Simplifying the mosaic description of DNA sequences

By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share compositional similarity with one or more distant (non--neighbouring) domains. We thus obtain a coarse--grained description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly reducing its organizational complexity. This procedure gives a new means of evaluating genomic complexity as one examines organisms ranging from bacteria to human. The mosaic organization of DNA sequences could have originated from the insertion of fragments of one genome (the parasite) inside another (the host), and we present numerical experiments that are suggestive of this scenario.Comment: 16 pages, 1 figure, Accepted for publication in Phys. Rev.

Robust Inside-Outside Segmentation Using Generalized Winding Numbers

Solid shapes in computer graphics are often represented with boundary descriptions, e.g. triangle meshes, but animation, physicallybased simulation, and geometry processing are more realistic and accurate when explicit volume representations are available. Tetrahedral meshes which exactly contain (interpolate) the input boundary description are desirable but difficult to construct for a large class of input meshes. Character meshes and CAD models are often composed of many connected components with numerous selfintersections, non-manifold pieces, and open boundaries, precluding existing meshing algorithms. We propose an automatic algorithm handling all of these issues, resulting in a compact discretization of the input’s inner volume. We only require reasonably consistent orientation of the input triangle mesh. By generalizing the winding number for arbitrary triangle meshes, we define a function that is a perfect segmentation for watertight input and is well-behaved otherwise. This function guides a graphcut segmentation of a constrained Delaunay tessellation (CDT), providing a minimal description that meets the boundary exactly and may be fed as input to existing tools to achieve element quality. We highlight our robustness on a number of examples and show applications of solving PDEs, volumetric texturing and elastic simulation

MORSE: Semantic-ally Drive-n MORpheme SEgment-er

We present in this paper a novel framework for morpheme segmentation which uses the morpho-syntactic regularities preserved by word representations, in addition to orthographic features, to segment words into morphemes. This framework is the first to consider vocabulary-wide syntactico-semantic information for this task. We also analyze the deficiencies of available benchmarking datasets and introduce our own dataset that was created on the basis of compositionality. We validate our algorithm across datasets and present state-of-the-art results

Will the US Economy Recover in 2010? A Minimal Spanning Tree Study

We calculated the cross correlations between the half-hourly times series of the ten Dow Jones US economic sectors over the period February 2000 to August 2008, the two-year intervals 2002--2003, 2004--2005, 2008--2009, and also over 11 segments within the present financial crisis, to construct minimal spanning trees (MSTs) of the US economy at the sector level. In all MSTs, a core-fringe structure is found, with consumer goods, consumer services, and the industrials consistently making up the core, and basic materials, oil and gas, healthcare, telecommunications, and utilities residing predominantly on the fringe. More importantly, we find that the MSTs can be classified into two distinct, statistically robust, topologies: (i) star-like, with the industrials at the center, associated with low-volatility economic growth; and (ii) chain-like, associated with high-volatility economic crisis. Finally, we present statistical evidence, based on the emergence of a star-like MST in Sep 2009, and the MST staying robustly star-like throughout the Greek Debt Crisis, that the US economy is on track to a recovery.Comment: elsarticle class, includes amsmath.sty, graphicx.sty and url.sty. 68 pages, 16 figures, 8 tables. Abridged version of the manuscript presented at the Econophysics Colloquim 2010, incorporating reviewer comment