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Manifold learning techniques for dynamical systems and time series have shown their utility for a broad spectrum of applications in recent years. While these methods are effective at learning a low-dimensional representation, they are often insufficient for visualizing the global and local structure of the data. In this paper, we present DIG (Dynamical Information Geometry), a visualization method for multivariate time series data that extracts an information geometry from a diffusion framework. Specifically, we implement a novel group of distances in the context of diffusion operators, which may be useful to reveal structure in the data that may not be accessible by the commonly used diffusion distances. Finally, we present a case study applying our visualization tool to EEG data to visualize sleep stages.
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This study investigates the theoretical foundations of t-distributed stochastic neighbor embedding (t-SNE), a popular nonlinear dimension reduction and data visualization method. A novel theoretical framework for the analysis of t-SNE based on the gradient descent approach is presented. For the early exaggeration stage of t-SNE, we show its asymptotic equivalence to a power iteration based on the underlying graph Laplacian, characterize its limiting behavior, and uncover its deep connection to Laplacian spectral clustering, and fundamental principles including early stopping as implicit regularization. The results explain the intrinsic mechanism and the empirical benefits of such a computational strategy. For the embedding stage of t-SNE, we characterize the kinematics of the low-dimensional map throughout the iterations, and identify an amplification phase, featuring the intercluster repulsion and the expansive behavior of the low-dimensional map. The general theory explains the fast convergence rate and the exceptional empirical performance of t-SNE for visualizing clustered data, brings forth the interpretations of the t-SNE output, and provides theoretical guidance for selecting tuning parameters in various applications.
Stochastic linear bandits with high-dimensional sparse features are a practical model for a variety of domains, including personalized medicine and online advertising. We derive a novel $Omega(n^{2/3})$ dimension-free minimax regret lower bound for sparse linear bandits in the data-poor regime where the horizon is smaller than the ambient dimension and where the feature vectors admit a well-conditioned exploration distribution. This is complemented by a nearly matching upper bound for an explore-then-commit algorithm showing that that $Theta(n^{2/3})$ is the optimal rate in the data-poor regime. The results complement existing bounds for the data-rich regime and provide another example where carefully balancing the trade-off between information and regret is necessary. Finally, we prove a dimension-free $O(sqrt{n})$ regret upper bound under an additional assumption on the magnitude of the signal for relevant features.
One of the fundamental problems in machine learning is the estimation of a probability distribution from data. Many techniques have been proposed to study the structure of data, most often building around the assumption that observations lie on a lower-dimensional manifold of high probability. It has been more difficult, however, to exploit this insight to build explicit, tractable density models for high-dimensional data. In this paper, we introduce the deep density model (DDM), a new approach to density estimation. We exploit insights from deep learning to construct a bijective map to a representation space, under which the transformation of the distribution of the data is approximately factorized and has identical and known marginal densities. The simplicity of the latent distribution under the model allows us to feasibly explore it, and the invertibility of the map to characterize contraction of measure across it. This enables us to compute normalized densities for out-of-sample data. This combination of tractability and flexibility allows us to tackle a variety of probabilistic tasks on high-dimensional datasets, including: rapid computation of normalized densities at test-time without evaluating a partition function; generation of samples without MCMC; and characterization of the joint entropy of the data.
The complexity of human cancer often results in significant heterogeneity in response to treatment. Precision medicine offers potential to improve patient outcomes by leveraging this heterogeneity. Individualized treatment rules (ITRs) formalize precision medicine as maps from the patient covariate space into the space of allowable treatments. The optimal ITR is that which maximizes the mean of a clinical outcome in a population of interest. Patient-derived xenograft (PDX) studies permit the evaluation of multiple treatments within a single tumor and thus are ideally suited for estimating optimal ITRs. PDX data are characterized by correlated outcomes, a high-dimensional feature space, and a large number of treatments. Existing methods for estimating optimal ITRs do not take advantage of the unique structure of PDX data or handle the associated challenges well. In this paper, we explore machine learning methods for estimating optimal ITRs from PDX data. We analyze data from a large PDX study to identify biomarkers that are informative for developing personalized treatment recommendations in multiple cancers. We estimate optimal ITRs using regression-based approaches such as Q-learning and direct search methods such as outcome weighted learning. Finally, we implement a superlearner approach to combine a set of estimated ITRs and show that the resulting ITR performs better than any of the input ITRs, mitigating uncertainty regarding user choice of any particular ITR estimation methodology. Our results indicate that PDX data are a valuable resource for developing individualized treatment strategies in oncology.
A number of universally consistent dependence measures have been recently proposed for testing independence, such as distance correlation, kernel correlation, multiscale graph correlation, etc. They provide a satisfactory solution for dependence testing in low-dimensions, but often exhibit decreasing power for high-dimensional data, a phenomenon that has been recognized but remains mostly unchartered. In this paper, we aim to better understand the high-dimensional testing scenarios and explore a procedure that is robust against increasing dimension. To that end, we propose the maximum marginal correlation method and characterize high-dimensional dependence structures via the notion of dependent dimensions. We prove that the maximum method can be valid and universally consistent for testing high-dimensional dependence under regularity conditions, and demonstrate when and how the maximum method may outperform other methods. The methodology can be implemented by most existing dependence measures, has a superior testing power in a variety of common high-dimensional settings, and is computationally efficient for big data analysis when using the distance correlation chi-square test.
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