The Magnetic Topology of the Weak-Lined T Tauri Star V410 - A Simultaneous Temperature and Magnetic Field Inversion

We present a detailed temperature and magnetic investigation of the T Tauri star V410 Tau by means of a simultaneous Doppler- and Zeeman-Doppler Imaging. Moreover we introduce a new line profile reconstruction method based on a singular value decomposition (SVD) to extract the weak polarized line profiles. One of the key features of the line profile reconstruction is that the SVD line profiles are amenable to radiative transfer modeling within our Zeeman-Doppler Imaging code iMap. The code also utilizes a new iterative regularization scheme which is independent of any additional surface constraints. To provide more stability a vital part of our inversion strategy is the inversion of both Stokes I and Stokes V profiles to simultaneously reconstruct the temperature and magnetic field surface distribution of V410 Tau. A new image-shear analysis is also implemented to allow the search for image and line profile distortions induced by a differential rotation of the star. The magnetic field structure we obtain for V410 Tau shows a good spatial correlation with the surface temperature and is dominated by a strong field within the cool polar spot. The Zeeman-Doppler maps exhibit a large-scale organization of both polarities around the polar cap in the form of a twisted bipolar structure. The magnetic field reaches a value of almost 2 kG within the polar region but smaller fields are also present down to lower latitudes. The pronounced non-axisymmetric field structure and the non-detection of a differential rotation for V410 Tau supports the idea of an underlying $\alpha^2$-type dynamo, which is predicted for weak-lined T Tauri stars.Comment: Accepted for A&A, 18 pages, 10 figure

Bayesian Sparse Factor Analysis of Genetic Covariance Matrices

Quantitative genetic studies that model complex, multivariate phenotypes are important for both evolutionary prediction and artificial selection. For example, changes in gene expression can provide insight into developmental and physiological mechanisms that link genotype and phenotype. However, classical analytical techniques are poorly suited to quantitative genetic studies of gene expression where the number of traits assayed per individual can reach many thousand. Here, we derive a Bayesian genetic sparse factor model for estimating the genetic covariance matrix (G-matrix) of high-dimensional traits, such as gene expression, in a mixed effects model. The key idea of our model is that we need only consider G-matrices that are biologically plausible. An organism's entire phenotype is the result of processes that are modular and have limited complexity. This implies that the G-matrix will be highly structured. In particular, we assume that a limited number of intermediate traits (or factors, e.g., variations in development or physiology) control the variation in the high-dimensional phenotype, and that each of these intermediate traits is sparse -- affecting only a few observed traits. The advantages of this approach are two-fold. First, sparse factors are interpretable and provide biological insight into mechanisms underlying the genetic architecture. Second, enforcing sparsity helps prevent sampling errors from swamping out the true signal in high-dimensional data. We demonstrate the advantages of our model on simulated data and in an analysis of a published Drosophila melanogaster gene expression data set.Comment: 35 pages, 7 figure

Tensor Graphical Lasso (TeraLasso)

This paper introduces a multi-way tensor generalization of the Bigraphical Lasso (BiGLasso), which uses a two-way sparse Kronecker-sum multivariate-normal model for the precision matrix to parsimoniously model conditional dependence relationships of matrix-variate data based on the Cartesian product of graphs. We call this generalization the {\bf Te}nsor g{\bf ra}phical Lasso (TeraLasso). We demonstrate using theory and examples that the TeraLasso model can be accurately and scalably estimated from very limited data samples of high dimensional variables with multiway coordinates such as space, time and replicates. Statistical consistency and statistical rates of convergence are established for both the BiGLasso and TeraLasso estimators of the precision matrix and estimators of its support (non-sparsity) set, respectively. We propose a scalable composite gradient descent algorithm and analyze the computational convergence rate, showing that the composite gradient descent algorithm is guaranteed to converge at a geometric rate to the global minimizer of the TeraLasso objective function. Finally, we illustrate the TeraLasso using both simulation and experimental data from a meteorological dataset, showing that we can accurately estimate precision matrices and recover meaningful conditional dependency graphs from high dimensional complex datasets.Comment: accepted to JRSS-

Dissecting high-dimensional phenotypes with bayesian sparse factor analysis of genetic covariance matrices.

Quantitative genetic studies that model complex, multivariate phenotypes are important for both evolutionary prediction and artificial selection. For example, changes in gene expression can provide insight into developmental and physiological mechanisms that link genotype and phenotype. However, classical analytical techniques are poorly suited to quantitative genetic studies of gene expression where the number of traits assayed per individual can reach many thousand. Here, we derive a Bayesian genetic sparse factor model for estimating the genetic covariance matrix (G-matrix) of high-dimensional traits, such as gene expression, in a mixed-effects model. The key idea of our model is that we need consider only G-matrices that are biologically plausible. An organism's entire phenotype is the result of processes that are modular and have limited complexity. This implies that the G-matrix will be highly structured. In particular, we assume that a limited number of intermediate traits (or factors, e.g., variations in development or physiology) control the variation in the high-dimensional phenotype, and that each of these intermediate traits is sparse - affecting only a few observed traits. The advantages of this approach are twofold. First, sparse factors are interpretable and provide biological insight into mechanisms underlying the genetic architecture. Second, enforcing sparsity helps prevent sampling errors from swamping out the true signal in high-dimensional data. We demonstrate the advantages of our model on simulated data and in an analysis of a published Drosophila melanogaster gene expression data set

Automatic Differentiation Variational Inference

Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist only provides a probabilistic model and a dataset, nothing else. ADVI automatically derives an efficient variational inference algorithm, freeing the scientist to refine and explore many models. ADVI supports a broad class of models-no conjugacy assumptions are required. We study ADVI across ten different models and apply it to a dataset with millions of observations. ADVI is integrated into Stan, a probabilistic programming system; it is available for immediate use

Decomposable Principal Component Analysis

We consider principal component analysis (PCA) in decomposable Gaussian graphical models. We exploit the prior information in these models in order to distribute its computation. For this purpose, we reformulate the problem in the sparse inverse covariance (concentration) domain and solve the global eigenvalue problem using a sequence of local eigenvalue problems in each of the cliques of the decomposable graph. We demonstrate the application of our methodology in the context of decentralized anomaly detection in the Abilene backbone network. Based on the topology of the network, we propose an approximate statistical graphical model and distribute the computation of PCA

Hyperspectral Unmixing Overview: Geometrical, Statistical, and Sparse Regression-Based Approaches

Imaging spectrometers measure electromagnetic energy scattered in their instantaneous field view in hundreds or thousands of spectral channels with higher spectral resolution than multispectral cameras. Imaging spectrometers are therefore often referred to as hyperspectral cameras (HSCs). Higher spectral resolution enables material identification via spectroscopic analysis, which facilitates countless applications that require identifying materials in scenarios unsuitable for classical spectroscopic analysis. Due to low spatial resolution of HSCs, microscopic material mixing, and multiple scattering, spectra measured by HSCs are mixtures of spectra of materials in a scene. Thus, accurate estimation requires unmixing. Pixels are assumed to be mixtures of a few materials, called endmembers. Unmixing involves estimating all or some of: the number of endmembers, their spectral signatures, and their abundances at each pixel. Unmixing is a challenging, ill-posed inverse problem because of model inaccuracies, observation noise, environmental conditions, endmember variability, and data set size. Researchers have devised and investigated many models searching for robust, stable, tractable, and accurate unmixing algorithms. This paper presents an overview of unmixing methods from the time of Keshava and Mustard's unmixing tutorial [1] to the present. Mixing models are first discussed. Signal-subspace, geometrical, statistical, sparsity-based, and spatial-contextual unmixing algorithms are described. Mathematical problems and potential solutions are described. Algorithm characteristics are illustrated experimentally.Comment: This work has been accepted for publication in IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensin