Avaliação de compostos com actividade inibidora da glicoproteína-P

A resistência a múltiplos fármacos é um grande problema na terapia anti-cancerígena, sendo a glicoproteína-P (P-gp) uma das responsáveis por esta resistência. A realização deste trabalho incidiu principalmente no desenvolvimento de modelos matemáticos/estatísticos e “químicos”. Para os modelos matemáticos/estatísticos utilizamos métodos de Machine Learning como o Support Vector Machine (SVM) e o Random Forest, (RF) em relação aos modelos químicos utilizou-se farmacóforos. Os métodos acima mencionados foram aplicados a diversas proteínas P-gp, p53 e complexo p53-MDM2, utilizando duas famílias: as pifitrinas para a p53 e flavonóides para P-gp e, em menor medida, um grupo diversificado de moléculas de diversas famílias químicas. Nos modelos obtidos pelo SVM quando aplicados à P-gp e à família dos flavonóides, obtivemos bons valores através do kernel Radial Basis Function (RBF), com precisão de conjunto de treino de 94% e especificidade de 96%. Quanto ao conjunto de teste com previsão de 70% e especificidade de 67%, sendo que o número de falsos negativos foi o mais baixo comparativamente aos restantes kernels. Aplicando o RF à família dos flavonóides verificou-se que o conjunto de treino apresenta 86% de precisão e uma especificidade de 90%, quanto ao conjunto de teste obtivemos uma previsão de 70% e uma especificidade de 60%, existindo a particularidade de o número de falsos negativos ser o mais baixo. Repetindo o procedimento anterior (RF) e utilizando um total de 63 descritores, os resultados apresentaram valores inferiores obtendo-se para o conjunto de treino 79% de precisão e 82% de especificidade. Aplicando o modelo ao conjunto de teste obteve-se 70% de previsão e 60% de especificidade. Comparando os dois métodos, escolhemos o método SVM com o kernel RBF como modelo que nos garante os melhores resultados de classificação. Aplicamos o método SVM à P-gp e a um conjunto de moléculas não flavonóides que são transportados pela P-gp, obteve-se bons valores através do kernel RBF, com precisão de conjunto de treino de 95% e especificidade de 93%. Quanto ao conjunto de teste, obtivemos uma previsão de 70% e uma especificidade de 69%, existindo a particularidade de o número de falsos negativos ser o mais baixo. Aplicou-se o método do farmacóforo a três alvos, sendo estes, um conjunto de inibidores flavonóides e de substratos não flavonóides para a P-gp, um grupo de piftrinas para a p53 e um conjunto diversificado de estruturas para a ligação da p53-MDM2. Em cada um dos quatro modelos de farmacóforos obtidos identificou-se três características, sendo que as características referentes ao anel aromático e ao dador de ligações de hidrogénio estão presentes em todos os modelos obtidos. Realizando o rastreio em diversas bases de dados utilizando os modelos, obtivemos hits com uma grande diversidade estrutural.

Low cost non-intrusive home energy monitoring

This thesis presents a low cost non-intrusive home energy monitor built on top of Non-Intrusive Load Monitoring (NILM) concepts and techniques. NILM solutions are already considered low cost alternatives to the big majority of existing commercial energy monitors but the goal here is to make its cost even lower by using a mini netbook as a whole in one solution. The mini netbook is installed in the homes main circuit breaker and computes power consumption by reading current and voltage from the built-in sound card. At the same time, feedback to the users is provided using the 11’’ LCD screen as well as other built-in I/O modules. Our meter is also capable of detecting changes in power and tries to find out which appliance lead to that change and it is being used as part of an eco-feedback platform that was build to study the long terms of energy eco-feedback in individuals. In this thesis the steps that were taken to come up with such a system are presented, from the basics of AC power measurements to the implementation of an event detector and classifier that was used to disaggregate the power load. In the last chapter results from some validation tests that have been performed are presented in order to validate the experiment. It is believed that such a system will not only be important as an energy monitor, but also as an open system than can be easily changed to accommodate and test new or existing nonintrusive load monitoring techniques.

Estimativa da área foliar do antúrio com o uso de funções de regressão

O presente trabalho teve como objetivo determinar quais variáveis dimensionais da folha são mais adequadas para utilização na estimativa da área foliar do antúrio (Anthurium andraeanum), cv. Apalai, por meio de equação de regressão linear, e comparar o desempenho de diferentes funções de regressão obtidas com o uso de aprendizado de máquina (AM). A variável que melhor estimou a área foliar foi o produto das dimensões lineares (comprimento e largura), CxL, sendo a equação proposta Af = 0.9672 *C x L, com coeficiente de determinação (R²) de 0,99. Verificou-se, também, com o uso de AM, que as funções lineares são mais adequadas para a estimação da área foliar dessa espécie vegetal.

Uma arquitetura baseada em agentes para configuração dinâmica de aplicações inteligentes em ambiente foundation fieldbus

The industrial automation is directly linked to the development of information tecnology. Better hardware solutions, as well as improvements in software development methodologies make possible the rapid growth of the productive process control. In this thesis, we propose an architecture that will allow the joining of two technologies in hardware (industrial network) and software field (multiagent systems). The objective of this proposal is to join those technologies in a multiagent architecture to allow control strategies implementations in to field devices. With this, we intend develop an agents architecture to detect and solve problems which may occur in the industrial network environment. Our work ally machine learning with industrial context, become proposed multiagent architecture adaptable to unfamiliar or unexpected production environment. We used neural networks and presented an allocation strategies of these networks in industrial network field devices. With this we intend to improve decision support at plant level and allow operations human intervention independent

Máquina de vetores-suporte intervalar

The Support Vector Machines (SVM) has attracted increasing attention in machine learning area, particularly on classification and patterns recognition. However, in some cases it is not easy to determinate accurately the class which given pattern belongs. This thesis involves the construction of a intervalar pattern classifier using SVM in association with intervalar theory, in order to model the separation of a pattern set between distinct classes with precision, aiming to obtain an optimized separation capable to treat imprecisions contained in the initial data and generated during the computational processing. The SVM is a linear machine. In order to allow it to solve real-world problems (usually nonlinear problems), it is necessary to treat the pattern set, know as input set, transforming from nonlinear nature to linear problem. The kernel machines are responsible to do this mapping. To create the intervalar extension of SVM, both for linear and nonlinear problems, it was necessary define intervalar kernel and the Mercer s theorem (which caracterize a kernel function) to intervalar function

Predição de promotores de Bacillus subtilis usando técnicas de aprendizado de máquina

One of the most important goals of bioinformatics is the ability to identify genes in uncharacterized DNA sequences on world wide database. Gene expression on prokaryotes initiates when the RNA-polymerase enzyme interacts with DNA regions called promoters. In these regions are located the main regulatory elements of the transcription process. Despite the improvement of in vitro techniques for molecular biology analysis, characterizing and identifying a great number of promoters on a genome is a complex task. Nevertheless, the main drawback is the absence of a large set of promoters to identify conserved patterns among the species. Hence, a in silico method to predict them on any species is a challenge. Improved promoter prediction methods can be one step towards developing more reliable ab initio gene prediction methods. In this work, we present an empirical comparison of Machine Learning (ML) techniques such as Na¨ýve Bayes, Decision Trees, Support Vector Machines and Neural Networks, Voted Perceptron, PART, k-NN and and ensemble approaches (Bagging and Boosting) to the task of predicting Bacillus subtilis. In order to do so, we first built two data set of promoter and nonpromoter sequences for B. subtilis and a hybrid one. In order to evaluate of ML methods a cross-validation procedure is applied. Good results were obtained with methods of ML like SVM and Naïve Bayes using B. subtilis. However, we have not reached good results on hybrid database

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.

An Optimum-Path Forest framework for intrusion detection in computer networks

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Efficient supervised optimum-path forest classification for large datasets

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Desenvolvimento de chatterbots educacionais: um estudo de caso voltado ao ensino de algoritmos

In development of Synthetic Agents for Education, the doubt still resides about what would be a behavior that could be considered, in fact, plausible for this agent's type, which can be considered as effective on the transmission of the knowledge by the agent and the function of emotions this process. The purpose of this labor has an investigative nature in an attempt to discover what aspects are important for this behavior consistent and practical development of a chatterbot with the function of virtual tutor, within the context of learning algorithms. In this study, we explained the agents' basics, Intelligent Tutoring Systems, bots, chatterbots and how these systems need to provide credibility to report on their behavior. Models of emotions, personality and humor to computational agents are also covered, as well as previous studies by other researchers at the area. After that, the prototype is detailed, the research conducted, a summary of results achieved, the architectural model of the system, vision of computing and macro view of the features implemented.

Uso de confiabilidade na rotulação de exemplos em problemas de classificação multirrótulo com aprendizado semissupervisionado

The techniques of Machine Learning are applied in classification tasks to acquire knowledge through a set of data or information. Some learning methods proposed in literature are methods based on semissupervised learning; this is represented by small percentage of labeled data (supervised learning) combined with a quantity of label and non-labeled examples (unsupervised learning) during the training phase, which reduces, therefore, the need for a large quantity of labeled instances when only small dataset of labeled instances is available for training. A commom problem in semi-supervised learning is as random selection of instances, since most of paper use a random selection technique which can cause a negative impact. Much of machine learning methods treat single-label problems, in other words, problems where a given set of data are associated with a single class; however, through the requirement existent to classify data in a lot of domain, or more than one class, this classification as called multi-label classification. This work presents an experimental analysis of the results obtained using semissupervised learning in troubles of multi-label classification using reliability parameter as an aid in the classification data. Thus, the use of techniques of semissupervised learning and besides methods of multi-label classification, were essential to show the results

In silico network topology-based prediction of gene essentiality

The identification of genes essential for survival is important for the understanding of the minimal requirements for cellular life and for drug design. As experimental studies with the purpose of building a catalog of essential genes for a given organism are time-consuming and laborious, a computational approach which could predict gene essentiality with high accuracy would be of great value. We present here a novel computational approach, called NTPGE (Network Topology-based Prediction of Gene Essentiality), that relies on the network topology features of a gene to estimate its essentiality. The first step of NTPGE is to construct the integrated molecular network for a given organism comprising protein physical, metabolic and transcriptional regulation interactions. The second step consists in training a decision-tree-based machine-learning algorithm on known essential and non-essential genes of the organism of interest, considering as learning attributes the network topology information for each of these genes. Finally, the decision-tree classifier generated is applied to the set of genes of this organism to estimate essentiality for each gene. We applied the NTPGE approach for discovering the essential genes in Escherichia coli and then assessed its performance. (C) 2007 Elsevier B.V. All rights reserved.

Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)