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MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ

Yıl 2012, Cilt: 27 Sayı: 3, 0 - , 19.02.2013

Öz

Ciddi rahatsızlıklardan biri olan meme kanserinin erken teşhis edilmesi hastalığın tedavisinde önemli rol oynar. Bu çalışmada meme kanseri hastalığında etkin rol oynayan genlerin belirlenmesi için veri füzyonu ve genetik algoritma tabanlı yeni bir nitelik seçme metodu önerilmektedir. Yapılan çalışma iki aşamadan oluşmaktadır: İlk aşamada filtreleme yöntemi ile gen ifade verisi indirgenmiş, ikinci aşamada genetik algoritma ile meme kanserinde etkin rol alan genlerin tespiti gerçekleştirilmiştir. Destek vektör makinesi, genetik algoritma için uygunluk fonksiyonu olarak kullanılmıştır. Yapılan çalışmada belirlenen 10 gen ile sınıflandırma doğruluk oranı %94,65 elde edilmiştir.

Kaynakça

  • Segal, E.,Wang, H. ve Koller, D., “Discovering Molecular Pathways From Protein Interaction And Gene Expression Data”, Bioinformatics, Cilt 19, 264-272, 2003.
  • Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O.P., Wilfond, B., Borg, A., Trent, J., “Gene-Expression Profiles in Hereditary Breast Cancer”, The New England Journal of Medicine, Cilt 344, 539-548, 2001.
  • van de Vijver, M.J, He, Y.D., van't Veer, L.J., Dai, H., Hart, A.A., Voskuil, D.W., Schreiber, G.J., Peterse, J.L., Roberts, C., Marton, M.J., Parrish, M., Atsma, D., Witteveen, A., Glas, A., Delahaye, L., van der Velde, T., Bartelink, H., Rodenhuis, S., Rutgers, E.T., Friend, S.H., Bernards, R., “A Gene-Expression Signature As A Predictor Of Survival In Breast Cancer”, The
  • New England Journal of Medicine, Cilt 347, 1999-2009, 2002.
  • Peng, Y., Wu, Z., Jiang, J., “A Novel Feature Selection Approach For Biomedical Data Classification”, Journal of Biomedical Informatics, Cilt 43, 15-23, 2010.
  • Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D. ve Levine, A. J., “Broad Patterns Of Gene Expression Revealed By Clustering Analysis Of Tumor And Normal Colon Tissues Probed By Oligonucleotide Arrays”, Cell Biology, Cilt 96, 6745-6750, 1999.
  • Dudoit, S., Fridlyand, J ve Speed, T., P., “Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data”, American Statistical Association, Cilt 97, 77-87, 2002.
  • Horng, J.T., Wub, L.C., Liu, B.J., Kuo, J.L., Kuo, W.H., Zhang, J.J., "An Expert System To Classify Microarray Gene Expression Data Using Gene Selection By Decision Tree", Expert Systems with Applications, Cilt 36, 9072-9081, 2009.
  • Wang, Y., Tetko, I.V., Hall, M.A., Frank, E., Facius, A., Mayer, K., Mewes, H., “Gene Selection From Microarray Data For Cancer Classification-A Machine Learning Approach”, Computational Biology and Chemistry, Cilt 29, 37-46, 2005.
  • Uriarte, R., D. ve Andrés, S.,A., “Gene Selection And Classification Of Microarray Data Using Random Forest”, BMC Bioinformatics, Cilt 7, 1-13, 2006.
  • Li, L., Jiang, W., Li, X., Moser, K.L., Guo, Z., Du, L., Wang, Q., Topol, E., Wang, Q., Rao, S., “A Robust Hybrid Between Genetic Algorithm And Support Vector Machine For Extracting An Optimal Feature Gene Subset”, Genomics, Cilt 85, 16-23, 2005.
  • Antonov, A.V., Tetko, I.V., Kosykh, D., Surmeli, D., Mewes, H.W., “Exploiting Scale-Free Information From Expression Data For Cancer Classification”, Computational Biology and Chemistry, Cilt 29, 288–293, 2005.
  • Saeys, Y., Inza, I. ve Larranaga, P., “A Review Of Feature Selection Techniques In Bioinformatics”, Bioınformatics, Cilt 23, 2507–2517, 2007.
  • Maldonado, S., Weber, R., “A Wrapper Method For Feature Selection Using Support Vector Machines”, Information Sciences, Cilt 179, 2208–2217, 2009.
  • Huang, C., L. Ve Wang, C., J., “A GA-Based Feature Selection And Parameters Optimization For Support Vector Machines”, Expert Systems with Applications, Cilt 31, 231–240, 2006.
  • Liu, H. ve Motoda, H., “Computational Methods Of Feature Selection”, Chapman & Hall/CRC, Taylor & Francis Group 6000 Broken Sound Parkway NW, 26-27, 2008.
  • Inza, I., Larranaga, P., Blanco, R., Cerrolaza, A.J., “Filter Versus Wrapper Gene Selection Approaches In DNA Microarray Domains”, Artificial Intelligence in Medicine, Cilt 31, 91-103, 2004.
  • Goldberg, E.D., “Genetic Algorithms in Search, Optimization, and Machine Learning”, Addison-Wesley Longman, Inc., New York, 1989.
  • Michalewicz, Z., “Genetic Algorithms + Data Structures = Evolution Programs”, Springer, Berlin, 1992.
  • Şen, Z., ”Genetik Algoritma Ve En İyileme Yöntemleri”, Su Vakfı Yayınları, 2004
  • Lee, C., P., Lin, W., S., Chen, Y., M. ve Kuo B., J., ”Gene Selection And Sample Classification On Microarray Data Based On Adaptive Genetic Algorithm/K-Nearest Neighbor Method”, Expert Systems with Applications, Cilt 38, 4661–4667, 2011.
  • Li, L., Weinberg, C., R., Darden, T.A. ve Pedersen, L.G., “Gene Selection For Sample Classification Based On Gene Expression Data: Study Of Sensitivity To Choice Of Parameters Of The GA/KNN Method”, Bioinformatics, Cilt. 17, 1131–1142, 2001.
  • Hernandez, J.,C., Duval, D., ve Hao, J., K., “A Genetic Embedded Approach for Gene Selection and Classification of Microarray Data”, EvoBIO'07 Proceedings of the 5th European
  • conference on Evolutionary computation, machine learning and data mining in bioinformatics, Springer-Verlag Berlin, Heidelberg 2007.
  • Lee, C., P. ve Leu, Y., “A Novel Hybrid Feature Selection Method For Microarray Data Analysis”, Applied Soft Computing, Cilt 11, 208–213, 2011.
  • Özkan, Y., “Veri Madenciliği Yöntemleri”, Papatya Yayıncılık, İstanbul, 2008.
  • Cristianini, N. ve Taylor, J.S., “An Introduction to Support Vector Machines: And Other Kernel-based Learning Methods”, Cambridge Univ. Press, 2000.
  • Lasko, T.,A., Bhagwat, J., G., Zou, K., H. ve Ohno-Machado, L., “The Use Of Receiver Operating Characteristic Curves In Biomedical Informatics”, Journal of Biomedical Informatics, Cilt 38, 404–415, 2005.
  • http://bioinformatics.nki.nl/data.php
  • Veer,L.J,V.,Dai,H., Vijver, M.J.V., He, Y.D., Hart, A. A. M., Mao, M., Peterse, H.L., Kooy, K.V.D., Marton, M.J., Witteveen, A.T., Schreiber, G.J., Kerkhoven, R.M., Roberts, C., Linsley, P.S., Bernards, R., Friend, S.H., “Gene Expression Profiling Predicts Clinical Outcome Of Breast Cancer”, Nature, Cilt 415, 530-536, 2002.
Yıl 2012, Cilt: 27 Sayı: 3, 0 - , 19.02.2013

Öz

Kaynakça

  • Segal, E.,Wang, H. ve Koller, D., “Discovering Molecular Pathways From Protein Interaction And Gene Expression Data”, Bioinformatics, Cilt 19, 264-272, 2003.
  • Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O.P., Wilfond, B., Borg, A., Trent, J., “Gene-Expression Profiles in Hereditary Breast Cancer”, The New England Journal of Medicine, Cilt 344, 539-548, 2001.
  • van de Vijver, M.J, He, Y.D., van't Veer, L.J., Dai, H., Hart, A.A., Voskuil, D.W., Schreiber, G.J., Peterse, J.L., Roberts, C., Marton, M.J., Parrish, M., Atsma, D., Witteveen, A., Glas, A., Delahaye, L., van der Velde, T., Bartelink, H., Rodenhuis, S., Rutgers, E.T., Friend, S.H., Bernards, R., “A Gene-Expression Signature As A Predictor Of Survival In Breast Cancer”, The
  • New England Journal of Medicine, Cilt 347, 1999-2009, 2002.
  • Peng, Y., Wu, Z., Jiang, J., “A Novel Feature Selection Approach For Biomedical Data Classification”, Journal of Biomedical Informatics, Cilt 43, 15-23, 2010.
  • Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D. ve Levine, A. J., “Broad Patterns Of Gene Expression Revealed By Clustering Analysis Of Tumor And Normal Colon Tissues Probed By Oligonucleotide Arrays”, Cell Biology, Cilt 96, 6745-6750, 1999.
  • Dudoit, S., Fridlyand, J ve Speed, T., P., “Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data”, American Statistical Association, Cilt 97, 77-87, 2002.
  • Horng, J.T., Wub, L.C., Liu, B.J., Kuo, J.L., Kuo, W.H., Zhang, J.J., "An Expert System To Classify Microarray Gene Expression Data Using Gene Selection By Decision Tree", Expert Systems with Applications, Cilt 36, 9072-9081, 2009.
  • Wang, Y., Tetko, I.V., Hall, M.A., Frank, E., Facius, A., Mayer, K., Mewes, H., “Gene Selection From Microarray Data For Cancer Classification-A Machine Learning Approach”, Computational Biology and Chemistry, Cilt 29, 37-46, 2005.
  • Uriarte, R., D. ve Andrés, S.,A., “Gene Selection And Classification Of Microarray Data Using Random Forest”, BMC Bioinformatics, Cilt 7, 1-13, 2006.
  • Li, L., Jiang, W., Li, X., Moser, K.L., Guo, Z., Du, L., Wang, Q., Topol, E., Wang, Q., Rao, S., “A Robust Hybrid Between Genetic Algorithm And Support Vector Machine For Extracting An Optimal Feature Gene Subset”, Genomics, Cilt 85, 16-23, 2005.
  • Antonov, A.V., Tetko, I.V., Kosykh, D., Surmeli, D., Mewes, H.W., “Exploiting Scale-Free Information From Expression Data For Cancer Classification”, Computational Biology and Chemistry, Cilt 29, 288–293, 2005.
  • Saeys, Y., Inza, I. ve Larranaga, P., “A Review Of Feature Selection Techniques In Bioinformatics”, Bioınformatics, Cilt 23, 2507–2517, 2007.
  • Maldonado, S., Weber, R., “A Wrapper Method For Feature Selection Using Support Vector Machines”, Information Sciences, Cilt 179, 2208–2217, 2009.
  • Huang, C., L. Ve Wang, C., J., “A GA-Based Feature Selection And Parameters Optimization For Support Vector Machines”, Expert Systems with Applications, Cilt 31, 231–240, 2006.
  • Liu, H. ve Motoda, H., “Computational Methods Of Feature Selection”, Chapman & Hall/CRC, Taylor & Francis Group 6000 Broken Sound Parkway NW, 26-27, 2008.
  • Inza, I., Larranaga, P., Blanco, R., Cerrolaza, A.J., “Filter Versus Wrapper Gene Selection Approaches In DNA Microarray Domains”, Artificial Intelligence in Medicine, Cilt 31, 91-103, 2004.
  • Goldberg, E.D., “Genetic Algorithms in Search, Optimization, and Machine Learning”, Addison-Wesley Longman, Inc., New York, 1989.
  • Michalewicz, Z., “Genetic Algorithms + Data Structures = Evolution Programs”, Springer, Berlin, 1992.
  • Şen, Z., ”Genetik Algoritma Ve En İyileme Yöntemleri”, Su Vakfı Yayınları, 2004
  • Lee, C., P., Lin, W., S., Chen, Y., M. ve Kuo B., J., ”Gene Selection And Sample Classification On Microarray Data Based On Adaptive Genetic Algorithm/K-Nearest Neighbor Method”, Expert Systems with Applications, Cilt 38, 4661–4667, 2011.
  • Li, L., Weinberg, C., R., Darden, T.A. ve Pedersen, L.G., “Gene Selection For Sample Classification Based On Gene Expression Data: Study Of Sensitivity To Choice Of Parameters Of The GA/KNN Method”, Bioinformatics, Cilt. 17, 1131–1142, 2001.
  • Hernandez, J.,C., Duval, D., ve Hao, J., K., “A Genetic Embedded Approach for Gene Selection and Classification of Microarray Data”, EvoBIO'07 Proceedings of the 5th European
  • conference on Evolutionary computation, machine learning and data mining in bioinformatics, Springer-Verlag Berlin, Heidelberg 2007.
  • Lee, C., P. ve Leu, Y., “A Novel Hybrid Feature Selection Method For Microarray Data Analysis”, Applied Soft Computing, Cilt 11, 208–213, 2011.
  • Özkan, Y., “Veri Madenciliği Yöntemleri”, Papatya Yayıncılık, İstanbul, 2008.
  • Cristianini, N. ve Taylor, J.S., “An Introduction to Support Vector Machines: And Other Kernel-based Learning Methods”, Cambridge Univ. Press, 2000.
  • Lasko, T.,A., Bhagwat, J., G., Zou, K., H. ve Ohno-Machado, L., “The Use Of Receiver Operating Characteristic Curves In Biomedical Informatics”, Journal of Biomedical Informatics, Cilt 38, 404–415, 2005.
  • http://bioinformatics.nki.nl/data.php
  • Veer,L.J,V.,Dai,H., Vijver, M.J.V., He, Y.D., Hart, A. A. M., Mao, M., Peterse, H.L., Kooy, K.V.D., Marton, M.J., Witteveen, A.T., Schreiber, G.J., Kerkhoven, R.M., Roberts, C., Linsley, P.S., Bernards, R., Friend, S.H., “Gene Expression Profiling Predicts Clinical Outcome Of Breast Cancer”, Nature, Cilt 415, 530-536, 2002.
Toplam 30 adet kaynakça vardır.

Ayrıntılar

Birincil Dil Türkçe
Bölüm Makaleler
Yazarlar

Oktay Yıldız Bu kişi benim

Mesut Tez Bu kişi benim

H. Şakir Bilge Bu kişi benim

M. Ali Akcayol Bu kişi benim

İnan Güler Bu kişi benim

Yayımlanma Tarihi 19 Şubat 2013
Gönderilme Tarihi 19 Şubat 2013
Yayımlandığı Sayı Yıl 2012 Cilt: 27 Sayı: 3

Kaynak Göster

APA Yıldız, O., Tez, M., Bilge, H. Ş., Akcayol, M. A., vd. (2013). MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ. Gazi Üniversitesi Mühendislik Mimarlık Fakültesi Dergisi, 27(3).
AMA Yıldız O, Tez M, Bilge HŞ, Akcayol MA, Güler İ. MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ. GUMMFD. Mart 2013;27(3).
Chicago Yıldız, Oktay, Mesut Tez, H. Şakir Bilge, M. Ali Akcayol, ve İnan Güler. “MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ”. Gazi Üniversitesi Mühendislik Mimarlık Fakültesi Dergisi 27, sy. 3 (Mart 2013).
EndNote Yıldız O, Tez M, Bilge HŞ, Akcayol MA, Güler İ (01 Mart 2013) MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ. Gazi Üniversitesi Mühendislik Mimarlık Fakültesi Dergisi 27 3
IEEE O. Yıldız, M. Tez, H. Ş. Bilge, M. A. Akcayol, ve İ. Güler, “MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ”, GUMMFD, c. 27, sy. 3, 2013.
ISNAD Yıldız, Oktay vd. “MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ”. Gazi Üniversitesi Mühendislik Mimarlık Fakültesi Dergisi 27/3 (Mart 2013).
JAMA Yıldız O, Tez M, Bilge HŞ, Akcayol MA, Güler İ. MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ. GUMMFD. 2013;27.
MLA Yıldız, Oktay vd. “MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ”. Gazi Üniversitesi Mühendislik Mimarlık Fakültesi Dergisi, c. 27, sy. 3, 2013.
Vancouver Yıldız O, Tez M, Bilge HŞ, Akcayol MA, Güler İ. MEME KANSERİ SINIFLANDIRMASI İÇİN VERİ FÜZYONU VE GENETİK ALGORİTMA TABANLI GEN SEÇİMİ. GUMMFD. 2013;27(3).