An Infinitesimal Probabilistic Model for Principal Component Analysis of Manifold Valued Data

We provide a probabilistic and infinitesimal view of how the principal component analysis procedure (PCA) can be generalized to analysis of nonlinear manifold valued data. Starting with the probabilistic PCA interpretation of the Euclidean PCA procedure, we show how PCA can be generalized to manifolds in an intrinsic way that does not resort to linearization of the data space. The underlying probability model is constructed by mapping a Euclidean stochastic process to the manifold using stochastic development of Euclidean semimartingales. The construction uses a connection and bundles of covariant tensors to allow global transport of principal eigenvectors, and the model is thereby an example of how principal fiber bundles can be used to handle the lack of global coordinate system and orientations that characterizes manifold valued statistics. We show how curvature implies non-integrability of the equivalent of Euclidean principal subspaces, and how the stochastic flows provide an alternative to explicit construction of such subspaces. We describe estimation procedures for inference of parameters and prediction of principal components, and we give examples of properties of the model on embedded surfaces

Anisotropically weighted and nonholonomically constrained evolutions on manifolds

We present evolution equations for a family of paths that results from anisotropically weighting curve energies in non-linear statistics of manifold valued data. This situation arises when performing inference on data that have non-trivial covariance and are anisotropic distributed. The family can be interpreted as most probable paths for a driving semi-martingale that through stochastic development is mapped to the manifold. We discuss how the paths are projections of geodesics for a sub-Riemannian metric on the frame bundle of the manifold, and how the curvature of the underlying connection appears in the sub-Riemannian Hamilton-Jacobi equations. Evolution equations for both metric and cometric formulations of the sub-Riemannian metric are derived. We furthermore show how rank-deficient metrics can be mixed with an underlying Riemannian metric, and we relate the paths to geodesics and polynomials in Riemannian geometry. Examples from the family of paths are visualized on embedded surfaces, and we explore computational representations on finite dimensional landmark manifolds with geometry induced from right-invariant metrics on diffeomorphism groups

A Meshfree Generalized Finite Difference Method for Surface PDEs

In this paper, we propose a novel meshfree Generalized Finite Difference Method (GFDM) approach to discretize PDEs defined on manifolds. Derivative approximations for the same are done directly on the tangent space, in a manner that mimics the procedure followed in volume-based meshfree GFDMs. As a result, the proposed method not only does not require a mesh, it also does not require an explicit reconstruction of the manifold. In contrast to existing methods, it avoids the complexities of dealing with a manifold metric, while also avoiding the need to solve a PDE in the embedding space. A major advantage of this method is that all developments in usual volume-based numerical methods can be directly ported over to surfaces using this framework. We propose discretizations of the surface gradient operator, the surface Laplacian and surface Diffusion operators. Possibilities to deal with anisotropic and discontinous surface properties (with large jumps) are also introduced, and a few practical applications are presented

Kinetics and Mechanism of Metal Nanoparticle Growth via Optical Extinction Spectroscopy and Computational Modeling: The Curious Case of Colloidal Gold

An overarching computational framework unifying several optical theories to describe the temporal evolution of gold nanoparticles (GNPs) during a seeded growth process is presented. To achieve this, we used the inexpensive and widely available optical extinction spectroscopy, to obtain quantitative kinetic data. In situ spectra collected over a wide set of experimental conditions were regressed using the physical model, calculating light extinction by ensembles of GNPs during the growth process. This model provides temporal information on the size, shape, and concentration of the particles and any electromagnetic interactions between them. Consequently, we were able to describe the mechanism of GNP growth and divide the process into distinct genesis periods. We provide explanations for several longstanding mysteries, for example, the phenomena responsible for the purple-greyish hue during the early stages of GNP growth, the complex interactions between nucleation, growth, and aggregation events, and a clear distinction between agglomeration and electromagnetic interactions. The presented theoretical formalism has been developed in a generic fashion so that it can readily be adapted to other nanoparticulate formation scenarios such as the genesis of various metal nanoparticles.Comment: Main text and supplementary information (accompanying MATLAB codes available on the journal webpage

Recent advances in directional statistics

Mainstream statistical methodology is generally applicable to data observed in Euclidean space. There are, however, numerous contexts of considerable scientific interest in which the natural supports for the data under consideration are Riemannian manifolds like the unit circle, torus, sphere and their extensions. Typically, such data can be represented using one or more directions, and directional statistics is the branch of statistics that deals with their analysis. In this paper we provide a review of the many recent developments in the field since the publication of Mardia and Jupp (1999), still the most comprehensive text on directional statistics. Many of those developments have been stimulated by interesting applications in fields as diverse as astronomy, medicine, genetics, neurology, aeronautics, acoustics, image analysis, text mining, environmetrics, and machine learning. We begin by considering developments for the exploratory analysis of directional data before progressing to distributional models, general approaches to inference, hypothesis testing, regression, nonparametric curve estimation, methods for dimension reduction, classification and clustering, and the modelling of time series, spatial and spatio-temporal data. An overview of currently available software for analysing directional data is also provided, and potential future developments discussed.Comment: 61 page

Computational methods to predict and enhance decision-making with biomedical data.

The proposed research applies machine learning techniques to healthcare applications. The core ideas were using intelligent techniques to find automatic methods to analyze healthcare applications. Different classification and feature extraction techniques on various clinical datasets are applied. The datasets include: brain MR images, breathing curves from vessels around tumor cells during in time, breathing curves extracted from patients with successful or rejected lung transplants, and lung cancer patients diagnosed in US from in 2004-2009 extracted from SEER database. The novel idea on brain MR images segmentation is to develop a multi-scale technique to segment blood vessel tissues from similar tissues in the brain. By analyzing the vascularization of the cancer tissue during time and the behavior of vessels (arteries and veins provided in time), a new feature extraction technique developed and classification techniques was used to rank the vascularization of each tumor type. Lung transplantation is a critical surgery for which predicting the acceptance or rejection of the transplant would be very important. A review of classification techniques on the SEER database was developed to analyze the survival rates of lung cancer patients, and the best feature vector that can be used to predict the most similar patients are analyzed

Towards Precision LSST Weak-Lensing Measurement - I: Impacts of Atmospheric Turbulence and Optical Aberration

The weak-lensing science of the LSST project drives the need to carefully model and separate the instrumental artifacts from the intrinsic lensing signal. The dominant source of the systematics for all ground based telescopes is the spatial correlation of the PSF modulated by both atmospheric turbulence and optical aberrations. In this paper, we present a full FOV simulation of the LSST images by modeling both the atmosphere and the telescope optics with the most current data for the telescope specifications and the environment. To simulate the effects of atmospheric turbulence, we generated six-layer phase screens with the parameters estimated from the on-site measurements. For the optics, we combined the ray-tracing tool ZEMAX and our simulated focal plane data to introduce realistic aberrations and focal plane height fluctuations. Although this expected flatness deviation for LSST is small compared with that of other existing cameras, the fast f-ratio of the LSST optics makes this focal plane flatness variation and the resulting PSF discontinuities across the CCD boundaries significant challenges in our removal of the systematics. We resolve this complication by performing PCA CCD-by-CCD, and interpolating the basis functions using conventional polynomials. We demonstrate that this PSF correction scheme reduces the residual PSF ellipticity correlation below 10^-7 over the cosmologically interesting scale. From a null test using HST/UDF galaxy images without input shear, we verify that the amplitude of the galaxy ellipticity correlation function, after the PSF correction, is consistent with the shot noise set by the finite number of objects. Therefore, we conclude that the current optical design and specification for the accuracy in the focal plane assembly are sufficient to enable the control of the PSF systematics required for weak-lensing science with the LSST.Comment: Accepted to PASP. High-resolution version is available at http://dls.physics.ucdavis.edu/~mkjee/LSST_weak_lensing_simulation.pd

Virtual cardiac monolayers for electrical wave propagation

The complex structure of cardiac tissue is considered to be one of the main determinants of an arrhythmogenic substrate. This study is aimed at developing the first mathematical model to describe the formation of cardiac tissue, using a joint in silico-in vitro approach. First, we performed experiments under various conditions to carefully characterise the morphology of cardiac tissue in a culture of neonatal rat ventricular cells. We considered two cell types, namely, cardiomyocytes and fibroblasts. Next, we proposed a mathematical model, based on the Glazier-Graner-Hogeweg model, which is widely used in tissue growth studies. The resultant tissue morphology was coupled to the detailed electrophysiological Korhonen-Majumder model for neonatal rat ventricular cardiomyocytes, in order to study wave propagation. The simulated waves had the same anisotropy ratio and wavefront complexity as those in the experiment. Thus, we conclude that our approach allows us to reproduce the morphological and physiological properties of cardiac tissue