270,054 research outputs found
Advanced Multilevel Node Separator Algorithms
A node separator of a graph is a subset S of the nodes such that removing S
and its incident edges divides the graph into two disconnected components of
about equal size. In this work, we introduce novel algorithms to find small
node separators in large graphs. With focus on solution quality, we introduce
novel flow-based local search algorithms which are integrated in a multilevel
framework. In addition, we transfer techniques successfully used in the graph
partitioning field. This includes the usage of edge ratings tailored to our
problem to guide the graph coarsening algorithm as well as highly localized
local search and iterated multilevel cycles to improve solution quality even
further. Experiments indicate that flow-based local search algorithms on its
own in a multilevel framework are already highly competitive in terms of
separator quality. Adding additional local search algorithms further improves
solution quality. Our strongest configuration almost always outperforms
competing systems while on average computing 10% and 62% smaller separators
than Metis and Scotch, respectively
Recent Advances in Graph Partitioning
We survey recent trends in practical algorithms for balanced graph
partitioning together with applications and future research directions
Enhancement of Underwater Video Mosaics for Post-Processing
Mosaics of seafloor created from still images or video acquired underwater have proved to be useful for construction of maps of forensic and archeological sites, species\u27 abundance estimates, habitat characterization, etc. Images taken by a camera mounted on a stable platform are registered (at first pair-wise and then globally) and assembled in a high resolution visual map of the surveyed area. While this map is usually sufficient for a human orientation and even quantitative measurements, it often contains artifacts that complicate an automatic post-processing (for example, extraction of shapes for organism counting, or segmentation for habitat characterization). The most prominent artifacts are inter-frame seams caused by inhomogeneous artificial illumination, and local feature misalignments due to parallax effects - result of an attempt to represent a 3D world on a 2D map. In this paper we propose two image processing techniques for mosaic quality enhancement - median mosaic-based illumination correction suppressing appearance of inter-frame seams, and micro warping decreasing influence of parallax effects
Going the distance for protein function prediction: a new distance metric for protein interaction networks
Due to an error introduced in the production process, the x-axes in the first panels of Figure 1 and Figure 7 are not formatted correctly. The correct Figure 1 can be viewed here: http://dx.doi.org/10.1371/annotation/343bf260-f6ff-48a2-93b2-3cc79af518a9In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a limited ability to capture fine-grained neighborhood distinctions, because most proteins are close to each other, and there are many ties in proximity. We introduce diffusion state distance (DSD), a new metric based on a graph diffusion property, designed to capture finer-grained distinctions in proximity for transfer of functional annotation in PPI networks. We present a tool that, when input a PPI network, will output the DSD distances between every pair of proteins. We show that replacing the shortest-path metric by DSD improves the performance of classical function prediction methods across the board.MC, HZ, NMD and LJC were supported in part by National Institutes of Health (NIH) R01 grant GM080330. JP was supported in part by NIH grant R01 HD058880. This material is based upon work supported by the National Science Foundation under grant numbers CNS-0905565, CNS-1018266, CNS-1012910, and CNS-1117039, and supported by the Army Research Office under grant W911NF-11-1-0227 (to MEC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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