Next Generation Cluster Editing

This work aims at improving the quality of structural variant prediction from the mapped reads of a sequenced genome. We suggest a new model based on cluster editing in weighted graphs and introduce a new heuristic algorithm that allows to solve this problem quickly and with a good approximation on the huge graphs that arise from biological datasets

Invariance of the Cuntz splice

We show that the Cuntz splice induces stably isomorphic graph $C^*$-algebras.Comment: Our arguments to prove invariance of the Cuntz splice for unital graph C*-algebras in arXiv:1505.06773 applied with only minor changes in the general case. Since most of the results of that preprint have since been superseded by other forthcoming work, we do not intend to publish it, whereas this work is intended for publication. arXiv admin note: substantial text overlap with arXiv:1505.0677

A new graph-based method for pairwise global network alignment

<p>Abstract</p> <p>Background</p> <p>In addition to component-based comparative approaches, <it>network alignments </it>provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical sequence alignment, the comparison of networks becomes computationally more challenging, as most meaningful assumptions instantly lead to <it>NP</it>-hard problems. Most previous algorithmic work on network alignments is heuristic in nature.</p> <p>Results</p> <p>We introduce the graph-based <it>maximum structural matching </it>formulation for pairwise global network alignment. We relate the formulation to previous work and prove <it>NP</it>-hardness of the problem.</p> <p>Based on the new formulation we build upon recent results in computational structural biology and present a novel Lagrangian relaxation approach that, in combination with a branch-and-bound method, computes provably optimal network alignments. The Lagrangian algorithm alone is a powerful heuristic method, which produces solutions that are often near-optimal and – unlike those computed by pure heuristics – come with a quality guarantee.</p> <p>Conclusion</p> <p>Computational experiments on the alignment of protein-protein interaction networks and on the classification of metabolic subnetworks demonstrate that the new method is reasonably fast and has advantages over pure heuristics. Our software tool is freely available as part of the L<smcaps>I</smcaps>SA library.</p

Time-dependent magnetotransport of a wave packet in a quantum wire with embedded quantum dots

We consider wave packet propagation in a quantum wire with either an embedded antidot or an embedded parallel double open quantum dot under the influence of a uniform magnetic field. The magnetoconductance and the time evolution of an electron wave packet are calculated based on the Lippmann-Schwinger formalism. This approach allows us to look at arbitrary embedded potential profiles and illustrate the results by performing computational simulations for the conductance and the time evolution of the electron wave packet through the quantum wire. In the double-dot system we observe a long-lived resonance state that enhances the spatial spreading of the wave packet, and quantum skipping-like trajectories are induced when the envelop function of the wave packet covers several subbands in appropriate magnetic fields.Comment: RevTeX, 9 pages with 8 included postscript figure

(Bi-)Cohen-Macaulay simplicial complexes and their associated coherent sheaves

Via the BGG correspondence a simplicial complex Delta on [n] is transformed into a complex of coherent sheaves on P^n-1. We show that this complex reduces to a coherent sheaf F exactly when the Alexander dual Delta^* is Cohen-Macaulay. We then determine when both Delta and Delta^* are Cohen-Macaulay. This corresponds to F being a locally Cohen-Macaulay sheaf. Lastly we conjecture for which range of invariants of such Delta it must be a cone.Comment: 16 pages, some minor change