Abstract

The call for papers resulted in a high number of submis- sions, from which we have been able to select 12 excellent papers dealing with the different aspects of satellite commu- nications and navigation. Multiple-input multiple-output (MIMO) techniques are attracting a considerable amount of attention from within the terrestrial wireless community. The first paper of this spe- cial issue, “Multisatellite MIMO communications at Ku band and above: investigations on spatial multiplexing for capac- ity improvement and selection diversity for interference mit- igation,” considers the application of such technology over a satellite platform operating in the Ku band and above. The paper considers how MIMO can be used to increase capac- ity by using a satellite spatial multiplexing system and how antenna selection can be used to mitigate interference. The next paper “Investigations in satellite MIMO channel model- ing: accent on polarization” looks at MIMO systems from the polarization diversity point of view and dwells on the satellite cooperative communication concepts. Switch and stay combining (SSC) is a form of diversity technique used in digital receivers to compensate for fade events introduced by the mobile channel. The third paper “Performance analysis of SSC diversity receivers over corre- lated Ricean fading satellite channels” investigates the per- formance of dual-branch SSC receivers for different fading channel characteristics. The next four papers deal with the emerging scenario of mobile digital video broadcasting (DVB-S2 and RCS mo- bile). Alternative approaches to counteracting fading chan- nels introduced when operating in a train environment re- ceiving satellite DVB-S2 are presented in the paper “Ad- vanced fade countermeasures for DVB-S2 systems in railway scenarios.” Here, as a result of simulation analysis, antenna diversity and packet-level forward error correction mecha- nisms are proposed and their impact is evaluated with respect to the receiver design and system complexity. The theme of DVB-S2 is continued with the paper “Capacity versus bit er- ror rate trade-off in the DVB-S2 forward link,” which inves- tigates how satellite capacity can be optimised for DVB-S2 transmissions. The DVB return channel via satellite (DVB- RCS) is then addressed in “Frequency estimation in iterative interference cancellation applied to multibeam satellite sys- tems,” which considers the application of interference cancel- lation on the reverse link of a multibeam satellite system, us- ing DVB-RCS with convolutional coding as an example. The paper “A QoS architecture for DVB-RCS next-generation satellite networks” proceeds to design and emulate a quality- of-service (QoS) architecture that demonstrates using real multimedia applications how QoS can be supported over a DVB-RCS network. 2 EURASIP Journal on Wireless Communications and Networking Synchronization aspects are dealt with in “Maximum likelihood timing and carrier synchronization in burst-mode satellite transmissions.” The paper addresses the problem of achieving synchronisation for a burst-mode satellite trans- mission over an AWGN channel. The subject of burst trans- mission continues with the paper “Burst format design for optimum joint estimation of Doppler-shift and Doppler- rate in packet satellite communications,” which considers optimising the burst-format of packet-oriented transmis- sions by proposing very-low-complexity algorithms for car- rier Doppler-shift and Doppler-rate estimation. A network comprising satellite and high-altitude plat- forms is considered in the paper “TCP-call admission con- trol interaction in multiplatform space architectures.” Cross- layer techniques are implemented by means of TCP feeding back into call admission control (CAC) procedures for the purpose of prevention of congestion and improvement in QoS. Finally, since navigation is an extremely important part of the satellite system family, we have included two papers. The first paper “Efficient delay tracking methods with side- lobes cancellation for BOC-modulated signals” deals with bi- nary offset carrier (BOC) modulation, which is adopted in typical navigation systems. The paper considers how to improve the tracking of the main lobe of the BOC-modulated signal by using sidelobe suppression techniques. An alternative approach based on filter bank processing is presented in “Analysis of filter-bank-based methods for fast serial acqui- sition of BOC-modulated signals” to conclude the special issue. Document type: Part of book or chapter of book

Abstract

Image Processing (IP) applications have become popular with the advent of efficient algorithms and low-cost CMOS cameras with high resolution. However, IP applications are compute-intensive, consume a lot of energy and have long processing times. Image approximation has been proposed by recent works for an energy-efficient design of these applications. It also reduces the impact of long processing times. The challenge here is that the IP applications often work as a part of bigger closed-loop control systems, e.g. advanced driver assistance system (ADAS). The impact of image approximations that tolerate certain error on these image-based control (IBC) systems is very important. However, there is a lack of tool support to evaluate the performance of such closed-loop IBC systems when the IP is approximated. We propose a framework - for both software-in-the-loop (SiL) and hardware-in-the-loop (HiL) simulation - for performance evaluation of image approximation on a closed-loop automotive IBC system (IMACS). Both simulation setups model the 3D environment in 3ds Max, and simulate the system dynamics, camera position and environment in V-REP. Our SiL setup simulates the system software in C++ or Matlab. Here, V-REP runs as a server and the software as a client in synchronous mode. Our HiL simulation setup runs the system software in the NVIDIA Drive PX2 platform and communicates to V-REP using application programming interfaces (APIs) for synchronous execution. We show the effectiveness of our framework using a vision-based lateral control example.

Abstract

In order to improve the efficiency of transportation networks, it is critical to forecast traffic congestion. Large-scale traffic congestion data have become available and accessible, yet they need to be properly represented in order to avoid overfitting, reduce the requirements of computational resources, and be utilized effectively by various methodologies and models. Inspired by pooling operations in deep learning, we propose a representation framework for traffic congestion data in urban road traffic networks. This framework consists of grid-based partition of urban road traffic networks and a pooling operation to reduce multiple values into an aggregated one. We also propose using a pooling operation to calculate the maximum value in each grid (MAV). Raw snapshots of traffic congestion maps are transformed and represented as a series of matrices which are used as inputs to a spatiotemporal congestion prediction network (STCN) to evaluate the effectiveness of representation when predicting traffic congestion. STCN combines convolutional neural networks (CNNs) and long short-term memory neural network (LSTMs) for their spatiotemporal capability. CNNs can extract spatial features and dependencies of traffic congestion between roads, and LSTMs can learn their temporal evolution patterns and correlations. An empirical experiment on an urban road traffic network shows that when incorporated into our proposed representation framework, MAV outperforms other pooling operations in the effectiveness of the representation of traffic congestion data for traffic congestion prediction, and that the framework is cost-efficient in terms of computational resources. Document type: Article

Abstract

Summary"/jats:title""jats:p"We designed a PyQt graphical user interface – Sequanix – aiming at democratizing the use of Snakemake pipelines. Although the primary goal of Sequanix was to facilitate the execution of NGS Snakemake pipelines available in the Sequana project ("jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://sequana.readthedocs.io""http://sequana.readthedocs.io"/jats:ext-link"), it can also handle any Snakemake pipelines. Therefore, Sequanix should be useful to all Snakemake developers willing to expose their pipelines to a wider audience."/jats:p""/jats:sec""jats:sec""jats:title"Availability"/jats:title""jats:p"Source code available on "jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://github.com/sequana/sequana""http://github.com/sequana/sequana"/jats:ext-link" and standalone on "jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://bioconda.github.io""http://bioconda.github.io"/jats:ext-link" (sequana package)."/jats:p""/jats:sec Document type: Article

Abstract

We present a simplified model of the strategic allocation of trajectories in a generic airspace for commercial flights. In this model, two types of companies, characterised by different cost functions and different strategies, compete for the allocation of trajectories in the airspace. With an analytical model and numerical simulations, we show that the relative advantage of the two populations -- companies -- depends on external factors like traffic demand as well as on the composition of the population. We show that there exists a stable equilibrium state which depends on the traffic demand. We also show that the equilibrium solution is not the optimal at the global level, but rather that it tends to favour one of the two business models -- the archetype for low-cost companies. Finally, linking the cost of allocated flights with the fitness of a company, we study the evolutionary dynamics of the system, investigating the fluctuations of population composition around the equilibrium and the speed of convergence towards it. We prove that in the presence of noise due to finite populations, the equilibrium point is shifted and is reached more slowly. Document type: Article

Abstract

"jats:sec" "jats:title"Motivation"/jats:title" "jats:p"With its capacity for high-resolution data output in one region of interest, chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a state-of-the-art next-generation sequencing technique that provides epigenetic insights, and regularly advances current medical research. However, 4C-seq data are complex and prone to biases, and while specialized programs exist, an unbiased, extensive benchmarking is still lacking. Furthermore, neither substantial datasets with fully characterized ground truth, nor simulation programs for realistic 4C-seq data have been published."/jats:p" "/jats:sec" "jats:sec" "jats:title"Results"/jats:title" "jats:p"We conducted a benchmarking study on 66 4C-seq samples from 20 datasets, and developed a novel 4C-seq simulation software, Basic4CSim, to allow for detailed comparisons of 4C-seq algorithms on 50 simulated datasets with 10–120 samples each. Simulations and benchmarking were adapted to address different characteristics of 4C-seq data. Simulated data were compared with published samples to validate simulation settings. We identified differences between 4C-seq algorithms in terms of precision, recall, interaction structure, and run time, and observed general trends. Novel differential pipeline versions of single-sample based 4C-seq algorithms were included in the benchmarking. While no single tool was optimally suited for both near-cis and far-cis, and both single-sample and differential analyses, choosing a high-performing algorithm variant did improve results considerably. For near-cis scenarios, r3Cseq, peakC and FourCSeq offered high precision, while fourSig demonstrated high overall F1 scores in far-cis analyses. Finally, 4C-seq simulations may aid in the development of improved analysis algorithms."/jats:p" "/jats:sec" "jats:sec" "jats:title"Availability and implementation"/jats:title" "jats:p"Basic4CSim is available at https://github.com/walter–ca/Basic4CSim."/jats:p" "/jats:sec" "jats:sec" "jats:title"Supplementary information"/jats:title" "jats:p"Supplementary data are available at Bioinformatics online."/jats:p" "/jats:sec Document type: Article

Abstract

Congested traffic problems on very dense networks lead, at the limit, to minimization problems posed on measures on curves as shown in Baillon and Carlier (Netw. Heterog. Media 7:219–241, 2012 ). Here, we go one step further by showing that these problems can be reformulated in terms of the minimization of an integral functional over a set of vector fields with prescribed divergence as in Beckmann (Econometrica 20:643–660, 1952 ). We prove a Sobolev regularity result for their minimizers despite the fact that the Euler–Lagrange equation of the dual is highly degenerate and anisotropic. This somehow extends the analysis of Brasco et al. (J. Math. Pures Appl. 93:652–671, 2010 ) to the anisotropic case. Copyright Springer Science+Business Media New York 2013

Abstract

Motivation Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments. We propose ViraPipe, a scalable metagenome analysis pipeline that is able to analyze thousands of human microbiomes in parallel in tolerable time. The pipeline is tuned for analyzing viral metagenomes and the software is applicable for other metagenomic analyses as well. ViraPipe integrates parallel BWA-MEM read aligner, MegaHit De novo assembler, and BLAST and HMMER3 sequence search tools. We show the scalability of ViraPipe by running experiments on mining virus related genomes from NGS datasets in a distributed Spark computing cluster. Results ViraPipe analyses 768 human samples in 210 minutes on a Spark computing cluster comprising 23 nodes and 1288 cores in total. The speedup of ViraPipe executed on 23 nodes was 11x compared to the sequential analysis pipeline executed on a single node. The whole process includes parallel decompression, read interleaving, BWA-MEM read alignment, filtering and normalizing of non-human reads, De novo contigs assembling, and searching of sequences with BLAST and HMMER3 tools. Contact ilari.maarala@aalto.fi. Availability and implementation https://github.com/NGSeq/ViraPipe.