Using the Fisher Kernel Method to Detect Remote Protein Homologies
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Protein homology detection by HMM--HMM comparison
Bioinformatics
Ensemble classifier for protein fold pattern recognition
Bioinformatics
Bioinformatics
Probabilistic multi-class multi-kernel learning
Bioinformatics
Letters: Adaptive local hyperplane classification
Neurocomputing
Protein fold recognition with adaptive local hyperplane algorithm
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Face recognition with adaptive local hyperplane algorithm
Pattern Analysis & Applications
Letters: Fusion of classifiers for protein fold recognition
Neurocomputing
ICANN/ICONIP'03 Proceedings of the 2003 joint international conference on Artificial neural networks and neural information processing
A generic classifier-ensemble approach for biomedical named entity recognition
PAKDD'12 Proceedings of the 16th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining - Volume Part I
Ensemble of diversely trained support vector machines for protein fold recognition
ACIIDS'13 Proceedings of the 5th Asian conference on Intelligent Information and Database Systems - Volume Part I
Enhancing protein fold prediction accuracy using evolutionary and structural features
PRIB'13 Proceedings of the 8th IAPR international conference on Pattern Recognition in Bioinformatics
A survey of multiple classifier systems as hybrid systems
Information Fusion
Hi-index | 12.05 |
Recognition of protein folding patterns is an important step in protein structure and function predictions. Traditional sequence similarity-based approach fails to yield convincing predictions when proteins have low sequence identities, while the taxonometric approach is a reliable alternative. From a pattern recognition perspective, protein fold recognition involves a large number of classes with only a small number of training samples, and multiple heterogeneous feature groups derived from different propensities of amino acids. This raises the need for a classification method that is able to handle the data complexity with a high prediction accuracy for practical applications. To this end, a novel ensemble classifier, called MarFold, is proposed in this paper which combines three margin-based classifiers for protein fold recognition. The effectiveness of our method is demonstrated with the benchmark D-B dataset with 27 classes. The overall prediction accuracy obtained by MarFold is 71.7%, which surpasses the existing fold recognition methods by 3.1-15.7%. Moreover, one component classifier for MarFold, called ALH, has obtained a prediction accuracy of 65.5%, which is 4.7-9.5% higher than the prediction accuracies for the published methods using single classifiers. Additionally, the feature set of pairwise frequency information about the amino acids, which is adopted by MarFold, is found to be important for discriminating folding patterns. These results imply that the MarFold method and its operation engine ALH might become useful vehicles for protein fold recognition, as well as other bioinformatics tasks. The MarFold method and the datasets can be obtained from: (http://www-staff.it.uts.edu.au/~lbcao/publication/MarFold.7z).