acceptable degree of the properties listed above, but noise sensitivity remains an issue. Therefore, we selected distance transform medial axis methods as our skeletonization strategy, and focused on creating a new noise-free approach to solve the contour noise problem. To effectively classify an object, or perform any other task with features based on its shape, the descriptor needs to be a normalized, compact form: $\Phi$ should map every shape $\Omega$ to the same vector space $\mathrm{R}^{n}$. This is not possible with skeletonization methods because the skeletons of different objects have different numbers of branches and different numbers of points, even when they belong to the same category. Consequently, we developed a strategy to extract features from the skeleton through the map $\Phi$, which we used as an input to a machine learning approach. After developing our method for robust skeletonization, the next step is to use such skeleton into the machine learning pipeline to classify object into previously defined categories. We developed a set of skeletal features that were used as input data to the machine learning architectures. We ran experiments on MPEG7 and ModelNet40 dataset to test our approach in both 2D and 3D. Our experiments show results comparable with the state-of-the-art in shape classification and retrieval. Our experiments also show that our pipeline and our skeletal features exhibit some degree of invariance to isometric transformations. In this study, we sought to design an isometric invariant shape descriptor through robust skeletonization enforced by a feature extraction pipeline that exploits such invariance through a machine learning methodology. We conducted a set of classification and retrieval experiments over well-known benchmarks to validate our proposed method. (Tomado de la fuente)En esta disertación se explora el problema de cómo describir la forma de un objeto en 2D y 3D con un conjunto de características que sean invariantes a transformaciones isométricas. La metodología propuesta en este documento se enfoca en la Transformada del Eje Medio (Medial Axis Transform) y sus propiedades topológicas. Nuestro objetivo es estudiar dos problemas. El primero es encontrar una representación matemática de la forma de un objeto que exhiba invarianza a las operaciones de rotación, translación y reflexión. El segundo problema es como construir un modelo de machine learning que use esas invarianzas para las tareas de clasificación y consulta de objetos a través de su forma. El método propuesto en esta tesis muestra resultados competitivos en comparación con otros métodos del estado del arte. En este trabajo basamos nuestra representación de forma en la transformada del eje medio, a veces llamada esqueleto topológico. Algunas propiedades conocidas y bien estudiadas de la transformada del eje medio son: conservación de la homotopía, invarianza a la rotación, su grosor consiste en un solo pixel (1D), y la habilidad para reconstruir el objeto original a través de ella. Estas propiedades hacen de la transformada del eje medio un punto de partida adecuado para crear características de forma. Sin embargo, en este punto surgen varios problemas dado que no todos los métodos de esqueletización satisfacen, al mismo tiempo, todas las propiedades mencionadas anteriormente. En general, los esqueletos basados en enfoques de erosión morfológica conservan la topología del objeto, pero son sensibles al ruido y no permiten una reconstrucción adecuada. Además, no son invariantes a las rotaciones. Otro método de esqueletización son los esqueletos de Voronoi. Los esqueletos de Voronoi también conservan la topología y son invariantes a la rotación, pero no tienen información sobre el grosor del objeto, lo que hace imposible su reconstrucción. Cuanto más denso sea el muestreo del contorno del objeto, mejor será la aproximación. Sin embargo, un muestreo más denso hace que el diagrama de Voronoi sea más costoso computacionalmente. Por el contrario, los métodos basados en la transformada de la distancia permiten la reconstrucción del objeto original, ya que proporcionan la distancia desde cada píxel del esqueleto hasta su punto más cercano en el contorno. Además, exhiben un grado aceptable de las propiedades enumeradas anteriormente, aunque la sensibilidad al ruido sigue siendo un problema. Por lo tanto, en este documento seleccionamos los métodos basados en la transformada de la distancia como nuestra estrategia de esqueletización, y nos enfocamos en crear un nuevo enfoque que resuelva el problema del ruido en el contorno. Para clasificar eficazmente un objeto o realizar cualquier otra tarea con características basadas en su forma, el descriptor debe ser compacto y estar normalizado: $\Phi$ debe relacionar cada forma $\Omega$ al mismo espacio vectorial $\mathrm{R}^{n}$. Esto no es posible con los métodos de esqueletización en el estado del arte, porque los esqueletos de diferentes objetos tienen diferentes números de ramas y diferentes números de puntos incluso cuando pertenecen a la misma categoría. Consecuentemente, en nuestra propuesta desarrollamos una estrategia para extraer características del esqueleto a través de la función $\Phi$, que usamos como entrada para un enfoque de aprendizaje automático. % TODO completar con resultados. Después de desarrollar nuestro método de esqueletización robusta, el siguiente paso es usar dicho esqueleto en un modelo de aprendizaje de máquina para clasificar el objeto en categorías previamente definidas. Para ello se desarrolló un conjunto de características basadas en el eje medio que se utilizaron como datos de entrada para la arquitectura de aprendizaje automático. Realizamos experimentos en los conjuntos de datos: MPEG7 y ModelNet40 para probar nuestro enfoque tanto en 2D como en 3D. Nuestros experimentos muestran resultados comparables con el estado del arte en clasificación y consulta de formas (retrieval). Nuestros experimentos también muestran que el modelo desarrollado junto con nuestras características basadas en el eje medio son invariantes a las transformaciones isométricas. (Tomado de la fuente)Beca para Doctorados Nacionales de Colciencias, convocatoria 725 de 2015DoctoradoDoctor en IngenieríaVisión por computadora y aprendizaje automátic

Quantifying Membrane Topology at the Nanoscale

Changes in the shape of cellular membranes are linked with viral replication, Alzheimer\u27s, heart disease and an abundance of other maladies. Some membranous organelles, such as the endoplasmic reticulum and the Golgi, are only 50 nm in diameter. As such, membrane shape changes are conventionally studied with electron microscopy (EM), which preserves cellular ultrastructure and achieves a resolution of 2 nm or better. However, immunolabeling in EM is challenging, and often destroys the cell, making it difficult to study interactions between membranes and other proteins. Additionally, cells must be fixed in EM imaging, making it impossible to study mechanisms of disease. To address these problems, this thesis advances nanoscale imaging and analysis of membrane shape changes and their associated proteins using super-resolution single-molecule localization microscopy. This thesis is divided into three parts. In the first, a novel correlative orientation-independent differential interference contrast (OI-DIC) and single-molecule localization microscopy (SMLM) instrument is designed to address challenges with live-cell imaging of membrane nanostructure. SMLM super-resolution fluorescence techniques image with ~ 20 nm resolution, and are compatible with live-cell imaging. However, due to SMLM\u27s slow imaging speeds, most cell movement is under-sampled. OI-DIC images fast, is gentle enough to be used with living cells and can image cellular structure without labelling, but is diffraction-limited. Combining SMLM with OI-DIC allows for imaging of cellular context that can supplement sparse super-resolution data in real time. The second part of the thesis describes an open-source software package for visualizing and analyzing SMLM data. SMLM imaging yields localization point clouds, which requires non-standard visualization and analysis techniques. Existing techniques are described, and necessary new ones are implemented. These tools are designed to interpret data collected from the OI-DIC/SMLM microscope, as well as from other optical setups. Finally, a tool for extracting membrane structure from SMLM point clouds is described. SMLM data is often noisy, containing multiple localizations per fluorophore and many non-specific localizations. SMLM\u27s resolution reveals labelling discontinuities, which exacerbate sparsity of localizations. It is non-trivial to reconstruct the continuous shape of a membrane from a discrete set of points, and even more difficult in the presence of the noise profile characteristic of most SMLM point clouds. To address this, a surface reconstruction algorithm for extracting continuous surfaces from SMLM data is implemented. This method employs biophysical curvature constraints to improve the accuracy of the surface

Numerical solution of gravitational dynamics in asymptotically anti-de Sitter spacetimes

A variety of gravitational dynamics problems in asymptotically anti-de Sitter (AdS) spacetime are amenable to efficient numerical solution using a common approach involving a null slicing of spacetime based on infalling geodesics, convenient exploitation of the residual diffeomorphism freedom, and use of spectral methods for discretizing and solving the resulting differential equations. Relevant issues and choices leading to this approach are discussed in detail. Three examples, motivated by applications to non-equilibrium dynamics in strongly coupled gauge theories, are discussed as instructive test cases. These are gravitational descriptions of homogeneous isotropization, collisions of planar shocks, and turbulent fluid flows in two spatial dimensions.Comment: 70 pages, 19 figures; v4: fixed minus sign typo in last term of eqn. (3.47