Automatic classification of enzyme family in protein annotation

Most of the tasks in genome annotation can be at least partially automated. Since this annotation is time-consuming, facilitating some parts of the process - thus freeing the specialist to carry out more valuable tasks - has been the motivation of many tools and annotation environments. In particular, annotation of protein function can benefit from knowledge about enzymatic processes. The use of sequence homology alone is not a good approach to derive this knowledge when there are only a few homologues of the sequence to be annotated. The alternative is to use motifs. This paper uses a symbolic machine learning approach to derive rules for the classification of enzymes according to the Enzyme Commission (EC). Our results show that, for the top class, the average global classification error is 3.13%. Our technique also produces a set of rules relating structural to functional information, which is important to understand the protein tridimensional structure and determine its biological function. © 2009 Springer Berlin Heidelberg.

Avaliação estatística de métodos de poda aplicados em neurônios intermediários da rede neural MLP

There are several papers on pruning methods in the artificial neural networks area. However, with rare exceptions, none of them presents an appropriate statistical evaluation of such methods. In this article, we proved statistically the ability of some methods to reduce the number of neurons of the hidden layer of a multilayer perceptron neural network (MLP), and to maintain the same landing of classification error of the initial net. They are evaluated seven pruning methods. The experimental investigation was accomplished on five groups of generated data and in two groups of real data. Three variables were accompanied in the study: apparent classification error rate in the test group (REA); number of hidden neurons, obtained after the application of the pruning method; and number of training/retraining epochs, to evaluate the computational effort. The non-parametric Friedman's test was used to do the statistical analysis.

Portable Hardness tester for timber classification

Hardness is a property largely used in material specifications, mechanical and metallurgical research and quality control of several materials. Specifically for timber, Janka hardness is a simple, quick and easy test, with good correlations with the compression parallel to grain strength, a strong reference in structural classification for this material. More recently, international studies have reported the use of Brinell hardness for timber assessment which resumes the advantages previously mentioned for Janka hardness and make it easier to be performed in the field, especially because of the lower magnitude of the involved loads. A first generation of an equipment for field evaluation of hardness in wood - Portable Hardness tester for wood - based on Brinell hardness has already been developed by the Research Group on Forest Products from FCA/UNESP, Brazil, with very good correlations between the evaluated hardness and several other mechanical properties of the material when performing tests with different species of native and reforested wood (traditionally used as ties - sleepers - in railways). This paper presents results obtained in the experimental program with the first generation of this equipment and preliminary tests with its second generation, which uses accelerometers to substitute the indentation measurements in wood. For the first generation of the equipment functional and calibration tests were carried out using 16 native and reforestation timber lots, among there E. citriodora, E. tereticornis, E. saligna, E. urophylla, E. grandis, Goupia glabra and Bagassa guianenses, with different origins and ages. The results obtained confirm its potential in the classification of specimens, with inclusion errors varying from 4.5% to 16.6%.