IOPT Petri Net State Space Generation Algorithm with Maximal-Step Execution Semantics

This paper presents an algorithm to efficiently generate the state-space of systems specified using the IOPT Petri-net modeling formalism. IOPT nets are a non-autonomous Petri-net class, based on Place-Transition nets with an extended set of features designed to allow the rapid prototyping and synthesis of system controllers through an existing hardware-software co-design framework. To obtain coherent and deterministic operation, IOPT nets use a maximal-step execution semantics where, in a single execution step, all enabled transitions will fire simultaneously. This fact increases the resulting state-space complexity and can cause an arc "explosion" effect. Real-world applications, with several million states, will reach a higher order of magnitude number of arcs, leading to the need for high performance state-space generator algorithms. The proposed algorithm applies a compilation approach to read a PNML file containing one IOPT model and automatically generate an optimized C program to calculate the corresponding state-space.

QSAR modeling of antitubercular activity of diverse organic compounds

Tuberculosis (TB) is a worldwide infectious disease that has shown over time extremely high mortality levels. The urgent need to develop new antitubercular drugs is due to the increasing rate of appearance of multi-drug resistant strains to the commonly used drugs, and the longer durations of therapy and recovery, particularly in immuno-compromised patients. The major goal of the present study is the exploration of data from different families of compounds through the use of a variety of machine learning techniques so that robust QSAR-based models can be developed to further guide in the quest for new potent anti-TB compounds. Eight QSAR models were built using various types of descriptors (from ADRIANA.Code and Dragon software) with two publicly available structurally diverse data sets, including recent data deposited in PubChem. QSAR methodologies used Random Forests and Associative Neural Networks. Predictions for the external evaluation sets obtained accuracies in the range of 0.76-0.88 (for active/inactive classifications) and Q(2)=0.66-0.89 for regressions. Models developed in this study can be used to estimate the anti-TB activity of drug candidates at early stages of drug development (C) 2011 Elsevier B.V. All rights reserved.

Increase of the delivered energy probability in DES using a fuzzy probabilistic modeling

The paper proposes a methodology to increase the probability of delivering power to any load point by identifying new investments in distribution energy systems. The proposed methodology is based on statistical failure and repair data of distribution components and it uses a fuzzy-probabilistic modeling for the components outage parameters. The fuzzy membership functions of the outage parameters of each component are based on statistical records. A mixed integer nonlinear programming optimization model is developed in order to identify the adequate investments in distribution energy system components which allow increasing the probability of delivering power to any customer in the distribution system at the minimum possible cost for the system operator. To illustrate the application of the proposed methodology, the paper includes a case study that considers a 180 bus distribution network.

Lightweight user modeling – a case study

In the context of previous publications, we propose a new lightweight UM process, intended to work as a tourism recommender system in a commercial environment. The new process tackles issues like cold start, gray sheep and over specialization through a rich user model and the application of a gradual forgetting function to the collected user action history. Also, significant performance improvements were achieved regarding the previously proposed UM process.

Modeling group decision meeting participants with an Agent-based approach

This paper aims to present a multi-agent model for a simulation, whose goal is to help one specific participant of multi-criteria group decision making process.This model has five main intervenient types: the human participant, who is using the simulation and argumentation support system; the participant agents, one associated to the human participant and the others simulating the others human members of the decision meeting group; the directory agent; the proposal agents, representing the different alternatives for a decision (the alternatives are evaluated based on criteria); and the voting agent responsiblefor all voting machanisms.At this stage it is proposed a two phse algorithm. In the first phase each participantagent makes his own evaluation of the proposals under discussion, and the voting agent proposes a simulation of a voting process.In the second phase, after the dissemination of the voting results,each one ofthe partcipan agents will argue to convince the others to choose one of the possible alternatives. The arguments used to convince a specific participant are dependent on agent knowledge about that participant. This two-phase algorithm is applied iteratively.

Modeling Allee Effect from Beta(p, 2) Densities

In this work we develop and investigate generalized populational growth models, adjusted from Beta(p, 2) densities, with Allee effect. The use of a positive parameter leads the presented generalization, which yields some more flexible models with variable extinction rates. An Allee limit is incorporated so that the models under study have strong Allee effect.

Algoritmo neurogenético com vistas para o planejamento de rotas de robôs móveis autônomos

Pós-graduação em Ciência da Computação - IBILCE

User modeling and recommendation strategies for tourism

Mestrado em Engenharia Informática

An application of structural equation modeling of test dispositional optimism as mediator or moderator in quality of life in patients with chronic disease

The aim of the present study was to test a hypothetical model to examine if dispositional optimism exerts a moderating or a mediating effect between personality traits and quality of life, in Portuguese patients with chronic diseases. A sample of 540 patients was recruited from central hospitals in various districts of Portugal. All patients completed self-reported questionnaires assessing socio-demographic and clinical variables, personality, dispositional optimism, and quality of life. Structural equation modeling (SEM) was used to analyze the moderating and mediating effects. Results suggest that dispositional optimism exerts a mediator rather than a moderator role between personality traits and quality of life, suggesting that “the expectation that good things will happen” contributes to a better general well-being and better mental functioning.

Aplicação de algoritmos genéticos para sintonia de controladores

Mestrado em Engenharia Electrotécnica e de Computadores

Monte Carlo modeling and simulations of the High Definition (HD120) micro MLC and validation against measurements for a 6 MV beam

Purpose: The most recent Varian® micro multileaf collimator(MLC), the High Definition (HD120) MLC, was modeled using the BEAMNRCMonte Carlo code. This model was incorporated into a Varian medical linear accelerator, for a 6 MV beam, in static and dynamic mode. The model was validated by comparing simulated profiles with measurements. Methods: The Varian® Trilogy® (2300C/D) accelerator model was accurately implemented using the state-of-the-art Monte Carlo simulation program BEAMNRC and validated against off-axis and depth dose profiles measured using ionization chambers, by adjusting the energy and the full width at half maximum (FWHM) of the initial electron beam. The HD120 MLC was modeled by developing a new BEAMNRC component module (CM), designated HDMLC, adapting the available DYNVMLC CM and incorporating the specific characteristics of this new micro MLC. The leaf dimensions were provided by the manufacturer. The geometry was visualized by tracing particles through the CM and recording their position when a leaf boundary is crossed. The leaf material density and abutting air gap between leaves were adjusted in order to obtain a good agreement between the simulated leakage profiles and EBT2 film measurements performed in a solid water phantom. To validate the HDMLC implementation, additional MLC static patterns were also simulated and compared to additional measurements. Furthermore, the ability to simulate dynamic MLC fields was implemented in the HDMLC CM. The simulation results of these fields were compared with EBT2 film measurements performed in a solid water phantom. Results: Overall, the discrepancies, with and without MLC, between the opened field simulations and the measurements using ionization chambers in a water phantom, for the off-axis profiles are below 2% and in depth-dose profiles are below 2% after the maximum dose depth and below 4% in the build-up region. On the conditions of these simulations, this tungsten-based MLC has a density of 18.7 g cm− 3 and an overall leakage of about 1.1 ± 0.03%. The discrepancies between the film measured and simulated closed and blocked fields are below 2% and 8%, respectively. Other measurements were performed for alternated leaf patterns and the agreement is satisfactory (to within 4%). The dynamic mode for this MLC was implemented and the discrepancies between film measurements and simulations are within 4%. Conclusions: The Varian® Trilogy® (2300 C/D) linear accelerator including the HD120 MLC was successfully modeled and simulated using the Monte CarloBEAMNRC code by developing an independent CM, the HDMLC CM, either in static and dynamic modes.

Comparison of different breast planning techniques and algorithms for radiation therapy treatment

This work aims at investigating the impact of treating breast cancer using different radiation therapy (RT) techniques – forwardly-planned intensity-modulated, f-IMRT, inversely-planned IMRT and dynamic conformal arc (DCART) RT – and their effects on the whole-breast irradiation and in the undesirable irradiation of the surrounding healthy tissues. Two algorithms of iPlan BrainLAB treatment planning system were compared: Pencil Beam Convolution (PBC) and commercial Monte Carlo (iMC). Seven left-sided breast patients submitted to breast-conserving surgery were enrolled in the study. For each patient, four RT techniques – f-IMRT, IMRT using 2-fields and 5-fields (IMRT2 and IMRT5, respectively) and DCART – were applied. The dose distributions in the planned target volume (PTV) and the dose to the organs at risk (OAR) were compared analyzing dose–volume histograms; further statistical analysis was performed using IBM SPSS v20 software. For PBC, all techniques provided adequate coverage of the PTV. However, statistically significant dose differences were observed between the techniques, in the PTV, OAR and also in the pattern of dose distribution spreading into normal tissues. IMRT5 and DCART spread low doses into greater volumes of normal tissue, right breast, right lung and heart than tangential techniques. However, IMRT5 plans improved distributions for the PTV, exhibiting better conformity and homogeneity in target and reduced high dose percentages in ipsilateral OAR. DCART did not present advantages over any of the techniques investigated. Differences were also found comparing the calculation algorithms: PBC estimated higher doses for the PTV, ipsilateral lung and heart than the iMC algorithm predicted.

Image upsampling algorithms applied on Nuclear Medicine: comparision of hqnx and nxSaI algorithms families with two interpolation algorithms - nearest neighbour and bicubic interpolation

Introduction: Image resizing is a normal feature incorporated into the Nuclear Medicine digital imaging. Upsampling is done by manufacturers to adequately fit more the acquired images on the display screen and it is applied when there is a need to increase - or decrease - the total number of pixels. This paper pretends to compare the “hqnx” and the “nxSaI” magnification algorithms with two interpolation algorithms – “nearest neighbor” and “bicubic interpolation” – in the image upsampling operations. Material and Methods: Three distinct Nuclear Medicine images were enlarged 2 and 4 times with the different digital image resizing algorithms (nearest neighbor, bicubic interpolation nxSaI and hqnx). To evaluate the pixel’s changes between the different output images, 3D whole image plot profiles and surface plots were used as an addition to the visual approach in the 4x upsampled images. Results: In the 2x enlarged images the visual differences were not so noteworthy. Although, it was clearly noticed that bicubic interpolation presented the best results. In the 4x enlarged images the differences were significant, with the bicubic interpolated images presenting the best results. Hqnx resized images presented better quality than 4xSaI and nearest neighbor interpolated images, however, its intense “halo effect” affects greatly the definition and boundaries of the image contents. Conclusion: The hqnx and the nxSaI algorithms were designed for images with clear edges and so its use in Nuclear Medicine images is obviously inadequate. Bicubic interpolation seems, from the algorithms studied, the most suitable and its each day wider applications seem to show it, being assumed as a multi-image type efficient algorithm.

Machine Learning Algorithms at Myocardial Perfusion Imaging - a Preliminary Study

Introduction: A major focus of data mining process - especially machine learning researches - is to automatically learn to recognize complex patterns and help to take the adequate decisions strictly based on the acquired data. Since imaging techniques like MPI – Myocardial Perfusion Imaging on Nuclear Cardiology, can implicate a huge part of the daily workflow and generate gigabytes of data, there could be advantages on Computerized Analysis of data over Human Analysis: shorter time, homogeneity and consistency, automatic recording of analysis results, relatively inexpensive, etc.Objectives: The aim of this study relates with the evaluation of the efficacy of this methodology on the evaluation of MPI Stress studies and the process of decision taking concerning the continuation – or not – of the evaluation of each patient. It has been pursued has an objective to automatically classify a patient test in one of three groups: “Positive”, “Negative” and “Indeterminate”. “Positive” would directly follow to the Rest test part of the exam, the “Negative” would be directly exempted from continuation and only the “Indeterminate” group would deserve the clinician analysis, so allowing economy of clinician’s effort, increasing workflow fluidity at the technologist’s level and probably sparing time to patients. Methods: WEKA v3.6.2 open source software was used to make a comparative analysis of three WEKA algorithms (“OneR”, “J48” and “Naïve Bayes”) - on a retrospective study using the comparison with correspondent clinical results as reference, signed by nuclear cardiologist experts - on “SPECT Heart Dataset”, available on University of California – Irvine, at the Machine Learning Repository. For evaluation purposes, criteria as “Precision”, “Incorrectly Classified Instances” and “Receiver Operating Characteristics (ROC) Areas” were considered. Results: The interpretation of the data suggests that the Naïve Bayes algorithm has the best performance among the three previously selected algorithms. Conclusions: It is believed - and apparently supported by the findings - that machine learning algorithms could significantly assist, at an intermediary level, on the analysis of scintigraphic data obtained on MPI, namely after Stress acquisition, so eventually increasing efficiency of the entire system and potentially easing both roles of Technologists and Nuclear Cardiologists. In the actual continuation of this study, it is planned to use more patient information and significantly increase the population under study, in order to allow improving system accuracy.