Masking Strategies for Image Manifolds

We consider the problem of selecting an optimal mask for an image manifold, i.e., choosing a subset of the pixels of the image that preserves the manifold's geometric structure present in the original data. Such masking implements a form of compressive sensing through emerging imaging sensor platforms for which the power expense grows with the number of pixels acquired. Our goal is for the manifold learned from masked images to resemble its full image counterpart as closely as possible. More precisely, we show that one can indeed accurately learn an image manifold without having to consider a large majority of the image pixels. In doing so, we consider two masking methods that preserve the local and global geometric structure of the manifold, respectively. In each case, the process of finding the optimal masking pattern can be cast as a binary integer program, which is computationally expensive but can be approximated by a fast greedy algorithm. Numerical experiments show that the relevant manifold structure is preserved through the data-dependent masking process, even for modest mask sizes

An Efficient Dual Approach to Distance Metric Learning

Distance metric learning is of fundamental interest in machine learning because the distance metric employed can significantly affect the performance of many learning methods. Quadratic Mahalanobis metric learning is a popular approach to the problem, but typically requires solving a semidefinite programming (SDP) problem, which is computationally expensive. Standard interior-point SDP solvers typically have a complexity of $O(D^{6.5})$ (with $D$ the dimension of input data), and can thus only practically solve problems exhibiting less than a few thousand variables. Since the number of variables is $D (D+1) / 2$, this implies a limit upon the size of problem that can practically be solved of around a few hundred dimensions. The complexity of the popular quadratic Mahalanobis metric learning approach thus limits the size of problem to which metric learning can be applied. Here we propose a significantly more efficient approach to the metric learning problem based on the Lagrange dual formulation of the problem. The proposed formulation is much simpler to implement, and therefore allows much larger Mahalanobis metric learning problems to be solved. The time complexity of the proposed method is $O (D ^ 3)$, which is significantly lower than that of the SDP approach. Experiments on a variety of datasets demonstrate that the proposed method achieves an accuracy comparable to the state-of-the-art, but is applicable to significantly larger problems. We also show that the proposed method can be applied to solve more general Frobenius-norm regularized SDP problems approximately

Dimensionality Reduction Mappings

A wealth of powerful dimensionality reduction methods has been established which can be used for data visualization and preprocessing. These are accompanied by formal evaluation schemes, which allow a quantitative evaluation along general principles and which even lead to further visualization schemes based on these objectives. Most methods, however, provide a mapping of a priorly given finite set of points only, requiring additional steps for out-of-sample extensions. We propose a general view on dimensionality reduction based on the concept of cost functions, and, based on this general principle, extend dimensionality reduction to explicit mappings of the data manifold. This offers simple out-of-sample extensions. Further, it opens a way towards a theory of data visualization taking the perspective of its generalization ability to new data points. We demonstrate the approach based on a simple global linear mapping as well as prototype-based local linear mappings.

Network Topology Mapping from Partial Virtual Coordinates and Graph Geodesics

For many important network types (e.g., sensor networks in complex harsh environments and social networks) physical coordinate systems (e.g., Cartesian), and physical distances (e.g., Euclidean), are either difficult to discern or inapplicable. Accordingly, coordinate systems and characterizations based on hop-distance measurements, such as Topology Preserving Maps (TPMs) and Virtual-Coordinate (VC) systems are attractive alternatives to Cartesian coordinates for many network algorithms. Herein, we present an approach to recover geometric and topological properties of a network with a small set of distance measurements. In particular, our approach is a combination of shortest path (often called geodesic) recovery concepts and low-rank matrix completion, generalized to the case of hop-distances in graphs. Results for sensor networks embedded in 2-D and 3-D spaces, as well as a social networks, indicates that the method can accurately capture the network connectivity with a small set of measurements. TPM generation can now also be based on various context appropriate measurements or VC systems, as long as they characterize different nodes by distances to small sets of random nodes (instead of a set of global anchors). The proposed method is a significant generalization that allows the topology to be extracted from a random set of graph shortest paths, making it applicable in contexts such as social networks where VC generation may not be possible.Comment: 17 pages, 9 figures. arXiv admin note: substantial text overlap with arXiv:1712.1006

Visualizing dimensionality reduction of systems biology data

One of the challenges in analyzing high-dimensional expression data is the detection of important biological signals. A common approach is to apply a dimension reduction method, such as principal component analysis. Typically, after application of such a method the data is projected and visualized in the new coordinate system, using scatter plots or profile plots. These methods provide good results if the data have certain properties which become visible in the new coordinate system and which were hard to detect in the original coordinate system. Often however, the application of only one method does not suffice to capture all important signals. Therefore several methods addressing different aspects of the data need to be applied. We have developed a framework for linear and non-linear dimension reduction methods within our visual analytics pipeline SpRay. This includes measures that assist the interpretation of the factorization result. Different visualizations of these measures can be combined with functional annotations that support the interpretation of the results. We show an application to high-resolution time series microarray data in the antibiotic-producing organism Streptomyces coelicolor as well as to microarray data measuring expression of cells with normal karyotype and cells with trisomies of human chromosomes 13 and 21