The Parameterized Complexity of Centrality Improvement in Networks

The centrality of a vertex v in a network intuitively captures how important v is for communication in the network. The task of improving the centrality of a vertex has many applications, as a higher centrality often implies a larger impact on the network or less transportation or administration cost. In this work we study the parameterized complexity of the NP-complete problems Closeness Improvement and Betweenness Improvement in which we ask to improve a given vertex' closeness or betweenness centrality by a given amount through adding a given number of edges to the network. Herein, the closeness of a vertex v sums the multiplicative inverses of distances of other vertices to v and the betweenness sums for each pair of vertices the fraction of shortest paths going through v. Unfortunately, for the natural parameter "number of edges to add" we obtain hardness results, even in rather restricted cases. On the positive side, we also give an island of tractability for the parameter measuring the vertex deletion distance to cluster graphs

Coherent interaction of laser pulses in a resonant optically dense extended medium under the regime of strong field-matter coupling

Nonstationary pump-probe interaction between short laser pulses propagating in a resonant optically dense coherent medium is considered. A special attention is paid to the case, where the density of two-level particles is high enough that a considerable part of the energy of relatively weak external laser-fields can be coherently absorbed and reemitted by the medium. Thus, the field of medium reaction plays a key role in the interaction processes, which leads to the collective behavior of an atomic ensemble in the strongly coupled light-matter system. Such behavior results in the fast excitation interchanges between the field and a medium in the form of the optical ringing, which is analogous to polariton beating in the solid-state optics. This collective oscillating response, which can be treated as successive beats between light wave-packets of different group velocities, is shown to significantly affect propagation and amplification of the probe field under its nonlinear interaction with a nearly copropagating pump pulse. Depending on the probe-pump time delay, the probe transmission spectra show the appearance of either specific doublet or coherent dip. The widths of these features are determined by the density-dependent field-matter coupling coefficient and increase during the propagation. Besides that, the widths of the coherent features, which appear close to the resonance in the broadband probe-spectrum, exceed the absorption-line width, since, under the strong-coupling regime, the frequency of the optical ringing exceeds the rate of incoherent relaxation. Contrary to the stationary strong-field effects, the density- and coordinate-dependent transmission spectra of the probe manifest the importance of the collective oscillations and cannot be obtained in the framework of the single-atom model.Comment: 10 pages, 8 figures, to be published in Phys. Rev.

Evaluating 35 Methods to Generate Structural Connectomes Using Pairwise Classification

There is no consensus on how to construct structural brain networks from diffusion MRI. How variations in pre-processing steps affect network reliability and its ability to distinguish subjects remains opaque. In this work, we address this issue by comparing 35 structural connectome-building pipelines. We vary diffusion reconstruction models, tractography algorithms and parcellations. Next, we classify structural connectome pairs as either belonging to the same individual or not. Connectome weights and eight topological derivative measures form our feature set. For experiments, we use three test-retest datasets from the Consortium for Reliability and Reproducibility (CoRR) comprised of a total of 105 individuals. We also compare pairwise classification results to a commonly used parametric test-retest measure, Intraclass Correlation Coefficient (ICC).Comment: Accepted for MICCAI 2017, 8 pages, 3 figure

Cosmic ray tests of the D0 preshower detector

The D0 preshower detector consists of scintillator strips with embedded wavelength-shifting fibers, and a readout using Visible Light Photon Counters. The response to minimum ionizing particles has been tested with cosmic ray muons. We report results on the gain calibration and light-yield distributions. The spatial resolution is investigated taking into account the light sharing between strips, the effects of multiple scattering and various systematic uncertainties. The detection efficiency and noise contamination are also investigated.Comment: 27 pages, 24 figures, submitted to NIM

Safe and complete contig assembly via omnitigs

Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from $G$ as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201

Structural subnetwork evolution across the life-span: rich-club, feeder, seeder

The impact of developmental and aging processes on brain connectivity and the connectome has been widely studied. Network theoretical measures and certain topological principles are computed from the entire brain, however there is a need to separate and understand the underlying subnetworks which contribute towards these observed holistic connectomic alterations. One organizational principle is the rich-club - a core subnetwork of brain regions that are strongly connected, forming a high-cost, high-capacity backbone that is critical for effective communication in the network. Investigations primarily focus on its alterations with disease and age. Here, we present a systematic analysis of not only the rich-club, but also other subnetworks derived from this backbone - namely feeder and seeder subnetworks. Our analysis is applied to structural connectomes in a normal cohort from a large, publicly available lifespan study. We demonstrate changes in rich-club membership with age alongside a shift in importance from 'peripheral' seeder to feeder subnetworks. Our results show a refinement within the rich-club structure (increase in transitivity and betweenness centrality), as well as increased efficiency in the feeder subnetwork and decreased measures of network integration and segregation in the seeder subnetwork. These results demonstrate the different developmental patterns when analyzing the connectome stratified according to its rich-club and the potential of utilizing this subnetwork analysis to reveal the evolution of brain architectural alterations across the life-span