Multitask learning for protein subcellular location prediction

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 8, Issue 3, 2011, Pages 748-759

  Xu, Qian ^a   Pan, Sinno Jialin ^a   Xue, Hannah Hong ^a   Yang, Qiang ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

multitask learning; Protein subcellular localization

Indexed keywords

ACCURATE PREDICTION; ANNOTATED TRAINING DATA; BIOLOGICAL POINTS; DATA SPARSITY PROBLEMS; DRUG TARGETS; GENOME ANNOTATION; INDIVIDUAL LEARNING; LOCALIZATION ACCURACY; LOCATION INFORMATION; MACHINE LEARNING METHODS; MULTI-TASK KERNELS; MULTIPLE MODELS; MULTITASK LEARNING; PREDICTION OF PROTEIN FUNCTION; PROTEIN SUBCELLULAR LOCALIZATION; PROTEIN SUBCELLULAR LOCATION; SUBCELLULAR LOCALIZATIONS; SUPERTYPE;

BIOLOGY; FORECASTING; MULTI AGENT SYSTEMS; PROTEINS; SUPPORT VECTOR MACHINES;

LEARNING ALGORITHMS;

PROTEIN;

ALGORITHM; ANIMAL; ARTICLE; ARTIFICIAL INTELLIGENCE; BACTERIUM; BIOLOGICAL MODEL; BIOLOGY; CELL FRACTIONATION; CHEMISTRY; FUNGUS; HUMAN; METABOLISM; METHODOLOGY; PROTEIN DATABASE; SPECIES DIFFERENCE;

ALGORITHMS; ANIMALS; ARTIFICIAL INTELLIGENCE; BACTERIA; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; FUNGI; HUMANS; MODELS, BIOLOGICAL; PROTEINS; SPECIES SPECIFICITY; SUBCELLULAR FRACTIONS;

EID: 79952849335     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2010.22     Document Type: Article

References (70)

1. K. C. Chou and H. B. Shen, "Cell-Ploc: A Package of Web Servers for Predicting Subcellular Localization of Proteins in Various Organisms, " Nature Protocol, vol. 3, pp. 153-162, 2008.
2. E. C. Su, H. S. Chiu, A. Lo, J. K. Hwang, T. Y. Sung, and W. L. Hsu, "Protein Subcellular Localization Prediction Based on Compartment-Specific Feature and Structure Conservation, " BMC Bioinformatics, vol. 8, article no. 330, 2007.
3. M. Claros, S. Brunak, and G. Heijne, "Prediction of N-Terminal Protein Sorting Signals, " Current Opinion in Structural Biology, vol. 7, pp. 394-398, 1997. (Pubitemid 27281410)
4. H. Nakashima and K. Nishikawa, "Discrimination of Intracellular and Extracellular Proteins Using Amino Acid Composition and Residue-Pair Frequencies, " J. Molecular Biology, vol. 238, no. 1, pp. 54-61, 1994. (Pubitemid 24156401)
5. K. C. Chou and D. W. Elrod, "Protein Subcellular Location Prediction, " Protein Eng., vol. 12, no. 2, pp. 107-118, 1999. (Pubitemid 29103689)
6. K. C. Chou and Y. D. Cai, "Using Functional Domain Composition and Support Vector Machines for Prediction of Protein Subcellular Location, " J. Biology Chemistry, vol. 277, no. 48, pp. 45765-45769, 2002.
7. K. C. Chou, "Prediction of Protein Cellular Attributes Using Pseudo-Amino Acid Composition, " Proteins, vol. 43, no. 3, pp. 246-255, 2001.
8. G. P. Zhou and K. Doctor, "Subcellular Location Prediction of Apoptosis Proteins, " Proteins, vol. 50, no. 1, pp. 44-48, 2003. (Pubitemid 36090607)
9. K. C. Chou and H. B. Shen, "Predicting Protein Subcellular Location by Fusing Multiple Classifiers, " J. Cellular Biochemistry, vol. 99, no. 2, pp. 517-527, 2006.
10. K. C. Chou and H. B. Shen, "Predicting Eukaryotic Protein Subcellular Location by Fusing Optimized Evidence-Theoretic K-Nearest Neighbor Classifiers, " J. Proteome Research, vol. 5, no. 8, pp. 1888-1897, 2006.
11. K. C. Chou and H. B. Shen, "Hum-Ploc: A Novel Ensemble Classifier for Predicting Human Protein Subcellular Localization, " Biochemical Biophysical Research Comm., vol. 347, no. 8, pp. 150-157, 2006.
12. H. B. Shen and K. C. Chou, "Gpos-Ploc: An Ensemble Classifier for Predicting Subcellular Localization of Gram-Positive Bacterial Proteins, " Protein Eng. Design Selection, vol. 20, no. 1, pp. 39-46, 2007.
13. H. B. Shen and K. C. Chou, "Nuc-Ploc: A New Web-Server for Predicting Protein Subnuclear Localization by Fusing Pseaa Composition and Psepssm, " Protein Eng. Design and Selection, vol. 20, no. 11, pp. 561-567, 2007.
14. K. C. Chou and H. B. Shen, "Large-Scale Plant Protein Subcellular Location Prediction, " J. Cellular Biochemistry, vol. 100, no. 3, pp. 665-678, 2007.
15. K. C. Chou and H. B. Shen, "Euk-Mploc: A Fusion Classifier for Large-Scale Eukaryotic Protein Subcellular Location Prediction by Incorporating Multiple Sites, " J. Proteome Research, vol. 6, no. 5, pp. 1728-1734, 2007.
16. K. C. Chou, "A Novel Approach to Predicting Protein Structural Classes in a (20-1)-d Amino Acid Composition Space, " Proteins: Structure, Function and Genetics, vol. 21, no. 4, pp. 319-344, 1995.
17. K. C. Chou and Y. D. Cai, "Predicting Protein Structural Class by Functional Domain Composition, " Biochemical and Biophysical Research Comm., vol. 321, no. 4, pp. 1007-1009, 2004.
18. K. D. Kedarisetti, L. A. Kurgan, and S. Dick, "Classifier Ensembles for Protein Structural Class Prediction with Varying Homology, " Biochemical and Biophysical Research Comm., vol. 348, no. 3, pp. 981-988, 2006. (Pubitemid 44233512)
19. X. Xiao, P. Wang, and K. C. Chou, "Predicting Protein Quaternary Structural Attribute by Hybridizing Functional Domain Composition and Pseudo Amino Acid Composition, " J. Applied Crystallography, vol. 42, pp. 169-173, 2009.
20. K. C. Chou and H. B. Shen, "Foldrate: A Web-Server for Predicting Protein Folding Rates from Primary Sequence, " Open Bioinformatics J., vol. 3, pp. 31-50, 2009.
21. H. B. Shen, J. N. Song, and K. C. Chou, "Prediction of Protein Folding Rates from Primary Sequence by Fusing Multiple Sequential Features, " J. Biomedical Science and Eng., vol. 2, pp. 136-143, 2009.
22. K. C. Chou and H. B. Shen, "Memtype-21: A Web Server for Predicting Membrane Proteins and Their Types by Incorporating Evolution Information through Pse-Pssm, " Biochemical and Biophysical Research Comm., vol. 360, no. 2, pp. 339-345, 2007.
23. H. B. Shen and K. C. Chou, "Ezypred: A Top-Down Approach for Predicting Enzyme Functional Classes and Subclasses, " Biochemical and Biophysical Research Comm., vol. 364, no. 1, pp. 53-59, 2007.
24. X. Xiao, P. Wang, and K. C. Chou, "Gpcr-Ca: A Cellular Automaton Image Approach for Predicting G-Protein-Coupled Receptor Functional Classes, " J. Computational Chemistry, vol. 30, pp. 1414-1423, 2009.
25. K. C. Chou, "Prediction of G-Protein-Coupled Receptor Classes, " J. Proteome Research, vol. 4, no. 4, pp. 1413-1418, 2004.
26. K. C. Chou and H. B. Shen, "Protident: A Web Server for Identifying Proteases and Their Types by Fusing Functional Domain and Sequential Evolution Information, " Biochemical Biophysical Research Comm., vol. 376, no. 2, pp. 321-325, 2008.
27. K. C. Chou, "A Vectorized Sequence-Coupling Model for Predicting hiv Protease Cleavage Sites in Proteins, " J. Biological Chemistry, vol. 269, pp. 16938-16948, 1993.
28. K. C. Chou, "Review: Prediction of hiv Protease Cleavage Sites in Proteins, " Analytical Biochemistry, vol. 233, pp. 1-14, 1996.
29. H. B. Shen and K. C. Chou, "Hivcleave: A Web-Server for Predicting hiv Protease Cleavage Sites in Proteins, " Analytical Biochemistry, vol. 375, pp. 388-390, 2008.
30. K. C. Chou and H. B. Shen, "Review: Recent Advances in Developing Web-Servers for Predicting Protein Attributes, " Natural Science, vol. 2, pp. 63-92, 2009.
31. H. B. Shen, J. Yang, and K. C. Chou, "Euk-Ploc: An Ensemble Classifier for Large-Scale Eukaryotic Protein Subcellular Location Prediction, " Amino Acids, vol. 33, pp. 57-67, 2007. (Pubitemid 47101466)
32. H. B. Shen and K. C. Chou, "Hum-mploc: An Ensemble Classifier for Large-Scale Human Protein Subcellular Location Prediction by Incorporating Samples with Multiple Sites, " Biochemical Biophysiacl Research Comm., vol. 355, no. 4, pp. 1006-1011, 2007.
33. R. Caruana, "Multitask Learning: A Knowledge-Based Source of Inductive Bias, " Machine Learning, vol. 28, pp. 41-75, 1997.
34. B. Bakker and T. Heskes, "Task Clustering and Gating for Bayesian Multi-Task Learning, " J. Machine Learing Research, vol. 4, pp. 83-99, 2003.
35. T. Evgeniou, C. A. Micchelli, and M. Pontil, "Learning Multiple Tasks with Kernel Methods, " J. Machine Learing Research, vol. 6, pp. 615-637, 2005.
36. R. K. Ando and T. Zhang, "A Framework for Learning Predictive Structures from Multiple Tasks and Unlabeled Data, " J. Machine Learning Research, vol. 6, pp. 1817-1853, 2005.
37. J. Baxter, "A Model for Inductive Bias Learning, " J. Artifical Intelligence Research, vol. 12, pp. 149-198, 2000.
38. S. Ben-David and R. Schuller, "Exploiting Task Relatedness for Multiple Task Learning, " Proc. Ann. Conf. Computational Learning Theory, 2003.
39. L. Jacob and J.-P. Vert, "Efficient Peptide-mhc-I Binding Prediction for Alleles with Few Known Binders, " Bioinformatics, vol. 3, pp. 358-366, 2008. (Pubitemid 351189011)
40. E. A. Argyriou and M. Pontil, "Multitask Feature Learning, " Proc. Ann. Conf. Neural Information Processing System (NIPS), 2006.
41. G. M. Allenby and P. E. Rossi, "Marketing Models of Consumer Heterogeneity, " J. Econometircs, vol. 89, nos. 1/2, pp. 57-78, 1999. (Pubitemid 128416645)
42. N. Arora, G. M. Allenby, and J. L. Ginter, "A Hierarchical Bayes Model of Primary and Secondary Demand, " Marketing Science, vol. 17, no. 1, pp. 29-44, 1998.
43. N. D. Lawrence and J. C. Platt, "Learning to Learn with the Informative Vector Machine, " Proc. 21st Int'l Conf. Machine Learning, 2004.
44. E. Bonilla, K. M. Chai, and C. Williams, "Multi-Task Gaussian Process Prediction, " Proc. 20th Ann. Conf. Neural Information Processing Systems, 2008.
45. A. Schwaighofer, V. Tresp, and K. Yu, "Learning Gaussian Process Kernels via Hierarchical Bayes, " Proc. 20th Ann. Conf. Neural Information Processing Systems, 2005.
46. A. Argyriou, C. A. Micchelli, M. Pontil, and Y. Ying, "A Spectral Regularization Framework for Multi-Task Structure Learning, " Proc. 20th Ann. Conf. Neural Information Processing Systems, 2008.
47. T. Jebara, "Multi-Task Feature and Kernel Selection for Svms, " Proc. 21st Int'l Conf. Machine Learnings, 2004.
48. S. Bickel, J. Bogojeska, T. Lengauer, and T. Scheffer, "Multi-Task Learning for hiv Therapy Screening, " Proc. 25th Int'l Conf. Machine Learning, pp. 56-63, 2008.
49. J. Bi, T. Xiong, S. Yu, M. Dundra, and R. Rao, "An Improved Multi-Task Learning Approach with Applications in Medical Diagnosis, " Machine Learning and Knowledge Discovery in Databases, vol. 5211, pp. 117-132, 2008.
50. T. Evgeniou and M. Pontil, "Regularized Multi-Task Learning, " Proc. ACM SIGKDD, 2004.
51. V. N. Vapnik, Statistical Learning Theory. Wiley, 1998.
52. T. Guo, S. Hua, X. Ji, and Z. Sun, "Dbsubloc: Database of Protein Subcellular Localization, " Nucleic Acids Research, vol. 32, pp. 122-124, 2004.
53. J. Wang, W.-K. Sung, A. Krishnan, and K.-B. Li, "Protein Subcellular Localization Prediction for Gram-Negative Bacteria Using Amino Acid Subalphabets and a Combination of Multiple Support Vector Machines, " BMC Bioinformatics, vol. 6, p. 174, 2005.
54. K. C. Chou and C. T. Zhang, "Review: Prediction of Protein Structural Classes, " Critical Rev. Biochemistry and Molecular Biology, vol. 30, no. 4, pp. 275-349, 1995.
55. K. C. Chou and H. B. Shen, "Review: Recent Progresses in Protein Subcellular Location Prediction, " Analytical Biochemistry, vol. 370, no. 1, pp. 1-16, 2007.
56. X. B. Zhou, C. Chen, Z. C. Li, and X. Y. Zou, "Using Chou's Amphiphilic Pseudo-Amino Acid Composition and Support Vector Machine for Prediction of Enzyme Subfamily Classes, " J. Theoretical Biology, vol. 248, no. 3, pp. 546-551, 2007. (Pubitemid 47368372)
57. H. Lin, "The Modified Mahalanobis Discriminant for Predicting Outer Membrane Proteins by Using Chou's Pseudo Amino Acid Composition, " J. Theoretical Biology, vol. 252, no. 2, pp. 350-356, 2008.
58. G. Y. Zhang and B. S. Fang, "Predicting the Cofactors of Oxidoreductases Based on Amino Acid Composition Distribution and Chou's Amphiphilic Pseudo Amino Acid Composition, " J. Theoretical Biology, vol. 253, no. 2, pp. 310-315, 2008.
59. G. Y. Zhang, H. C. Li, and B. S. Fang, "Predicting Lipase Types by Improved Chou's Pseudo-Amino Acid Composition, " Protein and Peptide Letters, vol. 15, pp. 1132-1137, 2008.
60. X. Jiang, R. Wei, T. L. Zhang, and Q. Gu, "Using the Concept of Chou's Pseudo Amino Acid Composition to Predict Apoptosis Proteins Subcellular Location: An Approach by Approximate Entropy, " Protein and Peptide Letters, vol. 15, pp. 392-396, 2008. (Pubitemid 351679342)
61. F. M. Li and Q. Z. Li, "Predicting Protein Subcellular Location Using Chou's Pseudo Amino Acid Composition and Improved Hybrid Approach, " Protein and Peptide Letters, vol. 15, pp. 612-616, 2008.
62. H. Lin, H. Ding, F. B. Guo, A. Y. Zhang, and J. Huang, "Predicting Subcellular Localization of Mycobacterial Proteins by Using Chou's Pseudo Amino Acid Composition, " Protein and Peptide Letters, vol. 15, pp. 739-744, 2008.
63. T. Wang, J. Yang, H. B. Shen, and K. C. Chou, "Predicting Membrane Protein Types by the llda Algorithm, " Protein and Peptide Letters, vol. 15, pp. 915-921, 2008.
64. Y. S. Ding and T. L. Zhang, "Using Chou's Pseudo Amino Acid Composition to Predict Subcellular Localization of Apoptosis Proteins: An Approach with Immune Genetic Algorithm-Based Ensemble Classifier, " Pattern Recognition Letters, vol. 29, no. 13, pp. 1887-1892, 2008.
65. C. Chen, L. Chen, X. Zou, and P. Cai, "Prediction of Protein Secondary Structure Content by Using the Concept of Chou's Pseudo Amino Acid Composition and Support Vector Machine, " Protein and Peptide Letters, vol. 16, pp. 27-31, 2009.
66. H. B. Shen and K. C. Chou, "Quatident: A Web Server for Identifying Protein Quaternary Structural Attribute by Fusing Functional Domain and Sequential Evolution Information, " Biochemical Biophysical Research Comm., vol. 8, no. 3, pp. 1577-1584, 2009.
67. H. B. Shen and K. C. Chou, "Identification of Proteases and Their Types, " Analytical Biochemistry, vol. 385, no. 1, pp. 153-160, 2009.
68. Y. S. Ding, T. L. Zhang, Q. Gu, P. Y. Zhao, and K. C. Chou, "Using Maximum Entropy Model to Predict Protein Secondary Structure with Single Sequence, " Protein and Peptide Letters, vol. 16, pp. 552-560, 2009.
69. H. B. Shen and K. C. Chou, "Predicting Protein Fold Pattern with Functional Domain and Sequential Evolution Information, " J. Theoretical Biology, vol. 256, no. 3, pp. 441-446, 2009.
70. S. Hua and Z. Sun, "Support Vector Machine Approach for Protein Subcellular Localization Prediction, " Bioinformatics, vol. 7, pp. 721-728, 2001. (Pubitemid 32851380)