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Added by
Alexander Gorban
Publication date
2011
fields
Informatics Engineering
and research's language is
English
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In many physical, statistical, biological and other investigations it is desirable to approximate a system of points by objects of lower dimension and/or complexity. For this purpose, Karl Pearson invented principal component analysis in 1901 and found lines and planes of closest fit to system of points. The famous k-means algorithm solves the approximation problem too, but by finite sets instead of lines and planes. This chapter gives a brief practical introduction into the methods of construction of general principal objects, i.e. objects embedded in the middle of the multidimensional data set. As a basis, the unifying framework of mean squared distance approximation of finite datasets is selected. Principal graphs and manifolds are constructed as generalisations of principal components and k-means principal points. For this purpose, the family of expectation/maximisation algorithms with nearest generalisations is presented. Construction of principal graphs with controlled complexity is based on the graph grammar approach.
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We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.
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Principal Component Analysis (PCA) is one of the most important methods to handle high dimensional data. However, most of the studies on PCA aim to minimize the loss after projection, which usually measures the Euclidean distance, though in some fields, angle distance is known to be more important and critical for analysis. In this paper, we propose a method by adding constraints on factors to unify the Euclidean distance and angle distance. However, due to the nonconvexity of the objective and constraints, the optimized solution is not easy to obtain. We propose an alternating linearized minimization method to solve it with provable convergence rate and guarantee. Experiments on synthetic data and real-world datasets have validated the effectiveness of our method and demonstrated its advantages over state-of-art clustering methods.
Dimensionality reduction on Riemannian manifolds is challenging due to the complex nonlinear data structures. While probabilistic principal geodesic analysis~(PPGA) has been proposed to generalize conventional principal component analysis (PCA) onto manifolds, its effectiveness is limited to data with a single modality. In this paper, we present a novel Gaussian latent variable model that provides a unique way to integrate multiple PGA models into a maximum-likelihood framework. This leads to a well-defined mixture model of probabilistic principal geodesic analysis (MPPGA) on sub-populations, where parameters of the principal subspaces are automatically estimated by employing an Expectation Maximization algorithm. We further develop a mixture Bayesian PGA (MBPGA) model that automatically reduces data dimensionality by suppressing irrelevant principal geodesics. We demonstrate the advantages of our model in the contexts of clustering and statistical shape analysis, using synthetic sphere data, real corpus callosum, and mandible data from human brain magnetic resonance~(MR) and CT images.
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