14,472 research outputs found

    Fast Quasi-Threshold Editing

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    We introduce Quasi-Threshold Mover (QTM), an algorithm to solve the quasi-threshold (also called trivially perfect) graph editing problem with edge insertion and deletion. Given a graph it computes a quasi-threshold graph which is close in terms of edit count. This edit problem is NP-hard. We present an extensive experimental study, in which we show that QTM is the first algorithm that is able to scale to large real-world graphs in practice. As a side result we further present a simple linear-time algorithm for the quasi-threshold recognition problem.Comment: 26 pages, 4 figures, submitted to ESA 201

    Scalable Community Detection

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    PACE solver description: The KaPoCE exact cluster editing algorithm

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    The cluster editing problem is to transform an input graph into a cluster graph by performing a minimum number of edge editing operations. A cluster graph is a graph where each connected component is a clique. An edit operation can be either adding a new edge or removing an existing edge. In this write-up we outline the core techniques used in the exact cluster editing algorithm of the KaPoCE framework (contains also a heuristic solver), submitted to the exact track of the 2021 PACE challenge

    PACE Solver Description: The KaPoCE Exact Cluster Editing Algorithm

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    The cluster editing problem is to transform an input graph into a cluster graph by performing a minimum number of edge editing operations. A cluster graph is a graph where each connected component is a clique. An edit operation can be either adding a new edge or removing an existing edge. In this write-up we outline the core techniques used in the exact cluster editing algorithm of the KaPoCE framework (contains also a heuristic solver), submitted to the exact track of the 2021 PACE challenge

    Minimum error correction-based haplotype assembly: considerations for long read data

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    The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the genome-phenotype association. Haplotype assembly is a well-known approach for reconstructing haplotypes, exploiting reads generated by DNA sequencing devices. The Minimum Error Correction (MEC) metric is often used for reconstruction of haplotypes from reads. However, problems with the MEC metric have been reported. Here, we investigate the MEC approach to demonstrate that it may result in incorrectly reconstructed haplotypes for devices that produce error-prone long reads. Specifically, we evaluate this approach for devices developed by Illumina, Pacific BioSciences and Oxford Nanopore Technologies. We show that imprecise haplotypes may be reconstructed with a lower MEC than that of the exact haplotype. The performance of MEC is explored for different coverage levels and error rates of data. Our simulation results reveal that in order to avoid incorrect MEC-based haplotypes, a coverage of 25 is needed for reads generated by Pacific BioSciences RS systems.Comment: 17 pages, 6 figure

    Continuous-wave room-temperature diamond maser

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    The maser, older sibling of the laser, has been confined to relative obscurity due to its reliance on cryogenic refrigeration and high-vacuum systems. Despite this it has found application in deep-space communications and radio astronomy due to its unparalleled performance as a low-noise amplifier and oscillator. The recent demonstration of a room-temperature solid- state maser exploiting photo-excited triplet states in organic pentacene molecules paves the way for a new class of maser that could find applications in medicine, security and sensing, taking advantage of its sensitivity and low noise. However, to date, only pulsed operation has been observed in this system. Furthermore, organic maser molecules have poor thermal and mechanical properties, and their triplet sub-level decay rates make continuous emission challenging: alternative materials are therefore required. Therefore, inorganic materials containing spin-defects such as diamond and silicon carbide have been proposed. Here we report a continuous-wave (CW) room-temperature maser oscillator using optically pumped charged nitrogen-vacancy (NV) defect centres in diamond. This demonstration unlocks the potential of room-temperature solid-state masers for use in a new generation of microwave devices.Comment: 7 pages, 4 figure

    Numerical characterization of intraoperative and chronic electrodes in deep brain stimulation

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    An intraoperative electrode (microelectrode) is used in the deep bra In stImulation (DBS) technique to pinpoint the brain target and to choose the best parameters for the electrical stimulus. However, when the intraoperative electrode is replaced with the chronic one (macroelectrode), the observed effects do not always coincide with predictions. To investigate the causes of such discrepancies, a 3D model of the basal ganglia has been considered and realistic models of both intraoperative and chronic electrodes have been developed and numerically solved. Results of simulations of the electric potential (V) and the activating function (AF) along neuronal fibers show that the different geometries and sizes of the two electrodes do not change the distributions and polarities of these functions, but rather the amplitudes. This effect is similar to the one produced by the presence of different tissue layers (edema or glial tissue) in the pen-electrode space. Conversely, an inaccurate positioning of the chronic electrode with respect to the intraoperative one (electric centers not coincident) may induce a completely different electric stimulation in some groups of fibers

    Low-frequency cortical activity is a neuromodulatory target that tracks recovery after stroke.

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    Recent work has highlighted the importance of transient low-frequency oscillatory (LFO; <4 Hz) activity in the healthy primary motor cortex during skilled upper-limb tasks. These brief bouts of oscillatory activity may establish the timing or sequencing of motor actions. Here, we show that LFOs track motor recovery post-stroke and can be a physiological target for neuromodulation. In rodents, we found that reach-related LFOs, as measured in both the local field potential and the related spiking activity, were diminished after stroke and that spontaneous recovery was closely correlated with their restoration in the perilesional cortex. Sensorimotor LFOs were also diminished in a human subject with chronic disability after stroke in contrast to two non-stroke subjects who demonstrated robust LFOs. Therapeutic delivery of electrical stimulation time-locked to the expected onset of LFOs was found to significantly improve skilled reaching in stroke animals. Together, our results suggest that restoration or modulation of cortical oscillatory dynamics is important for the recovery of upper-limb function and that they may serve as a novel target for clinical neuromodulation
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