Aprendizado de máquina simbólico e técnicas fractais para caracterizar rejeição em biópsia miocárdica

This work combines symbolic machine learning and multiscale fractal techniques to generate models that characterize cellular rejection in myocardial biopsies and that can base a diagnosis support system. The models express the knowledge by the features threshold, fractal dimension, lacunarity, number of clusters, spatial percolation and percolation probability, all obtained with myocardial biopsies processing. Models were evaluated and the most significant was the one generated by the C4.5 algorithm for the features spatial percolation and number of clusters. The result is relevant and contributes to the specialized literature since it determines a standard diagnosis protocol. © 2013 Springer.

The Development of a Universal In Silico Predictor of Protein-Protein Interactions

Protein-protein interactions (PPIs) are essential for understanding the function of biological systems and have been characterized using a vast array of experimental techniques. These techniques detect only a small proportion of all PPIs and are labor intensive and time consuming. Therefore, the development of computational methods capable of predicting PPIs accelerates the pace of discovery of new interactions. This paper reports a machine learning-based prediction model, the Universal In Silico Predictor of Protein-Protein Interactions (UNISPPI), which is a decision tree model that can reliably predict PPIs for all species (including proteins from parasite-host associations) using only 20 combinations of amino acids frequencies from interacting and non-interacting proteins as learning features. UNISPPI was able to correctly classify 79.4% and 72.6% of experimentally supported interactions and non-interacting protein pairs, respectively, from an independent test set. Moreover, UNISPPI suggests that the frequencies of the amino acids asparagine, cysteine and isoleucine are important features for distinguishing between interacting and non-interacting protein pairs. We envisage that UNISPPI can be a useful tool for prioritizing interactions for experimental validation. © 2013 Valente et al.

Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

Background: Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal's life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.Results: The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.Conclusions: These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle. © 2013 Mokry et al.; licensee BioMed Central Ltd.

OPF-MRF: Optimum-path forest and Markov random fields for contextual-based image classification

Some machine learning methods do not exploit contextual information in the process of discovering, describing and recognizing patterns. However, spatial/temporal neighboring samples are likely to have same behavior. Here, we propose an approach which unifies a supervised learning algorithm - namely Optimum-Path Forest - together with a Markov Random Field in order to build a prior model holding a spatial smoothness assumption, which takes into account the contextual information for classification purposes. We show its robustness for brain tissue classification over some images of the well-known dataset IBSR. © 2013 Springer-Verlag.

Estimativa da radiação solar ultravioleta em Botucatu/SP Brasil utilizando técnicas de aprendizado de máquina

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Construção e análise da rede integrada de interações entre genes humanos envolvida com a regulação da trnsição G1/S do ciclo celular plea adesão à matriz extracelular

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Analisando a determinação sexual de vertebrados com base em redes de interação entre proteínas

Pós-graduação em Ciências Biológicas (Genética) - IBB

Construção, caracterização global e local de redes biológicas

A Biologia Sistêmica visa a compreensão da vida através de modelos integrativos que enfatizem as interações entre os diferentes agentes biológicos. O objetivo é buscar por leis universais, não nas partes componentes dos sistemas mas sim nos padrões de interação dos elementos constituintes. As redes complexas biológicas são uma poderosa abstração matemática que permite a representação de grandes volumes de dados e a posterior formulação de hipóteses biológicas. Nesta tese apresentamos as redes biológicas integradas que incluem interações oriundas do metabolismo, interação física de proteínas e regulação. Discutimos sua construção e ferramentas para sua análise global e local. Apresentamos também resultados do uso de ferramentas de aprendizado de máquina que nos permitem compreender a relação entre propriedades topológicas e a essencialidade gênica e a previsão de genes mórbidos e alvos para drogas em humanos

Pattern recognition issues on anisotropic smoothed particle hydrodynamics

This is a preliminary theoretical discussion on the computational requirements of the state of the art smoothed particle hydrodynamics (SPH) from the optics of pattern recognition and artificial intelligence. It is pointed out in the present paper that, when including anisotropy detection to improve resolution on shock layer, SPH is a very peculiar case of unsupervised machine learning. On the other hand, the free particle nature of SPH opens an opportunity for artificial intelligence to study particles as agents acting in a collaborative framework in which the timed outcomes of a fluid simulation forms a large knowledge base, which might be very attractive in computational astrophysics phenomenological problems like self-propagating star formation.

Prediction of Oncogenic Interactions and Cancer-Related Signaling Networks Based on Network Topology

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

NodePM: A Remote Monitoring Alert System for Energy Consumption Using Probabilistic Techniques

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

Classificação de tábuas de madeira usando processamento de imagens digitais e aprendizado de máquina

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Interface para classificação de dados por máquinas de vetores de suporte

In this project the Pattern Recognition Problem is approached with the Support Vector Machines (SVM) technique, a binary method of classification that provides the best solution separating the data in the better way with a hiperplan and an extension of the input space dimension, as a Machine Learning solution. The system aims to classify two classes of pixels chosen by the user in the interface in the interest selection phase and in the background selection phase, generating all the data to be used in the LibSVM library, a library that implements the SVM, illustrating the library operation in a casual way. The data provided by the interface is organized in three types, RGB (Red, Green and Blue color system), texture (calculated) or RGB + texture. At last the project showed successful results, where the classification of the image pixels was showed as been from one of the two classes, from the interest selection area or from the background selection area. The simplest user view of results classification is the RGB type of data arrange, because it’s the most concrete way of data acquisition

An evolutionary approach to improve connectivity prediction in mobile wireless sensor networks

Connectivity is the basic factor for the proper operation of any wireless network. In a mobile wireless sensor network it is a challenge for applications and protocols to deal with connectivity problems, as links might get up and down frequently. In these scenarios, having knowledge of the node remaining connectivity time could both improve the performance of the protocols (e.g. handoff mechanisms) and save possible scarce nodes resources (CPU, bandwidth, and energy) by preventing unfruitful transmissions. The current paper provides a solution called Genetic Machine Learning Algorithm (GMLA) to forecast the remainder connectivity time in mobile environments. It consists in combining Classifier Systems with a Markov chain model of the RF link quality. The main advantage of using an evolutionary approach is that the Markov model parameters can be discovered on-the-fly, making it possible to cope with unknown environments and mobility patterns. Simulation results show that the proposal is a very suitable solution, as it overcomes the performance obtained by similar approaches.

A method using artificial neural networks to morphologically assess mouse blastocyst quality

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