In Defense of One-Vs-All Classification
The Journal of Machine Learning Research
Protein homology detection using string alignment kernels
Bioinformatics
Remote homology detection based on oligomer distances
Bioinformatics
MPI-HMMER-Boost: Distributed FPGA Acceleration
Journal of VLSI Signal Processing Systems
Learning from imbalanced data in surveillance of nosocomial infection
Artificial Intelligence in Medicine
Protein classification with multiple algorithms
PCI'05 Proceedings of the 10th Panhellenic conference on Advances in Informatics
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Large-scale sequencing projects have led to a vast amount of protein sequences, which have to be assigned to functional categories. Currently, profile hidden markov models and kernel-based machine learning methods provide the most accurate results for protein classification. However, the prediction of new sequences with these approaches is computationally expensive. We present an approach for fast scoring of protein sequences by means of feature-based protein sequence representation and multi-class multi-label machine learning techniques. Using the Pfam database, we show that our method provides high computational efficiency and that the approach is well-suitable for pre-filtering of large sequence sets.