Unified radio and network control across heterogeneous hardware platforms

Experimentation is an important step in the investigation of techniques for handling spectrum scarcity or the development of new waveforms in future wireless networks. However, it is impractical and not cost effective to construct custom platforms for each future network scenario to be investigated. This problem is addressed by defining Unified Programming Interfaces that allow common access to several platforms for experimentation-based prototyping, research, and development purposes. The design of these interfaces is driven by a diverse set of scenarios that capture the functionality relevant to future network implementations while trying to keep them as generic as possible. Herein, the definition of this set of scenarios is presented as well as the architecture for supporting experimentation-based wireless research over multiple hardware platforms. The proposed architecture for experimentation incorporates both local and global unified interfaces to control any aspect of a wireless system while being completely agnostic to the actual technology incorporated. Control is feasible from the low-level features of individual radios to the entire network stack, including hierarchical control combinations. A testbed to enable the use of the above architecture is utilized that uses a backbone network in order to be able to extract measurements and observe the overall behaviour of the system under test without imposing further communication overhead to the actual experiment. Based on the aforementioned architecture, a system is proposed that is able to support the advancement of intelligent techniques for future networks through experimentation while decoupling promising algorithms and techniques from the capabilities of a specific hardware platform

Deployment Strategies of Multiple Aerial BSs for User Coverage and Power Efficiency Maximization

Unmanned aerial vehicle (UAV) based aerial base stations (BSs) can provide rapid communication services to ground users and are thus promising for future communication systems. In this paper, we consider a scenario where no functional terrestrial BSs are available and the aim is deploying multiple aerial BSs to cover a maximum number of users within a certain target area. To this end, we first propose a naive successive deployment method, which converts the non-convex constraints in the involved optimization into a combination of linear constraints through geometrical relaxation. Then we investigate a deployment method based on K-means clustering. The method divides the target area into K convex subareas, where within each subarea, a mixed integer non-linear problem (MINLP) is solved. An iterative power efficient technique is further proposed to improve coverage probability with reduced power. Finally, we propose a robust technique for compensating the loss of coverage probability in the existence of inaccurate user location information (ULI). Our simulation results show that, the proposed techniques achieve an up to 30% higher coverage probability when users are not distributed uniformly. In addition, the proposed simultaneous deployment techniques, especially the one using iterative algorithm improve power-efficiency by up to 15% compared to the benchmark circle packing theory

ExplorePipolin: a pipeline for identification and exploration of pipolins, novel mobile genetic elements widespread among bacteria

Trabajo de fin de máster en Bioinformática y Biología ComputacionalPipolins constitute a new group of self-synthesizing or self-replicating mobile genetic elements (MGEs), encoding for their own replicative DNA polymerase B. These elements have been found to be mostly integrated into the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Since a reduced number of pipolins has been identified and described so far, their origin and role remains unknown as well as there is little evidence of their horizontal transfer. A bioinformatics software capable of automatic identification and analysis of pipolins from bacterial genomes might ensure the progress in the accumulation of knowledge about these mobile genetic elements. Therefore, the main goal of the current project was to design and implement a pilot version of a pipeline for the identification and analysis of pipolins from Escherichia coli genomes. The pipeline should be flexible enough to easily extend it to other bacteria in the future. As a sub-goal, it was decided to perform a detailed analysis of pipolins of E. coli strains and isolates, available from the NCBI database and from the Spanish E. coli Reference Laboratory (LREC) collectio

Chronic-Pain Protective Behavior Detection with Deep Learning

In chronic pain rehabilitation, physiotherapists adapt physical activity to patients' performance based on their expression of protective behavior, gradually exposing them to feared but harmless and essential everyday activities. As rehabilitation moves outside the clinic, technology should automatically detect such behavior to provide similar support. Previous works have shown the feasibility of automatic protective behavior detection (PBD) within a specific activity. In this paper, we investigate the use of deep learning for PBD across activity types, using wearable motion capture and surface electromyography data collected from healthy participants and people with chronic pain. We approach the problem by continuously detecting protective behavior within an activity rather than estimating its overall presence. The best performance reaches mean F1 score of 0.82 with leave-one-subject-out cross validation. When protective behavior is modelled per activity type, performance is mean F1 score of 0.77 for bend-down, 0.81 for one-leg-stand, 0.72 for sit-to-stand, 0.83 for stand-to-sit, and 0.67 for reach-forward. This performance reaches excellent level of agreement with the average experts' rating performance suggesting potential for personalized chronic pain management at home. We analyze various parameters characterizing our approach to understand how the results could generalize to other PBD datasets and different levels of ground truth granularity.Comment: 24 pages, 12 figures, 7 tables. Accepted by ACM Transactions on Computing for Healthcar

Fog-supported delay-constrained energy-saving live migration of VMs over multiPath TCP/IP 5G connections

The incoming era of the fifth-generation fog computing-supported radio access networks (shortly, 5G FOGRANs) aims at exploiting computing/networking resource virtualization, in order to augment the limited resources of wireless devices through the seamless live migration of virtual machines (VMs) toward nearby fog data centers. For this purpose, the bandwidths of the multiple wireless network interface cards of the wireless devices may be aggregated under the control of the emerging MultiPathTCP (MPTCP) protocol. However, due to the fading and mobility-induced phenomena, the energy consumptions of the current state-of-the-art VM migration techniques may still offset their expected benefits. Motivated by these considerations, in this paper, we analytically characterize and implement in software and numerically test the optimal minimum-energy settable-complexity bandwidth manager (SCBM) for the live migration of VMs over 5G FOGRAN MPTCP connections. The key features of the proposed SCBM are that: 1) its implementation complexity is settable on-line on the basis of the target energy consumption versus implementation complexity tradeoff; 2) it minimizes the network energy consumed by the wireless device for sustaining the migration process under hard constraints on the tolerated migration times and downtimes; and 3) by leveraging a suitably designed adaptive mechanism, it is capable to quickly react to (possibly, unpredicted) fading and/or mobility-induced abrupt changes of the wireless environment without requiring forecasting. The actual effectiveness of the proposed SCBM is supported by extensive energy versus delay performance comparisons that cover: 1) a number of heterogeneous 3G/4G/WiFi FOGRAN scenarios; 2) synthetic and real-world workloads; and, 3) MPTCP and wireless connections

Efficient Algorithms for Prokaryotic Whole Genome Assembly and Finishing

De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) using both overlapping reads and linked reads until the assembly runs into an ambiguous repeat region. These contigs are further bridged into scaffolds using linked read information. However, errors can be made in both phases of assembly due to high error threshold of overlap acceptance and linking based on too few mate reads. Identical as well as similar repeat regions can often cause errors in overlap and mate-pair evidence. In addition, the problem of setting the correct threshold to minimize errors and optimize assembly of reads is not trivial and often requires a time-consuming trial and error process to obtain optimal results. The typical trial-and-error with multiple assembler, which can be computationally intensive, and is very inefficient, especially when users must learn how to use a wide variety of assemblers, many of which may be serial requiring long execution time and will not return usable or accurate results. Further, we show that the comparison of assembly results may not provide the users with a clear winner under all circumstances. Therefore, we propose a novel scaffolding tool, Correlative Algorithm for Repeat Placement (CARP), capable of joining short low error contigs using mate pair reads, computationally resolved repeat structures and synteny with one or more reference organisms. The CARP tool requires a set of repeat sequences such as insertion sequences (IS) that can be found computationally found without assembling the genome. Development of methods to identify such repeating regions directly from raw sequence reads or draft genomes led to the development of the ISQuest software package. ISQuest identifies bacterial ISs and their sequence elements—inverted and direct repeats—in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs in hundreds of partially assembled genomes within hours; making it a valuable high-throughput tool for a global search of IS and repeat elements. The CARP tool matches very low error contigs with strong overlap using the ambiguous partial repeat sequence at the ends of the contig annotated using the repeat sequences discovered using ISQuest. These matches are verified by synteny with genomes of one or more reference organisms. We show that the CARP tool can be used to verify low mate pair evidence regions, independently find new joins and significantly reduce the number of scaffolds. Finally, we are demonstrate a novel viewer that presents to the user the computationally derived joins along with the evidence used to make the joins. The viewer allows the user to independently assess their confidence in the joins made by the finishing tools and make an informed decision of whether to invest the resources necessary to confirm a particular portion of the assembly. Further, we allow users to manually record join evidence, re-order contigs, and track the assembly finishing process