On the Reconstruction of Geodesic Subspaces of RN\mathbb{R}^N

We consider the topological and geometric reconstruction of a geodesic subspace of $\mathbb{R}^N$ both from the \v{C}ech and Vietoris-Rips filtrations on a finite, Hausdorff-close, Euclidean sample. Our reconstruction technique leverages the intrinsic length metric induced by the geodesics on the subspace. We consider the distortion and convexity radius as our sampling parameters for a successful reconstruction. For a geodesic subspace with finite distortion and positive convexity radius, we guarantee a correct computation of its homotopy and homology groups from the sample. For geodesic subspaces of $\mathbb{R}^2$, we also devise an algorithm to output a homotopy equivalent geometric complex that has a very small Hausdorff distance to the unknown shape of interest

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

On The Effect of Hyperedge Weights On Hypergraph Learning

Hypergraph is a powerful representation in several computer vision, machine learning and pattern recognition problems. In the last decade, many researchers have been keen to develop different hypergraph models. In contrast, no much attention has been paid to the design of hyperedge weights. However, many studies on pairwise graphs show that the choice of edge weight can significantly influence the performances of such graph algorithms. We argue that this also applies to hypegraphs. In this paper, we empirically discuss the influence of hyperedge weight on hypegraph learning via proposing three novel hyperedge weights from the perspectives of geometry, multivariate statistical analysis and linear regression. Extensive experiments on ORL, COIL20, JAFFE, Sheffield, Scene15 and Caltech256 databases verify our hypothesis. Similar to graph learning, several representative hyperedge weighting schemes can be concluded by our experimental studies. Moreover, the experiments also demonstrate that the combinations of such weighting schemes and conventional hypergraph models can get very promising classification and clustering performances in comparison with some recent state-of-the-art algorithms

Data-Driven Shape Analysis and Processing

Data-driven methods play an increasingly important role in discovering geometric, structural, and semantic relationships between 3D shapes in collections, and applying this analysis to support intelligent modeling, editing, and visualization of geometric data. In contrast to traditional approaches, a key feature of data-driven approaches is that they aggregate information from a collection of shapes to improve the analysis and processing of individual shapes. In addition, they are able to learn models that reason about properties and relationships of shapes without relying on hard-coded rules or explicitly programmed instructions. We provide an overview of the main concepts and components of these techniques, and discuss their application to shape classification, segmentation, matching, reconstruction, modeling and exploration, as well as scene analysis and synthesis, through reviewing the literature and relating the existing works with both qualitative and numerical comparisons. We conclude our report with ideas that can inspire future research in data-driven shape analysis and processing.Comment: 10 pages, 19 figure

Improved processing of microarray data using image reconstruction techniques

Spotted cDNA microarray data analysis suffers from various problems such as noise from a variety of sources, missing data, inconsistency, and, of course, the presence of outliers. This paper introduces a new method that dramatically reduces the noise when processing the original image data. The proposed approach recreates the microarray slide image, as it would have been with all the genes removed. By subtracting this background recreation from the original, the gene ratios can be calculated with more precision and less influence from outliers and other artifacts that would normally make the analysis of this data more difficult. The new technique is also beneficial, as it does not rely on the accurate fitting of a region to each gene, with its only requirement being an approximate coordinate. In experiments conducted, the new method was tested against one of the mainstream methods of processing spotted microarray images. Our method is shown to produce much less variation in gene measurements. This evidence is supported by clustering results that show a marked improvement in accuracy

Signal Estimation with Additive Error Metrics in Compressed Sensing

Compressed sensing typically deals with the estimation of a system input from its noise-corrupted linear measurements, where the number of measurements is smaller than the number of input components. The performance of the estimation process is usually quantified by some standard error metric such as squared error or support set error. In this correspondence, we consider a noisy compressed sensing problem with any arbitrary error metric. We propose a simple, fast, and highly general algorithm that estimates the original signal by minimizing the error metric defined by the user. We verify that our algorithm is optimal owing to the decoupling principle, and we describe a general method to compute the fundamental information-theoretic performance limit for any error metric. We provide two example metrics --- minimum mean absolute error and minimum mean support error --- and give the theoretical performance limits for these two cases. Experimental results show that our algorithm outperforms methods such as relaxed belief propagation (relaxed BP) and compressive sampling matching pursuit (CoSaMP), and reaches the suggested theoretical limits for our two example metrics.Comment: to appear in IEEE Trans. Inf. Theor