Nano-CF: a Coordination Framework for macro-programming in wireless sensor networks

Wireless Sensor Networks (WSN) are being used for a number of applications involving infrastructure monitoring, building energy monitoring and industrial sensing. The difficulty of programming individual sensor nodes and the associated overhead have encouraged researchers to design macro-programming systems which can help program the network as a whole or as a combination of subnets. Most of the current macro-programming schemes do not support multiple users seamlessly deploying diverse applications on the same shared sensor network. As WSNs are becoming more common, it is important to provide such support, since it enables higher-level optimizations such as code reuse, energy savings, and traffic reduction. In this paper, we propose a macro-programming framework called Nano-CF, which, in addition to supporting in-network programming, allows multiple applications written by different programmers to be executed simultaneously on a sensor networking infrastructure. This framework enables the use of a common sensing infrastructure for a number of applications without the users having to worrying about the applications already deployed on the network. The framework also supports timing constraints and resource reservations using the Nano-RK operating system. Nano- CF is efficient at improving WSN performance by (a) combining multiple user programs, (b) aggregating packets for data delivery, and (c) satisfying timing and energy specifications using Rate- Harmonized Scheduling. Using representative applications, we demonstrate that Nano-CF achieves 90% reduction in Source Lines-of-Code (SLoC) and 50% energy savings from aggregated data delivery.

A parallel programming model for ada

Over the last three decades, computer architects have been able to achieve an increase in performance for single processors by, e.g., increasing clock speed, introducing cache memories and using instruction level parallelism. However, because of power consumption and heat dissipation constraints, this trend is going to cease. In recent times, hardware engineers have instead moved to new chip architectures with multiple processor cores on a single chip. With multi-core processors, applications can complete more total work than with one core alone. To take advantage of multi-core processors, parallel programming models are proposed as promising solutions for more effectively using multi-core processors. This paper discusses some of the existent models and frameworks for parallel programming, leading to outline a draft parallel programming model for Ada.

Demo: automatic personal identification system for security in critical services: a case study

The demonstration proposal moves from the capabilities of a wireless biometric badge [4], which integrates a localization and tracking service along with an automatic personal identification mechanism, to show how a full system architecture is devised to enable the control of physical accesses to restricted areas. The system leverages on the availability of a novel IEEE 802.15.4/Zigbee Cluster Tree network model, on enhanced security levels and on the respect of all the users' privacy issues.

The dark side of DEMMON: what is behind the scene in engineering large-scale wireless sensor networks

Most research work on WSNs has focused on protocols or on specific applications. There is a clear lack of easy/ready-to-use WSN technologies and tools for planning, implementing, testing and commissioning WSN systems in an integrated fashion. While there exists a plethora of papers about network planning and deployment methodologies, to the best of our knowledge none of them helps the designer to match coverage requirements with network performance evaluation. In this paper we aim at filling this gap by presenting an unified toolset, i.e., a framework able to provide a global picture of the system, from the network deployment planning to system test and validation. This toolset has been designed to back up the EMMON WSN system architecture for large-scale, dense, real-time embedded monitoring. It includes network deployment planning, worst-case analysis and dimensioning, protocol simulation and automatic remote programming and hardware testing tools. This toolset has been paramount to validate the system architecture through DEMMON1, the first EMMON demonstrator, i.e., a 300+ node test-bed, which is, to the best of our knowledge, the largest single-site WSN test-bed in Europe to date.

A framework for programming sensor networks with scheduling and resource-sharing optimizations

Several projects in the recent past have aimed at promoting Wireless Sensor Networks as an infrastructure technology, where several independent users can submit applications that execute concurrently across the network. Concurrent multiple applications cause significant energy-usage overhead on sensor nodes, that cannot be eliminated by traditional schemes optimized for single-application scenarios. In this paper, we outline two main optimization techniques for reducing power consumption across applications. First, we describe a compiler based approach that identifies redundant sensing requests across applications and eliminates those. Second, we cluster the radio transmissions together by concatenating packets from independent applications based on Rate-Harmonized Scheduling.

sMapReduce: a programming pattern for wireless sensor networks

Wireless Sensor Networks (WSNs) are increasingly used in various application domains like home-automation, agriculture, industries and infrastructure monitoring. As applications tend to leverage larger geographical deployments of sensor networks, the availability of an intuitive and user friendly programming abstraction becomes a crucial factor in enabling faster and more efficient development, and reprogramming of applications. We propose a programming pattern named sMapReduce, inspired by the Google MapReduce framework, for mapping application behaviors on to a sensor network and enabling complex data aggregation. The proposed pattern requires a user to create a network-level application in two functions: sMap and Reduce, in order to abstract away from the low-level details without sacrificing the control to develop complex logic. Such a two-fold division of programming logic is a natural-fit to typical sensor networking operation which makes sensing and topological modalities accessible to the user.

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Automatic tunning of Okumura-Hata model on railway communications

This paper presents the Genetic Algorithms (GA) as an efficient solution for the Okumura-Hata prediction model tuning on railways communications. A method for modelling the propagation model tuning parameters was presented. The algorithm tuning and validation were based on real networks measurements carried out on four different propagation scenarios and several performance indicators were used. It was shown that the proposed GA is able to produce significant improvements over the original model. The algorithm developed is currently been used on real GSM-R network planning process for an enhanced resources usage.

Direct search optimization application programming interface with remote access

Search Optimization methods are needed to solve optimization problems where the objective function and/or constraints functions might be non differentiable, non convex or might not be possible to determine its analytical expressions either due to its complexity or its cost (monetary, computational, time,...). Many optimization problems in engineering and other fields have these characteristics, because functions values can result from experimental or simulation processes, can be modelled by functions with complex expressions or by noise functions and it is impossible or very difficult to calculate their derivatives. Direct Search Optimization methods only use function values and do not need any derivatives or approximations of them. In this work we present a Java API that including several methods and algorithms, that do not use derivatives, to solve constrained and unconstrained optimization problems. Traditional API access, by installing it on the developer and/or user computer, and remote API access to it, using Web Services, are also presented. Remote access to the API has the advantage of always allow the access to the latest version of the API. For users that simply want to have a tool to solve Nonlinear Optimization Problems and do not want to integrate these methods in applications, also two applications were developed. One is a standalone Java application and the other a Web-based application, both using the developed API.

A Java expression evaluator for nonlinear programming

Finding the optimal value for a problem is usual in many areas of knowledge where in many cases it is needed to solve Nonlinear Optimization Problems. For some of those problems it is not possible to determine the expression for its objective function and/or its constraints, they are the result of experimental procedures, might be non-smooth, among other reasons. To solve such problems it was implemented an API contained methods to solve both constrained and unconstrained problems. This API was developed to be used either locally on the computer where the application is being executed or remotely on a server. To obtain the maximum flexibility both from the programmers’ and users’ points of view, problems can be defined as a Java class (because this API was developed in Java) or as a simple text input that is sent to the API. For this last one to be possible it was also implemented on the API an expression evaluator. One of the drawbacks of this expression evaluator is that it is slower than the Java native code. In this paper it is presented a solution that combines both options: the problem can be expressed at run-time as a string of chars that are converted to Java code, compiled and loaded dynamically. To wide the target audience of the API, this new expression evaluator is also compatible with the AMPL format.

Web-based application programming interface to solve nonlinear optimization problems

Nonlinear Optimization Problems are usual in many engineering fields. Due to its characteristics the objective function of some problems might not be differentiable or its derivatives have complex expressions. There are even cases where an analytical expression of the objective function might not be possible to determine either due to its complexity or its cost (monetary, computational, time, ...). In these cases Nonlinear Optimization methods must be used. An API, including several methods and algorithms to solve constrained and unconstrained optimization problems was implemented. This API can be accessed not only as traditionally, by installing it on the developer and/or user computer, but it can also be accessed remotely using Web Services. As long as there is a network connection to the server where the API is installed, applications always access to the latest API version. Also an Web-based application, using the proposed API, was developed. This application is to be used by users that do not want to integrate methods in applications, and simply want to have a tool to solve Nonlinear Optimization Problems.

Fatty liver automatic diagnosis from ultrasound images

In this paper an automatic classification algorithm is proposed for the diagnosis of the liver steatosis, also known as, fatty liver, from ultrasound images. The features, automatically extracted from the ultrasound images used by the classifier, are basically the ones used by the physicians in the diagnosis of the disease based on visual inspection of the ultrasound images. The main novelty of the method is the utilization of the speckle noise that corrupts the ultrasound images to compute textural features of the liver parenchyma relevant for the diagnosis. The algorithm uses the Bayesian framework to compute a noiseless image, containing anatomic and echogenic information of the liver and a second image containing only the speckle noise used to compute the textural features. The classification results, with the Bayes classifier using manually classified data as ground truth show that the automatic classifier reaches an accuracy of 95% and a 100% of sensitivity.

Type System for the ComponentJ Programming Language

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Informática.

REXIB: Remote Experiments Interface Builder

Remote Experimentation is an educational resource that allows teachers to strengthen the practical contents of science & engineering courses. However, building up the interfaces to remote experiments is not a trivial task. Although teachers normally master the practical contents addressed by a particular remote experiment they usually lack the programming skills required to quickly build up the corresponding web interface. This paper describes the automatic generation of experiment interfaces through a web-accessible Java application. The application displays a list of existent modules and once the requested modules have been selected, it generates the code that enables the browser to display the experiment interface. The tools? main advantage is enabling non-tech teachers to create their own remote experiments.

A stochastic programming approach for the development of offering strategies for a wind power producer

A stochastic programming approach is proposed in this paper for the development of offering strategies for a wind power producer. The optimization model is characterized by making the analysis of several scenarios and treating simultaneously two kinds of uncertainty: wind power and electricity market prices. The approach developed allows evaluating alternative production and offers strategies to submit to the electricity market with the ultimate goal of maximizing profits. An innovative comparative study is provided, where the imbalances are treated differently. Also, an application to two new realistic case studies is presented. Finally, conclusions are duly drawn.