An experimental comparison of classification algorithms for hierarchical prediction of protein function

1 Computing Laboratory and Centre for BioMedical Informatics, University of Kent, Canterbury, CT2 7NF, UK Email: {a.d.secker, a.a.freitas}@kent.ac.uk 2 Edward Jenner Institute, Compton, Newbury, Berkshire, RG20 7NN, UK Email: m.davies@mail.cryst.bbk.ac.uk, darren.flower@jenner.ac.uk 3 Departments of Computer Science and Electronics, University of York, Heslington, YO10 5DD, UK Email: {jtimmis, miguel}@cs.york.ac.uk

[1]  Jaak Vilo,et al.  Prediction of the coupling specificity of G protein coupled receptors to their G proteins , 2001, ISMB.

[2]  T. Lundstedt,et al.  Classification of G‐protein coupled receptors by alignment‐independent extraction of principal chemical properties of primary amino acid sequences , 2002, Protein science : a publication of the Protein Society.

[3]  M. Bouvier,et al.  Structural and functional aspects of G protein-coupled receptor oligomerization. , 1998, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[4]  Kolakowski Lf GCRDB: A G-PROTEIN-COUPLED RECEPTOR DATABASE , 1994 .

[5]  T. Lundstedt,et al.  Proteochemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands. , 2002, Molecular pharmacology.

[6]  S. Sathiya Keerthi,et al.  Improvements to Platt's SMO Algorithm for SVM Classifier Design , 2001, Neural Computation.

[7]  Amanda Clare,et al.  Predicting gene function in Saccharomyces cerevisiae , 2003, ECCB.

[8]  Jonathan Timmis,et al.  Artificial Immune Recognition System (AIRS): An Immune-Inspired Supervised Learning Algorithm , 2004, Genetic Programming and Evolvable Machines.

[9]  Ying Huang,et al.  Classifying G-protein Coupled Receptors with Support Vector Machine , 2004, ISNN.

[10]  D R Flower,et al.  Modelling G-protein-coupled receptors for drug design. , 1999, Biochimica et biophysica acta.

[11]  Zheng-Zhi Wang,et al.  Classification of G-protein coupled receptors at four levels. , 2006, Protein engineering, design & selection : PEDS.

[12]  Ian H. Witten,et al.  Generating Accurate Rule Sets Without Global Optimization , 1998, ICML.

[13]  Alex A. Freitas,et al.  A Tutorial on Hierarchical Classification with Applications in Bioinformatics. , 2007 .