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2017 | OriginalPaper | Chapter

Classifying Non-linear Gene Expression Data Using a Novel Hybrid Rotation Forest Method

Authors : Huijuan Lu, Yaqiong Meng, Ke Yan, Yu Xue, Zhigang Gao

Published in: Intelligent Computing Methodologies

Publisher: Springer International Publishing

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Abstract

Rotation forest (RoF) is an ensemble classifier based on the combination of linear analysis theories and decision tree algorithms. In existing works, the RoF has demonstrated high classification accuracy and good performance with a reasonable number of base classifiers. However, the classification accuracy drops drastically for linearly inseparable datasets. This paper presents a hybrid algorithm integrating kernel principal component analysis and RoF algorithm (KPCA-RoF) to solve the classification problem in linearly inseparable cases. We choose the radial basis function (RBF) kernel for the PCA algorithm to establish the nonlinear mapping and segmentation for gene data. Moreover, we focus on the determination of suitable parameters in the kernel functions for better performance. Experimental results show that our algorithm solves linearly inseparable problem and improves the classification accuracy.

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Literature
1.
go back to reference Wang, W., Wang, Z., Bu, X., Li, R., Zhou, M., Hu, Z.: Discovering of tumor-targeting peptides using bi-functional microarray. Adv. Healthcare Mater. 4(18), 2802–2808 (2015)CrossRef Wang, W., Wang, Z., Bu, X., Li, R., Zhou, M., Hu, Z.: Discovering of tumor-targeting peptides using bi-functional microarray. Adv. Healthcare Mater. 4(18), 2802–2808 (2015)CrossRef
2.
go back to reference Stanbury, J.F., Baade, P.D., Yu, Y., Yu, X.Q.: Impact of geographic area level on measuring socioeconomic disparities in cancer survival in New South Wales, Australia: a period analysis. Cancer Epidemiol. 43, 56–62 (2016)CrossRef Stanbury, J.F., Baade, P.D., Yu, Y., Yu, X.Q.: Impact of geographic area level on measuring socioeconomic disparities in cancer survival in New South Wales, Australia: a period analysis. Cancer Epidemiol. 43, 56–62 (2016)CrossRef
3.
go back to reference Liszewski, K.: Exploiting Gene-Expression Data (2012) Liszewski, K.: Exploiting Gene-Expression Data (2012)
4.
go back to reference Liu, Y., Lu, H., Yan, K., Xia, H., An, C.: Applying cost-sensitive extreme learning machine and dissimilarity integration to gene expression data classification. Comput. Intell. Neurosci. 2017, 1–9 (2016)CrossRef Liu, Y., Lu, H., Yan, K., Xia, H., An, C.: Applying cost-sensitive extreme learning machine and dissimilarity integration to gene expression data classification. Comput. Intell. Neurosci. 2017, 1–9 (2016)CrossRef
5.
go back to reference Wang, Z., Zhang, J.: Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc. Natl. Acad. Sci. 108(16), E67–E76 (2011)CrossRef Wang, Z., Zhang, J.: Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc. Natl. Acad. Sci. 108(16), E67–E76 (2011)CrossRef
6.
go back to reference Pastinen, T., Sladek, R., Gurd, S., Ge, B., Lepage, P., Lavergne, K., Verner, A.: A survey of genetic and epigenetic variation affecting human gene expression. Physiol. Genomics 16(2), 184–193 (2004)CrossRef Pastinen, T., Sladek, R., Gurd, S., Ge, B., Lepage, P., Lavergne, K., Verner, A.: A survey of genetic and epigenetic variation affecting human gene expression. Physiol. Genomics 16(2), 184–193 (2004)CrossRef
7.
go back to reference Lu, H.J., An, C.L., Zheng, E.H., Lu, Y.: Dissimilarity based ensemble of extreme learning machine for gene expression data classification. Neurocomputing 128, 22–30 (2014)CrossRef Lu, H.J., An, C.L., Zheng, E.H., Lu, Y.: Dissimilarity based ensemble of extreme learning machine for gene expression data classification. Neurocomputing 128, 22–30 (2014)CrossRef
8.
go back to reference Langdon, W.B., Buxton, B.F.: Genetic programming for mining DNA chip data from cancer patients. Genetic Programm. Evolvable Mach. 5(3), 251–257 (2004)CrossRef Langdon, W.B., Buxton, B.F.: Genetic programming for mining DNA chip data from cancer patients. Genetic Programm. Evolvable Mach. 5(3), 251–257 (2004)CrossRef
9.
go back to reference Furey, T.S., Cristianini, N., Duffy, N., Bednarski, D.W., Schummer, M., Haussler, D.: Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 16(10), 906–914 (2000)CrossRef Furey, T.S., Cristianini, N., Duffy, N., Bednarski, D.W., Schummer, M., Haussler, D.: Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 16(10), 906–914 (2000)CrossRef
10.
go back to reference Rodriguez, J.J., Kuncheva, L.I., Alonso, C.J.: Rotation forest: a new classifier ensemble method. IEEE Trans. Pattern Anal. Mach. Intell. 28(10), 1619–1630 (2006)CrossRef Rodriguez, J.J., Kuncheva, L.I., Alonso, C.J.: Rotation forest: a new classifier ensemble method. IEEE Trans. Pattern Anal. Mach. Intell. 28(10), 1619–1630 (2006)CrossRef
11.
go back to reference Su Chong, J., Shenggen, L.Y., et al.: Improving random forest and rotation forest for highly imbalanced datasets. Intell. Data Anal. 19(6), 1409–1432 (2015)CrossRef Su Chong, J., Shenggen, L.Y., et al.: Improving random forest and rotation forest for highly imbalanced datasets. Intell. Data Anal. 19(6), 1409–1432 (2015)CrossRef
12.
go back to reference Suykens, J.A., Vandewalle, J.: Least squares support vector machine classifiers. Neural Process. Lett. 9(3), 293–300 (1999)CrossRefMATH Suykens, J.A., Vandewalle, J.: Least squares support vector machine classifiers. Neural Process. Lett. 9(3), 293–300 (1999)CrossRefMATH
13.
go back to reference Gu, B., Sheng, V.S., Tay, K.Y., Romano, W., Li, S.: Incremental support vector learning for ordinal regression. IEEE Trans. Neural Netw. Learn. Syst. 26(7), 1403–1416 (2015)MathSciNetCrossRef Gu, B., Sheng, V.S., Tay, K.Y., Romano, W., Li, S.: Incremental support vector learning for ordinal regression. IEEE Trans. Neural Netw. Learn. Syst. 26(7), 1403–1416 (2015)MathSciNetCrossRef
14.
go back to reference Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. In: Advances in Neural Information Processing Systems, pp. 1097–1105 (2012) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. In: Advances in Neural Information Processing Systems, pp. 1097–1105 (2012)
15.
go back to reference Mika, S., Schölkopf, B., Smola, A.J., Müller, K.R., Scholz, M., Rätsch, G.: Kernel PCA and de-noising in feature spaces. In: NIPS, vol. 11, pp. 536–542, December 1998 Mika, S., Schölkopf, B., Smola, A.J., Müller, K.R., Scholz, M., Rätsch, G.: Kernel PCA and de-noising in feature spaces. In: NIPS, vol. 11, pp. 536–542, December 1998
16.
go back to reference Schölkopf, B., Smola, A., Müller, K.-R.: Kernel principal component analysis. In: Gerstner, W., Germond, A., Hasler, M., Nicoud, J.-D. (eds.) ICANN 1997. LNCS, vol. 1327, pp. 583–588. Springer, Heidelberg (1997). doi:10.1007/BFb0020217 Schölkopf, B., Smola, A., Müller, K.-R.: Kernel principal component analysis. In: Gerstner, W., Germond, A., Hasler, M., Nicoud, J.-D. (eds.) ICANN 1997. LNCS, vol. 1327, pp. 583–588. Springer, Heidelberg (1997). doi:10.​1007/​BFb0020217
17.
18.
go back to reference Olshen, L.B.J.F.R., Stone, C.J.: Classification and regression trees. Wadsworth Int. Group 93(99), 101 (1984)MATH Olshen, L.B.J.F.R., Stone, C.J.: Classification and regression trees. Wadsworth Int. Group 93(99), 101 (1984)MATH
19.
go back to reference Quinlan, J.R.: C4. 5: Programs for Machine Learning. Elsevier, Amsterdam (2014) Quinlan, J.R.: C4. 5: Programs for Machine Learning. Elsevier, Amsterdam (2014)
21.
go back to reference Rodriguez, J.J., Kuncheva, L.I., Alonso, C.J.: Rotation forest: a new classifier ensemble method. IEEE Trans. Pattern Anal. Mach. Intell. 28(10), 1619–1630 (2006)CrossRef Rodriguez, J.J., Kuncheva, L.I., Alonso, C.J.: Rotation forest: a new classifier ensemble method. IEEE Trans. Pattern Anal. Mach. Intell. 28(10), 1619–1630 (2006)CrossRef
22.
go back to reference Kuncheva, L.I., Rodríguez, J.J.: An experimental study on rotation forest ensembles. In: Haindl, M., Kittler, J., Roli, F. (eds.) MCS 2007, vol. 4472, pp. 459–468. Springer, Heidelberg (2007). doi:10.1007/978-3-540-72523-7_46 Kuncheva, L.I., Rodríguez, J.J.: An experimental study on rotation forest ensembles. In: Haindl, M., Kittler, J., Roli, F. (eds.) MCS 2007, vol. 4472, pp. 459–468. Springer, Heidelberg (2007). doi:10.​1007/​978-3-540-72523-7_​46
23.
go back to reference Zhang, C.X., Zhang, J.S.: RotBoost: a technique for combining rotation forest and AdaBoost. Pattern Recogn. Lett. 29(10), 1524–1536 (2008)CrossRef Zhang, C.X., Zhang, J.S.: RotBoost: a technique for combining rotation forest and AdaBoost. Pattern Recogn. Lett. 29(10), 1524–1536 (2008)CrossRef
24.
go back to reference Mousavi, R., Eftekhari, M., Haghighi, M.G.: A new approach to human microRNA target prediction using ensemble pruning and rotation forest. J. Bioinform. Comput. Biol. 13(06), 1550017 (2015)CrossRef Mousavi, R., Eftekhari, M., Haghighi, M.G.: A new approach to human microRNA target prediction using ensemble pruning and rotation forest. J. Bioinform. Comput. Biol. 13(06), 1550017 (2015)CrossRef
25.
go back to reference Wong, L., You, Z.H., Ming, Z., Li, J., Chen, X., Huang, Y.A.: Detection of interactions between proteins through rotation forest and local phase quantization descriptors. Int. J. Mol. Sci. 17(1), 21 (2015)CrossRef Wong, L., You, Z.H., Ming, Z., Li, J., Chen, X., Huang, Y.A.: Detection of interactions between proteins through rotation forest and local phase quantization descriptors. Int. J. Mol. Sci. 17(1), 21 (2015)CrossRef
26.
go back to reference Ayerdi, B., Romay, M.G.: Hyperspectral image analysis by spectral-spatial processing and anticipative hybrid extreme rotation forest classification. IEEE Trans. Geosci. Remote Sens. 54(5), 2627–2639 (2016)CrossRef Ayerdi, B., Romay, M.G.: Hyperspectral image analysis by spectral-spatial processing and anticipative hybrid extreme rotation forest classification. IEEE Trans. Geosci. Remote Sens. 54(5), 2627–2639 (2016)CrossRef
27.
go back to reference Kuang, F., Xu, W., Zhang, S.: A novel hybrid KPCA and SVM with GA model for intrusion detection. Appl. Soft Comput. 18, 178–184 (2014)CrossRef Kuang, F., Xu, W., Zhang, S.: A novel hybrid KPCA and SVM with GA model for intrusion detection. Appl. Soft Comput. 18, 178–184 (2014)CrossRef
28.
go back to reference Mengqi, N., Jingjing, D., Tianzhen, W., Diju, G., Jingang, H., Benbouzid, M.E.H.: A hybrid kernel PCA, hypersphere SVM and extreme learning machine approach for nonlinear process online fault detection. In: IECON 2015-41st Annual Conference of the IEEE Industrial Electronics Society, pp. 002106–002111. IEEE, November 2015 Mengqi, N., Jingjing, D., Tianzhen, W., Diju, G., Jingang, H., Benbouzid, M.E.H.: A hybrid kernel PCA, hypersphere SVM and extreme learning machine approach for nonlinear process online fault detection. In: IECON 2015-41st Annual Conference of the IEEE Industrial Electronics Society, pp. 002106–002111. IEEE, November 2015
29.
go back to reference Luo, K., Li, S., Ren Deng, W.Z., Cai, H.: Multivariate statistical kernel PCA for nonlinear process fault diagnosis in military barracks. Int. J. Hybrid Inf. Technol. 9(1), 195–206 (2016)CrossRef Luo, K., Li, S., Ren Deng, W.Z., Cai, H.: Multivariate statistical kernel PCA for nonlinear process fault diagnosis in military barracks. Int. J. Hybrid Inf. Technol. 9(1), 195–206 (2016)CrossRef
30.
go back to reference Boujnouni, M.E., Jedra, M., Zahid, N.: Support vector domain description with a new confidence coefficient. In: 2014 9th International Conference on Intelligent Systems: Theories and Applications (SITA-2014), pp. 1–8. IEEE, May 2014 Boujnouni, M.E., Jedra, M., Zahid, N.: Support vector domain description with a new confidence coefficient. In: 2014 9th International Conference on Intelligent Systems: Theories and Applications (SITA-2014), pp. 1–8. IEEE, May 2014
31.
go back to reference Amari, S.I., Wu, S.: Improving support vector machine classifiers by modifying kernel functions. Neural Netw. 12(6), 783–789 (1999)CrossRef Amari, S.I., Wu, S.: Improving support vector machine classifiers by modifying kernel functions. Neural Netw. 12(6), 783–789 (1999)CrossRef
32.
go back to reference Devijver, P.A., Kittler, J.: Pattern Recognition: A Statistical Approach. Prentice Hall, Upper Saddle River (1982)MATH Devijver, P.A., Kittler, J.: Pattern Recognition: A Statistical Approach. Prentice Hall, Upper Saddle River (1982)MATH
33.
go back to reference Brereton, R.G.: The F distribution and its relationship to the chi squared and t distributions. J. Chemom. 29(11), 582–586 (2015)CrossRef Brereton, R.G.: The F distribution and its relationship to the chi squared and t distributions. J. Chemom. 29(11), 582–586 (2015)CrossRef
Metadata
Title
Classifying Non-linear Gene Expression Data Using a Novel Hybrid Rotation Forest Method
Authors
Huijuan Lu
Yaqiong Meng
Ke Yan
Yu Xue
Zhigang Gao
Copyright Year
2017
DOI
https://doi.org/10.1007/978-3-319-63315-2_64

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