制度:新 ; 報告番号:甲3199号 ; 学位の種類:博士(工学) ; 授与年月日:2011/3/15 ; 早大学位記番号:新549

Chen Benhui

English

制度:新 ; 報告番号:甲3199号 ; 学位の種類:博士(工学) ; 授与年月日:2011/3/15 ; 早大学位記番号:新5495textthesi

Chen, Benhui

32138

Waseda University Repository

 早稲田大学 博士（工学） 学位申請 研究業績書   Ｎｏ．  氏  名  CHEN Benhui  印 （ 2010  年 10 月 26 現在）  論文欄には、著者(連名含む)、論文タイトル、雑誌名（国際学術会議名、国内学術会議名）、巻、号、ページ及びページ数、発行年を記載すること。また、当該論文のコピーを添付すること。採録決定したが未発行の論文については、論文原稿のコピーと採録決定通知書のコピーを提出すること。特許公告の１頁目を添付すること。Write authors including co-authors, title of the paper, name of the journal or conference, volume, number, pages and year.  Attach the preprint of your paper (the copy is acceptable).  When unpublished, although accepted, attach the notice of its acceptance letter to your paper.  For patent, attach 1st page of the announcement.  種 類 別 著 者 、 題 目 、 掲 載 誌 名 、 巻 号 、 頁 、 発 表 年 （ 月 ） 等   学 術 誌 原著 論 文                      査 読 の ある 国 際 会議・シ ン ポジ ウ ム 論文      ○ 1. B e n h u i  Chen and Jinglu Hu, “An Adaptive Niching EDA with Balance Searching Based on Clustering Analysis”, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol.E93-A, No.10, pp.1792-1799, Oct. 2010.  ○ 2. B en h u i  Chen, Weifeng Gu and Jinglu Hu, “An Improved Multi-label Classification Method and Its Application to Functional Genomics”, International Journal of Computational Biology and Drug Design, Vol.3 No.2, pp.133-145, Sep. 2010.  ○ 3. Benhui Chen, Jinglu Hu. “A Hybrid EDA for Protein Folding Based on HP Model”, IEEJ Transactions on Electrical and Electronics Engineering (TEEE), Vol.5 No.4, pp.459-466, July 2010.  ○ 4. Benhui Chen, Liangpeng Ma and Jinglu Hu. “An Improved Multi-label Classification Method Based on SVM with Delicate Decision Boundary”, International Journal of Innovative Computing, Information and Control (IJICIC). Vol.6 No.4, pp.1605-1614, April 2010.  5. Benhui Chen, Jinglu Hu, Lihua Duan and Yinglong Gu. “Network Administrator Assistance System Based on Fuzzy C-means Analysis”, Journal of Advanced Computational Intelligence and Intelligent Informatics (JACIII), Vol.13 No.2, pp. 91-96, Mar. 2009.  ○ 6.Benhui Chen, Feiran Sun and Jinglu Hu, “Local Linear Multi-SVM Method for Gene Function Classification”, in Proc. of World Congress on Nature and Biologically Inspired Computing (NaBIC 2010), Kitakyushu, Japan, Dec. 2010 (to appear).  ○ 7. Benhui Chen and Jinglu Hu, “Hierarchical Multi-label Classification Incorporating Prior Information for Gene Function Prediction”, in Proc. of the 10th International Conference on Intelligent Systems Design and Applications (ISDA) (ISDA'10), Cairo, Egypt, Nov. 2010 (to appear).  ○  8. Benhui Chen and Jinglu Hu, “An Adaptive Niching EDA Based on Clustering Analysis”, in Proc. of IEEE World Congress on Computational Intelligence 2010 (WCCI 2010) -- Congress on Evolutionary Computation (CEC 2010) , pp. 858-864, Barcelona, Spain, July 2010.  ○ 9. Benhui Chen, Weifeng Gu and Jinglu Hu, “An Improved Multi-label Classification Based on Label Ranking and Delicate Boundary SVM”, in Proc. of IEEE World Congress on Computational Intelligence 2010 (WCCI 2010) -- International Joint Conference on Neural Networks (IJCNN 2010) , pp. 786-791, Barcelona, Spain, July 2010.  早稲田大学 博士（工学） 学位申請 研究業績書   Ｎｏ．  氏  名  CHEN Benhui  印 （ 2010  年 10 月 26 現在）  論文欄には、著者(連名含む)、論文タイトル、雑誌名（国際学術会議名、国内学術会議名）、巻、号、ページ及びページ数、発行年を記載すること。また、当該論文のコピーを添付すること。採録決定したが未発行の論文については、論文原稿のコピーと採録決定通知書のコピーを提出すること。特許公告の１頁目を添付すること。Write authors including co-authors, title of the paper, name of the journal or conference, volume, number, pages and year.  Attach the preprint of your paper (the copy is acceptable).  When unpublished, although accepted, attach the notice of its acceptance letter to your paper.  For patent, attach 1st page of the announcement.   ○ 10. Benhui Chen and Jinglu Hu, “A Novel Clustering Based Niching EDA for Protein Folding”, in Proc. of World Congress on Nature and Biologically Inspired Computing (NaBIC 2009), pp. 748-753, Coimbatore, India, Dec. 2009.  ○ 11. Benhui Chen, Long Li and Jinglu Hu, “An Improved Backtracking Method for EDAs Based Protein Folding”, in Proc. of ICROS-SICE International Joint Conference 2009, pp.4669-4674, Fukuoka, Japan, Aug. 2009.  ○ 12. Benhui Chen, Long Li and Jinglu Hu, “A Novel EDAs Based Method for HP Model Protein Folding”, in Proc. of 2009 IEEE Congress on Evolutionary Computation (CEC 2009), pp. 309-315, Trondheim, Norway, May 2009.  ○ 13. Benhui Chen, Liangpeng Ma and Jinglu Hu, “A New SVM Based Method for Solving Multi-label Classification Problem”, in Proc. of the 3rd International Symposium on Computational Intelligence and Industrial Applications (ISCIIA 2008), pp. 325-334, Dali, China, Nov. 2008.  14. Weifeng Gu, Bebhui Chen and Jinglu Hu, “Combining Binary-SVM and Pairwise Label Constraints for Multi-label Classification”, in Proc of 2010 IEEE International Conference on Systems, Man and Cybernetics (SMC'10) (Istanbul), Oct. 2010 (to appear).  15. Jinglu Hu and Benhui Chen, “A New Method for Identifying Nonlinear Polynomial Model Using Genetic Algorithm, in Proc. of the 3rd International Symposium on Computational Intelligence and Industrial Applications (ISCIIA 2008), pp. 75-84, Dali, China, Nov. 2008. (Best Paper Award)  

Study on the predictions of gene function and protein structure using multi-SVM and hybrid EDA

DSpace at Waseda University

   早稲田大学大学院情報生産システム研究科     博 士 論 文 概 要         論  文  題  目   Study on the Predictions of Gene Function and Protein Structure Using Multi-SVM and Hybrid EDA        申  請  者   CHEN, Benhui   情報生産システム工学専攻 ニューロコンピューティング研究      2010 年 11 月 2 H o w  t o  e f f i c i en t l y  e x t r a c t  t h e  u s e f u l  i n f o r m a t i o n  f r o m  h i g h  t h r o u g h p u t  b i o l o g i c a l  d a t a  i s  o n e  o f  t h e  m a i n  c h a l l en g e s  i n  b i o i n f o r m a t i c s .  M a c h i n e  l e a r n i n g  t e c h n i q u e s  s u ch  a s  S u p p o r t  V e c t o r  M a c h i n e s  ( S V M s ) ,  N e u r a l  N e t w o r k s  ( N N s )  a n d  E s t i ma t i o n  o f  D i s t r i b u t i o n  A l g o r i t h ms  ( E D A s )  h a v e  b e en  e f f e c t i v e  i n  a n a l y z i n g  b i o l o g i c a l  d a t a  b e c a u s e  o f  t h e i r  c a p ab i l i t i e s  i n  h a n d l i n g  u nc e r t a i n  d a t a  n o i s e  a n d  i n  g en e r a l i z a t i o n .  G e n e  f u n c t i o n  p r ed i c t i o n  an d  p r o t e i n  s t r u c t u r e  p r e d i c t i o n  a r e  t wo  i mp o r t a n t  d o m a i n s  w h e r e  m a c h i n e  l e a r n i n g  t e c h n i q u e s  a r e  a p p l i e d  i n  b i o i n f o r m a t i c s .  F r o m t h e  v i e w  o f  m a c h i n e  l e a r n i n g ,  t h e  g e n e  f u n c t i o n  p r e d i c t i o n s  c a n  b e  s e e n  a s  mu l t i - l a b e l  c l a s s i f i c a t i o n  o r  h i e r a r c h i c a l  mu l t i - l ab e l  c l a s s i f i c a t i o n  ( H M C )  t a s k s ;  t h e  p r o t e i n  s t r u c t u r e  p r e d i c t i o n s  c a n  b e  s e e n  a s  o p t i mi z a t i o n  t a s k s  t h a t  s e a r c h  f o r  t h e  p r o t e i n  f o l d i n g  s t r u c t u r e  w i t h  mi n i mu m e n e r g y  b a s ed  o n  i t s  a mi n o  a c i d  s e q u e n c e .    F o r  c o mp l i c a t e d  t a s k s  i n  b i o i n f o r ma t i c s ,  ap p l y i n g  m a c h i n e  l e a r n i n g  m e t h o d s  s i mp l y  u su a l l y  c a n n o t  o b t a i n  e x p e c t a b l e  r e s u l t s .  T h e  d i f f e r e n t  c h a r a c t e r i s t i c s  a n d  c h a l l e n g e s  o f  t h e  t a s k s  w i l l  r e q u i r e  n o v e l  mo d i f i c a t i o n s  o f  ex i s t i n g  ma c h i n e  l e a r n i n g  m e t h o d s .  I n  t h i s  t h e s i s ,  so me  i mp r o v e d  me t h o d s  b a s ed  o n  mu l t i - S V M  an d  h y b r i d  E D A a r e  d e v e l o p e d  f o r  s o l v i n g  c o mp l i c a t e d  t a sk s  i n  t h e  p r e d i c t i o n s  o f  g en e  f u n c t i o n  a n d  p r o t e i n  H P  mo d e l .  A c c o r d i n g  t o  t h e  c h a r a c t e r i s t i c s  o f  ap p l i c a t i o n s ,  t h e  p r i o r  k n o w l e d g e  o f  t a s k s  an d  t h e  i n f o r m a t i o n  o f  b i o l o g i c a l  d a t a  a r e  e x t r a c t e d  b y  s o me  d e l i c a t e  t e c h n i q u e s .  T h e  o b t a i n e d  k n o w l e d g e  a n d  i n f o r ma t i o n  a r e  u s e d  t o  e n h a n c e  m a c h i n e  l e a r n i n g  me t h o d s .  S V M s  b a s e d  m e t h o d s  a r e  d ev e l o p ed  f o r  so l v i n g  d i f f e r e n t  a p p l i c a t i o n s  o f  t h e  g e n e  f u n c t i o n  p r e d i c t i o n .  E D A s  b a s e d  me t h o d s  a r e  p r o p o s e d  f o r  s o l v i n g  p r o t e i n  H P  mo d e l  p r o b l e ms .  T h e  D i l l ' s  H P - l a t t i c e  mo d e l  i s  a  s i mp l i f i e d  mo d e l  o f  p r o t e i n  s t r u c t u r e  p r e d i c t i o n .  I t  i s  a  u s e f u l  t o o l  f o r  i n v e s t i g a t i n g  g en e r a l  p r o p e r t i e s  o f  p r o t e i n  f o l d i n g .    T h e  t h e s i s  i s  o r g a n i z e d  f r o m 7  c h ap t e r s  a s  f o l l o w s .   C h a p t e r  1  b r i e f l y  i n t r o d u c e s  p r e d i c t i o n s  o f  g e n e  f u n c t i o n  a n d  p r o t e i n  s t r u c t u r e ,  o u r  mo t i v a t i o n ,  g o a l s  o f  t h i s  w o r k  a n d  o u t l i n e  o f  t h e  t h e s i s .   C h a p t e r  2  p r o p o s e s  a  n e w  mu l t i - S V M  sy s t e m  c a l l e d  co mp o s i t e  k e r n e l  b a s e d  S V M  ( c k - S V M )  mo d e l  f o r  s o l v i n g  n o n l i n e a r  c l a s s i f i c a t i o n  t a s k s  i n  g e n e  f u n c t i o n  p r e d i c t i o n .  I n  g e n e  f u n c t i o n  c l a s s i f i c a t i o n ,  t h e r e  a r e  s o me  d a t a s e t s  w i t h  c h a r a c t e r i s t i c s  o f  h i g h  n o i s e ,  l a r g e  n u mb e r  o f  i n p u t  f e a t u r e s  a n d  r e l a t i v e l y  s ma l l  n u m b e r  o f  t r a i n i n g  e x a m p l e s .  F o r  t h o s e  d a t a s e t s ,  c o n v e n t i o n a l  n o n l i n e a r  c l a s s i f i c a t i o n  me t h o d s  a r e  u n a v a i l a b l e  d u e  t o  t h e  o v e r - f i t t i n g  p r o b l e m .  T h e  p r o p o s ed  c k - S V M  mo d e l  r e a l i z e s  a  n o n l i n e a r  s e p a r a t i n g  b o u n d a r y  b y  e s t i m a t i n g  a  s e r i e s  o f   3 p i e c e w i s e  l o c a l  l i n e a r  b o u n d a r i e s .  A  l o c a l  l i n e a r  mu l t i - S V M  sy s t e m i s  e s t i ma t e d  b y  a  co mp o s i t e  k e r n e l  i n c o r p o r a t i n g  p r i o r  k n o w l e d g e  o f  t r a i n i n g  d a t a .  I n s t e a d  o f  b u i l d i n g  mu l t i p l e  l o c a l  S V M  mo d e l s  s e p a r a t e l y ,  t h e  p r i o r  k n o w l e d g e  o f  l o c a l  s u b s e t s  i s  u s e d  t o  co n s t r u c t  a  c o mp o s i t e  k e r n e l ,  a n d  t h e  l o c a l  l i n e a r  mu l t i - S V M  mo d e l  i s  r e a l i z e d  e x a c t l y  i n  t h e  s a me  w ay  a s  a  s i n g l e  S V M  mo d e l  b y  u s i n g  t h e  c o mp o s i t e  k e r n e l .  T h e  p r o p o s e d  ck - S V M  i s  a  c o n t r o l l a b l e  s u p p o r t  v e c t o r  m a c h i n e  mo d e l ,  i t  c a n  s o l v e  n o n l i n e a r  t a s k s  a n d  a v o i d  o v e r - f i t t i n g  i n  c e r t a i n  d eg r e e  b y  i n t r o d u c i n g  mu l t i p l e  l o c a l  l i n e a r  b o u n d a r i e s .   C h a p t e r  3  p r o p o s e s  a  mu l t i - l a b e l  c l a s s i f i c a t i o n  m e t h o d  b a s e d  o n  l a b e l  r a n k i n g  an d  d e l i c a t e  d e c i s i o n  b o u n d a r y  S V M .  I n  mu l t i - l a b e l  g e n e  c l a s s i f i c a t i o n ,  a  t r a i n i n g  e x a mp l e  i s  a s s o c i a t e d  w i t h  a  s e t  o f  l a b e l s  a n d  t h e  t a s k  i s  t o  p r ed i c t  t h e  l a b e l  s e t  f o r  e a c h  u n s e e n  i n s t a n c e .  T h e  ma i n  ch a l l e n g e  o f  t h i s  p r o b l e m i s  t h a t  c l a s s e s  a r e  u s u a l l y  o v e r l a p p e d  a n d  c o r r e l a t e d .  L a b e l  r a n k i n g  b a s e d  m e t h o d  r e q u i r e s  a  r e a l - v a l u ed  s c o r e  f o r  e a c h  c l a s s  ( l ab e l )  t o  o r d e r  a  l a b e l  r a n k ,  t h en  c l a s s i f i e s  a  n e w  i n s t a n c e  i n t o  t h e  c l a s s e s  t h a t  r a n k i n g  s c o r e  a b o v e  a  t h r e s h o ld .  I n  o r d e r  t o  o b t a i n  a  p r o p e r  l a b e l  r a n k ,  a n  i mp r o v e d  p r o b a b i l i s t i c  S V M  w i t h  d e l i c a t e  d e c i s i o n  b o u n d a r y  i s  p r o p o s e d  a s  t h e  s c o r i n g  m e t h o d .  I t  c a n  i mp r o v e  t h e  p r o b a b i l i s t i c  l ab e l  r a n k  b y  i n t r o d u c i n g  t h e  i n f o r ma t i o n  o f  o v e r l ap p e d  t r a i n i n g  s a mp l e s  i n t o  l e a r n i n g  p r o c ed u r e .  I n s t e a d  o f  e s t i m a t i n g  a  s t a t i c  t h r e s h o l d  f o r  a l l  t e s t i n g  i n s t a n c e s ,  a n  i n s t a n c e - i n d e p e n d e n t  t h r e s h o l d i n g  s t r a t eg y  i s  p r o p o s e d  t o  d e c i d e  t h e  c l a s s i f i c a t i o n  r e s u l t s .  I t  c a n  e s t i m a t e  a n  ap p r o p r i a t e  t h r e s h o l d  f o r  e a c h  t e s t i n g  i n s t an c e  a c c o r d i n g  t o  t h e  c h a r a c t e r i s t i c s  o f  i n s t a n c e  a n d  l a b e l  r a n k .   C h a p t e r  4  p r o p o s e s  a  h i e r a r c h i c a l  m u l t i - l a b e l  c l a s s i f i c a t i o n  me t h o d  b a s e d  o n  o v e r - s a mp l i n g  a n d  h i e r a r c h y  c o n s t r a i n t .  H i e r a r c h i c a l  mu l t i - l a b e l  c l a s s i f i c a t i o n  ( H M C )  i s  a  s p e c i a l  v a r i a n t  o f  mu l t i - l ab e l  c l a s s i f i c a t i o n  wh e r e  t h e  c l a s s e s  a r e  o r g a n i z e d  i n  a  h i e r a r c h y .  G e n e  F u n C a t  p r e d i c t i o n  p r o b l e m  i s  a  d i f f i c u l t  H M C  t a s k .  I n  F u n C a t  d a t a s e t s ,  t h e r e  a r e  h u n d r e d s  o f  f u n c t i o n a l  c l a s s e s  s t r u c t u r ed  b y  a  p r e d e f i n e d  h i e r a r c h y ,  an d  t h e  e x a mp l e  d i s t r i b u t i o n s  o f  c l a s s e s  a r e  u s u a l l y  h i g h  d eg r e e  s k e w e d  ( i m b a l a n c e d )  w i t h  n e g a t i v e  mo r e  t h an  p o s i t i v e .  T w o  me a s u r e s  a r e  i mp l e me n t e d  i n  t h e  p r o p o s e d  me t h o d  t o  i mp r o v e  t h e  H M C  p e r f o r ma n c e  b y  i n t r o d u c i n g  t h e  h i e r a r c h y  c o n s t r a i n t  i n t o  l e a r n i n g  p r o c ed u r e s .  F i r s t l y ,  f o r  i mb a l a n c e d  f u n c t i o n a l  c l a s s e s ,  a  h i e r a r c h i c a l  S M O T E  i s  p r o p o s e d  a s  o v e r - s a m p l i n g  p r e p r o c e s s i n g  t o  e n h a n c e  t h e  S V M  l e a r n i n g  e f f i c i e n cy .  S e co n d l y ,  a n  i mp r o v ed  T r u e  P a t h  R u l e  co n s i s t en cy  a p p r o a c h  i s  i n t r o d u c e d  t o  en s e mb l e  t h e  r e s u l t s  o f  b i n a r y  p r o b a b i l i s t i c  S V M  c l a s s i f i c a t i o n s .  I t  c a n  co r r e c t  t h e  c l a s s i f i c a t i o n  r e s u l t s  an d  g u a r a n t e e  t h e  h i e r a r c h y  co n s t r a i n t  o f  c l a s s e s .   4 C h a p t e r  5  p r o p o s e s  a  h y b r i d  E D A  f o r  so l v i n g  t h e  p r o t e i n  s t r u c t u r e  p r e d i c t i o n  p r o b l e m  o n  H P  m o d e l .  T h e  p r o t e i n  H P  mo d e l  p r e d i c t i o n  i s  a n  N P - c o m p l e t e  o p t i mi z a t i o n  p r o b l e m.  T h e  t a s k  i s  t o  p r e d i c t  t h e  m i n i mu m e n e r g y  l a t t i c e  s t r u c t u r e  o f  a  p r o t e i n  f r o m i t s  s i mp l i f i e d  t wo - l e t t e r  ( H  a n d  P )  a mi n o  a c i d  s e q u e n c e .  E A s  b a s ed  m e t h o d s  c a n  b e  u s e d  t o  s o l v e  t h i s  N P - co mp l e t e  p r o b l e m .  B u t  f o r  l o n g  p r o t e i n  s e q u e n c e s ,  t h e  c o n v en t i o n a l  m e t h o d s  c a n  o n l y  f i n d  t h e  s u b o p t i mu m s o l u t i o n s .  I n  o r d e r  t o  s e l e c t  b e t t e r  i n d i v i d u a l s  f o r  p r o b ab i l i s t i c  mo d e l  o f  E D A ,  a  co mp o s i t e  f i t n e s s  f u n c t i o n  c o n t a i n i n g  t h e  i n f o r m a t i o n  o f  f o l d i n g  s t r u c t u r e  c o r e  ( H - C o r e )  i s  i n t r o d u c e d  t o  r e p l a c e  t h e  t r a d i t i o n a l  f i t n e s s  f u n c t i o n  o f  H P  mo d e l .  T h e n ,  l o c a l  s e a r c h  w i t h  g u i d e d  o p e r a t o r s  i s  u t i l i z e d  t o  r e f i n e  f o u n d  s o l u t i o n s  f o r  i mp r o v i n g  e f f i c i en cy  o f  E D A .  I n  ad d i t i o n ,  a n  i mp r o v e d  b a c k t r a c k i n g - b a s e d  r e p a i r i n g  me t h o d  i s  p r o p o s e d  t o  r e p a i r  i n v a l i d  i n d i v i d u a l s  s a mp l e d  b y  t h e  p r o b a b i l i s t i c  mo d e l  o f  E D A .  I t  c a n  s i g n i f i c a n t l y  r e d u c e  t h e  n u mb e r  o f  b a c k t r a c k i n g  s e a r c h i n g  o p e r a t i o n  an d  t h e  c o mp u t a t i o n a l  co s t  f o r  l o n g  s e q u e n c e  p r o t e i n .   C h a p t e r  6  p r o p o s e s  an  a d ap t i v e  n i c h i n g  E D A  w i t h  b a l a n c e  s e a r c h i n g  b a s e d  o n  c l u s t e r i n g  an a l y s i s .  F o r  o p t i mi z a t i o n  p r o b l e m s  w i t h  i r r e g u l a r  a n d  c o mp l e x  mu l t i mo d a l  l a n d s c a p e s ,  E D A s  a l w ay s  s u f f e r  f r o m t h e  d r a w b a c k  o f  p r e m a t u r e  c o n v e r g e n c e  s i mi l a r  t o  o t h e r  ev o l u t i o n a r y  a l g o r i t h ms .  I n  t h e  p r o p o s ed  a d ap t i v e  n i c h i n g  E D A ,  t h e  A f f i n i t y  P r o p ag a t i o n  ( A P )  c l u s t e r i n g  i s  u s e d  t o  a d a p t i v e l y  p a r t i t i o n  t h e  p o p u l a t i o n  i n t o  n i c h e s  d u r i n g  a  r u n  o f  E D A  f i r s t l y .  T h e n ,  a  n i c h e  c a p a c i t y  s e l e c t i o n  m e c h a n i s m b a s e d  o n  t h e  B o l t z ma n n  s c h e m e  i s  i n t r o d u c e d  t o  r e a l i z e  a  b a l a n c e  s e a r c h i n g  b e t w e e n  e x p lo r a t i o n  an d  e x p l o i t a t i o n .  T wo  d i f f e r e n t  s e l e c t i o n  s t r a t eg i e s ,  n o v e l t y - p r o p o r t i o n a t e  s e l e c t i o n  b a s e d  o n  t h e  s e a r c h i n g  h i s t o r y  i n f o r ma t i o n  an d  f i t n e s s - p r o p o r t i o n a t e  s e l e c t i o n  b a s e d  o n  t h e  b e s t  f i t n e s s  i n  a  n i c h e ,  a r e  a s s e m b l e d  b y  a  B o l t z ma n n  w e i g h t .  T u n e d  b y  t h e  B o l t z ma n n  w e i g h t ,  a t  t h e  b eg i n n i n g  p h a s e  o f  s e a r c h i n g ,  t h e  d o mi n a t i n g  n o v e l t y - p r o p o r t i o n a t e  s e l e c t i o n  c a n  g u i d e  t h e  E D A  s e a r c h i n g  t o  c o v e r  t h e  s e a r c h  sp a c e  a s  mu c h  a s  p o s s i b l e ;  a t  t h e  e n d  p h a s e  o f  s e a r c h i n g ,  t h e  d o mi n a t i n g  f i t n e s s - p r o p o r t i o n a t e  s e l e c t i o n  c a n  e n f o r c e  t h e  E D A  s e a r c h i n g  t o  e x p l o i t  t h e  a l r e a d y  f o u n d  p r o mi s i n g  a r e a s .  T h e  p r o p o s e d  ad a p t i v e  n i c h i n g  E D A  i s  u s e d  f o r  s o l v i n g  t h e  p r o t e i n  H P  mo d e l  p r e d i c t i o n .  I n  a d d i t i o n ,  t h r e e  b en c h ma r k  f u n c t i o n a l  mu l t i m o d a l  o p t i mi z a t i o n  p r o b l e ms  a r e  a l so  u s e d  t o  e v a l u a t e  t h e  p r o p o s e d  m e t h o d .   C h a p t e r  7  su m ma r i z e s  t h e  t h e s i s  an d  g i v e s  s u g g e s t i o n s  f o r  f u r t h e r  r e s e a r c h .  

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Study on the predictions of gene function and protein structure using multi-SVM and hybrid EDA

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