#!/usr/bin/perl
require 5.008;
use strict;
use warnings;
my %measure;
my %evaluated;
my %stat;
my @marginal;
my @icu;
my $threshold = -1.868;
&load_measures;
&load_parameters;
my ($rid, $icu) = &read_case;
&inference;
sub inference{
my @counts;
my @ln;
my $N = $marginal[0] + $marginal[1];
while(my($measure, $trend) = each %evaluated){
next unless defined $measure{$measure};
my $href = $stat{$measure};
if(defined $href->{$trend}){
push @counts, $href->{$trend};
}else{
my @values = @marginal;
foreach my $trend (keys %$href){ #take out from marginals, significant pattern counts
$values[$_] -= $stat{$measure}{$trend}[$_] for (0..1);
}
push @counts, \@values;
}
}
foreach my $s (0..1){
$ln[$s] = log($marginal[$s]) - log $N;
my $i = 1;
foreach my $c_aref (@counts){
$ln[$s] += log($c_aref->[$s] + 1) - log($c_aref->[0] + $c_aref->[1] + 2);
$i++;
}
$ln[$s] += log($icu[$icu][$s]); $i++;
$ln[$s] /= $i;
}
my $lnP_mortality = $ln[1]-log(exp($ln[0]) + exp($ln[1]));
my $prediction = $lnP_mortality > $threshold ? 1 : 0;
print "$rid,$prediction,", &calibrate402(exp($lnP_mortality)), "\n";
#print "$rid,$prediction,", exp($lnP_mortality), "\n";
}
sub calibrate402{
my $p = shift;
if($p >= 0.173){
$p = -155.02 * $p * $p + 72.053 * $p - 7.3446;
}else{
$p = 71.367 * $p * $p - 12.394 * $p + 0.4959;
}
return 0.001 if $p < 0.001;
return 0.70 if $p > 0.70;
return $p;
}
sub load_parameters{
open my $ifh, $0 or die "Cannot read $0!\n$!";
while(<$ifh>){
last if /^#BeginParameters/;
}
while(<$ifh>){
last if /^#EndParameters/;
chomp;
s/^#//;
my ($head, @tail) = split /\t/, $_;
if($head eq 'marginals'){
@marginal = @tail;
}else{
my $trend = shift @tail;
$stat{$head}{$trend} = \@tail;
}
}
close $ifh;
$icu[1][1] = 0.140;
$icu[2][1] = 0.049;
$icu[3][1] = 0.186;
$icu[4][1] = 0.145;
$icu[$_][0] = 1 - $icu[$_][1] for (1..4);
}
sub read_case{
my %static;
$static{$_} = 1 for ('Age', 'BMI', 'Gender', 'Height','Weight','ICUType');
my %observed;
my $rid;
my $icu;
while(<STDIN>){
next unless /^\d\d:/;
chomp;
my ($time,$measure,$value) = split /\,/, $_;
$rid = $value and next if $measure eq 'RecordID';
$icu = $value and next if $measure eq 'ICUType';
next unless (defined $measure{$measure} or $measure =~ /^.eight$/);
next unless $value =~ /\d/;
next if $value == -1;
$time =~ s/://;
$time += 0; #make it numeric
next if $time > 4800;
my $aref;
if($static{$measure}){
$observed{$measure} = [0,0] unless defined $observed{$measure};
$aref = $observed{$measure};
}else{
my $day = $time < 2400 ? 1 : 2;
$observed{$measure}{$day} = [0,0] unless defined $observed{$measure}{$day};
$aref = $observed{$measure}{$day};
}
$aref->[0] += $value;
$aref->[1] ++;
}
#my %evaluated;
if(defined $observed{Height} and defined $observed{Weight}){
my $height = $observed{Height}[0] / (100* $observed{Height}[1]);
my $weight = $observed{Weight}[0] / ($observed{Weight}[1]);
$observed{BMI} = [$weight / ($height * $height),1];
}
foreach my $measure (keys %measure){
my $aref;
if($static{$measure}){
$aref = $observed{$measure};
if($aref){
$evaluated{$measure} = &evaluate($measure, $aref);
}else{
$evaluated{$measure} .= 'U';
}
}else{
for my $day (1..2){
$aref = $observed{$measure}{$day};
if($aref){
$evaluated{$measure} .= &evaluate($measure, $aref);
}else{
$evaluated{$measure} .= 'U';
}
}
}
}
return $rid, $icu;
}
sub evaluate{
my $measure = shift;
my $aref = shift;
my $mean = $aref->[0] / $aref->[1];
if($mean <= $measure{$measure}{low}){
return 'L';
}elsif($mean > $measure{$measure}{high}){
return 'H';
}else{
return 'N';
}
}
sub load_measures{
open my $ifh, $0 or die "Cannot read $0!\n$!";
while(<$ifh>){
last if /^#BeginRanges/;
}
while(<$ifh>){
last if /^#EndRanges/;
chomp;
s/^#//;
my ($measure, $low, $high) = split /\s*\t\s*/, $_;
#$measure =~ s/\s*:$//;
$measure{$measure}{low} = $low;
$measure{$measure}{high} = $high;
}
close $ifh;
}
#BeginRanges
#ALP 96.80 96.80 0.26 [-,+] [172/1122, 150/568]
#ALT 52.00 512.60 0.23 [-,+,+] [200/1156, 100/475, 28/90]
#AST 77.50 77.50 0.24 [-,+] [193/1166, 136/559]
#Age 81.20 99.60 0.24 [-,+,-] [396/3288, 157/655, 1/57]
#Albumin 2.76 2.76 0.25 [+,-] [157/619, 146/996]
#BMI 20.55 20.55 0.16 [+,-,U+] [28/141, 233/1964, 293/1895]
#BUN 42.40 42.40 0.30 [-,+] [383/3382, 167/554]
#Bilirubin 1.00 1.00 0.27 [-,+] [176/1156, 151/562]
#Cholesterol 202.30 218.90 0.08 [+,-,+] [42/257, 0/24, 4/24]
#Creatinine 1.74 1.74 0.27 [-,+] [364/3257, 186/679]
#DiasABP 54.53 54.53 0.17 [+,-] [143/842, 266/1957]
#FiO2 0.34 0.60 0.20 [+,-,+] [8/38, 319/2106, 117/573]
#GCS 8.28 8.28 0.32 [+,-] [225/703, 324/3233]
#Glucose 167.80 167.80 0.24 [-,+] [403/3284, 144/603]
#HCO3 18.62 30.17 0.30 [+,-,+] [134/361, 380/3361, 35/202]
#HCT 28.60 30.02 0.17 [-,+,-] [159/1161, 97/585, 294/2190]
#HR 59.90 104.15 0.22 [+,-,+] [15/78, 423/3367, 111/492]
#K 3.40 4.80 0.19 [+,-,+] [32/175, 443/3371, 72/358]
#Lactate 2.65 2.65 0.26 [-,+] [239/1627, 146/556]
#MAP 66.54 91.09 0.19 [+,-,+] [46/157, 286/2155, 74/480]
#MechVent 0.72 0.72 0.20 [-,+] [32/704, 363/1825]
#Mg 2.18 2.18 0.18 [-,+] [381/2970, 166/927]
#NIDiasABP 48.04 48.04 0.19 [+,-] [138/727, 349/2756]
#NIMAP 65.90 65.90 0.21 [+,-] [135/645, 352/2836]
#NISysABP 99.15 99.15 0.21 [+,-] [119/531, 369/2962]
#Na 132.70 143.88 0.25 [+,-,+] [54/207, 406/3365, 88/353]
#PaCO2 32.50 50.50 0.28 [+,-,+] [109/315, 321/2488, 44/220]
#PaO2 102.50 102.50 0.21 [+,-] [146/695, 327/2328]
#Platelets 99.68 389.78 0.23 [+,-,+] [112/425, 406/3304, 32/203]
#RespRate 26.11 26.11 0.16 [-,+,U+] [73/1036, 14/65, 467/2899]
#SaO2 96.10 98.90 0.20 [+,-,+] [93/459, 154/1229, 18/104]
#SysABP 105.18 105.18 0.22 [+,-] [126/566, 283/2233]
#Temp 36.26 37.99 0.24 [+,-,+] [99/382, 416/3384, 34/170]
#TroponinI 2.93 5.56 0.10 [+,-,+] [32/110, 4/21, 21/74]
#TroponinT 0.05 2.21 0.23 [-,+,-] [33/201, 130/558, 19/104]
#Urine 64.46 64.46 0.30 [+,-] [230/766, 307/3117]
#WBC 4.02 18.72 0.23 [+,-,+] [24/95, 420/3386, 106/446]
#pH 7.35 7.46 0.22 [+,-,+] [110/512, 309/2306, 55/222]
#EndRanges
#BeginParameters
#marginals 3446 554
#ALP HH 167 62
#ALP HL 30 10
#ALP HU 190 64
#ALP LH 18 5
#ALP LL 246 53
#ALP LU 542 80
#ALP UH 35 16
#ALP UL 140 32
#ALP UU 2078 232
#ALT HH 39 22
#ALT LL 213 51
#ALT LN 13 8
#ALT LU 591 114
#ALT NL 22 2
#ALT NN 165 47
#ALT NU 149 31
#ALT UL 135 33
#ALT UN 38 12
#ALT UU 2053 226
#AST HH 187 77
#AST HL 52 6
#AST HU 159 33
#AST LH 19 13
#AST LL 213 39
#AST LU 586 113
#AST UH 42 14
#AST UL 138 34
#AST UU 2050 225
#Age H 56 1
#Age L 2892 396
#Age N 498 157
#Albumin HH 109 16
#Albumin HL 37 11
#Albumin HU 567 92
#Albumin LL 107 36
#Albumin LU 237 85
#Albumin UH 148 33
#Albumin UL 97 27
#Albumin UU 2134 251
#BMI H 1731 233
#BMI L 113 28
#BMI U 1602 293
#BUN HH 293 140
#BUN HL 91 20
#BUN LH 75 24
#BUN LL 2824 345
#BUN LU 66 13
#BUN UL 27 4
#BUN UU 60 4
#Bilirubin HH 204 82
#Bilirubin HL 25 7
#Bilirubin HU 146 41
#Bilirubin LH 18 9
#Bilirubin LL 230 37
#Bilirubin LU 573 99
#Bilirubin UH 40 17
#Bilirubin UL 155 35
#Bilirubin UU 2055 227
#Cholesterol HU 18 4
#Cholesterol LU 183 34
#Cholesterol NU 22 0
#Cholesterol UL 28 8
#Cholesterol UU 3187 508
#Creatinine HH 405 159
#Creatinine HL 72 13
#Creatinine LH 83 26
#Creatinine LL 2728 330
#Creatinine LU 65 13
#Creatinine UL 27 5
#Creatinine UU 60 4
#DiasABP HH 1225 200
#DiasABP HL 265 34
#DiasABP HU 136 3
#DiasABP LH 180 48
#DiasABP LL 403 90
#DiasABP LU 58 5
#DiasABP UH 88 15
#DiasABP UL 35 14
#DiasABP UU 1056 145
#FiO2 HH 145 57
#FiO2 HN 323 83
#FiO2 HU 174 7
#FiO2 NH 110 18
#FiO2 NL 31 7
#FiO2 NN 904 221
#FiO2 NU 425 15
#FiO2 UH 61 16
#FiO2 UN 83 15
#FiO2 UU 1173 110
#GCS HH 2536 254
#GCS HL 122 51
#GCS HU 15 2
#GCS LH 388 56
#GCS LL 316 181
#GCS UU 59 5
#Glucose HH 164 52
#Glucose HL 450 109
#Glucose HU 25 3
#Glucose LH 184 58
#Glucose LL 2218 300
#Glucose LU 157 13
#Glucose UH 16 0
#Glucose UL 126 12
#Glucose UU 106 7
#HCO3 HH 102 26
#HCO3 HN 54 12
#HCO3 LL 141 91
#HCO3 LN 146 48
#HCO3 NH 72 5
#HCO3 NL 92 27
#HCO3 NN 2628 318
#HCO3 NU 78 12
#HCO3 UN 44 6
#HCO3 UU 71 5
#HCT HH 1417 209
#HCT HL 328 51
#HCT HN 252 32
#HCT HU 51 10
#HCT LH 166 46
#HCT LL 602 98
#HCT LN 138 23
#HCT NH 95 18
#HCT NL 206 33
#HCT NN 80 16
#HCT UH 24 6
#HCT UU 60 4
#HR HH 233 78
#HR HN 211 49
#HR LL 40 6
#HR LN 67 13
#HR NH 168 34
#HR NL 48 7
#HR NN 2601 359
#HR UU 58 5
#K HH 97 26
#K HN 245 48
#K HU 22 2
#K LL 58 12
#K LN 139 24
#K NH 117 32
#K NL 189 39
#K NN 2235 341
#K NU 124 12
#K UH 12 4
#K UN 103 5
#K UU 89 7
#Lactate HH 59 56
#Lactate HL 193 37
#Lactate HU 224 43
#Lactate LH 24 13
#Lactate LL 383 86
#Lactate LU 730 109
#Lactate UH 22 10
#Lactate UL 163 31
#Lactate UU 1648 169
#MAP HH 197 35
#MAP HN 115 28
#MAP HU 52 2
#MAP LL 44 15
#MAP LN 76 25
#MAP LU 16 1
#MAP NH 198 28
#MAP NL 107 26
#MAP NN 1336 212
#MAP NU 122 3
#MAP UH 36 7
#MAP UL 11 10
#MAP UN 75 13
#MAP UU 1060 148
#MechVent HH 1462 363
#MechVent HU 568 10
#MechVent UH 104 22
#MechVent UU 1312 159
#Mg HH 426 103
#Mg HL 315 31
#Mg HU 40 7
#Mg LH 407 94
#Mg LL 1867 284
#Mg LU 138 16
#Mg UH 34 7
#Mg UL 123 5
#Mg UU 96 7
#NIDiasABP HH 1489 182
#NIDiasABP HL 153 41
#NIDiasABP HU 488 127
#NIDiasABP LH 177 22
#NIDiasABP LL 212 53
#NIDiasABP LU 136 50
#NIDiasABP UH 212 6
#NIDiasABP UL 129 6
#NIDiasABP UU 450 67
#NIMAP HH 1508 181
#NIMAP HL 130 38
#NIMAP HU 492 127
#NIMAP LH 224 30
#NIMAP LL 163 48
#NIMAP LU 134 51
#NIMAP UH 249 6
#NIMAP UL 94 6
#NIMAP UU 452 67
#NISysABP HH 1629 197
#NISysABP HL 115 37
#NISysABP HU 485 124
#NISysABP LH 182 32
#NISysABP LL 120 34
#NISysABP LU 133 51
#NISysABP UH 283 8
#NISysABP UL 58 5
#NISysABP UU 441 66
#Na HH 167 59
#Na HN 127 21
#Na LL 83 34
#Na LN 76 26
#Na NH 168 41
#Na NL 111 20
#Na NN 2475 324
#Na NU 93 11
#Na UN 55 7
#Na UU 69 6
#PaCO2 HH 84 16
#PaCO2 HN 52 21
#PaCO2 HU 42 9
#PaCO2 LL 74 50
#PaCO2 LN 74 31
#PaCO2 LU 64 18
#PaCO2 NH 49 14
#PaCO2 NL 127 42
#PaCO2 NN 1279 200
#PaCO2 NU 567 38
#PaCO2 UL 20 10
#PaCO2 UN 107 21
#PaCO2 UU 897 80
#PaO2 HH 856 192
#PaO2 HL 576 89
#PaO2 HU 499 35
#PaO2 LH 113 32
#PaO2 LL 197 64
#PaO2 LU 172 27
#PaO2 UH 90 17
#PaO2 UL 47 17
#PaO2 UU 896 81
#Platelets HH 119 21
#Platelets HN 77 15
#Platelets LL 215 76
#Platelets LN 32 15
#Platelets NH 26 4
#Platelets NL 193 49
#Platelets NN 2578 337
#Platelets NU 79 15
#Platelets UN 46 11
#Platelets UU 64 4
#RespRate HH 33 6
#RespRate HL 36 7
#RespRate LH 23 8
#RespRate LL 907 64
#RespRate UU 2432 467
#SaO2 HN 22 6
#SaO2 HU 60 8
#SaO2 LL 80 20
#SaO2 LN 67 18
#SaO2 LU 118 24
#SaO2 NH 20 7
#SaO2 NL 173 26
#SaO2 NN 350 47
#SaO2 NU 398 40
#SaO2 UH 15 9
#SaO2 UL 69 24
#SaO2 UN 136 33
#SaO2 UU 1919 289
#SysABP HH 1488 224
#SysABP HL 146 29
#SysABP HU 136 3
#SysABP LH 230 48
#SysABP LL 209 71
#SysABP LU 58 5
#SysABP UH 101 15
#SysABP UL 22 14
#SysABP UU 1056 145
#Temp HH 68 12
#Temp HN 110 22
#Temp LL 110 52
#Temp LN 313 59
#Temp NH 134 34
#Temp NL 145 46
#Temp NN 2473 312
#Temp NU 13 6
#Temp UU 59 5
#TroponinI HH 18 4
#TroponinI HU 26 13
#TroponinI LL 19 7
#TroponinI LU 52 21
#TroponinI UU 3298 497
#TroponinT HH 35 14
#TroponinT HU 39 3
#TroponinT LL 30 11
#TroponinT LU 142 22
#TroponinT NN 142 46
#TroponinT NU 227 66
#TroponinT UL 16 2
#TroponinT UN 18 5
#TroponinT UU 2765 372
#Urine HH 2236 215
#Urine HL 445 99
#Urine HU 35 3
#Urine LH 255 49
#Urine LL 344 164
#Urine LU 19 5
#Urine UU 100 17
#WBC HH 190 69
#WBC HN 228 38
#WBC LL 43 18
#WBC LN 41 7
#WBC NH 103 35
#WBC NL 34 6
#WBC NN 2590 343
#WBC NU 75 17
#WBC UN 51 9
#WBC UU 69 4
#pH HH 33 21
#pH HN 73 18
#pH HU 55 8
#pH LH 20 10
#pH LL 216 71
#pH LN 321 65
#pH LU 141 20
#pH NH 126 24
#pH NL 83 32
#pH NN 985 135
#pH NU 365 34
#pH UH 23 7
#pH UL 26 11
#pH UN 93 16
#pH UU 880 80
#EndParameters