A survey of dimensionality reduction techniques

Experimental life sciences like biology or chemistry have seen in the recent decades an explosion of the data available from experiments. Laboratory instruments become more and more complex and report hundreds or thousands measurements for a single experiment and therefore the statistical methods face challenging tasks when dealing with such high dimensional data. However, much of the data is highly redundant and can be efficiently brought down to a much smaller number of variables without a significant loss of information. The mathematical procedures making possible this reduction are called dimensionality reduction techniques; they have widely been developed by fields like Statistics or Machine Learning, and are currently a hot research topic. In this review we categorize the plethora of dimension reduction techniques available and give the mathematical insight behind them

Principal Manifolds and Nonlinear Dimension Reduction via Local Tangent Space Alignment

Nonlinear manifold learning from unorganized data points is a very challenging unsupervised learning and data visualization problem with a great variety of applications. In this paper we present a new algorithm for manifold learning and nonlinear dimension reduction. Based on a set of unorganized data points sampled with noise from the manifold, we represent the local geometry of the manifold using tangent spaces learned by fitting an affine subspace in a neighborhood of each data point. Those tangent spaces are aligned to give the internal global coordinates of the data points with respect to the underlying manifold by way of a partial eigendecomposition of the neighborhood connection matrix. We present a careful error analysis of our algorithm and show that the reconstruction errors are of second-order accuracy. We illustrate our algorithm using curves and surfaces both in 2D/3D and higher dimensional Euclidean spaces, and 64-by-64 pixel face images with various pose and lighting conditions. We also address several theoretical and algorithmic issues for further research and improvements

Parametrization of white matter manifold-like structures using principal surfaces

In this manuscript, we are concerned with data generated from a diffusion tensor imaging (DTI) experiment. The goal is to parameterize manifold-like white matter tracts, such as the corpus callosum, using principal surfaces. We approach the problem by finding a geometrically motivated surface-based representation of the corpus callosum and visualize the fractional anisotropy (FA) values projected onto the surface; the method applies to any other diffusion summary as well as to other white matter tracts. We provide an algorithm that 1) constructs the principal surface of a corpus callosum; 2) flattens the surface into a parametric 2D map; 3) projects associated FA values on the map. The algorithm was applied to a longitudinal study containing 466 diffusion tensor images of 176 multiple sclerosis (MS) patients observed at multiple visits. For each subject and visit the study contains a registered DTI scan of the corpus callosum at roughly 20,000 voxels. Extensive simulation studies demonstrate fast convergence and robust performance of the algorithm under a variety of challenging scenarios.Comment: 27 pages, 5 figures and 1 tabl

Auto-associative models, nonlinear Principal component analysis, manifolds and projection pursuit

In this paper, auto-associative models are proposed as candidates to the generalization of Principal Component Analysis. We show that these models are dedicated to the approximation of the dataset by a manifold. Here, the word "manifold" refers to the topology properties of the structure. The approximating manifold is built by a projection pursuit algorithm. At each step of the algorithm, the dimension of the manifold is incremented. Some theoretical properties are provided. In particular, we can show that, at each step of the algorithm, the mean residuals norm is not increased. Moreover, it is also established that the algorithm converges in a finite number of steps. Some particular auto-associative models are exhibited and compared to the classical PCA and some neural networks models. Implementation aspects are discussed. We show that, in numerous cases, no optimization procedure is required. Some illustrations on simulated and real data are presented

Tangent Bundle Manifold Learning via Grassmann&Stiefel Eigenmaps

One of the ultimate goals of Manifold Learning (ML) is to reconstruct an unknown nonlinear low-dimensional manifold embedded in a high-dimensional observation space by a given set of data points from the manifold. We derive a local lower bound for the maximum reconstruction error in a small neighborhood of an arbitrary point. The lower bound is defined in terms of the distance between tangent spaces to the original manifold and the estimated manifold at the considered point and reconstructed point, respectively. We propose an amplification of the ML, called Tangent Bundle ML, in which the proximity not only between the original manifold and its estimator but also between their tangent spaces is required. We present a new algorithm that solves this problem and gives a new solution for the ML also.Comment: 25 pages, 6 figure

Computational Machines in a Coexistence with Concrete Universals and Data Streams

We discuss that how the majority of traditional modeling approaches are following the idealism point of view in scientific modeling, which follow the set theoretical notions of models based on abstract universals. We show that while successful in many classical modeling domains, there are fundamental limits to the application of set theoretical models in dealing with complex systems with many potential aspects or properties depending on the perspectives. As an alternative to abstract universals, we propose a conceptual modeling framework based on concrete universals that can be interpreted as a category theoretical approach to modeling. We call this modeling framework pre-specific modeling. We further, discuss how a certain group of mathematical and computational methods, along with ever-growing data streams are able to operationalize the concept of pre-specific modeling

NPTC-net: Narrow-Band Parallel Transport Convolutional Neural Network on Point Clouds

Convolution plays a crucial role in various applications in signal and image processing, analysis, and recognition. It is also the main building block of convolution neural networks (CNNs). Designing appropriate convolution neural networks on manifold-structured point clouds can inherit and empower recent advances of CNNs to analyzing and processing point cloud data. However, one of the major challenges is to define a proper way to "sweep" filters through the point cloud as a natural generalization of the planar convolution and to reflect the point cloud's geometry at the same time. In this paper, we consider generalizing convolution by adapting parallel transport on the point cloud. Inspired by a triangulated surface-based method [Stefan C. Schonsheck, Bin Dong, and Rongjie Lai, arXiv:1805.07857.], we propose the Narrow-Band Parallel Transport Convolution (NPTC) using a specifically defined connection on a voxel-based narrow-band approximation of point cloud data. With that, we further propose a deep convolutional neural network based on NPTC (called NPTC-net) for point cloud classification and segmentation. Comprehensive experiments show that the proposed NPTC-net achieves similar or better results than current state-of-the-art methods on point cloud classification and segmentation.Comment: 18 pages, 6 figure

ViDaExpert: user-friendly tool for nonlinear visualization and analysis of multidimensional vectorial data

ViDaExpert is a tool for visualization and analysis of multidimensional vectorial data. ViDaExpert is able to work with data tables of "object-feature" type that might contain numerical feature values as well as textual labels for rows (objects) and columns (features). ViDaExpert implements several statistical methods such as standard and weighted Principal Component Analysis (PCA) and the method of elastic maps (non-linear version of PCA), Linear Discriminant Analysis (LDA), multilinear regression, K-Means clustering, a variant of decision tree construction algorithm. Equipped with several user-friendly dialogs for configuring data point representations (size, shape, color) and fast 3D viewer, ViDaExpert is a handy tool allowing to construct an interactive 3D-scene representing a table of data in multidimensional space and perform its quick and insightfull statistical analysis, from basic to advanced methods

EasiCS: the objective and fine-grained classification method of cervical spondylosis dysfunction

The precise diagnosis is of great significance in developing precise treatment plans to restore neck function and reduce the burden posed by the cervical spondylosis (CS). However, the current available neck function assessment method are subjective and coarse-grained. In this paper, based on the relationship among CS, cervical structure, cervical vertebra function, and surface electromyography (sEMG), we seek to develop a clustering algorithms on the sEMG data set collected from the clinical environment and implement the division. We proposed and developed the framework EasiCS, which consists of dimension reduction, clustering algorithm EasiSOM, spectral clustering algorithm EasiSC. The EasiCS outperform the commonly used seven algorithms overall

Geodesic convolutional neural networks on Riemannian manifolds

Feature descriptors play a crucial role in a wide range of geometry analysis and processing applications, including shape correspondence, retrieval, and segmentation. In this paper, we introduce Geodesic Convolutional Neural Networks (GCNN), a generalization of the convolutional networks (CNN) paradigm to non-Euclidean manifolds. Our construction is based on a local geodesic system of polar coordinates to extract "patches", which are then passed through a cascade of filters and linear and non-linear operators. The coefficients of the filters and linear combination weights are optimization variables that are learned to minimize a task-specific cost function. We use GCNN to learn invariant shape features, allowing to achieve state-of-the-art performance in problems such as shape description, retrieval, and correspondence