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We consider distributed caching of content across several small base stations (SBSs) in a wireless network, where the content is encoded using a maximum distance separable code. Specifically, we apply soft time-to-live (STTL) cache management policies, where coded packets may be evicted from the caches at periodic times. We propose a reinforcement learning (RL) approach to find coded STTL policies minimizing the overall network load. We demonstrate that such caching policies achieve almost the same network load as policies obtained through optimization, where the latter assumes perfect knowledge of the distribution of times between file requests as well the distribution of the number of SBSs within communication range of a user placing a request. We also suggest a multi-agent RL (MARL) framework for the scenario of non-uniformly distributed requests in space. For such a scenario, we show that MARL caching policies achieve lower network load as compared to optimized caching policies assuming a uniform request placement. We also provide convincing evidence that synchronous updates offer a lower network load than asynchronous updates for spatially homogeneous renewal request processes due to the memory of the renewal processes.

We consider distributed and dynamic caching of coded content at small base stations (SBSs) in an area served by a macro base station (MBS). Specifically, content is encoded using a maximum distance separable code and cached according to a time-to-live (TTL) cache eviction policy, which allows coded packets to be removed from the caches at periodic times. Mobile users requesting a particular content download coded packets from SBSs within communication range. If additional packets are required to decode the file, these are downloaded from the MBS. We formulate an optimization problem that is efficiently solved numerically, providing TTL caching policies minimizing the overall network load. We demonstrate that distributed coded caching using TTL caching policies can offer significant reductions in terms of network load when request arrivals are bursty. We show how the distributed coded caching problem utilizing TTL caching policies can be analyzed as a specific single cache, convex optimization problem. Our problem encompasses static caching and the single cache as special cases. We prove that, interestingly, static caching is optimal under a Poisson request process, and that for a single cache the optimization problem has a surprisingly simple solution., Comment: To appear in IEEE Transactions on Communications

Graph refinement, or the task of obtaining subgraphs of interest from over-complete graphs, can have many varied applications. In this work, we extract trees or collection of sub-trees from image data by, first deriving a graph-based representation of the volumetric data and then, posing the tree extraction as a graph refinement task. We present two methods to perform graph refinement. First, we use mean-field approximation (MFA) to approximate the posterior density over the subgraphs from which the optimal subgraph of interest can be estimated. Mean field networks (MFNs) are used for inference based on the interpretation that iterations of MFA can be seen as feed-forward operations in a neural network. This allows us to learn the model parameters using gradient descent. Second, we present a supervised learning approach using graph neural networks (GNNs) which can be seen as generalisations of MFNs. Subgraphs are obtained by training a GNN-based graph refinement model to directly predict edge probabilities. We discuss connections between the two classes of methods and compare them for the task of extracting airways from 3D, low-dose, chest CT data. We show that both the MFN and GNN models show significant improvement when compared to one baseline method, that is similar to a top performing method in the EXACT'09 Challenge, and a 3D U-Net based airway segmentation model, in detecting more branches with fewer false positives., Comment: Accepted for publication at Medical Image Analysis. 14 pages

In this work, we adapt a method based on multiple hypothesis tracking (MHT) that has been shown to give state-of-the-art vessel segmentation results in interactive settings, for the purpose of extracting trees. Regularly spaced tubular templates are fit to image data forming local hypotheses. These local hypotheses are used to construct the MHT tree, which is then traversed to make segmentation decisions. However, some critical parameters in this method are scale-dependent and have an adverse effect when tracking structures of varying dimensions. We propose to use statistical ranking of local hypotheses in constructing the MHT tree, which yields a probabilistic interpretation of scores across scales and helps alleviate the scale-dependence of MHT parameters. This enables our method to track trees starting from a single seed point. Our method is evaluated on chest CT data to extract airway trees and coronary arteries. In both cases, we show that our method performs significantly better than the original MHT method., Comment: Accepted for publication at the International Journal of Medical Physics and Practice

We present extraction of tree structures, such as airways, from image data as a graph refinement task. To this end, we propose a graph auto-encoder model that uses an encoder based on graph neural networks (GNNs) to learn embeddings from input node features and a decoder to predict connections between nodes. Performance of the GNN model is compared with mean-field networks in their ability to extract airways from 3D chest CT scans., Comment: Extended Abstract submitted to MIDL, 2018. 3 pages

We present tree extraction in 3D images as a graph refinement task, of obtaining a subgraph from an over-complete input graph. To this end, we formulate an approximate Bayesian inference framework on undirected graphs using mean field approximation (MFA). Mean field networks are used for inference based on the interpretation that iterations of MFA can be seen as feed-forward operations in a neural network. This allows us to learn the model parameters from training data using back-propagation algorithm. We demonstrate usefulness of the model to extract airway trees from 3D chest CT data. We first obtain probability images using a voxel classifier that distinguishes airways from background and use Bayesian smoothing to model individual airway branches. This yields us joint Gaussian density estimates of position, orientation and scale as node features of the input graph. Performance of the method is compared with two methods: the first uses probability images from a trained voxel classifier with region growing, which is similar to one of the best performing methods at EXACT'09 airway challenge, and the second method is based on Bayesian smoothing on these probability images. Using centerline distance as error measure the presented method shows significant improvement compared to these two methods., Comment: 10 pages. Preprint

Segmenting tree structures is common in several image processing applications. In medical image analysis, reliable segmentations of airways, vessels, neurons and other tree structures can enable important clinical applications. We present a framework for tracking tree structures comprising of elongated branches using probabilistic state-space models and Bayesian smoothing. Unlike most existing methods that proceed with sequential tracking of branches, we present an exploratory method, that is less sensitive to local anomalies in the data due to acquisition noise and/or interfering structures. The evolution of individual branches is modelled using a process model and the observed data is incorporated into the update step of the Bayesian smoother using a measurement model that is based on a multi-scale blob detector. Bayesian smoothing is performed using the RTS (Rauch-Tung-Striebel) smoother, which provides Gaussian density estimates of branch states at each tracking step. We select likely branch seed points automatically based on the response of the blob detection and track from all such seed points using the RTS smoother. We use covariance of the marginal posterior density estimated for each branch to discriminate false positive and true positive branches. The method is evaluated on 3D chest CT scans to track airways. We show that the presented method results in additional branches compared to a baseline method based on region growing on probability images., Comment: 10 pages. Pre-print of the paper accepted at Workshop on Graphs in Biomedical Image Analysis. MICCAI 2017. Quebec City

Chronic obstructive pulmonary disease (COPD) is a lung disease where early detection benefits the survival rate. COPD can be quantified by classifying patches of computed tomography images, and combining patch labels into an overall diagnosis for the image. As labeled patches are often not available, image labels are propagated to the patches, incorrectly labeling healthy patches in COPD patients as being affected by the disease. We approach quantification of COPD from lung images as a multiple instance learning (MIL) problem, which is more suitable for such weakly labeled data. We investigate various MIL assumptions in the context of COPD and show that although a concept region with COPD-related disease patterns is present, considering the whole distribution of lung tissue patches improves the performance. The best method is based on averaging instances and obtains an AUC of 0.742, which is higher than the previously reported best of 0.713 on the same dataset. Using the full training set further increases performance to 0.776, which is significantly higher (DeLong test) than previous results., Comment: Published at International Conference on Pattern Recognition (ICPR) 2014

We consider the caching of content in the mobile devices in a dense wireless network using maximum distance separable (MDS) codes. We focus on an area, served by a base station (BS), where mobile devices move around according to a random mobility model. Users requesting a particular file download coded packets from caching devices within a communication range, using device-to-device communication. If additional packets are required to decode the file, these are downloaded from the BS. We analyze the device mobility and derive a good approximation of the distribution of caching devices within the communication range of mobile devices at any given time. We then optimize the MDS codes to minimize the network load under a cache size constraint and show that using optimized MDS codes results in significantly lower network load compared to when caching the most popular files. We further show numerically that caching coded packets of each file on all mobile devices, i.e., maximal spreading, is optimal., Comment: Accepted for publication in the IEEE Transactions on Wireless Communications

Chronic obstructive pulmonary disease (COPD) is a lung disease which can be quantified using chest computed tomography (CT) scans. Recent studies have shown that COPD can be automatically diagnosed using weakly supervised learning of intensity and texture distributions. However, up till now such classifiers have only been evaluated on scans from a single domain, and it is unclear whether they would generalize across domains, such as different scanners or scanning protocols. To address this problem, we investigate classification of COPD in a multi-center dataset with a total of 803 scans from three different centers, four different scanners, with heterogenous subject distributions. Our method is based on Gaussian texture features, and a weighted logistic classifier, which increases the weights of samples similar to the test data. We show that Gaussian texture features outperform intensity features previously used in multi-center classification tasks. We also show that a weighting strategy based on a classifier that is trained to discriminate between scans from different domains, can further improve the results. To encourage further research into transfer learning methods for classification of COPD, upon acceptance of the paper we will release two feature datasets used in this study on http://bigr.nl/research/projects/copd, Comment: Accepted at Journal of Biomedical and Health Informatics

Knowledge of airway tree morphology has important clinical applications in diagnosis of chronic obstructive pulmonary disease. We present an automatic tree extraction method based on multiple hypothesis tracking and template matching for this purpose and evaluate its performance on chest CT images. The method is adapted from a semi-automatic method devised for vessel segmentation. Idealized tubular templates are constructed that match airway probability obtained from a trained classifier and ranked based on their relative significance. Several such regularly spaced templates form the local hypotheses used in constructing a multiple hypothesis tree, which is then traversed to reach decisions. The proposed modifications remove the need for local thresholding of hypotheses as decisions are made entirely based on statistical comparisons involving the hypothesis tree. The results show improvements in performance when compared to the original method and region growing on intensity images. We also compare the method with region growing on the probability images, where the presented method does not show substantial improvement, but we expect it to be less sensitive to local anomalies in the data., Comment: 12 pages. Presented at the MICCAI Pulmonary Image Analysis Workshop, Athens, Greece, 2016

We consider the use of distributed storage (DS) to reduce the communication cost of content delivery in wireless networks. Content is stored (cached) in a number of mobile devices using an erasure correcting code. Users retrieve content from other devices using device-to-device communication or from the base station (BS), at the expense of higher communication cost. We address the repair problem when a device storing data leaves the cell. We introduce a repair scheduling where repair is performed periodically and derive analytical expressions for the overall communication cost of content download and data repair as a function of the repair interval. The derived expressions are then used to evaluate the communication cost entailed by DS using several erasure correcting codes. Our results show that DS can reduce the communication cost with respect to the case where content is downloaded only from the BS, provided that repairs are performed frequently enough. If devices storing content arrive to the cell, the communication cost using DS is further reduced and, for large enough arrival rate, it is always beneficial. Interestingly, we show that MDS codes, which do not perform well for classical DS, can yield a low overall communication cost in wireless DS., Comment: After final editing for publication in TCOM

We consider distributed storage (DS) for a wireless network where mobile devices arrive and depart according to a Poisson random process. Content is stored in a number of mobile devices, using an erasure correcting code. When requesting a piece of content, a user retrieves the content from the mobile devices using device-to-device communication or, if not possible, from the base station (BS), at the expense of a higher communication cost. We consider the repair problem when a device that stores data leaves the network. In particular, we introduce a repair scheduling where repair is performed (from storage devices or the BS) periodically. We derive analytical expressions for the overall communication cost of repair and download as a function of the repair interval. We illustrate the analysis by giving results for maximum distance separable codes and regenerating codes. Our results indicate that DS can reduce the overall communication cost with respect to the case where content is only downloaded from the BS, provided that repairs are performed frequently enough. The required repair frequency depends on the code used for storage and the network parameters. In particular, minimum bandwidth regenerating codes require very frequent repairs, while maximum distance separable codes give better performance if repair is performed less frequently. We also show that instantaneous repair is not always optimal., Comment: To be presented at IEEE Information Theory Workshop (ITW) 2015, Jeju Island, Korea, October 2015

Graphene bilayer systems are known to exhibit a band gap when the layer symmetry is broken, by applying a perpendicular electric field. The resulting band structure resembles that of a conventional semiconductor with a parabolic dispersion. Here, we introduce a novel bilayer graphene heterostructure, where single-layer graphene is placed on top of another layer of graphene with a regular lattice of antidots. We dub this class of graphene systems GOAL: graphene on graphene antidot lattice. By varying the structure geometry, band structure engineering can be performed to obtain linearly dispersing bands (with a high concomitant mobility), which nevertheless can be made gapped with the perpendicular field. We analyze the electronic structure and transport properties of various types of GOALs, and draw general conclusions about their properties to aid their design in experiments., Comment: 13 pages, 10 figures, submitted

This paper presents two approaches to quantifying and visualizing variation in datasets of trees. The first approach localizes subtrees in which significant population differences are found through hypothesis testing and sparse classifiers on subtree features. The second approach visualizes the global metric structure of datasets through low-distortion embedding into hyperbolic planes in the style of multidimensional scaling. A case study is made on a dataset of airway trees in relation to Chronic Obstructive Pulmonary Disease., Comment: 22 pages

Methodological contributions: This paper introduces a family of kernels for analyzing (anatomical) trees endowed with vector valued measurements made along the tree. While state-of-the-art graph and tree kernels use combinatorial tree/graph structure with discrete node and edge labels, the kernels presented in this paper can include geometric information such as branch shape, branch radius or other vector valued properties. In addition to being flexible in their ability to model different types of attributes, the presented kernels are computationally efficient and some of them can easily be computed for large datasets (N of the order 10.000) of trees with 30-600 branches. Combining the kernels with standard machine learning tools enables us to analyze the relation between disease and anatomical tree structure and geometry. Experimental results: The kernels are used to compare airway trees segmented from low-dose CT, endowed with branch shape descriptors and airway wall area percentage measurements made along the tree. Using kernelized hypothesis testing we show that the geometric airway trees are significantly differently distributed in patients with Chronic Obstructive Pulmonary Disease (COPD) than in healthy individuals. The geometric tree kernels also give a significant increase in the classification accuracy of COPD from geometric tree structure endowed with airway wall thickness measurements in comparison with state-of-the-art methods, giving further insight into the relationship between airway wall thickness and COPD. Software: Software for computing kernels and statistical tests is available at http://image.diku.dk/aasa/software.php., Comment: 12 pages

We study graphene antidot lattices (GALs) in magnetic fields. Using a tight-binding model and a recursive Green's function technique that we extend to deal with periodic structures, we calculate Hofstadter butterflies of GALs. We compare the results to those obtained in a simpler gapped graphene model. A crucial difference emerges in the behaviour of the lowest Landau level, which in a gapped graphene model is independent of magnetic field. In stark contrast to this picture, we find that in GALs the band gap can be completely closed by applying a magnetic field. While our numerical simulations can only be performed on structures much smaller than can be experimentally realized, we find that the critical magnetic field for which the gap closes can be directly related to the ratio between the cyclotron radius and the neck width of the GAL. In this way, we obtain a simple scaling law for extrapolation of our results to more realistically sized structures and find resulting quenching magnetic fields that should be well within reach of experiments., Comment: 8 pages, 8 figures

We present a perturbative method for calculating the optical Hall conductivity in a tight-binding framework based on the Kubo formalism. The method involves diagonalization only of the Hamiltonian in absence of the magnetic field, and thus avoids the computational problems usually arising due to the huge magnetic unit cells required to maintain translational invariance in presence of a Peierls phase. A recipe for applying the method to numerical calculations of the magneto-optical response is presented. We apply the formalism to the case of ordinary and gapped graphene in a next-nearest neighbour tight-binding model as well as graphene antidot lattices. In both case, we find unique signatures in the Hall response, that are not captured in continuum (Dirac) approximations. These include a non-zero optical Hall conductivity even when the chemical potential is at the Dirac point energy. Numerical results suggest that this effect should be measurable in experiments., Comment: 7 pages, 4 figures, accepted in Physical Review B

We introduce graphene antidot lattice waveguides: nanostructured graphene where a region of pristine graphene is sandwiched between regions of graphene antidot lattices. The band gap in the surrounding antidot lattices enable localized states to emerge in the central waveguide region. We model the waveguides via a position-dependent mass term in the Dirac approximation of graphene, and arrive at analytical results for the dispersion relation and spinor eigenstates of the localized waveguide modes. To include atomistic details we also use a tight-binding model, which is in excellent agreement with the analytical results. The waveguides resemble graphene nanoribbons, but without the particular properties of ribbons that emerge due to the details of the edge. We show that electrons can be guided through kinks without additional resistance and that transport through the waveguides is robust against structural disorder., Comment: 9 pages, 7 figures, accepted for publication in Physical Review B

Periodic arrays of antidots, i.e. nanoscale perforations, in graphene enable tight confinement of carriers and efficient transport barriers. Such barriers evade the Klein tunneling mechanism by being of the mass rather than electrostatic type. While all graphene antidot lattices (GALs) may support directional barriers, we show, however, that a full transport gap exists only for certain orientations of the GAL. Moreover, we assess the applicability of gapped graphene and the Dirac continuum approach as simplified models of various antidot structures showing that, in particular, the former is an excellent approximation for transport in GALs supporting a bulk band gap. Finally, the transport properties of a GAL based resonant tunneling diode is analyzed indicating that such advanced graphene based devices may, indeed, be realized using GAL structures., Comment: 12 pages, 9 figures, accepted for publication on Journal of Applied Physics