The plethora of data from neuroimaging studies provide a rich opportunity to discover effects and generate hypotheses through exploratory data analysis. Brain pathologies often manifest in changes in shape along with deterioration and alteration of brain matter, i.e., changes in mass. We propose a morphometry approach using unbalanced optimal transport that detects and localizes changes in mass and separates them from changes due to the location of mass. The approach generates images of mass allocation and mass transport cost for each subject in the population. Voxelwise correlations with clinical variables highlight regions of mass allocation or mass transfer related to the variables. We demonstrate the method on the white and gray matter segmentations from the OASIS brain MRI data set. The separation of white and gray matter ensures that optimal transport does not transfer mass between different tissues types and separates gray and white matter related changes. The OASIS data set includes subjects ranging from healthy to mild and moderate dementia, and the results corroborate known pathology changes related to dementia that are not discovered with traditional voxel-based morphometry. The transport-based morphometry increases the explanatory power of regression on clinical variables compared to traditional voxel-based morphometry, indicating that transport cost and mass allocation images capture a larger portion of pathology induced changes.

This paper presents a multiscale approach to efficiently compute approximate optimal transport plans between point sets. It is particularly well-suited for point sets that are in high- dimensions, but are close to being intrinsically low- dimensional. The approach is based on an adaptive multiscale decomposition of the point sets. The multiscale decomposition yields a sequence of optimal transport problems, that are solved in a top-to-bottom fashion from the coarsest to the finest scale. We provide numerical evidence that this multiscale approach scales approximately linearly, in time and memory, in the number of nodes, instead of quadratically or worse for a direct solution. Empirically, the multiscale approach results in less than one percent relative error in the objective function. Furthermore, the multiscale plans constructed are of interest by themselves as they may be used to introduce novel features and notions of distances between point sets. An analysis of sets of brain MRI based on optimal transport distances illustrates the effectiveness of the proposed method on a real world data set. The application demonstrates that multiscale optimal transport distances have the potential to improve on state-of-the-art metrics currently used in computational anatomy.

We present a novel method for multitask learning (MTL) based on {\it manifold regularization}: assume that all task parameters lie on a manifold. This is the generalization of a common assumption made in the existing literature: task parameters share a common {\it linear} subspace. One proposed method uses the projection distance from the manifold to regularize the task parameters. The manifold structure and the task parameters are learned using an alternating optimization framework. When the manifold structure is fixed, our method decomposes across tasks which can be learnt independently. An approximation of the manifold regularization scheme is presented that preserves the convexity of the single task learning problem, and makes the proposed MTL framework efficient and easy to implement. We show the efficacy of our method on several datasets.

An important goal of scientific data analysis is to understand the behavior of a system or process based on a sample of the system. In many instances it is possible to observe both input parameters and system outputs, and characterize the system as a high-dimensional function. Such data sets arise, for instance, in large numerical simulations, as energy landscapes in optimization problems, or in the analysis of image data relating to biological or medical parameters. This paper proposes an approach to analyze and visualizing such data sets. The proposed method combines topological and geometric techniques to provide interactive visualizations of discretely sampled high-dimensional scalar fields. The method relies on a segmentation of the parameter space using an approximate Morse-Smale complex on the cloud of point samples. For each crystal of the Morse-Smale complex, a regression of the system parameters with respect to the output yields a curve in the parameter space. The result is a simplified geometric representation of the Morse-Smale complex in the high dimensional input domain. Finally, the geometric representation is embedded in 2D, using dimension reduction, to provide a visualization platform. The geometric properties of the regression curves enable the visualization of additional information about each crystal such as local and global shape, width, length, and sampling densities. The method is illustrated on several synthetic examples of two dimensional functions. Two use cases, using data sets from the UCI machine learning repository, demonstrate the utility of the proposed approach on real data. Finally, in collaboration with domain experts the proposed method is applied to two scientific challenges. The analysis of parameters of climate simulations and their relationship to predicted global energy flux and the concentrations of chemical species in a combustion simulation and their integration with temperature.

We present a manifold learning approach to dimensionality reduction that explicitly models the manifold as a mapping from low to high dimensional space. The manifold is represented as a parametrized surface represented by a set of parameters that are defined on the input samples. The representation also provides a natural mapping from high to low dimensional space, and a concatenation of these two mappings induces a projection operator onto the manifold. The explicit projection operator allows for a clearly defined objective function in terms of projection distance and reconstruction error. A formulation of the mappings in terms of kernel regression permits a direct optimization of the objective function and the extremal points converge to principal surfaces as the number of data to learn from increases. Principal surfaces have the desirable property that they, informally speaking, pass through the middle of a distribution. We provide a proof on the convergence to principal surfaces and illustrate the effectiveness of the proposed approach on synthetic and real data sets.

This paper investigates an approach to model the space of brain images through a low-dimensional manifold. A data driven method to learn a manifold from a collections of brain images is proposed. We hypothesize that the space spanned by a set of brain images can be captured, to some approximation, by a low-dimensional manifold, i.e. a parametrization of the set of images. The approach builds on recent advances in manifold learning that allow to uncover nonlinear trends in data. We combine this manifold learning with distance measures between images that capture shape, in order to learn the underlying structure of a database of brain images. The proposed method is generative. New images can be created from the manifold parametrization and existing images can be projected onto the manifold. By measuring projection distance of a held out set of brain images we evaluate the fit of the proposed manifold model to the data and we can compute statistical properties of the data using this manifold structure. We demonstrate this technology on a database of 436 MR brain images.

Non-linear dimensionality reduction of noisy data is a challenging problem encountered in a variety of data analysis applications. Recent results in the literature show that spectral decomposition, as used for example by the Laplacian Eigenmaps algorithm, provides a powerful tool for non-linear dimensionality reduction and manifold learning. In this paper, we discuss a significant shortcoming of these approaches, which we refer to as the repeated eigendirections problem. We propose a novel approach that combines successive 1-dimensional spectral embeddings with a data advection scheme that allows us to address this problem. The proposed method does not depend on a non-linear optimization scheme; hence, it is not prone to local minima. Experiments with artificial and real data illustrate the advantages of the proposed method over existing approaches. We also demonstrate that the approach is capable of correctly learning manifolds corrupted by significant amounts of noise.