The medial axis transform (MAT) is an important shape representation for shape approximation, shape recognition, and shape retrieval. Despite years of research, there is still a lack of effective methods for efficient, robust and accurate computation of the MAT. We present an efficient method, called {\em Q-MAT}, that uses quadratic error minimization to compute a structurally simple, geometrically accurate, and compact representation of the MAT. We introduce a new error metric for approximation and a new quantitative characterization of unstable branches of the MAT, and integrate them in an extension of the well-known quadric error metric (QEM) framework for mesh decimation. Q-MAT is fast, removes insignificant unstable branches effectively, and produces a simple and accurate piecewise linear approximation of the MAT. The method is thoroughly validated and compared with existing methods for MAT computation.

No abstract uploaded!

Due to vast sequence divergence among different viral groups, sequence alignment is not directly applicable to genome-wide comparative analysis of viruses. More and more attention has been paid to alignment-free methods for whole genome comparison and phylogenetic tree reconstruction. Among alignment-free methods, the recently proposed ‘‘Natural Vector (NV) representation” has successfully been used to study the phylogeny of multi-segmented viruses based on a 12-dimensional genome space derived from the nucleotide sequence structure. But the preference of proteomes over genomes for the determination of viral phylogeny was not deeply investigated. As the translated products of genes, proteins directly form the shape of viral structure and are vital for all metabolic pathways. In this study, using the NV representation of a protein sequence along with the Hausdorff distance suitable to compare point sets, we construct a 60-dimensional protein space to analyze the evolutionary relationships of 4021 viruses by whole-proteomes in the current NCBI Reference Sequence Database (RefSeq). We also take advantage of the previously developed natural graphical representation to recover viral phylogeny. Our results demonstrate that the proposed method is efficient and accurate for classifying viruses. The accuracy rates of our predictions such as for Baltimore II viruses are as high as 95.9% for family labels, 95.7% for subfamily labels and 96.5% for genus labels. Finally, we discover that proteomes lead to better viral classification when reliable protein sequences are abundant. In other cases, the accuracy rates using proteomes are still comparable to that of genomes.

No abstract uploaded!

Fixing a weakly unobstructed Lagrangian torus in a symplectic manifold X, we define a holomorphic function W known as the Floer potential. We construct a canonical A∞-functor from the Fukaya category of X to the category of matrix factorizations of W. It provides a unified way to construct matrix factorizations from Lagrangian Floer theory. The technique is applied to toric Fano manifolds to transform Lagrangian branes to matrix factorizations. Using the method, we also obtain an explicit expression of the matrix factorization mirror to the real locus of the complex projective space.