A conditional compression distance that unveils insights of the genomic evolution

We describe a compression-based distance for genomic sequences. Instead of using the usual conjoint information content, as in the classical Normalized Compression Distance (NCD), it uses the conditional information content. To compute this Normalized Conditional Compression Distance (NCCD), we need a normal conditional compressor, that we built using a mixture of static and dynamic finite-context models. Using this approach, we measured chromosomal distances between Hominidae primates and also between Muroidea (rat and mouse), observing several insights of evolution that so far have not been reported in the literature.Comment: Full version of DCC 2014 paper "A conditional compression distance that unveils insights of the genomic evolution

Information profiles for DNA pattern discovery

Finite-context modeling is a powerful tool for compressing and hence for representing DNA sequences. We describe an algorithm to detect genomic regularities, within a blind discovery strategy. The algorithm uses information profiles built using suitable combinations of finite-context models. We used the genome of the fission yeast Schizosaccharomyces pombe strain 972 h- for illustration, unveilling locations of low information content, which are usually associated with DNA regions of potential biological interest.Comment: Full version of DCC 2014 paper "Information profiles for DNA pattern discovery

A Tractable Model of the LTE Access Reservation Procedure for Machine-Type Communications

A canonical scenario in Machine-Type Communications (MTC) is the one featuring a large number of devices, each of them with sporadic traffic. Hence, the number of served devices in a single LTE cell is not determined by the available aggregate rate, but rather by the limitations of the LTE access reservation protocol. Specifically, the limited number of contention preambles and the limited amount of uplink grants per random access response are crucial to consider when dimensioning LTE networks for MTC. We propose a low-complexity model of LTE's access reservation protocol that encompasses these two limitations and allows us to evaluate the outage probability at click-speed. The model is based chiefly on closed-form expressions, except for the part with the feedback impact of retransmissions, which is determined by solving a fixed point equation. Our model overcomes the incompleteness of the existing models that are focusing solely on the preamble collisions. A comparison with the simulated LTE access reservation procedure that follows the 3GPP specifications, confirms that our model provides an accurate estimation of the system outage event and the number of supported MTC devices.Comment: Submitted, Revised, to be presented in IEEE Globecom 2015; v3: fixed error in eq. (4

What Can Wireless Cellular Technologies Do about the Upcoming Smart Metering Traffic?

The introduction of smart electricity meters with cellular radio interface puts an additional load on the wireless cellular networks. Currently, these meters are designed for low duty cycle billing and occasional system check, which generates a low-rate sporadic traffic. As the number of distributed energy resources increases, the household power will become more variable and thus unpredictable from the viewpoint of the Distribution System Operator (DSO). It is therefore expected, in the near future, to have an increased number of Wide Area Measurement System (WAMS) devices with Phasor Measurement Unit (PMU)-like capabilities in the distribution grid, thus allowing the utilities to monitor the low voltage grid quality while providing information required for tighter grid control. From a communication standpoint, the traffic profile will change drastically towards higher data volumes and higher rates per device. In this paper, we characterize the current traffic generated by smart electricity meters and supplement it with the potential traffic requirements brought by introducing enhanced Smart Meters, i.e., meters with PMU-like capabilities. Our study shows how GSM/GPRS and LTE cellular system performance behaves with the current and next generation smart meters traffic, where it is clearly seen that the PMU data will seriously challenge these wireless systems. We conclude by highlighting the possible solutions for upgrading the cellular standards, in order to cope with the upcoming smart metering traffic.Comment: Submitted; change: corrected location of eSM box in Fig. 1; May 22, 2015: Major revision after review; v4: revised, accepted for publicatio

IoT in the Support of Marketing Actions. Case study: Porto City Park

This study aims to understand how large databases generated from IoT systems can be used for Marketing and Organizational Management purposes. Through this research work, an attempt was made to highlight the importance of understanding the advantages of using data from an IoT system, especially regarding user behavior and developing well-segmented strategies, which will later translate into competitive advantages. In this work, it was made the study of a case, of a smart counter solution provided by Wavecom, implemented in Porto City Park, capable of sending real-time readings about the occupation of a given space. The theoretical contextualization of this study was based on exploratory research of relevant bibliographic works. In a statement, this work added value to fill gaps in the areas of the themes under study, offering a deeper understanding of the correlation between the large amounts of data generated by IoT systems and their use in Marketing

Smash plus plus : an alignment-free and memory-efficient tool to find genomic rearrangements

Background: The development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial owing to their role in chromosomal evolution, genetic disorders, and cancer. Results: We present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between 2 DNA sequences. This computational solution extracts information contents of the 2 sequences, exploiting a data compression technique to find rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image. Conclusions: Tested on several synthetic and real DNA sequences from bacteria, fungi, Aves, and Mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions were in accordance with previous studies, which took alignment-based approaches or performed FISH (fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was similar to 1 GB, which makes Smash++ feasible to run on present-day standard computers.Peer reviewe

A Reference-Free Lossless Compression Algorithm for DNA Sequences Using a Competitive Prediction of Two Classes of Weighted Models

The development of efficient data compressors for DNA sequences is crucial not only for reducing the storage and the bandwidth for transmission, but also for analysis purposes. In particular, the development of improved compression models directly influences the outcome of anthropological and biomedical compression-based methods. In this paper, we describe a new lossless compressor with improved compression capabilities for DNA sequences representing different domains and kingdoms. The reference-free method uses a competitive prediction model to estimate, for each symbol, the best class of models to be used before applying arithmetic encoding. There are two classes of models: weighted context models (including substitutional tolerant context models) and weighted stochastic repeat models. Both classes of models use specific sub-programs to handle inverted repeats efficiently. The results show that the proposed method attains a higher compression ratio than state-of-the-art approaches, on a balanced and diverse benchmark, using a competitive level of computational resources. An efficient implementation of the method is publicly available, under the GPLv3 license.Peer reviewe

Stiffness and strength-based lightweight design of truss structures using multi-material topology optimization

Authors wish also to thank Professor Krister Svanberg (Royal Institute of Technology, Stockholm, Sweden) for the MMA optimization code. Publisher Copyright: © 2021 9th International Conference on Computational Methods for Coupled Problems in Science and Engineering, COUPLED PROBLEMS 2021. All rights reserved.Stiffness and strength are important structural design criteria. However, most contributions to Topology Optimization (TO) deal with the compliance minimization problem. Controlling stresses in a structure is very important to avoid material failure, but that raises complications in TO, such as: nonlinearity, singularity and high computational cost. The total weight of a structure is also another important criterion in optimal design. The multi-material setting is considered in the present work as it opens the possibility to improve structural performance even further allowing extra weight reduction. Recursive SIMP is used as the material interpolation scheme and design solutions are sought using the ground structure approach. This means that truss-like (lattice) designs are obtained here. The problem is relaxed to the continuum by introducing an artificial density variable and it is solved by a gradientbased algorithm (MMA). A stress-constraint relaxation technique (qp-approach) is applied to overcome the stress singularity phenomenon. A continuation approach is used to guarantee discrete solutions, i.e., only the presence or absence of bars is identified. Therefore, design uniformity in terms of bars cross section areas is ensured. Hence, this work proposes a methodology to perform Multi-Material Topology Optimization (MMTO) of truss structures, with density-based design variables, and subject to stress constraints. To discuss the differences between stiffness and strength-oriented optimal designs, a compliance minimization problem subject to mass constraint is also considered. The example chosen demonstrates the viability of the proposed design methodology and it also reveals differences between the strongest and the stiffest designs.authorsversionpublishe