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DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer ! " # !"$ % & !" ' ( !" ) !" !" !") * ( !") + , , ) , DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer #-.$ / -01 2 3 (3 4 + ' ( + ( 1 ( + /( . , ( # $ #$ 5 -. ! " # !"$ ' 5 . 6 0( !" . 67 . 68 5 . 69 . 6: , # $ ; "6 " "7 "8 6 ; 6 6 7 6 DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer <6 7 " "8 <7 6= 6= " ( #>-$ + #>.$ * + ( ( ( ? ! ! ( 1 ' ) " #"$4 " ( #$ 6 " 6 " > , 3 #;-$3 + , ( 5 ;- ) ( ;- 1 ' + + ' /' , DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer . @ 02 5 5/ ( / ( 9AAAA 1 <8= ;- #5 66$ ( " ;- B 1C 6AA ! " # " 5 ' > + Æ 5 ;- * ;- ( ? <69= / A% 6AA + + 5 ( ? -. , ' DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer $ /% #$ >- 4 1 > 1 >- " ' > 1 >#5 6 $ 1 % >- ( -. ;- , + -. " #% & ' ( ) ' ( #.0!$ #.?$ ' 8 .? .0! .0! ' , .0! .? " .0! 6A .? 6A DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer * #$ ( 1 ( / ' #$ . % 1 1 "6 6 7 7 " 6 6 6 5 , #7$ # $ 1 1 0 1 -. ! " # !"$ !" !" DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer + , - -. . D >- >- , !" ', !" # $ * ( ( ( 5 E 6 ( A # A$ A , ; ' ; ( !" 5 ; ', 4 #$ + ! . 5 D >- ; 4 Ä !# $ Ê !# $ # $ 5 , , !" DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer ! ! C B ' .,/0 / ! & ! ! ! 0. ! 1 2 3 '( 4 2 3 ' ( + 1 ! ! /' ( 4 2 3 ' ( 4 . $ 4 " ,/0 % 5 !" , 67 -. -. , >- ; " ( ( " > 1 DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer + , >- 1 ( ; E < = ! # $ ; , 6$ $ , E < = #$ 6$ #$ $ ! + 4 E E ' '#$ 1 * , 4 + 4 E E E # $ E . 687 " " ; E < 6 = #6 :$ 7 8 9 ( <7 6 8 A= <#66$ #6 $ #66$ # 8$ #6 $ # 7$= ) <#66$ #6 $ #6 $ # 8$ #6 $ # 7$= 6 7 9 !" ', '4 #$ '#$ ' DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer , 1 3 3 < 6 = 4 # ¼ $ E # ¼ $ #66$ E # $ % , 66 1 <6F 68= % , % ( 4 # ¼ $ E 6 # # ¼ $ $ # ¼ $ #6 $ E # ¼ $ # ¼ $ ( E > ( 1 !" % 1 +%+ G # $ 5H ( 4 " 1 I 0 ; + DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer + , + . 3 + 6 / 0 0 0+ 0 0 0 + * + + * 8 + 7 + + ; ' #1 I$ #"$ #0$ E # $ # J $# J $ #67$ ( * * 1 ' 4 #68$ E J ' # < 6= $ 0 ' 2 3 ' # $ G ( E J J J J #69$ DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer 6 A , ( , , E A " 4 * ; 4 ¼ ¼ ¼ #¼ $ #$ #$ '#$ Æ < = , # !" < =$ * ( #$ #$ #$ " . 6 ¼ 4 ¼ #$ #$ ¼ !# $ 4 # ¼ $ " ; G #$ '#$ #¼ ¼ $ E ¼ # ¼ $ "( G ( ) (4 E E E A E E E A E E E E E E A 1 I . 5H ( ' /' DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer + , -. , !" 5 68 ; K E 6 1 Æ K ># $ #6 $ 1 , 9A E AA9 6AAA , ' -. , Æ # <6L= $ Significances 5 80 4 -log(P) Score Observed scores and critical values 100 60 40 20 3 2 1 0 0 0 10 20 30 40 50 60 70 80 90 100 Location (cM) 0 10 20 30 40 50 60 70 80 90 100 Location (cM) ' ( 3 ' ( ' ( %8 DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer ! " # " !" < 6 = & !" ' <6F 68= 3 !") ! < 6 67= ( 6AA 6AAAAA A 6AA " 6A6 7A6 .0! ' - .0! .0! 2 6AA 5 ( 5 691 :AM " FAM " + 1 6AA " A " 4 > ' + < 6= !" 2' 66 % ' 2' 68 " ' A8 ' A69 ' ( M 4 6AA + DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer 9 $ , !" (4 ( F N ( A 6AAA !8 68) 5 + :AM NAM 5 691 ( :AM%FAM ( 0( + M 9M 6AM LAM ( LM 69M 9M - 8M 5 69> 69M !" - ) <L= - #( ) $ ? #5 69/$ LAM + !" 5 <7 6= 9 68 " -. 7L9 6AA # < 6=$ 6AAAAA 5 69- AAAA68 AAA69 ! ( ' 5 ( # # ! " $$ ' " -+ + , ' #&;$ + -. + DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer * B. Missing data 100 90 90 80 80 70 70 Power (%) Power (%) A. Phenocopies 100 60 50 40 60 50 40 60% 70% 80% 85% 90% 30 20 10 30 4% 8% 15% 25% 20 10 0 0 0 1 2 3 4 5 6 7 8 Prediction error (cM) 9 10 0 1 C. HPM vs. TDT 2 3 4 5 6 7 8 Prediction error (cM) 9 10 D. Type 1 diabetes 100 5 90 80 4 60 -log(P) Power (%) 70 50 40 3 2 30 20 1 HPM TDT 10 0 0 0 1 2 3 4 5 6 7 8 Prediction error (cM) 9 10 0 2 4 6 8 10 12 Physical location (Mb) 14 / ,/0 "( :; 9 #( :; 9 4( " ,/0 % / *<! *< -< %( 8 9 !" ) ' 1 + ' ( DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer 9 - & !" !" 2' 69 % 2' 6 ( & !" &- <6= - <68= . 686 ( ' A8 ' A ( ; # E J $ J $ J J % $ $ $ $ + + #1+$ E $ 6 J $ E 9 Æ E % 9M 1 , + ' E J $ J $ J 6 9 + <A6= + AA + , ( F " ' 6A 5 6: & !" &- Æ & !" &- Æ Æ "# "$ % + DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer Difficult model 100 90 90 80 80 70 70 Power (%) Power (%) Easy model 100 60 50 40 30 60 50 40 30 20 20 QHPM QTDT 10 QHPM QTDT 10 0 0 0 1 2 3 4 5 6 7 8 Prediction error (cM) 9 10 0 1 2 3 4 5 6 7 8 9 10 Prediction error (cM) 9 =,/0 ' ( =% ' ( "( #( Æ & . % ( Æ 7 ( ) ( " I ( 1 !" !" # !")$ ( 1 /' ' !") !" !") !" .0! . 686 ' !" AA AA 6AA !") 69A + 69A 7AA DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer > . 686 .0! ( 6N ' ( : " 9AM !") ( 9AM ( !") 8 : .0! #!8 68) $ 6AAA ( ( 8 : ( !" .0! : 7 8A 6AAA + .0! 5 5 6F1 !") !" ' .0! #5 6F>$ ( !") .0! B. SNP data 100 90 90 80 80 70 70 Power (%) Power (%) A. Microsatellite data 100 60 50 40 30 60 50 40 30 20 20 HPMG HPM 10 HPMG HPM 10 0 0 0 1 2 3 4 5 6 7 8 Prediction error (cM) 9 10 0 1 2 3 4 5 6 7 8 Prediction error (cM) 9 10 4 ,/0. ,/0 ; ?$<! *<! *< -< . "( @9 #( @9 86/ $ % & 5 ' NAH ; <6A= AAA DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer ;- <9 F= / - <:= < A= . <6:= "! . <66= , ;- . ;- "! . !" 4 G G ( < 7= ( ! ; <N= " <6 = - . <6L= 5 !" !" G < 8= ( !" ' ' ' ; ;- , - + , ; O' #-$ <6N= ;- ( ' ( ) -01 ' 1 -01 ' 4 -01 ' DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer % + 5 # $ - ) -. . ! " D( !" 4 , , ' !" ( , 2 ( ' !" ' ' .0! ( Æ 1 !" ' 3 3( 2( !" > !") , ( !"4 ' .0! !" 4 !" ( DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer ) 4 -. 0 , 3 3 A%7A " !" ( " !" ;- ( ( " ( ( , Æ 2( <6F= !" , 3 , )& !" P * @ P " Q @ " P * ( !" & !" DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer % & 1 '( $)( ) -01 ?01 ; -01 # ?01$ ' #$ 6 E 6AAA 6 " E 6AAA * ? > ( # 1 -01 # ! + # ., # $ #$ 1 + ) ( +', + ) ( +' -$ 0 ; ( ' # $ -$ !)( -, 0 - . / , $ 1 -01 ( ( ) " #"$ , ( 6 " E 6AA " * 6 " 6 " 1 DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer 1 ' 0 ) DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer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ccepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer * > 8 G 8! % A @! 6 # 1! @ " 8H @.& ! 2$*C$+*! --- $ / 8! / B! D B! , ! , 0! F G 0 ! ! " A ! ! '8 (28**C8-+! * / 8! , ! D B %2 & ! " # # " ! +C+$! ! ':5 2II I>I4( - > 8 8! > : 0! A F : &2 . '%%0( ! 2C! --+ F % " & ! 2$$$C$*$! -- , ! / B! G D! D B! / 8! , 0! 0 ,! F G % & ! $2++C ! , ! / B! G D! D B! / 8! , 0! F G # # $%# $ ! --C*! + 8 7! , 7 @ & ! 2C$$! 8 7! G 7! F @! , 7 B . & ! & $! C! DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer > - *" ". I 5 AAA !- ! ( ! Q @H 5 ) / @ . ! , 1 I 5 ". !- I 6NN6 6NN: H ! ( 0 ? / 9A 6A > 1 ? 1 @--NL 6AAA /. 2/";O!@-- AA @-- - " > # AA6%$ 2 $ I 5 . ". " 1 6NN9 ; , ( . !- AA 6 !R 69 . 1 1 ) 2 . AAA / , " DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer + > + * 3 J79L N 6N6888 N !. S, 11 1 J79L N 6N688 9 S, 2 $ J79L N 6N688 F7 ! *S, & 3 - / . !*>( : # 7$ 50AAA68 I 5 ( J79L N 6N688886 1 DRAFT Accepted for publication in 'Data Mining in Bioinformatics' Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer