Aplicação de técnicas de aprendizado de máquina no reconhecimento de classes estruturais de proteínas

Nowadays, classifying proteins in structural classes, which concerns the inference of patterns in their 3D conformation, is one of the most important open problems in Molecular Biology. The main reason for this is that the function of a protein is intrinsically related to its spatial conformation. However, such conformations are very difficult to be obtained experimentally in laboratory. Thus, this problem has drawn the attention of many researchers in Bioinformatics. Considering the great difference between the number of protein sequences already known and the number of three-dimensional structures determined experimentally, the demand of automated techniques for structural classification of proteins is very high. In this context, computational tools, especially Machine Learning (ML) techniques, have become essential to deal with this problem. In this work, ML techniques are used in the recognition of protein structural classes: Decision Trees, k-Nearest Neighbor, Naive Bayes, Support Vector Machine and Neural Networks. These methods have been chosen because they represent different paradigms of learning and have been widely used in the Bioinfornmatics literature. Aiming to obtain an improvment in the performance of these techniques (individual classifiers), homogeneous (Bagging and Boosting) and heterogeneous (Voting, Stacking and StackingC) multiclassification systems are used. Moreover, since the protein database used in this work presents the problem of imbalanced classes, artificial techniques for class balance (Undersampling Random, Tomek Links, CNN, NCL and OSS) are used to minimize such a problem. In order to evaluate the ML methods, a cross-validation procedure is applied, where the accuracy of the classifiers is measured using the mean of classification error rate, on independent test sets. These means are compared, two by two, by the hypothesis test aiming to evaluate if there is, statistically, a significant difference between them. With respect to the results obtained with the individual classifiers, Support Vector Machine presented the best accuracy. In terms of the multi-classification systems (homogeneous and heterogeneous), they showed, in general, a superior or similar performance when compared to the one achieved by the individual classifiers used - especially Boosting with Decision Tree and the StackingC with Linear Regression as meta classifier. The Voting method, despite of its simplicity, has shown to be adequate for solving the problem presented in this work. The techniques for class balance, on the other hand, have not produced a significant improvement in the global classification error. Nevertheless, the use of such techniques did improve the classification error for the minority class. In this context, the NCL technique has shown to be more appropriated

Estratégias baseadas em aprendizado para coordenação de uma frota de robôs em tarefas cooperativas

In multi-robot systems, both control architecture and work strategy represent a challenge for researchers. It is important to have a robust architecture that can be easily adapted to requirement changes. It is also important that work strategy allows robots to complete tasks efficiently, considering that robots interact directly in environments with humans. In this context, this work explores two approaches for robot soccer team coordination for cooperative tasks development. Both approaches are based on a combination of imitation learning and reinforcement learning. Thus, in the first approach was developed a control architecture, a fuzzy inference engine for recognizing situations in robot soccer games, a software for narration of robot soccer games based on the inference engine and the implementation of learning by imitation from observation and analysis of others robotic teams. Moreover, state abstraction was efficiently implemented in reinforcement learning applied to the robot soccer standard problem. Finally, reinforcement learning was implemented in a form where actions are explored only in some states (for example, states where an specialist robot system used them) differently to the traditional form, where actions have to be tested in all states. In the second approach reinforcement learning was implemented with function approximation, for which an algorithm called RBF-Sarsa($lambda$) was created. In both approaches batch reinforcement learning algorithms were implemented and imitation learning was used as a seed for reinforcement learning. Moreover, learning from robotic teams controlled by humans was explored. The proposal in this work had revealed efficient in the robot soccer standard problem and, when implemented in other robotics systems, they will allow that these robotics systems can efficiently and effectively develop assigned tasks. These approaches will give high adaptation capabilities to requirements and environment changes.

Uma Análise Comparativa entre Sistemas de Combinação de Classificadores com Distribuição Vertical dos Dados

In systems that combine the outputs of classification methods (combination systems), such as ensembles and multi-agent systems, one of the main constraints is that the base components (classifiers or agents) should be diverse among themselves. In other words, there is clearly no accuracy gain in a system that is composed of a set of identical base components. One way of increasing diversity is through the use of feature selection or data distribution methods in combination systems. In this work, an investigation of the impact of using data distribution methods among the components of combination systems will be performed. In this investigation, different methods of data distribution will be used and an analysis of the combination systems, using several different configurations, will be performed. As a result of this analysis, it is aimed to detect which combination systems are more suitable to use feature distribution among the components

Aplicação de ontologias para métodos de negociação de um sistema multiagente para o reconhecimento de padrões

The use of intelligent agents in multi-classifier systems appeared in order to making the centralized decision process of a multi-classifier system into a distributed, flexible and incremental one. Based on this, the NeurAge (Neural Agents) system (Abreu et al 2004) was proposed. This system has a superior performance to some combination-centered methods (Abreu, Canuto, and Santana 2005). The negotiation is important to the multiagent system performance, but most of negotiations are defined informaly. A way to formalize the negotiation process is using an ontology. In the context of classification tasks, the ontology provides an approach to formalize the concepts and rules that manage the relations between these concepts. This work aims at using ontologies to make a formal description of the negotiation methods of a multi-agent system for classification tasks, more specifically the NeurAge system. Through ontologies, we intend to make the NeurAge system more formal and open, allowing that new agents can be part of such system during the negotiation. In this sense, the NeurAge System will be studied on the basis of its functioning and reaching, mainly, the negotiation methods used by the same ones. After that, some negotiation ontologies found in literature will be studied, and then those that were chosen for this work will be adapted to the negotiation methods used in the NeurAge.

Dilema da diversidade-acurácia: um estudo empírico no contexto de multiclassificadores

Multi-classifier systems, also known as ensembles, have been widely used to solve several problems, because they, often, present better performance than the individual classifiers that form these systems. But, in order to do so, it s necessary that the base classifiers to be as accurate as diverse among themselves this is also known as diversity/accuracy dilemma. Given its importance, some works have investigate the ensembles behavior in context of this dilemma. However, the majority of them address homogenous ensemble, i.e., ensembles composed only of the same type of classifiers. Thus, motivated by this limitation, this thesis, using genetic algorithms, performs a detailed study on the dilemma diversity/accuracy for heterogeneous ensembles

Um framework de agentes de recomendação para sistemas Web

The World Wide Web has been consolidated over the last years as a standard platform to provide software systems in the Internet. Nowadays, a great variety of user applications are available on the Web, varying from corporate applications to the banking domain, or from electronic commerce to the governmental domain. Given the quantity of information available and the quantity of users dealing with their services, many Web systems have sought to present recommendations of use as part of their functionalities, in order to let the users to have a better usage of the services available, based on their profile, history navigation and system use. In this context, this dissertation proposes the development of an agent-based framework that offers recommendations for users of Web systems. It involves the conception, design and implementation of an object-oriented framework. The framework agents can be plugged or unplugged in a non-invasive way in existing Web applications using aspect-oriented techniques. The framework is evaluated through its instantiation to three different Web systems

Analisando o desempenho do ClassAge: um sistema multiagentes para classificação de padrões

The use of multi-agent systems for classification tasks has been proposed in order to overcome some drawbacks of multi-classifier systems and, as a consequence, to improve performance of such systems. As a result, the NeurAge system was proposed. This system is composed by several neural agents which communicate and negotiate a common result for the testing patterns. In the NeurAge system, a negotiation method is very important to the overall performance of the system since the agents need to reach and agreement about a problem when there is a conflict among the agents. This thesis presents an extensive analysis of the NeurAge System where it is used all kind of classifiers. This systems is now named ClassAge System. It is aimed to analyze the reaction of this system to some modifications in its topology and configuration

Passivity in Implant-Supported Prosthesis

Because of the widespread use of implant-supported restorations and that the success of this treatment depends on the passivity of the different component systems of implant-prosthesis, a literature review was performed to highlight issues related to passivity in framework of implant-supported fixed prosthesis. A search of English-language peer-review literature was completed using MEDLINE database (PubMed) focusing on acceptable levels of passivity, misfit classification, problems related to misfit, methods to evaluate misfit, general factors that affect the passivity, and the biologic tolerance in the presence of misfit. The information obtained in the present review suggested that even if it is hard to obtain an implant-supported prosthesis with complete passivity, the professional should use the technological resources to offer better conditions for their patients. An acceptable clinical level of passivity that does not cause any problem to the biologic, aesthetic, and functional parameters of the patient should be sought.

Comparative analysis of differentially expressed sequence tags of sweet orange and mandarin infected with Xylella fastidiosa

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Real-time optical monitoring of the dip coating process

A significant part of film production by the coating industry is based on wet bench processes, where better understanding of their temporal dynamics could facilitate control and optimization. In this work, in situ laser interferometry is applied to study properties of flowing liquids and quantitatively monitor the dip coating batch process. Two oil standards Newtonian, non-volatile, with constant refractive indices and distinct flow properties - were measured under several withdrawing speeds. The dynamics of film physical thickness then depends on time as t(-1/2), and flow characterization becomes possible with high precision (linear slope uncertainty of +/-0.04%). Resulting kinematic viscosities for OP60 and OP400 are 1,17 +/- 0,03. St and 9,9 +/- 0,2 St, respectively. These results agree with nominal values, as provided by the manufacturer. For more complex films (a multi-component sol-gel Zirconyl Chloride aqueous solution) with a varying refractive index, through a direct polarimetric measurement, allowing also determination of the temporal evolution of physical thickness (uncertainty of +/- 0,007 microns) is also determined during dip coating.

Teaching real-time with a scheduler simulator

In this paper we describe a scheduler simulator for real-time tasks, RTsim, that can be used as a tool to teach real-time scheduling algorithms. It simulates a variety of preprogrammed scheduling policies for single and multi-processor systems and simple algorithm variants introduced by its user. Using RTsim students can conduct experiments that will allow them to understand the effects of each policy given different load conditions and learn which policy is better for different workloads. We show how to use RTsim as a learning tool and the results achieved with its application on the Real-Time Systems course taught at the B.Sc. on Computer Science at Paulista State University - Unesp - at Rio Preto.

Double optical monitoring of time-dependent film formation

A brief overview of optical monitoring for vacuum and wet bench film deposition processes is presented. Interferometric and polarimetric measurements are combined with regard to simultaneous real-time monitoring of refractive index and physical thickness. Monitor stability and accuracy are verified with transparent oil standards. This double optical technique is applied to dip coating with a multi-component Zirconyl Chloride aqueous solution, whose time varying refractive index and physical thickness curves indicate significant sensitivity to changes of film flow properties during the process.

Calibration uncertainty estimation for internal aerodynamic balance

Aerodynamic balances are employed in wind tunnels to estimate the forces and moments acting on the model under test. This paper proposes a methodology for the assessment of uncertainty in the calibration of an internal multi-component aerodynamic balance. In order to obtain a suitable model to provide aerodynamic loads from the balance sensor responses, a calibration is performed prior to the tests by applying known weights to the balance. A multivariate polynomial fitting by the least squares method is used to interpolate the calibration data points. The uncertainties of both the applied loads and the readings of the sensors are considered in the regression. The data reduction includes the estimation of the calibration coefficients, the predicted values of the load components and their corresponding uncertainties, as well as the goodness of fit.

Spatial electric load forecasting using a local movement approach

An agent based model for spatial electric load forecasting using a local movement approach for the spatiotemporal allocation of the new loads in the service zone is presented. The density of electrical load for each of the major consumer classes in each sub-zone is used as the current state of the agents. The spatial growth is simulated with a walking agent who starts his path in one of the activity centers of the city and goes to the limits of the city following a radial path depending on the different load levels. A series of update rules are established to simulate the S growth behavior and the complementarity between classes. The results are presented in future load density maps. The tests in a real system from a mid-size city show a high rate of success when compared with other techniques. The most important features of this methodology are the need for few data and the simplicity of the algorithm, allowing for future scalability. © 2009 IEEE.

Spatial load forecasting using a demand propagation approach

A method for spatial electric load forecasting using multi-agent systems, especially suited to simulate the local effect of special loads in distribution systems is presented. The method based on multi-agent systems uses two kinds of agents: reactive and proactive. The reactive agents represent each sub-zone in the service zone, characterizing each one with their corresponding load level, represented in a real number, and their relationships with other sub-zones represented in development probabilities. The proactive agent carry the new load expected to be allocated because of the new special load, this agent distribute the new load in a propagation pattern. The results are presented with maps of future expected load levels in the service zone. The method is tested with data from a mid-size city real distribution system, simulating the effect of a load with attraction and repulsion attributes. The method presents good results and performance. © 2011 IEEE.