Peptide programs: applying fragment programs to protein classification
Proceedings of the 2nd international workshop on Data and text mining in bioinformatics
Pattern recognition with a Bayesian kernel combination machine
Pattern Recognition Letters
Prediction of Protein Functions from Protein Interaction Networks: A Naïve Bayes Approach
PRICAI '08 Proceedings of the 10th Pacific Rim International Conference on Artificial Intelligence: Trends in Artificial Intelligence
Combining feature spaces for classification
Pattern Recognition
Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Multiple Kernel Learning of Environmental Data. Case Study: Analysis and Mapping of Wind Fields
ICANN '09 Proceedings of the 19th International Conference on Artificial Neural Networks: Part II
Combined classifier for unknown genome classification using chaos game representation features
ISB '10 Proceedings of the International Symposium on Biocomputing
Pattern Recognition
Multiple Kernel Learning Algorithms
The Journal of Machine Learning Research
Using rotation forest for protein fold prediction problem: an empirical study
EvoBIO'10 Proceedings of the 8th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Protein annotation from protein interaction networks and Gene Ontology
Journal of Biomedical Informatics
Predicting human miRNA target genes using a novel evolutionary methodology
SETN'12 Proceedings of the 7th Hellenic conference on Artificial Intelligence: theories and applications
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Motivation: Drawing inferences from large, heterogeneous sets of biological data requires a theoretical framework that is capable of representing, e.g. DNA and protein sequences, protein structures, microarray expression data, various types of interaction networks, etc. Recently, a class of algorithms known as kernel methods has emerged as a powerful framework for combining diverse types of data. The support vector machine (SVM) algorithm is the most popular kernel method, due to its theoretical underpinnings and strong empirical performance on a wide variety of classification tasks. Furthermore, several recently described extensions allow the SVM to assign relative weights to various datasets, depending upon their utilities in performing a given classification task. Results: In this work, we empirically investigate the performance of the SVM on the task of inferring gene functional annotations from a combination of protein sequence and structure data. Our results suggest that the SVM is quite robust to noise in the input datasets. Consequently, in the presence of only two types of data, an SVM trained from an unweighted combination of datasets performs as well or better than a more sophisticated algorithm that assigns weights to individual data types. Indeed, for this simple case, we can demonstrate empirically that no solution is significantly better than the naive, unweighted average of the two datasets. On the other hand, when multiple noisy datasets are included in the experiment, then the naive approach fares worse than the weighted approach. Our results suggest that for many applications, a naive unweighted sum of kernels may be sufficient. Availability: http://noble.gs.washington.edu/proj/seqstruct Contact: noble@gs.washington.edu Supplementary information: Supplementary Data are available at Bioinformatics online.