Using machine learning tools for protein database biocuration assistance.

Biocuration in the omics sciences has become paramount, as research in these fields rapidly evolves towards increasingly data-dependent models. As a result, the management of web-accessible publicly-available databases becomes a central task in biological knowledge dissemination. One relevant challenge for biocurators is the unambiguous identification of biological entities.

Systematic Analysis of Primary Sequence Domain Segments for the Discrimination Between Class C GPCR Subtypes.

G-protein-coupled receptors (GPCRs) are a large and diverse super-family of eukaryotic cell membrane proteins that play an important physiological role as transmitters of extracellular signal. In this paper, we investigate Class C, a member of this super-family that has attracted much attention in pharmacology. The limited knowledge about the complete 3D crystal structure of Class C receptors makes necessary the use of their primary amino acid sequences for analytical purposes.

MSClique: Multiple Structure Discovery through the Maximum Weighted Clique Problem.

We present a novel approach for feature correspondence and multiple structure discovery in computer vision. In contrast to existing methods, we exploit the fact that point-sets on the same structure usually lie close to each other, thus forming clusters in the image. Given a pair of input images, we initially extract points of interest and extract hierarchical representations by agglomerative clustering.

Label noise in subtype discrimination of class C G protein-coupled receptors: A systematic approach to the analysis of classification errors.

Background: The characterization of proteins in families and subfamilies, at different levels, entails the definition and use of class labels. When the adscription of a protein to a family is uncertain, or even wrong, this becomes an instance of what has come to be known as a label noise problem. Label noise has a potentially negative effect on any quantitative analysis of proteins that depends on label information.

Reducing the n-gram feature space of class C GPCRs to subtype-discriminating patterns.

G protein-coupled receptors (GPCRs) are a large and heterogeneous superfamily of receptors that are key cell players for their role as extracellular signal transmitters. Class C GPCRs, in particular, are of great interest in pharmacology. The lack of knowledge about their full 3-D structure prompts the use of their primary amino acid sequences for the construction of robust classifiers, capable of discriminating their different subtypes.

Comparing error minimized extreme learning machines and support vector sequential feed-forward neural networks.

Recently, error minimized extreme learning machines (EM-ELMs) have been proposed as a simple and efficient approach to build single-hidden-layer feed-forward networks (SLFNs) sequentially. They add random hidden nodes one by one (or group by group) and update the output weights incrementally to minimize the sum-of-squares error in the training set. Other very similar methods that also construct SLFNs sequentially had been reported earlier with the main difference that their hidden-layer weights are a subset of the data instead of being random.

Data mining of patients on weaning trials from mechanical ventilation using cluster analysis and neural networks.

The process of weaning from mechanical ventilation is one of the challenges in intensive care. 149 patients under extubation process (T-tube test) were studied: 88 patients with successful trials (group S), 38 patients who failed to maintain spontaneous breathing and were reconnected (group F), and 23 patients with successful test but that had to be reintubated before 48 hours (group R). Each patient was characterized using 8 time series and 6 statistics extracted from respiratory and cardiac signals.