New Directions for Contact Integrators

Contact integrators are a family of geometric numerical schemes which guarantee the conservation of the contact structure. In this work we review the construction of both the variational and Hamiltonian versions of these methods. We illustrate some of the advantages of geometric integration in the dissipative setting by focusing on models inspired by recent studies in celestial mechanics and cosmology.Comment: To appear as Chapter 24 in GSI 2021, Springer LNCS 1282

Variational Image Segmentation with Constraints

The research of Huizhu Pan addresses the problem of image segmentation with constraints though designing and solving various variational models. A novel constraint term is designed for the use of landmarks in image segmentation. Two region-based segmentation models were proposed where the segmentation contour passes through landmark points. A more stable and memory efficient solution to the self-repelling snakes model, a variational model with the topology preservation constraint, was also designed

Contributions of Continuous Max-Flow Theory to Medical Image Processing

Discrete graph cuts and continuous max-flow theory have created a paradigm shift in many areas of medical image processing. As previous methods limited themselves to analytically solvable optimization problems or guaranteed only local optimizability to increasingly complex and non-convex functionals, current methods based now rely on describing an optimization problem in a series of general yet simple functionals with a global, but non-analytic, solution algorithms. This has been increasingly spurred on by the availability of these general-purpose algorithms in an open-source context. Thus, graph-cuts and max-flow have changed every aspect of medical image processing from reconstruction to enhancement to segmentation and registration. To wax philosophical, continuous max-flow theory in particular has the potential to bring a high degree of mathematical elegance to the field, bridging the conceptual gap between the discrete and continuous domains in which we describe different imaging problems, properties and processes. In Chapter 1, we use the notion of infinitely dense and infinitely densely connected graphs to transfer between the discrete and continuous domains, which has a certain sense of mathematical pedantry to it, but the resulting variational energy equations have a sense of elegance and charm. As any application of the principle of duality, the variational equations have an enigmatic side that can only be decoded with time and patience. The goal of this thesis is to show the contributions of max-flow theory through image enhancement and segmentation, increasing incorporation of topological considerations and increasing the role played by user knowledge and interactivity. These methods will be rigorously grounded in calculus of variations, guaranteeing fuzzy optimality and providing multiple solution approaches to addressing each individual problem

Statistical distances and probability metrics for multivariate data, ensembles and probability distributions

The use of distance measures in Statistics is of fundamental importance in solving practical problems, such us hypothesis testing, independence contrast, goodness of fit tests, classification tasks, outlier detection and density estimation methods, to name just a few. The Mahalanobis distance was originally developed to compute the distance from a point to the center of a distribution taking into account the distribution of the data, in this case the normal distribution. This is the only distance measure in the statistical literature that takes into account the probabilistic information of the data. In this thesis we address the study of different distance measures that share a fundamental characteristic: all the proposed distances incorporate probabilistic information. The thesis is organized as follows: In Chapter 1 we motivate the problems addressed in this thesis. In Chapter 2 we present the usual definitions and properties of the different distance measures for multivariate data and for probability distributions treated in the statistical literature. In Chapter 3 we propose a distance that generalizes the Mahalanobis distance to the case where the distribution of the data is not Gaussian. To this aim, we introduce a Mercer Kernel based on the distribution of the data at hand. The Mercer Kernel induces distances from a point to the center of a distribution. In this chapter we also present a plug-in estimator of the distance that allows us to solve classification and outlier detection problems in an efficient way. In Chapter 4 of this thesis, we present two new distance measures for multivariate data that incorporate the probabilistic information contained in the sample. In this chapter we also introduce two estimation methods for the proposed distances and we study empirically their convergence. In the experimental section of Chapter 4 we solve classification problems and obtain better results than several standard classification methods in the literature of discriminant analysis. In Chapter 5 we propose a new family of probability metrics and we study its theoretical properties. We introduce an estimation method to compute the proposed distances that is based on the estimation of the level sets, avoiding in this way the difficult task of density estimation. In this chapter we show that the proposed distance is able to solve hypothesis tests and classification problems in general contexts, obtaining better results than other standard methods in statistics. In Chapter 6 we introduce a new distance for sets of points. To this end, we define a dissimilarity measure for points by using a Mercer Kernel that is extended later to a Mercer Kernel for sets of points. In this way, we are able to induce a dissimilarity index for sets of points that it is used as an input for an adaptive k-mean clustering algorithm. The proposed clustering algorithm considers an alignment of the sets of points by taking into account a wide range of possible wrapping functions. This chapter presents an application to clustering neuronal spike trains, a relevant problem in neural coding. Finally, in Chapter 7, we present the general conclusions of this thesis and the future research lines.En Estadística el uso de medidas de distancia resulta de vital importancia a la hora de resolver problemas de índole práctica. Algunos métodos que hacen uso de distancias en estadística son: Contrastes de hipótesis, de independencia, de bondad de ajuste, métodos de clasificación, detección de atípicos y estimación de densidad, entre otros. La distancia de Mahalanobis, que fue diseñada originalmente para hallar la distancia de un punto al centro de una distribución usando información de la distribución ambiente, en este caso la normal. Constituye el único ejemplo existente en estadística de distancia que considera información probabilística. En esta tesis abordamos el estudio de diferentes medidas de distancia que comparten una característica en común: todas ellas incorporan información probabilística. El trabajo se encuentra organizado de la siguiente manera: En el Capítulo 1 motivamos los problemas abordados en esta tesis. En el Capítulo 2 de este trabajo presentamos las definiciones y propiedades de las diferentes medidas de distancias para datos multivariantes y para medidas de probabilidad existentes en la literatura. En el Capítulo 3 se propone una distancia que generaliza la distancia de Mahalanobis al caso en que la distribución de los datos no es Gaussiana. Para ello se propone un Núcleo (kernel) de Mercer basado en la densidad (muestral) de los datos que nos confiere la posibilidad de inducir distancias de un punto a una distribución. En este capítulo presentamos además un estimador plug-in de la distancia que nos permite resolver, de manera práctica y eficiente, problemas de detección de atípicos y problemas de clasificación mejorando los resultados obtenidos al utilizar otros métodos de la literatura. Continuando con el estudio de medidas de distancia, en el Capítulo 4 de esta tesis se proponen dos nuevas medidas de distancia para datos multivariantes incorporando información probabilística contenida en la muestra. En este capítulo proponemos también dos métodos de estimación eficientes para las distancias propuestas y estudiamos de manera empírica su convergencia. En la sección experimental del Capítulo 4 se resuelven problemas de clasificación con las medidas de distancia propuestas, mejorando los resultados obtenidos con procedimientos habitualmente utilizados en la literatura de análisis discriminante. En el Capítulo 5 proponemos una familia de distancias entre medidas de probabilidad. Se estudian también las propiedades teóricas de la familia de métricas propuesta y se establece un método de estimación de las distancias basado en la estimación de los conjuntos de nivel (definidos en este capítulo), evitando así la estimación directa de la densidad. En este capítulo se resuelven diferentes problemas de índole práctica con las métricas propuestas: Contraste de hipótesis y problemas de clasificación en diferentes contextos. Los resultados empíricos de este capítulo demuestran que la distancia propuesta es superior a otros métodos habituales de la literatura. Para finalizar con el estudio de distancias, en el Capítulo 6 se propone una medida de distancia entre conjuntos de puntos. Para ello, se define una medida de similaridad entre puntos a través de un kernel de Mercer. A continuación se extiende el kernel para puntos a un kernel de Mercer para conjuntos de puntos. De esta forma, el Núcleo de Mercer para conjuntos de puntos es utilizado para inducir una métrica (un índice de disimilaridad) entre conjuntos de puntos. En este capítulo se propone un método de clasificación por k-medias que utiliza la métrica propuesta y que contempla, además, la posibilidad de alinear los conjuntos de puntos en cada etapa de la construcción de los clusters. En este capítulo presentamos una aplicación relativa al estudio de la decodificación neuronal, donde utilizamos el método propuesto para encontrar clusters de neuronas con patrones de funcionamiento similares. Finalmente en el Capítulo 7 se presentan las conclusiones generales de este trabajo y las futuras líneas de investigación.Programa Oficial de Doctorado en Ingeniería MatemáticaPresidente: Santiago Velilla Cerdán.- Secretario: Verónica Vinciotti.- Vocal: Emilio Carrizosa Prieg

Longitudinal clustering analysis and prediction of Parkinson\u27s disease progression using radiomics and hybrid machine learning

Background: We employed machine learning approaches to (I) determine distinct progression trajectories in Parkinson\u27s disease (PD) (unsupervised clustering task), and (II) predict progression trajectories (supervised prediction task), from early (years 0 and 1) data, making use of clinical and imaging features. Methods: We studied PD-subjects derived from longitudinal datasets (years 0, 1, 2 & 4; Parkinson\u27s Progressive Marker Initiative). We extracted and analyzed 981 features, including motor, non-motor, and radiomics features extracted for each region-of-interest (ROIs: left/right caudate and putamen) using our standardized standardized environment for radiomics analysis (SERA) radiomics software. Segmentation of ROIs on dopamine transposer - single photon emission computed tomography (DAT SPECT) images were performed via magnetic resonance images (MRI). After performing cross-sectional clustering on 885 subjects (original dataset) to identify disease subtypes, we identified optimal longitudinal trajectories using hybrid machine learning systems (HMLS), including principal component analysis (PCA) + K-Means algorithms (KMA) followed by Bayesian information criterion (BIC), Calinski-Harabatz criterion (CHC), and elbow criterion (EC). Subsequently, prediction of the identified trajectories from early year data was performed using multiple HMLSs including 16 Dimension Reduction Algorithms (DRA) and 10 classification algorithms. Results: We identified 3 distinct progression trajectories. Hotelling\u27s t squared test (HTST) showed that the identified trajectories were distinct. The trajectories included those with (I, II) disease escalation (2 trajectories, 27% and 38% of patients) and (III) stable disease (1 trajectory, 35% of patients). For trajectory prediction from early year data, HMLSs including the stochastic neighbor embedding algorithm (SNEA, as a DRA) as well as locally linear embedding algorithm (LLEA, as a DRA), linked with the new probabilistic neural network classifier (NPNNC, as a classifier), resulted in accuracies of 78.4% and 79.2% respectively, while other HMLSs such as SNEA + Lib_SVM (library for support vector machines) and t_SNE (t-distributed stochastic neighbor embedding) + NPNNC resulted in 76.5% and 76.1% respectively. Conclusions: This study moves beyond cross-sectional PD subtyping to clustering of longitudinal disease trajectories. We conclude that combining medical information with SPECT-based radiomics features, and optimal utilization of HMLSs, can identify distinct disease trajectories in PD patients, and enable effective prediction of disease trajectories from early year data

Mathematical Imaging and Surface Processing

Within the last decade image and geometry processing have become increasingly rigorous with solid foundations in mathematics. Both areas are research fields at the intersection of different mathematical disciplines, ranging from geometry and calculus of variations to PDE analysis and numerical analysis. The workshop brought together scientists from all these areas and a fruitful interplay took place. There was a lively exchange of ideas between geometry and image processing applications areas, characterized in a number of ways in this workshop. For example, optimal transport, first applied in computer vision is now used to define a distance measure between 3d shapes, spectral analysis as a tool in image processing can be applied in surface classification and matching, and so on. We have also seen the use of Riemannian geometry as a powerful tool to improve the analysis of multivalued images. This volume collects the abstracts for all the presentations covering this wide spectrum of tools and application domains

Robust and Optimal Methods for Geometric Sensor Data Alignment

Geometric sensor data alignment - the problem of finding the rigid transformation that correctly aligns two sets of sensor data without prior knowledge of how the data correspond - is a fundamental task in computer vision and robotics. It is inconvenient then that outliers and non-convexity are inherent to the problem and present significant challenges for alignment algorithms. Outliers are highly prevalent in sets of sensor data, particularly when the sets overlap incompletely. Despite this, many alignment objective functions are not robust to outliers, leading to erroneous alignments. In addition, alignment problems are highly non-convex, a property arising from the objective function and the transformation. While finding a local optimum may not be difficult, finding the global optimum is a hard optimisation problem. These key challenges have not been fully and jointly resolved in the existing literature, and so there is a need for robust and optimal solutions to alignment problems. Hence the objective of this thesis is to develop tractable algorithms for geometric sensor data alignment that are robust to outliers and not susceptible to spurious local optima. This thesis makes several significant contributions to the geometric alignment literature, founded on new insights into robust alignment and the geometry of transformations. Firstly, a novel discriminative sensor data representation is proposed that has better viewpoint invariance than generative models and is time and memory efficient without sacrificing model fidelity. Secondly, a novel local optimisation algorithm is developed for nD-nD geometric alignment under a robust distance measure. It manifests a wider region of convergence and a greater robustness to outliers and sampling artefacts than other local optimisation algorithms. Thirdly, the first optimal solution for 3D-3D geometric alignment with an inherently robust objective function is proposed. It outperforms other geometric alignment algorithms on challenging datasets due to its guaranteed optimality and outlier robustness, and has an efficient parallel implementation. Fourthly, the first optimal solution for 2D-3D geometric alignment with an inherently robust objective function is proposed. It outperforms existing approaches on challenging datasets, reliably finding the global optimum, and has an efficient parallel implementation. Finally, another optimal solution is developed for 2D-3D geometric alignment, using a robust surface alignment measure. Ultimately, robust and optimal methods, such as those in this thesis, are necessary to reliably find accurate solutions to geometric sensor data alignment problems