Improving drug discovery using hybrid softcomputing methods

Virtual screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, but it has been demonstrated that diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact. This problem is circumvented by a novel VS methodology named BINDSURF that scans the whole protein surface in order to find new hotspots, where ligands might potentially interact with, and which is implemented in last generation massively parallel GPU hardware, allowing fast processing of large ligand databases. BINDSURF can thus be used in drug discovery, drug design, drug repurposing and therefore helps considerably in clinical research. However, the accuracy of most VS methods and concretely BINDSURF is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to improve accuracy of the scoring functions used in BINDSURF we propose a hybrid novel approach where neural networks (NNET) and support vector machines (SVM) methods are trained with databases of known active (drugs) and inactive compounds, being this information exploited afterwards to improve BINDSURF VS predictions.

Improvement of Virtual Screening Predictions using Computational Intelligence Methods

Virtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. However, the accuracy of most VS methods is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to improve accuracy of scoring functions used in most VS methods we propose a hybrid novel approach where neural networks (NNET) and support vector machines (SVM) methods are trained with databases of known active (drugs) and inactive compounds, this information being exploited afterwards to improve VS predictions.

Improving drug discovery using a neural networks based parallel scoring function

Virtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, but it has been demonstrated that diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact. This problem is circumvented by a novel VS methodology named BINDSURF that scans the whole protein surface to find new hotspots, where ligands might potentially interact with, and which is implemented in massively parallel Graphics Processing Units, allowing fast processing of large ligand databases. BINDSURF can thus be used in drug discovery, drug design, drug repurposing and therefore helps considerably in clinical research. However, the accuracy of most VS methods is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to solve this problem, we propose a novel approach where neural networks are trained with databases of known active (drugs) and inactive compounds, and later used to improve VS predictions.

Active Foreground Region Extraction and Tracking for Sports Video Annotation

Automatic video segmentation plays a vital role in sports videos annotation. This paper presents a fully automatic and computationally efficient algorithm for analysis of sports videos. Various methods of automatic shot boundary detection have been proposed to perform automatic video segmentation. These investigations mainly concentrate on detecting fades and dissolves for fast processing of the entire video scene without providing any additional feedback on object relativity within the shots. The goal of the proposed method is to identify regions that perform certain activities in a scene. The model uses some low-level feature video processing algorithms to extract the shot boundaries from a video scene and to identify dominant colours within these boundaries. An object classification method is used for clustering the seed distributions of the dominant colours to homogeneous regions. Using a simple tracking method a classification of these regions to active or static is performed. The efficiency of the proposed framework is demonstrated over a standard video benchmark with numerous types of sport events and the experimental results show that our algorithm can be used with high accuracy for automatic annotation of active regions for sport videos.

Football Video Annotation Based on Player Motion Recognition Using Enhanced Entropy

This paper presents a semi-parametric Algorithm for parsing football video structures. The approach works on a two interleaved based process that closely collaborate towards a common goal. The core part of the proposed method focus perform a fast automatic football video annotation by looking at the enhance entropy variance within a series of shot frames. The entropy is extracted on the Hue parameter from the HSV color system, not as a global feature but in spatial domain to identify regions within a shot that will characterize a certain activity within the shot period. The second part of the algorithm works towards the identification of dominant color regions that could represent players and playfield for further activity recognition. Experimental Results shows that the proposed football video segmentation algorithm performs with high accuracy.

Model Probability in Self-organising Maps

Growing models have been widely used for clustering or topology learning. Traditionally these models work on stationary environments, grow incrementally and adapt their nodes to a given distribution based on global parameters. In this paper, we present an enhanced unsupervised self-organising network for the modelling of visual objects. We first develop a framework for building non-rigid shapes using the growth mechanism of the self-organising maps, and then we define an optimal number of nodes without overfitting or underfitting the network based on the knowledge obtained from information-theoretic considerations. We present experimental results for hands and we quantitatively evaluate the matching capabilities of the proposed method with the topographic product.

Descubrimiento de fármacos basado en cribado virtual refinado con enfoques neuronales paralelos

En el campo de la medicina clínica es crucial poder determinar la seguridad y la eficacia de los fármacos actuales y además acelerar el descubrimiento de nuevos compuestos activos. Para ello se llevan a cabo ensayos de laboratorio, que son métodos muy costosos y que requieren mucho tiempo. Sin embargo, la bioinformática puede facilitar enormemente la investigación clínica para los fines mencionados, ya que proporciona la predicción de la toxicidad de los fármacos y su actividad en enfermedades nuevas, así como la evolución de los compuestos activos descubiertos en ensayos clínicos. Esto se puede lograr gracias a la disponibilidad de herramientas de bioinformática y métodos de cribado virtual por ordenador (CV) que permitan probar todas las hipótesis necesarias antes de realizar los ensayos clínicos, tales como el docking estructural, mediante el programa BINDSURF. Sin embargo, la precisión de la mayoría de los métodos de CV se ve muy restringida a causa de las limitaciones presentes en las funciones de afinidad o scoring que describen las interacciones biomoleculares, e incluso hoy en día estas incertidumbres no se conocen completamente. En este trabajo abordamos este problema, proponiendo un nuevo enfoque en el que las redes neuronales se entrenan con información relativa a bases de datos de compuestos conocidos (proteínas diana y fármacos), y se aprovecha después el método para incrementar la precisión de las predicciones de afinidad del método de CV BINDSURF.

SARASOM: a supervised architecture based on the recurrent associative SOM

We present and evaluate a novel supervised recurrent neural network architecture, the SARASOM, based on the associative self-organizing map. The performance of the SARASOM is evaluated and compared with the Elman network as well as with a hidden Markov model (HMM) in a number of prediction tasks using sequences of letters, including some experiments with a reduced lexicon of 15 words. The results were very encouraging with the SARASOM learning better and performing with better accuracy than both the Elman network and the HMM.

Estudio e implementación del centro de procesamiento de datos de la empresa Peoplepass S.A

142 p.

Sistema drone para monitoreo de ganado bovino por reconocimiento de imágenes

61 p.

Segurança contra intrusão em redes informáticas

Devido ao facto de hoje em dia a informação que é processada numa rede informática empresarial, ser cada vez mais de ordem confidencial, torna-se necessário que essa informação esteja o mais protegida possível. Ao mesmo tempo, é necessário que esta a informação esteja disponível com a devida rapidez, para os parceiros certos, num mundo cada vez mais globalizado. Com este trabalho pretende-se efectuar o estudo e implementação da segurança, numa pequena e genérica rede de testes, que facilmente seja extrapolada, para uma rede da dimensão, de uma grande empresa com potenciais ramificações por diversos locais. Pretende-se implementar/monitorização segurança quer externamente, (Internet service provider ISP) quer internamente (activos de rede, postos de trabalho/utilizadores). Esta análise é baseada na localização (local, wireless ou remota), e, sempre que seja detectada qualquer anomalia, seja identificada a sua localização, sendo tomadas automaticamente acções de protecção. Estas anomalias poderão ser geridas recorrendo a ferramentas open source ou comerciais, que façam a recolha de toda a informação necessária, e tomem acções de correcção ou alerta mediante o tipo de anomalia.

Soluções para monitorização, salvaguarda de configurações e segurança na rede do banco BNP Paribas Personal Finance S. A. em Vila Nova De Gaia

Mestrado em Engenharia Electrotécnica e de Computadores - Área de Especialização de Telecomunicações

Redes, comunicações e segurança informática

Este trabalho começa por apresentar uma instalação de rede informática local efetuada sob supervisão do candidato e parcialmente por ele, descrevendo de seguida algumas considerações que na altura se lhe levantaram. Sendo ligada à saúde, para além das preocupações normais de instalação de qualquer solução, a questão humana e social foi particularmente sentida. Várias organizações e pessoas individuais necessitam de implementar e utilizar soluções de comunicações informáticas, pelo que a privacidade e confiabilidade das informações processadas se torna um assunto premente. No sentido de obter uma resposta para este problema, o candidato evoluiu para a área da criptografia e segurança de comunicações, implementado alguns dos protocolos existentes e estudando-os com maior rigor. É justamente a descrição dessa evolução e da segurança com que se pode contar quando se utilizam meios informáticos o âmbito deste trabalho, focando principalmente o impacto que tem na sua utilização.

Controlo preditivo sobre redes de sensores e actuadores sem fios com tolerância a falhas de comunicação

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Redes locais de computadores Uma visão global e prática

O presente trabalho tem por objectivo, a elaboração de um manual prático que permita aos leitores, sejam ou não, técnicos de redes, instalar uma rede local básica em casa ou no local de trabalho, sem recorrer a sessões de formação presenciais. São abordados vários aspectos essenciais para a compreensão dos paradigmas de redes locais. Faz-se também, um estudo prático e sucinto de todos os componentes envolvidos no processo de comunicação, numa rede local. Assim sendo, este manual permitirá ao leitor compreender o funcionamento de uma rede local, assim como o processo de instalação e configuração.