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Support Vector Machines (SVMs) ensembles have been widely used to improve classification accuracy in complicated pattern recognition tasks. In this work we propose to apply an ensemble of SVMs coupled with feature-subset selection methods to aleviate the curse of dimensionality associated with expression-based classification of DNA microarray data. We compare the single SVM classifier to SVM ensembles...
This work presents a system for knowledge discovery from protein databases, based on an Artificial Immune System. The discovered rules have the advantage of representing comprehensible knowledge to biologist users. This task leads to a very challenging problem since a protein can be assigned multiple classes (functions or Gene Ontology (GO) terms) across several levels of the GO's term hierarchy....
In this paper, we apply an evolutionary optimization classifier, referred to as genetic algorithm-based multiple classifier (GaMC), to the long-range contacts prediction. As a result, about 44.1% contacts between long-range residues (with a sequence separation of at least 24 amino acids) are founded around the sequence profile (SP) centre when evaluating the top L/5 (L is the sequence length of protein)...
Neural activity is very important source for data mining and can be used as a control signal for brain-computer interfaces (BCIs). Particularly, Magnetic signals of neurons are enriched with information about the movement of different part of the body such as wrist movement. In this paper, we use MEG (Magneto encephalography) signals of two subjects recorded during wrist movement task in four directions...
In this paper, we examine the problem of classifying protein fold structure without sequence similarity, by using classification techniques. The representation of the problem in an attribute-based manner allows the application of many well established machine learning algorithms. We study the performance of several algorithms such as decision trees, Naive Bayes, instance-based, and generalized exemplar...
Identifying protein-protein interaction sites have important connotations ranging from rational drug design to analysis metabolic and signal transduction networks. In this paper, we presented an adapted Bayesian classifier based on tree augmented naiumlve Bayesian classifier to predict interface residues of protein-protein interaction sites. This classifier used fixed structure which could denote...
Protein secondary structure prediction is a bridge between amino acid sequence and tertiary prediction. Various methods have been used to improve the prediction accuracy and have been developed greatly. Protein classification is a multi-class classification problem. For traditional method, the three structure are predicted in the same time. But it can be degraded to a set of binary classification...
Microarray technology has been widely applied to search for biomarkers of diseases, diagnose diseases and analyze gene regulatory network. Abundance of expression data from microarray experiments are processed by informatics tools, such as supporting vector machines (SVM), artificial neural network (ANN), and so on. These methods achieve good results in single dataset. Nevertheless, most analyses...
Dimensionality reduction has been demonstrated to improve the performance of the k-nearest neighbor (kNN) classifier for high-dimensional data sets, such as microarrays. However, the effectiveness of different dimensionality reduction methods varies, and it has been shown that no single method constantly outperforms the others. In contrast to using a single method, two approaches to fusing the result...
We present a classification algorithm built on our adaptation of the Generalized Lotka-Volterra model, well-known in mathematical ecology. The training algorithm itself consists only of computing several scalars, per each training vector, using a single global user parameter and then solving a linear system of equations. Construction of the system matrix is driven by our model and based on kernel...
Promoter recognition has been attempted using different paradigms such as motif/binding regions alone or whole promoter itself. In an earlier paper, a scheme is proposed to use 2-gram features to represent a promoter. These 2-grams gave a comparable performance with the existing methods in the literature. An in-depth analysis of data sets using 2-grams is performed. The analysis presented a scenario...
Classification is a major task in the gene sequence analysis. Based on the general principle of artificial immune system, this paper first constructed a classifier which inducted antibody-antigen identification, immune colonel reproduction, hypermutation, affinity mature and the network suppression, by simulating how the antigens stimulate the immune network and how the immune network responds. Then,...
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