RESULTS ========================================================== SET A ========================================================== === Run information === Scheme: weka.classifiers.trees.J48 -C 0.25 -M 2 Relation: cerevisiae_SET_A Instances: 3089 Attributes: 13 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ BLAST_yeast <= 0 | CAI <= 0.145: 0 (1212.0/245.0) | CAI > 0.145 | | GC <= 0.361 | | | BLAST_closeyeast = 0: 1 (1.0) | | | BLAST_closeyeast = 1: 1 (0.0) | | | BLAST_closeyeast = 2: 1 (2.0) | | | BLAST_closeyeast = 3 | | | | L_aa <= 461: 0 (5.0) | | | | L_aa > 461 | | | | | GC <= 0.353 | | | | | | Nc <= 48.52: 1 (3.0) | | | | | | Nc > 48.52: 0 (9.0/2.0) | | | | | GC > 0.353: 1 (6.0) | | | BLAST_closeyeast = 4 | | | | L_aa <= 177: 0 (6.0) | | | | L_aa > 177 | | | | | CHR_POSN <= 0.890021: 1 (52.0/18.0) | | | | | CHR_POSN > 0.890021: 0 (6.0/1.0) | | | BLAST_closeyeast = 5 | | | | CAI <= 0.187: 1 (4.0) | | | | CAI > 0.187: 0 (4.0/1.0) | | | BLAST_closeyeast = 6: 0 (3.0/1.0) | | GC > 0.361 | | | BLAST_closeyeast = 0: 0 (2.0) | | | BLAST_closeyeast = 1: 0 (5.0) | | | BLAST_closeyeast = 2 | | | | CLOSE_STOP_RATIO <= 0.030303: 1 (3.0/1.0) | | | | CLOSE_STOP_RATIO > 0.030303: 0 (10.0) | | | BLAST_closeyeast = 3 | | | | INTRON = 0 | | | | | CLOSE_STOP_RATIO <= 0.041379 | | | | | | L_aa <= 334: 0 (24.0/2.0) | | | | | | L_aa > 334 | | | | | | | CLOSE_STOP_RATIO <= 0.030177 | | | | | | | | CHR_POSN <= 0.108328: 1 (3.0) | | | | | | | | CHR_POSN > 0.108328: 0 (26.0/3.0) | | | | | | | CLOSE_STOP_RATIO > 0.030177: 1 (36.0/15.0) | | | | | CLOSE_STOP_RATIO > 0.041379: 0 (106.0/14.0) | | | | INTRON = 1 | | | | | CAI <= 0.176: 1 (3.0) | | | | | CAI > 0.176 | | | | | | CHR <= 14 | | | | | | | CAI <= 0.258: 0 (6.0) | | | | | | | CAI > 0.258: 1 (3.0/1.0) | | | | | | CHR > 14: 1 (2.0) | | | BLAST_closeyeast = 4: 0 (494.0/137.0) | | | BLAST_closeyeast = 5 | | | | INTRON = 0: 0 (244.0/100.0) | | | | INTRON = 1 | | | | | GC <= 0.411: 0 (2.0) | | | | | GC > 0.411: 1 (3.0) | | | BLAST_closeyeast = 6 | | | | INTRON = 0 | | | | | GC <= 0.38: 1 (5.0) | | | | | GC > 0.38 | | | | | | CLOSE_STOP_RATIO <= 0.045292 | | | | | | | L_aa <= 526 | | | | | | | | CLOSE_STOP_RATIO <= 0.040562 | | | | | | | | | RARE_AA_RATIO <= 0.050228 | | | | | | | | | | CHR <= 6: 1 (7.0/2.0) | | | | | | | | | | CHR > 6: 0 (11.0/1.0) | | | | | | | | | RARE_AA_RATIO > 0.050228: 0 (11.0) | | | | | | | | CLOSE_STOP_RATIO > 0.040562: 1 (4.0) | | | | | | | L_aa > 526: 1 (18.0/4.0) | | | | | | CLOSE_STOP_RATIO > 0.045292 | | | | | | | CAI <= 0.441: 0 (23.0/2.0) | | | | | | | CAI > 0.441: 1 (4.0/1.0) | | | | INTRON = 1: 1 (2.0) BLAST_yeast > 0 | L_aa <= 481: 0 (346.0/22.0) | L_aa > 481 | | CAI <= 0.171: 0 (236.0/31.0) | | CAI > 0.171 | | | CLOSE_STOP_RATIO <= 0.03593 | | | | L_aa <= 1009 | | | | | GC <= 0.412: 1 (14.0/4.0) | | | | | GC > 0.412: 0 (17.0/3.0) | | | | L_aa > 1009: 1 (9.0/1.0) | | | CLOSE_STOP_RATIO > 0.03593 | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | BLAST_closeyeast = 2: 0 (0.0) | | | | BLAST_closeyeast = 3: 0 (11.0/1.0) | | | | BLAST_closeyeast = 4 | | | | | Nc <= 42.4: 1 (3.0) | | | | | Nc > 42.4 | | | | | | L_aa <= 749: 0 (11.0) | | | | | | L_aa > 749 | | | | | | | BLAST_yeast <= 2 | | | | | | | | Nc <= 44.53: 1 (2.0) | | | | | | | | Nc > 44.53 | | | | | | | | | GC <= 0.4: 0 (4.0) | | | | | | | | | GC > 0.4: 1 (2.0) | | | | | | | BLAST_yeast > 2: 0 (2.0) | | | | BLAST_closeyeast = 5 | | | | | BLAST_yeast <= 1 | | | | | | CHR <= 4: 1 (6.0/1.0) | | | | | | CHR > 4: 0 (4.0) | | | | | BLAST_yeast > 1: 0 (23.0/1.0) | | | | BLAST_closeyeast = 6: 0 (29.0/3.0) Number of Leaves : 59 Size of the tree : 102 Time taken to build model: 0.34 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 2341 75.785 % Incorrectly Classified Instances 748 24.215 % Kappa statistic 0.035 Mean absolute error 0.3438 Root mean squared error 0.429 Relative absolute error 96.2435 % Root relative squared error 101.5117 % Total Number of Instances 3089 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.972 0.947 0.772 0.972 0.86 0 0.053 0.028 0.362 0.053 0.092 1 === Confusion Matrix === a b <-- classified as 2303 67 | a = 0 681 38 | b = 1 -------------- Evaluation of Information Gain Ratio ------------------------------------ === Run information === Evaluator: weka.attributeSelection.GainRatioAttributeEval Search: weka.attributeSelection.Ranker -T -1.7976931348623157E308 -N -1 Relation: cerevisiae_SET_A Instances: 3089 Attributes: 13 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON SGD-ess Evaluation mode: evaluate on all training data === Attribute Selection on all input data === Search Method: Attribute ranking. Attribute Evaluator (supervised, Class (nominal): 13 SGD-ess): Gain Ratio feature evaluator Ranked attributes: 0.01948 7 BLAST_yeast 0.01081 1 CAI 0.01015 2 Nc 0.00778 3 GC 0.00518 8 BLAST_closeyeast 0.00395 9 BLAST_proks 0.00103 12 INTRON 0 4 L_aa 0 10 CHR 0 11 CHR_POSN 0 5 CLOSE_STOP_RATIO 0 6 RARE_AA_RATIO Selected attributes: 7,1,2,3,8,9,12,4,10,11,5,6 : 12 ========================================================== SET B ========================================================== WITH 0.25 CONFIDENCE LEVEL PRUNING === Run information === Scheme: weka.classifiers.trees.J48 -C 0.25 -M 2 Relation: cerevisiae_SET_B Instances: 3089 Attributes: 9 Hydro TM_HELIX PRED_mitochondria PRED_cytoplasm PRED_er PRED_nucleus PRED_vacuole PRED_other SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ : 0 (3089.0/719.0) Number of Leaves : 1 Size of the tree : 1 Time taken to build model: 0.06 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 2368 76.6591 % Incorrectly Classified Instances 721 23.3409 % Kappa statistic 0.0002 Mean absolute error 0.357 Root mean squared error 0.423 Relative absolute error 99.9218 % Root relative squared error 100.089 % Total Number of Instances 3089 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.999 0.999 0.767 0.999 0.868 0 0.001 0.001 0.25 0.001 0.003 1 === Confusion Matrix === a b <-- classified as 2367 3 | a = 0 718 1 | b = 1 WITH 0.5 CONFIDENCE LEVEL PRUNING === Run information === Scheme: weka.classifiers.trees.J48 -C 0.5 -M 2 Relation: cerevisiae_SET_B Instances: 3089 Attributes: 9 Hydro TM_HELIX PRED_mitochondria PRED_cytoplasm PRED_er PRED_nucleus PRED_vacuole PRED_other SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ PRED_er = 0: 0 (2952.0/681.0) PRED_er = 1 | Hydro <= -0.420055 | | Hydro <= -0.752567 | | | Hydro <= -0.800875: 0 (18.0/3.0) | | | Hydro > -0.800875: 1 (3.0) | | Hydro > -0.752567: 0 (26.0) | Hydro > -0.420055: 0 (90.0/32.0) Number of Leaves : 5 Size of the tree : 9 Time taken to build model: 0.08 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 2367 76.6267 % Incorrectly Classified Instances 722 23.3733 % Kappa statistic 0.0156 Mean absolute error 0.3534 Root mean squared error 0.4217 Relative absolute error 98.9184 % Root relative squared error 99.7815 % Total Number of Instances 3089 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.994 0.983 0.769 0.994 0.867 0 0.017 0.006 0.444 0.017 0.032 1 === Confusion Matrix === a b <-- classified as 2355 15 | a = 0 707 12 | b = 1 -------------- Evaluation of Information Gain Ratio ------------------------------------ === Run information === Evaluator: weka.attributeSelection.GainRatioAttributeEval Search: weka.attributeSelection.Ranker -T -1.7976931348623157E308 -N -1 Relation: cerevisiae_SET_B Instances: 3089 Attributes: 9 Hydro TM_HELIX PRED_mitochondria PRED_cytoplasm PRED_er PRED_nucleus PRED_vacuole PRED_other SGD-ess Evaluation mode: evaluate on all training data === Attribute Selection on all input data === Search Method: Attribute ranking. Attribute Evaluator (supervised, Class (nominal): 9 SGD-ess): Gain Ratio feature evaluator Ranked attributes: 0.03889 6 PRED_nucleus 0.03402 7 PRED_vacuole 0.0233 3 PRED_mitochondria 0.01735 2 TM_HELIX 0.01479 1 Hydro 0.0129 8 PRED_other 0.00271 4 PRED_cytoplasm 0.00137 5 PRED_er Selected attributes: 6,7,3,2,1,8,4,5 : 8 ========================================================== SET C ========================================================== === Run information === Scheme: weka.classifiers.trees.J48 -C 0.25 -M 2 Relation: cerevisiae_SET_C Instances: 3089 Attributes: 9 mRNA_EXPR INTXN_PARTNERS EXPT_mitochondria EXPT_cytoplam EXPT_er EXPT_nucleus EXPT_vacuole EXPT_other SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ INTXN_PARTNERS <= 82: 0 (2673.0/510.0) INTXN_PARTNERS > 82 | EXPT_nucleus = 0 | | EXPT_other = 0: 0 (120.0/26.0) | | EXPT_other = 1 | | | mRNA_EXPR <= 0.8: 0 (12.0/2.0) | | | mRNA_EXPR > 0.8: 1 (66.0/24.0) | EXPT_nucleus = 1 | | mRNA_EXPR <= 12.9 | | | EXPT_cytoplam = 0: 1 (124.0/37.0) | | | EXPT_cytoplam = 1 | | | | INTXN_PARTNERS <= 212: 1 (72.0/23.0) | | | | INTXN_PARTNERS > 212: 0 (8.0/1.0) | | mRNA_EXPR > 12.9: 0 (14.0/2.0) Number of Leaves : 8 Size of the tree : 15 Time taken to build model: 0.06 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 2438 78.9252 % Incorrectly Classified Instances 651 21.0748 % Kappa statistic 0.2384 Mean absolute error 0.3244 Root mean squared error 0.4067 Relative absolute error 90.7876 % Root relative squared error 96.2352 % Total Number of Instances 3089 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.961 0.776 0.803 0.961 0.875 0 0.224 0.039 0.634 0.224 0.331 1 === Confusion Matrix === a b <-- classified as 2277 93 | a = 0 558 161 | b = 1 -------------- Evaluation of Information Gain Ratio ------------------------------------ === Run information === Evaluator: weka.attributeSelection.GainRatioAttributeEval Search: weka.attributeSelection.Ranker -T -1.7976931348623157E308 -N -1 Relation: cerevisiae_SET_C Instances: 3089 Attributes: 9 mRNA_EXPR INTXN_PARTNERS EXPT_mitochondria EXPT_cytoplam EXPT_er EXPT_nucleus EXPT_vacuole EXPT_other SGD-ess Evaluation mode: evaluate on all training data === Attribute Selection on all input data === Search Method: Attribute ranking. Attribute Evaluator (supervised, Class (nominal): 9 SGD-ess): Gain Ratio feature evaluator Ranked attributes: 0.037404 2 INTXN_PARTNERS 0.027664 6 EXPT_nucleus 0.025542 3 EXPT_mitochondria 0.025036 7 EXPT_vacuole 0.010497 1 mRNA_EXPR 0.006421 4 EXPT_cytoplam 0.005974 8 EXPT_other 0.000231 5 EXPT_er Selected attributes: 2,6,3,7,1,4,8,5 : 8 ========================================================== SET AB ========================================================== === Run information === Scheme: weka.classifiers.trees.J48 -C 0.25 -M 2 Relation: cerevisiae_SET_AB Instances: 3089 Attributes: 21 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON Hydro TM_HELIX PRED_mitochondria PRED_cytoplasm PRED_er PRED_nucleus PRED_vacuole PRED_other SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ PRED_nucleus = 0 | BLAST_yeast <= 0 | | PRED_vacuole = 0 | | | PRED_mitochondria = 0 | | | | CAI <= 0.145: 0 (624.0/93.0) | | | | CAI > 0.145 | | | | | PRED_other = 0 | | | | | | BLAST_closeyeast = 0: 0 (1.0) | | | | | | BLAST_closeyeast = 1: 0 (5.0) | | | | | | BLAST_closeyeast = 2: 0 (9.0/1.0) | | | | | | BLAST_closeyeast = 3: 0 (125.0/31.0) | | | | | | BLAST_closeyeast = 4 | | | | | | | TM_HELIX <= 0 | | | | | | | | PRED_cytoplasm = 0 | | | | | | | | | RARE_AA_RATIO <= 0.059342 | | | | | | | | | | RARE_AA_RATIO <= 0.046113: 0 (17.0/2.0) | | | | | | | | | | RARE_AA_RATIO > 0.046113: 1 (23.0/9.0) | | | | | | | | | RARE_AA_RATIO > 0.059342: 0 (29.0/1.0) | | | | | | | | PRED_cytoplasm = 1 | | | | | | | | | GC <= 0.363 | | | | | | | | | | L_aa <= 164: 0 (4.0) | | | | | | | | | | L_aa > 164 | | | | | | | | | | | CLOSE_STOP_RATIO <= 0.039474: 1 (7.0) | | | | | | | | | | | CLOSE_STOP_RATIO > 0.039474 | | | | | | | | | | | | CAI <= 0.172 | | | | | | | | | | | | | CAI <= 0.153: 0 (2.0) | | | | | | | | | | | | | CAI > 0.153: 1 (9.0/1.0) | | | | | | | | | | | | CAI > 0.172: 0 (3.0) | | | | | | | | | GC > 0.363: 0 (148.0/38.0) | | | | | | | TM_HELIX > 0: 0 (60.0/14.0) | | | | | | BLAST_closeyeast = 5 | | | | | | | TM_HELIX <= 5 | | | | | | | | BLAST_proks = 0 | | | | | | | | | PRED_cytoplasm = 0 | | | | | | | | | | CHR <= 12 | | | | | | | | | | | L_aa <= 605 | | | | | | | | | | | | L_aa <= 513 | | | | | | | | | | | | | Nc <= 53.22 | | | | | | | | | | | | | | L_aa <= 292: 0 (3.0/1.0) | | | | | | | | | | | | | | L_aa > 292: 1 (8.0) | | | | | | | | | | | | | Nc > 53.22: 0 (2.0) | | | | | | | | | | | | L_aa > 513: 0 (4.0) | | | | | | | | | | | L_aa > 605: 1 (9.0) | | | | | | | | | | CHR > 12: 0 (11.0/1.0) | | | | | | | | | PRED_cytoplasm = 1 | | | | | | | | | | CLOSE_STOP_RATIO <= 0.063147 | | | | | | | | | | | L_aa <= 353: 1 (24.0/9.0) | | | | | | | | | | | L_aa > 353 | | | | | | | | | | | | Hydro <= -0.418097 | | | | | | | | | | | | | Hydro <= -0.563969 | | | | | | | | | | | | | | CAI <= 0.305: 0 (7.0) | | | | | | | | | | | | | | CAI > 0.305: 1 (3.0/1.0) | | | | | | | | | | | | | Hydro > -0.563969: 1 (6.0) | | | | | | | | | | | | Hydro > -0.418097: 0 (34.0/3.0) | | | | | | | | | | CLOSE_STOP_RATIO > 0.063147: 1 (6.0) | | | | | | | | BLAST_proks = 1: 0 (4.0/1.0) | | | | | | | | BLAST_proks = 2: 0 (0.0) | | | | | | | | BLAST_proks = 3: 0 (1.0) | | | | | | | | BLAST_proks = 4: 0 (0.0) | | | | | | | | BLAST_proks = 5: 0 (0.0) | | | | | | | TM_HELIX > 5: 0 (7.0) | | | | | | BLAST_closeyeast = 6 | | | | | | | INTRON = 0 | | | | | | | | CHR_POSN <= 0.229283: 0 (7.0) | | | | | | | | CHR_POSN > 0.229283 | | | | | | | | | CHR <= 7 | | | | | | | | | | PRED_cytoplasm = 0 | | | | | | | | | | | CHR_POSN <= 0.425895: 0 (2.0) | | | | | | | | | | | CHR_POSN > 0.425895: 1 (2.0) | | | | | | | | | | PRED_cytoplasm = 1: 1 (13.0/2.0) | | | | | | | | | CHR > 7 | | | | | | | | | | CHR <= 11: 0 (8.0) | | | | | | | | | | CHR > 11 | | | | | | | | | | | CHR <= 13: 1 (3.0) | | | | | | | | | | | CHR > 13 | | | | | | | | | | | | CHR <= 14: 0 (2.0) | | | | | | | | | | | | CHR > 14 | | | | | | | | | | | | | CHR_POSN <= 0.809042 | | | | | | | | | | | | | | RARE_AA_RATIO <= 0.070175: 1 (5.0) | | | | | | | | | | | | | | RARE_AA_RATIO > 0.070175: 0 (3.0/1.0) | | | | | | | | | | | | | CHR_POSN > 0.809042: 0 (3.0) | | | | | | | INTRON = 1: 1 (2.0) | | | | | PRED_other = 1 | | | | | | GC <= 0.364: 1 (3.0/1.0) | | | | | | GC > 0.364: 0 (59.0/8.0) | | | PRED_mitochondria = 1: 0 (244.0/23.0) | | PRED_vacuole = 1: 0 (54.0/1.0) | BLAST_yeast > 0: 0 (491.0/31.0) PRED_nucleus = 1 | CAI <= 0.156 | | Hydro <= -0.497629: 0 (444.0/106.0) | | Hydro > -0.497629 | | | BLAST_closeyeast = 0: 0 (0.0) | | | BLAST_closeyeast = 1: 0 (1.0) | | | BLAST_closeyeast = 2: 0 (2.0) | | | BLAST_closeyeast = 3 | | | | CLOSE_STOP_RATIO <= 0.041116 | | | | | BLAST_yeast <= 1 | | | | | | L_aa <= 830 | | | | | | | GC <= 0.485: 1 (15.0/1.0) | | | | | | | GC > 0.485: 0 (2.0) | | | | | | L_aa > 830 | | | | | | | CHR <= 4: 0 (4.0) | | | | | | | CHR > 4 | | | | | | | | CHR <= 8: 1 (2.0) | | | | | | | | CHR > 8: 0 (4.0/1.0) | | | | | BLAST_yeast > 1 | | | | | | GC <= 0.396: 1 (3.0/1.0) | | | | | | GC > 0.396: 0 (3.0) | | | | CLOSE_STOP_RATIO > 0.041116: 0 (49.0/12.0) | | | BLAST_closeyeast = 4 | | | | RARE_AA_RATIO <= 0.049405: 1 (10.0) | | | | RARE_AA_RATIO > 0.049405: 0 (120.0/50.0) | | | BLAST_closeyeast = 5 | | | | RARE_AA_RATIO <= 0.082687: 1 (14.0/3.0) | | | | RARE_AA_RATIO > 0.082687 | | | | | Hydro <= -0.20129: 0 (4.0) | | | | | Hydro > -0.20129: 1 (3.0/1.0) | | | BLAST_closeyeast = 6 | | | | CAI <= 0.137: 1 (3.0) | | | | CAI > 0.137: 0 (2.0) | CAI > 0.156 | | CAI <= 0.489 | | | GC <= 0.434 | | | | Hydro <= -0.832264 | | | | | INTRON = 0 | | | | | | Hydro <= -0.932 | | | | | | | CHR_POSN <= 0.488559 | | | | | | | | RARE_AA_RATIO <= 0.048104: 0 (15.0) | | | | | | | | RARE_AA_RATIO > 0.048104 | | | | | | | | | CHR <= 10 | | | | | | | | | | CHR <= 5: 1 (4.0/1.0) | | | | | | | | | | CHR > 5: 0 (5.0) | | | | | | | | | CHR > 10: 1 (6.0) | | | | | | | CHR_POSN > 0.488559 | | | | | | | | CHR_POSN <= 0.926212: 1 (11.0/1.0) | | | | | | | | CHR_POSN > 0.926212: 0 (3.0) | | | | | | Hydro > -0.932: 0 (22.0/2.0) | | | | | INTRON = 1: 1 (2.0) | | | | Hydro > -0.832264 | | | | | BLAST_closeyeast = 0: 1 (1.0) | | | | | BLAST_closeyeast = 1: 1 (0.0) | | | | | BLAST_closeyeast = 2: 1 (1.0) | | | | | BLAST_closeyeast = 3 | | | | | | TM_HELIX <= 1 | | | | | | | L_aa <= 1033 | | | | | | | | L_aa <= 691 | | | | | | | | | Hydro <= -0.454632: 1 (6.0) | | | | | | | | | Hydro > -0.454632: 0 (3.0) | | | | | | | | L_aa > 691: 0 (8.0) | | | | | | | L_aa > 1033: 1 (7.0) | | | | | | TM_HELIX > 1: 0 (2.0) | | | | | BLAST_closeyeast = 4: 1 (84.0/31.0) | | | | | BLAST_closeyeast = 5 | | | | | | INTRON = 0 | | | | | | | RARE_AA_RATIO <= 0.047733: 1 (18.0/1.0) | | | | | | | RARE_AA_RATIO > 0.047733 | | | | | | | | BLAST_yeast <= 1: 1 (39.0/14.0) | | | | | | | | BLAST_yeast > 1: 0 (3.0) | | | | | | INTRON = 1 | | | | | | | GC <= 0.405: 0 (3.0) | | | | | | | GC > 0.405: 1 (2.0) | | | | | BLAST_closeyeast = 6 | | | | | | CLOSE_STOP_RATIO <= 0.049505 | | | | | | | CLOSE_STOP_RATIO <= 0.022599: 0 (2.0) | | | | | | | CLOSE_STOP_RATIO > 0.022599 | | | | | | | | L_aa <= 1001: 1 (17.0/1.0) | | | | | | | | L_aa > 1001: 0 (2.0) | | | | | | CLOSE_STOP_RATIO > 0.049505: 0 (4.0) | | | GC > 0.434: 0 (22.0/4.0) | | CAI > 0.489: 0 (16.0/1.0) Number of Leaves : 96 Size of the tree : 172 Time taken to build model: 0.45 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 2342 75.8174 % Incorrectly Classified Instances 747 24.1826 % Kappa statistic 0.2074 Mean absolute error 0.3071 Root mean squared error 0.4375 Relative absolute error 85.9595 % Root relative squared error 103.539 % Total Number of Instances 3089 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.906 0.729 0.804 0.906 0.852 0 0.271 0.094 0.467 0.271 0.343 1 === Confusion Matrix === a b <-- classified as 2147 223 | a = 0 524 195 | b = 1 -------------- Evaluation of Information Gain Ratio ------------------------------------ === Run information === Evaluator: weka.attributeSelection.GainRatioAttributeEval Search: weka.attributeSelection.Ranker -T -1.7976931348623157E308 -N -1 Relation: cerevisiae_SET_AB Instances: 3089 Attributes: 21 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON Hydro TM_HELIX PRED_mitochondria PRED_cytoplasm PRED_er PRED_nucleus PRED_vacuole PRED_other SGD-ess Evaluation mode: evaluate on all training data === Attribute Selection on all input data === Search Method: Attribute ranking. Attribute Evaluator (supervised, Class (nominal): 21 SGD-ess): Gain Ratio feature evaluator Ranked attributes: 0.03889 18 PRED_nucleus 0.03402 19 PRED_vacuole 0.0233 15 PRED_mitochondria 0.01948 7 BLAST_yeast 0.01735 14 TM_HELIX 0.01479 13 Hydro 0.0129 20 PRED_other 0.01081 1 CAI 0.01015 2 Nc 0.00778 3 GC 0.00518 8 BLAST_closeyeast 0.00395 9 BLAST_proks 0.00271 16 PRED_cytoplasm 0.00137 17 PRED_er 0.00103 12 INTRON 0 4 L_aa 0 10 CHR 0 11 CHR_POSN 0 5 CLOSE_STOP_RATIO 0 6 RARE_AA_RATIO Selected attributes: 18,19,15,7,14,13,20,1,2,3,8,9,16,17,12,4,10,11,5,6 : 20 ========================================================== SET AC ========================================================== === Run information === Scheme: weka.classifiers.trees.J48 -C 0.25 -M 2 Relation: cerevisiae_SET_AC Instances: 3089 Attributes: 21 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON mRNA_EXPR INTXN_PARTNERS EXPT_mitochondria EXPT_cytoplam EXPT_er EXPT_nucleus EXPT_vacuole EXPT_other SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ INTXN_PARTNERS <= 82 | EXPT_vacuole = 0 | | EXPT_mitochondria = 0 | | | BLAST_yeast <= 0 | | | | INTXN_PARTNERS <= 6 | | | | | INTRON = 0: 0 (819.0/129.0) | | | | | INTRON = 1 | | | | | | INTXN_PARTNERS <= 1: 1 (3.0) | | | | | | INTXN_PARTNERS > 1 | | | | | | | EXPT_nucleus = 0: 0 (11.0) | | | | | | | EXPT_nucleus = 1 | | | | | | | | CHR <= 14: 0 (4.0) | | | | | | | | CHR > 14: 1 (3.0) | | | | INTXN_PARTNERS > 6 | | | | | EXPT_cytoplam = 0 | | | | | | EXPT_nucleus = 0 | | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | | BLAST_closeyeast = 1: 0 (1.0) | | | | | | | BLAST_closeyeast = 2: 0 (1.0) | | | | | | | BLAST_closeyeast = 3 | | | | | | | | EXPT_other = 0: 0 (23.0/5.0) | | | | | | | | EXPT_other = 1 | | | | | | | | | GC <= 0.364 | | | | | | | | | | L_aa <= 831: 1 (5.0) | | | | | | | | | | L_aa > 831 | | | | | | | | | | | GC <= 0.362 | | | | | | | | | | | | INTXN_PARTNERS <= 15: 0 (6.0) | | | | | | | | | | | | INTXN_PARTNERS > 15: 1 (3.0/1.0) | | | | | | | | | | | GC > 0.362: 1 (3.0) | | | | | | | | | GC > 0.364 | | | | | | | | | | CHR_POSN <= 0.479277 | | | | | | | | | | | L_aa <= 1229: 0 (16.0/3.0) | | | | | | | | | | | L_aa > 1229: 1 (4.0) | | | | | | | | | | CHR_POSN > 0.479277: 0 (24.0/1.0) | | | | | | | BLAST_closeyeast = 4 | | | | | | | | EXPT_er = 0: 0 (120.0/43.0) | | | | | | | | EXPT_er = 1 | | | | | | | | | INTXN_PARTNERS <= 31 | | | | | | | | | | Nc <= 50.81 | | | | | | | | | | | Nc <= 48.22: 1 (3.0) | | | | | | | | | | | Nc > 48.22: 0 (5.0/1.0) | | | | | | | | | | Nc > 50.81: 1 (7.0) | | | | | | | | | INTXN_PARTNERS > 31: 0 (4.0) | | | | | | | BLAST_closeyeast = 5 | | | | | | | | L_aa <= 506 | | | | | | | | | L_aa <= 277: 0 (7.0) | | | | | | | | | L_aa > 277 | | | | | | | | | | EXPT_er = 0 | | | | | | | | | | | CHR_POSN <= 0.502863: 0 (3.0) | | | | | | | | | | | CHR_POSN > 0.502863: 1 (8.0/1.0) | | | | | | | | | | EXPT_er = 1: 1 (3.0) | | | | | | | | L_aa > 506: 0 (8.0) | | | | | | | BLAST_closeyeast = 6: 0 (3.0) | | | | | | EXPT_nucleus = 1 | | | | | | | INTRON = 0 | | | | | | | | CAI <= 0.146 | | | | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | | | | | | BLAST_closeyeast = 2: 0 (4.0) | | | | | | | | | BLAST_closeyeast = 3 | | | | | | | | | | RARE_AA_RATIO <= 0.050633 | | | | | | | | | | | INTXN_PARTNERS <= 35: 1 (5.0) | | | | | | | | | | | INTXN_PARTNERS > 35: 0 (4.0/1.0) | | | | | | | | | | RARE_AA_RATIO > 0.050633 | | | | | | | | | | | mRNA_EXPR <= 0.3 | | | | | | | | | | | | CAI <= 0.131 | | | | | | | | | | | | | CLOSE_STOP_RATIO <= 0.026804: 0 (2.0) | | | | | | | | | | | | | CLOSE_STOP_RATIO > 0.026804: 1 (4.0) | | | | | | | | | | | | CAI > 0.131: 0 (3.0) | | | | | | | | | | | mRNA_EXPR > 0.3: 0 (13.0) | | | | | | | | | BLAST_closeyeast = 4 | | | | | | | | | | L_aa <= 688 | | | | | | | | | | | INTXN_PARTNERS <= 9: 1 (6.0) | | | | | | | | | | | INTXN_PARTNERS > 9 | | | | | | | | | | | | Nc <= 53.99: 0 (18.0/4.0) | | | | | | | | | | | | Nc > 53.99 | | | | | | | | | | | | | GC <= 0.383: 0 (4.0) | | | | | | | | | | | | | GC > 0.383: 1 (22.0/7.0) | | | | | | | | | | L_aa > 688: 0 (14.0/1.0) | | | | | | | | | BLAST_closeyeast = 5: 0 (2.0/1.0) | | | | | | | | | BLAST_closeyeast = 6: 1 (2.0) | | | | | | | | CAI > 0.146 | | | | | | | | | BLAST_closeyeast = 0: 1 (0.0) | | | | | | | | | BLAST_closeyeast = 1: 1 (0.0) | | | | | | | | | BLAST_closeyeast = 2: 1 (2.0) | | | | | | | | | BLAST_closeyeast = 3 | | | | | | | | | | CHR <= 11: 0 (5.0/1.0) | | | | | | | | | | CHR > 11: 1 (5.0/1.0) | | | | | | | | | BLAST_closeyeast = 4 | | | | | | | | | | mRNA_EXPR <= 0.3: 0 (3.0) | | | | | | | | | | mRNA_EXPR > 0.3: 1 (33.0/6.0) | | | | | | | | | BLAST_closeyeast = 5 | | | | | | | | | | CHR_POSN <= 0.447823 | | | | | | | | | | | CHR_POSN <= 0.284396 | | | | | | | | | | | | CHR <= 14: 1 (4.0) | | | | | | | | | | | | CHR > 14: 0 (3.0/1.0) | | | | | | | | | | | CHR_POSN > 0.284396: 0 (3.0) | | | | | | | | | | CHR_POSN > 0.447823: 1 (7.0) | | | | | | | | | BLAST_closeyeast = 6 | | | | | | | | | | GC <= 0.392: 1 (3.0) | | | | | | | | | | GC > 0.392: 0 (2.0) | | | | | | | INTRON = 1: 1 (4.0) | | | | | EXPT_cytoplam = 1 | | | | | | CAI <= 0.28: 0 (379.0/78.0) | | | | | | CAI > 0.28 | | | | | | | mRNA_EXPR <= 30.7 | | | | | | | | L_aa <= 326: 0 (15.0/1.0) | | | | | | | | L_aa > 326 | | | | | | | | | EXPT_nucleus = 0: 1 (21.0/6.0) | | | | | | | | | EXPT_nucleus = 1 | | | | | | | | | | mRNA_EXPR <= 3.5: 1 (2.0) | | | | | | | | | | mRNA_EXPR > 3.5: 0 (7.0) | | | | | | | mRNA_EXPR > 30.7: 1 (6.0) | | | BLAST_yeast > 0 | | | | EXPT_cytoplam = 0 | | | | | CLOSE_STOP_RATIO <= 0.030445 | | | | | | BLAST_proks = 0 | | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | | | | BLAST_closeyeast = 2: 0 (1.0) | | | | | | | BLAST_closeyeast = 3 | | | | | | | | EXPT_other = 0 | | | | | | | | | CHR <= 12: 0 (9.0) | | | | | | | | | CHR > 12: 1 (4.0/1.0) | | | | | | | | EXPT_other = 1 | | | | | | | | | CAI <= 0.182: 1 (4.0) | | | | | | | | | CAI > 0.182: 0 (2.0) | | | | | | | BLAST_closeyeast = 4 | | | | | | | | EXPT_other = 0 | | | | | | | | | CHR_POSN <= 0.412598: 0 (6.0) | | | | | | | | | CHR_POSN > 0.412598: 1 (4.0/1.0) | | | | | | | | EXPT_other = 1 | | | | | | | | | mRNA_EXPR <= 0.6: 1 (2.0) | | | | | | | | | mRNA_EXPR > 0.6: 0 (8.0/1.0) | | | | | | | BLAST_closeyeast = 5 | | | | | | | | CAI <= 0.261: 1 (3.0) | | | | | | | | CAI > 0.261: 0 (3.0) | | | | | | | BLAST_closeyeast = 6: 1 (1.0) | | | | | | BLAST_proks = 1 | | | | | | | CLOSE_STOP_RATIO <= 0.020243: 0 (2.0) | | | | | | | CLOSE_STOP_RATIO > 0.020243: 1 (5.0) | | | | | | BLAST_proks = 2: 0 (1.0) | | | | | | BLAST_proks = 3: 0 (0.0) | | | | | | BLAST_proks = 4: 0 (0.0) | | | | | | BLAST_proks = 5: 0 (0.0) | | | | | CLOSE_STOP_RATIO > 0.030445: 0 (151.0/15.0) | | | | EXPT_cytoplam = 1: 0 (349.0/23.0) | | EXPT_mitochondria = 1: 0 (307.0/28.0) | EXPT_vacuole = 1: 0 (107.0/6.0) INTXN_PARTNERS > 82 | EXPT_mitochondria = 0 | | GC <= 0.428 | | | EXPT_nucleus = 0 | | | | EXPT_other = 0 | | | | | mRNA_EXPR <= 1.2 | | | | | | L_aa <= 1337: 0 (20.0) | | | | | | L_aa > 1337 | | | | | | | Nc <= 51.99: 0 (3.0/1.0) | | | | | | | Nc > 51.99: 1 (2.0) | | | | | mRNA_EXPR > 1.2 | | | | | | BLAST_yeast <= 0 | | | | | | | L_aa <= 1157 | | | | | | | | GC <= 0.393: 1 (9.0/1.0) | | | | | | | | GC > 0.393 | | | | | | | | | CHR <= 5: 1 (6.0/1.0) | | | | | | | | | CHR > 5 | | | | | | | | | | RARE_AA_RATIO <= 0.065574: 0 (8.0/1.0) | | | | | | | | | | RARE_AA_RATIO > 0.065574: 1 (5.0/2.0) | | | | | | | L_aa > 1157: 0 (5.0) | | | | | | BLAST_yeast > 0: 0 (12.0/1.0) | | | | EXPT_other = 1 | | | | | mRNA_EXPR <= 0.8: 0 (11.0/2.0) | | | | | mRNA_EXPR > 0.8 | | | | | | BLAST_closeyeast = 0: 1 (0.0) | | | | | | BLAST_closeyeast = 1: 1 (0.0) | | | | | | BLAST_closeyeast = 2: 1 (0.0) | | | | | | BLAST_closeyeast = 3 | | | | | | | CAI <= 0.204 | | | | | | | | GC <= 0.359: 1 (2.0) | | | | | | | | GC > 0.359: 0 (4.0) | | | | | | | CAI > 0.204: 1 (3.0) | | | | | | BLAST_closeyeast = 4 | | | | | | | CHR_POSN <= 0.572761: 1 (12.0) | | | | | | | CHR_POSN > 0.572761 | | | | | | | | CAI <= 0.155: 0 (2.0) | | | | | | | | CAI > 0.155: 1 (8.0/2.0) | | | | | | BLAST_closeyeast = 5: 1 (12.0/3.0) | | | | | | BLAST_closeyeast = 6 | | | | | | | CHR <= 11 | | | | | | | | INTXN_PARTNERS <= 93: 1 (3.0) | | | | | | | | INTXN_PARTNERS > 93: 0 (6.0/1.0) | | | | | | | CHR > 11: 1 (5.0) | | | EXPT_nucleus = 1 | | | | BLAST_yeast <= 2 | | | | | EXPT_other = 0 | | | | | | INTXN_PARTNERS <= 213 | | | | | | | CHR <= 10 | | | | | | | | CHR <= 7 | | | | | | | | | BLAST_yeast <= 0 | | | | | | | | | | CAI <= 0.121 | | | | | | | | | | | Nc <= 50.47: 1 (2.0) | | | | | | | | | | | Nc > 50.47: 0 (7.0) | | | | | | | | | | CAI > 0.121 | | | | | | | | | | | L_aa <= 1208: 1 (47.0/6.0) | | | | | | | | | | | L_aa > 1208: 0 (2.0) | | | | | | | | | BLAST_yeast > 0 | | | | | | | | | | GC <= 0.413: 1 (3.0) | | | | | | | | | | GC > 0.413: 0 (3.0) | | | | | | | | CHR > 7 | | | | | | | | | RARE_AA_RATIO <= 0.058462: 1 (4.0/1.0) | | | | | | | | | RARE_AA_RATIO > 0.058462: 0 (8.0/1.0) | | | | | | | CHR > 10 | | | | | | | | INTXN_PARTNERS <= 88: 0 (2.0) | | | | | | | | INTXN_PARTNERS > 88: 1 (55.0/7.0) | | | | | | INTXN_PARTNERS > 213: 0 (7.0/1.0) | | | | | EXPT_other = 1 | | | | | | CLOSE_STOP_RATIO <= 0.018391: 0 (3.0) | | | | | | CLOSE_STOP_RATIO > 0.018391: 1 (29.0/2.0) | | | | BLAST_yeast > 2 | | | | | EXPT_cytoplam = 0: 0 (5.0) | | | | | EXPT_cytoplam = 1 | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | | | BLAST_closeyeast = 2: 0 (0.0) | | | | | | BLAST_closeyeast = 3: 0 (0.0) | | | | | | BLAST_closeyeast = 4: 0 (0.0) | | | | | | BLAST_closeyeast = 5: 1 (2.0) | | | | | | BLAST_closeyeast = 6: 0 (3.0) | | GC > 0.428 | | | BLAST_yeast <= 0 | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | BLAST_closeyeast = 2: 0 (0.0) | | | | BLAST_closeyeast = 3 | | | | | EXPT_cytoplam = 0: 1 (4.0) | | | | | EXPT_cytoplam = 1 | | | | | | GC <= 0.436: 1 (2.0) | | | | | | GC > 0.436: 0 (4.0) | | | | BLAST_closeyeast = 4 | | | | | EXPT_nucleus = 0: 0 (7.0) | | | | | EXPT_nucleus = 1 | | | | | | RARE_AA_RATIO <= 0.041816: 1 (3.0) | | | | | | RARE_AA_RATIO > 0.041816: 0 (10.0/2.0) | | | | BLAST_closeyeast = 5 | | | | | CHR <= 8: 0 (6.0) | | | | | CHR > 8: 1 (3.0/1.0) | | | | BLAST_closeyeast = 6 | | | | | CAI <= 0.609: 0 (3.0) | | | | | CAI > 0.609: 1 (4.0/1.0) | | | BLAST_yeast > 0: 0 (22.0) | EXPT_mitochondria = 1: 0 (28.0/1.0) Number of Leaves : 146 Size of the tree : 252 Time taken to build model: 0.52 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 2386 77.2418 % Incorrectly Classified Instances 703 22.7582 % Kappa statistic 0.2616 Mean absolute error 0.2927 Root mean squared error 0.4388 Relative absolute error 81.9389 % Root relative squared error 103.8275 % Total Number of Instances 3089 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.911 0.686 0.814 0.911 0.86 0 0.314 0.089 0.518 0.314 0.391 1 === Confusion Matrix === a b <-- classified as 2160 210 | a = 0 493 226 | b = 1 -------------- Evaluation of Information Gain Ratio ------------------------------------ === Run information === Evaluator: weka.attributeSelection.GainRatioAttributeEval Search: weka.attributeSelection.Ranker -T -1.7976931348623157E308 -N -1 Relation: cerevisiae_SET_AC Instances: 3089 Attributes: 21 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON mRNA_EXPR INTXN_PARTNERS EXPT_mitochondria EXPT_cytoplam EXPT_er EXPT_nucleus EXPT_vacuole EXPT_other SGD-ess Evaluation mode: evaluate on all training data === Attribute Selection on all input data === Search Method: Attribute ranking. Attribute Evaluator (supervised, Class (nominal): 21 SGD-ess): Gain Ratio feature evaluator Ranked attributes: 0.037404 14 INTXN_PARTNERS 0.027664 18 EXPT_nucleus 0.025542 15 EXPT_mitochondria 0.025036 19 EXPT_vacuole 0.019481 7 BLAST_yeast 0.010809 1 CAI 0.010497 13 mRNA_EXPR 0.010153 2 Nc 0.007776 3 GC 0.006421 16 EXPT_cytoplam 0.005974 20 EXPT_other 0.005178 8 BLAST_closeyeast 0.003949 9 BLAST_proks 0.001031 12 INTRON 0.000231 17 EXPT_er 0 4 L_aa 0 10 CHR 0 11 CHR_POSN 0 5 CLOSE_STOP_RATIO 0 6 RARE_AA_RATIO Selected attributes: 14,18,15,19,7,1,13,2,3,16,20,8,9,12,17,4,10,11,5,6 : 20 ========================================================== SET BC ========================================================== === Run information === Scheme: weka.classifiers.trees.J48 -C 0.25 -M 2 Relation: cerevisiae_SET_BC Instances: 3089 Attributes: 17 Hydro TM_HELIX PRED_mitochondria PRED_cytoplasm PRED_er PRED_nucleus PRED_vacuole PRED_other mRNA_EXPR INTXN_PARTNERS EXPT_mitochondria EXPT_cytoplam EXPT_er EXPT_nucleus EXPT_vacuole EXPT_other SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ INTXN_PARTNERS <= 82 | PRED_nucleus = 0: 0 (1886.0/275.0) | PRED_nucleus = 1 | | EXPT_cytoplam = 0 | | | INTXN_PARTNERS <= 3: 0 (118.0/27.0) | | | INTXN_PARTNERS > 3 | | | | EXPT_nucleus = 0: 0 (90.0/36.0) | | | | EXPT_nucleus = 1 | | | | | Hydro <= -0.485404 | | | | | | EXPT_other = 0: 0 (130.0/52.0) | | | | | | EXPT_other = 1 | | | | | | | Hydro <= -1.165408: 1 (3.0) | | | | | | | Hydro > -1.165408: 0 (8.0/1.0) | | | | | Hydro > -0.485404 | | | | | | mRNA_EXPR <= 0.4 | | | | | | | mRNA_EXPR <= 0.2: 0 (3.0) | | | | | | | mRNA_EXPR > 0.2 | | | | | | | | INTXN_PARTNERS <= 17: 0 (3.0) | | | | | | | | INTXN_PARTNERS > 17: 1 (9.0/3.0) | | | | | | mRNA_EXPR > 0.4 | | | | | | | INTXN_PARTNERS <= 66: 1 (47.0/6.0) | | | | | | | INTXN_PARTNERS > 66: 0 (4.0/1.0) | | EXPT_cytoplam = 1: 0 (372.0/68.0) INTXN_PARTNERS > 82 | EXPT_mitochondria = 0 | | PRED_nucleus = 0 | | | PRED_other = 0 | | | | EXPT_cytoplam = 0 | | | | | PRED_mitochondria = 0 | | | | | | Hydro <= -0.526923: 0 (17.0/2.0) | | | | | | Hydro > -0.526923 | | | | | | | PRED_vacuole = 0 | | | | | | | | TM_HELIX <= 0 | | | | | | | | | mRNA_EXPR <= 18.5 | | | | | | | | | | Hydro <= -0.476136 | | | | | | | | | | | EXPT_other = 0: 1 (2.0) | | | | | | | | | | | EXPT_other = 1: 0 (2.0) | | | | | | | | | | Hydro > -0.476136: 1 (23.0) | | | | | | | | | mRNA_EXPR > 18.5: 0 (3.0) | | | | | | | | TM_HELIX > 0: 0 (2.0) | | | | | | | PRED_vacuole = 1: 0 (3.0/1.0) | | | | | PRED_mitochondria = 1: 0 (2.0) | | | | EXPT_cytoplam = 1 | | | | | mRNA_EXPR <= 1.8: 0 (38.0/5.0) | | | | | mRNA_EXPR > 1.8 | | | | | | EXPT_other = 0 | | | | | | | EXPT_nucleus = 0 | | | | | | | | Hydro <= -0.276056 | | | | | | | | | INTXN_PARTNERS <= 109: 1 (7.0) | | | | | | | | | INTXN_PARTNERS > 109: 0 (23.0/10.0) | | | | | | | | Hydro > -0.276056: 0 (17.0/2.0) | | | | | | | EXPT_nucleus = 1 | | | | | | | | PRED_cytoplasm = 0 | | | | | | | | | Hydro <= -0.523304: 1 (3.0/1.0) | | | | | | | | | Hydro > -0.523304: 0 (4.0/1.0) | | | | | | | | PRED_cytoplasm = 1 | | | | | | | | | mRNA_EXPR <= 13.4 | | | | | | | | | | mRNA_EXPR <= 2.5: 0 (2.0) | | | | | | | | | | mRNA_EXPR > 2.5: 1 (15.0/2.0) | | | | | | | | | mRNA_EXPR > 13.4: 0 (6.0/1.0) | | | | | | EXPT_other = 1: 1 (4.0/1.0) | | | PRED_other = 1 | | | | INTXN_PARTNERS <= 129: 0 (8.0) | | | | INTXN_PARTNERS > 129: 1 (2.0) | | PRED_nucleus = 1 | | | EXPT_other = 0 | | | | EXPT_nucleus = 0: 0 (25.0/4.0) | | | | EXPT_nucleus = 1: 1 (120.0/38.0) | | | EXPT_other = 1 | | | | Hydro <= -0.838302 | | | | | INTXN_PARTNERS <= 114: 1 (5.0/1.0) | | | | | INTXN_PARTNERS > 114: 0 (10.0/2.0) | | | | Hydro > -0.838302: 1 (45.0/3.0) | EXPT_mitochondria = 1: 0 (28.0/1.0) Number of Leaves : 38 Size of the tree : 75 Time taken to build model: 0.23 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 2441 79.0223 % Incorrectly Classified Instances 648 20.9777 % Kappa statistic 0.2819 Mean absolute error 0.3008 Root mean squared error 0.4053 Relative absolute error 84.181 % Root relative squared error 95.9179 % Total Number of Instances 3089 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.943 0.712 0.814 0.943 0.873 0 0.288 0.057 0.603 0.288 0.39 1 === Confusion Matrix === a b <-- classified as 2234 136 | a = 0 512 207 | b = 1 -------------- Evaluation of Information Gain Ratio ------------------------------------ === Run information === Evaluator: weka.attributeSelection.GainRatioAttributeEval Search: weka.attributeSelection.Ranker -T -1.7976931348623157E308 -N -1 Relation: cerevisiae_SET_BC Instances: 3089 Attributes: 17 Hydro TM_HELIX PRED_mitochondria PRED_cytoplasm PRED_er PRED_nucleus PRED_vacuole PRED_other mRNA_EXPR INTXN_PARTNERS EXPT_mitochondria EXPT_cytoplam EXPT_er EXPT_nucleus EXPT_vacuole EXPT_other SGD-ess Evaluation mode: evaluate on all training data === Attribute Selection on all input data === Search Method: Attribute ranking. Attribute Evaluator (supervised, Class (nominal): 17 SGD-ess): Gain Ratio feature evaluator Ranked attributes: 0.038887 6 PRED_nucleus 0.037404 10 INTXN_PARTNERS 0.034023 7 PRED_vacuole 0.027664 14 EXPT_nucleus 0.025542 11 EXPT_mitochondria 0.025036 15 EXPT_vacuole 0.023299 3 PRED_mitochondria 0.017345 2 TM_HELIX 0.014788 1 Hydro 0.012899 8 PRED_other 0.010497 9 mRNA_EXPR 0.006421 12 EXPT_cytoplam 0.005974 16 EXPT_other 0.002706 4 PRED_cytoplasm 0.00137 5 PRED_er 0.000231 13 EXPT_er Selected attributes: 6,10,7,14,11,15,3,2,1,8,9,12,16,4,5,13 : 16 ========================================================== SET ABC ========================================================== === Run information === Scheme: weka.classifiers.trees.J48 -C 0.25 -M 2 Relation: cerevisiae_SET_ABC Instances: 3089 Attributes: 29 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON Hydro TM_HELIX PRED_mitochondria PRED_cytoplasm PRED_er PRED_nucleus PRED_vacuole PRED_other mRNA_EXPR INTXN_PARTNERS EXPT_mitochondria EXPT_cytoplam EXPT_er EXPT_nucleus EXPT_vacuole EXPT_other SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ INTXN_PARTNERS <= 82 | PRED_vacuole = 0 | | PRED_nucleus = 0 | | | BLAST_yeast <= 0 | | | | CAI <= 0.28 | | | | | EXPT_er = 0 | | | | | | INTXN_PARTNERS <= 12 | | | | | | | EXPT_nucleus = 0: 0 (609.0/57.0) | | | | | | | EXPT_nucleus = 1 | | | | | | | | INTRON = 0 | | | | | | | | | EXPT_cytoplam = 0 | | | | | | | | | | PRED_other = 0 | | | | | | | | | | | CLOSE_STOP_RATIO <= 0.040307: 0 (16.0) | | | | | | | | | | | CLOSE_STOP_RATIO > 0.040307 | | | | | | | | | | | | GC <= 0.392: 1 (7.0/1.0) | | | | | | | | | | | | GC > 0.392: 0 (5.0) | | | | | | | | | | PRED_other = 1: 1 (2.0) | | | | | | | | | EXPT_cytoplam = 1 | | | | | | | | | | CHR <= 11 | | | | | | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | | | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | | | | | | | | BLAST_closeyeast = 2: 0 (2.0) | | | | | | | | | | | BLAST_closeyeast = 3 | | | | | | | | | | | | CHR <= 7: 0 (12.0) | | | | | | | | | | | | CHR > 7 | | | | | | | | | | | | | CHR <= 8: 1 (2.0) | | | | | | | | | | | | | CHR > 8: 0 (4.0) | | | | | | | | | | | BLAST_closeyeast = 4 | | | | | | | | | | | | PRED_cytoplasm = 0 | | | | | | | | | | | | | Nc <= 56.43: 0 (18.0) | | | | | | | | | | | | | Nc > 56.43: 1 (3.0/1.0) | | | | | | | | | | | | PRED_cytoplasm = 1 | | | | | | | | | | | | | RARE_AA_RATIO <= 0.071344: 0 (19.0/3.0) | | | | | | | | | | | | | RARE_AA_RATIO > 0.071344 | | | | | | | | | | | | | | GC <= 0.466 | | | | | | | | | | | | | | | CHR <= 6: 1 (5.0) | | | | | | | | | | | | | | | CHR > 6 | | | | | | | | | | | | | | | | GC <= 0.4: 1 (3.0) | | | | | | | | | | | | | | | | GC > 0.4: 0 (2.0) | | | | | | | | | | | | | | GC > 0.466: 0 (3.0) | | | | | | | | | | | BLAST_closeyeast = 5 | | | | | | | | | | | | mRNA_EXPR <= 1.9: 0 (6.0/1.0) | | | | | | | | | | | | mRNA_EXPR > 1.9: 1 (5.0) | | | | | | | | | | | BLAST_closeyeast = 6: 0 (1.0) | | | | | | | | | | CHR > 11: 0 (54.0/2.0) | | | | | | | | INTRON = 1 | | | | | | | | | L_aa <= 238: 0 (4.0) | | | | | | | | | L_aa > 238: 1 (2.0) | | | | | | INTXN_PARTNERS > 12 | | | | | | | EXPT_other = 0: 0 (256.0/36.0) | | | | | | | EXPT_other = 1 | | | | | | | | TM_HELIX <= 0 | | | | | | | | | RARE_AA_RATIO <= 0.085057 | | | | | | | | | | PRED_er = 0 | | | | | | | | | | | PRED_cytoplasm = 0 | | | | | | | | | | | | Hydro <= -0.730285: 0 (10.0) | | | | | | | | | | | | Hydro > -0.730285 | | | | | | | | | | | | | EXPT_nucleus = 0 | | | | | | | | | | | | | | CHR <= 10 | | | | | | | | | | | | | | | PRED_other = 0: 1 (7.0) | | | | | | | | | | | | | | | PRED_other = 1 | | | | | | | | | | | | | | | | CHR <= 3: 0 (2.0) | | | | | | | | | | | | | | | | CHR > 3: 1 (8.0/1.0) | | | | | | | | | | | | | | CHR > 10: 0 (15.0/4.0) | | | | | | | | | | | | | EXPT_nucleus = 1: 1 (2.0) | | | | | | | | | | | PRED_cytoplasm = 1: 0 (51.0/13.0) | | | | | | | | | | PRED_er = 1: 1 (6.0/2.0) | | | | | | | | | RARE_AA_RATIO > 0.085057: 1 (6.0) | | | | | | | | TM_HELIX > 0: 0 (7.0) | | | | | EXPT_er = 1 | | | | | | CAI <= 0.12: 0 (18.0) | | | | | | CAI > 0.12 | | | | | | | PRED_other = 0 | | | | | | | | PRED_cytoplasm = 0 | | | | | | | | | PRED_er = 0 | | | | | | | | | | CHR_POSN <= 0.268241: 0 (15.0) | | | | | | | | | | CHR_POSN > 0.268241 | | | | | | | | | | | TM_HELIX <= 11 | | | | | | | | | | | | RARE_AA_RATIO <= 0.08046 | | | | | | | | | | | | | CHR_POSN <= 0.765739 | | | | | | | | | | | | | | CHR <= 7: 1 (5.0) | | | | | | | | | | | | | | CHR > 7 | | | | | | | | | | | | | | | Hydro <= -0.302507: 1 (4.0) | | | | | | | | | | | | | | | Hydro > -0.302507: 0 (8.0/1.0) | | | | | | | | | | | | | CHR_POSN > 0.765739: 0 (6.0) | | | | | | | | | | | | RARE_AA_RATIO > 0.08046: 0 (10.0) | | | | | | | | | | | TM_HELIX > 11: 1 (3.0) | | | | | | | | | PRED_er = 1 | | | | | | | | | | TM_HELIX <= 6 | | | | | | | | | | | Hydro <= -0.384545: 0 (5.0) | | | | | | | | | | | Hydro > -0.384545: 1 (26.0/8.0) | | | | | | | | | | TM_HELIX > 6: 0 (8.0/1.0) | | | | | | | | PRED_cytoplasm = 1 | | | | | | | | | CHR_POSN <= 0.58211: 1 (8.0/1.0) | | | | | | | | | CHR_POSN > 0.58211: 0 (5.0) | | | | | | | PRED_other = 1 | | | | | | | | INTXN_PARTNERS <= 4: 0 (11.0) | | | | | | | | INTXN_PARTNERS > 4: 1 (3.0/1.0) | | | | CAI > 0.28 | | | | | EXPT_other = 0 | | | | | | mRNA_EXPR <= 30.7 | | | | | | | BLAST_proks = 0 | | | | | | | | L_aa <= 483 | | | | | | | | | TM_HELIX <= 1 | | | | | | | | | | CAI <= 0.318 | | | | | | | | | | | GC <= 0.42: 1 (9.0/1.0) | | | | | | | | | | | GC > 0.42: 0 (5.0) | | | | | | | | | | CAI > 0.318 | | | | | | | | | | | Nc <= 37.77 | | | | | | | | | | | | CHR <= 14 | | | | | | | | | | | | | CLOSE_STOP_RATIO <= 0.047771: 0 (17.0/2.0) | | | | | | | | | | | | | CLOSE_STOP_RATIO > 0.047771: 1 (8.0/3.0) | | | | | | | | | | | | CHR > 14: 1 (3.0) | | | | | | | | | | | Nc > 37.77: 0 (21.0) | | | | | | | | | TM_HELIX > 1: 0 (4.0) | | | | | | | | L_aa > 483 | | | | | | | | | EXPT_nucleus = 0 | | | | | | | | | | mRNA_EXPR <= 4.3 | | | | | | | | | | | CLOSE_STOP_RATIO <= 0.046269: 0 (3.0) | | | | | | | | | | | CLOSE_STOP_RATIO > 0.046269: 1 (2.0) | | | | | | | | | | mRNA_EXPR > 4.3: 1 (15.0) | | | | | | | | | EXPT_nucleus = 1: 0 (2.0) | | | | | | | BLAST_proks = 1: 0 (7.0/1.0) | | | | | | | BLAST_proks = 2: 0 (0.0) | | | | | | | BLAST_proks = 3: 0 (1.0) | | | | | | | BLAST_proks = 4: 0 (0.0) | | | | | | | BLAST_proks = 5: 0 (0.0) | | | | | | mRNA_EXPR > 30.7: 1 (6.0) | | | | | EXPT_other = 1: 0 (6.0) | | | BLAST_yeast > 0: 0 (431.0/23.0) | | PRED_nucleus = 1 | | | EXPT_cytoplam = 0 | | | | INTXN_PARTNERS <= 3 | | | | | mRNA_EXPR <= 0.3: 0 (28.0/1.0) | | | | | mRNA_EXPR > 0.3 | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | | | BLAST_closeyeast = 2: 0 (4.0) | | | | | | BLAST_closeyeast = 3 | | | | | | | L_aa <= 728: 0 (19.0/1.0) | | | | | | | L_aa > 728 | | | | | | | | BLAST_yeast <= 14 | | | | | | | | | INTXN_PARTNERS <= 1: 1 (3.0) | | | | | | | | | INTXN_PARTNERS > 1 | | | | | | | | | | CHR_POSN <= 0.523346: 0 (4.0) | | | | | | | | | | CHR_POSN > 0.523346: 1 (2.0) | | | | | | | | BLAST_yeast > 14: 0 (4.0) | | | | | | BLAST_closeyeast = 4 | | | | | | | RARE_AA_RATIO <= 0.048689: 0 (12.0) | | | | | | | RARE_AA_RATIO > 0.048689 | | | | | | | | mRNA_EXPR <= 1.6 | | | | | | | | | EXPT_other = 0 | | | | | | | | | | RARE_AA_RATIO <= 0.051701: 1 (2.0) | | | | | | | | | | RARE_AA_RATIO > 0.051701: 0 (13.0/2.0) | | | | | | | | | EXPT_other = 1 | | | | | | | | | | Nc <= 53.16 | | | | | | | | | | | CAI <= 0.148: 0 (4.0) | | | | | | | | | | | CAI > 0.148: 1 (2.0) | | | | | | | | | | Nc > 53.16: 1 (4.0) | | | | | | | | mRNA_EXPR > 1.6: 1 (4.0) | | | | | | BLAST_closeyeast = 5 | | | | | | | CHR_POSN <= 0.417465: 0 (5.0) | | | | | | | CHR_POSN > 0.417465: 1 (5.0) | | | | | | BLAST_closeyeast = 6: 0 (3.0/1.0) | | | | INTXN_PARTNERS > 3 | | | | | EXPT_vacuole = 0 | | | | | | BLAST_proks = 0 | | | | | | | BLAST_yeast <= 0 | | | | | | | | BLAST_closeyeast = 0: 1 (0.0) | | | | | | | | BLAST_closeyeast = 1: 0 (1.0) | | | | | | | | BLAST_closeyeast = 2: 0 (3.0/1.0) | | | | | | | | BLAST_closeyeast = 3 | | | | | | | | | EXPT_nucleus = 0 | | | | | | | | | | Hydro <= -0.821791: 0 (7.0) | | | | | | | | | | Hydro > -0.821791 | | | | | | | | | | | EXPT_other = 0: 0 (5.0/1.0) | | | | | | | | | | | EXPT_other = 1 | | | | | | | | | | | | Hydro <= -0.460156: 1 (7.0) | | | | | | | | | | | | Hydro > -0.460156 | | | | | | | | | | | | | RARE_AA_RATIO <= 0.057413: 0 (5.0) | | | | | | | | | | | | | RARE_AA_RATIO > 0.057413: 1 (5.0/1.0) | | | | | | | | | EXPT_nucleus = 1 | | | | | | | | | | EXPT_other = 0: 0 (36.0/16.0) | | | | | | | | | | EXPT_other = 1 | | | | | | | | | | | GC <= 0.394: 1 (3.0) | | | | | | | | | | | GC > 0.394: 0 (2.0) | | | | | | | | BLAST_closeyeast = 4 | | | | | | | | | CAI <= 0.142 | | | | | | | | | | Nc <= 58.02 | | | | | | | | | | | EXPT_other = 0 | | | | | | | | | | | | GC <= 0.382: 0 (12.0) | | | | | | | | | | | | GC > 0.382 | | | | | | | | | | | | | GC <= 0.39: 1 (4.0) | | | | | | | | | | | | | GC > 0.39: 0 (21.0/4.0) | | | | | | | | | | | EXPT_other = 1 | | | | | | | | | | | | TM_HELIX <= 0 | | | | | | | | | | | | | L_aa <= 572 | | | | | | | | | | | | | | L_aa <= 243: 0 (2.0) | | | | | | | | | | | | | | L_aa > 243: 1 (10.0/1.0) | | | | | | | | | | | | | L_aa > 572 | | | | | | | | | | | | | | CLOSE_STOP_RATIO <= 0.057576: 0 (9.0) | | | | | | | | | | | | | | CLOSE_STOP_RATIO > 0.057576: 1 (2.0) | | | | | | | | | | | | TM_HELIX > 0: 0 (2.0) | | | | | | | | | | Nc > 58.02: 1 (12.0/2.0) | | | | | | | | | CAI > 0.142 | | | | | | | | | | EXPT_nucleus = 0 | | | | | | | | | | | EXPT_other = 0: 0 (2.0) | | | | | | | | | | | EXPT_other = 1 | | | | | | | | | | | | INTXN_PARTNERS <= 41: 1 (7.0/1.0) | | | | | | | | | | | | INTXN_PARTNERS > 41: 0 (5.0) | | | | | | | | | | EXPT_nucleus = 1: 1 (35.0/5.0) | | | | | | | | BLAST_closeyeast = 5: 1 (25.0/7.0) | | | | | | | | BLAST_closeyeast = 6 | | | | | | | | | Nc <= 49.61: 0 (2.0) | | | | | | | | | Nc > 49.61: 1 (4.0) | | | | | | | BLAST_yeast > 0 | | | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | | | | | BLAST_closeyeast = 2: 0 (0.0) | | | | | | | | BLAST_closeyeast = 3 | | | | | | | | | EXPT_nucleus = 0: 1 (5.0/1.0) | | | | | | | | | EXPT_nucleus = 1 | | | | | | | | | | CAI <= 0.183: 0 (8.0) | | | | | | | | | | CAI > 0.183: 1 (2.0) | | | | | | | | BLAST_closeyeast = 4 | | | | | | | | | CHR_POSN <= 0.861178 | | | | | | | | | | CAI <= 0.152: 0 (17.0) | | | | | | | | | | CAI > 0.152 | | | | | | | | | | | RARE_AA_RATIO <= 0.060533: 0 (9.0/1.0) | | | | | | | | | | | RARE_AA_RATIO > 0.060533: 1 (3.0) | | | | | | | | | CHR_POSN > 0.861178: 1 (2.0) | | | | | | | | BLAST_closeyeast = 5 | | | | | | | | | CHR <= 7: 0 (5.0) | | | | | | | | | CHR > 7: 1 (3.0/1.0) | | | | | | | | BLAST_closeyeast = 6: 1 (1.0) | | | | | | BLAST_proks = 1 | | | | | | | EXPT_nucleus = 0: 0 (2.0) | | | | | | | EXPT_nucleus = 1 | | | | | | | | mRNA_EXPR <= 0.7: 0 (4.0/1.0) | | | | | | | | mRNA_EXPR > 0.7: 1 (5.0) | | | | | | BLAST_proks = 2: 0 (1.0) | | | | | | BLAST_proks = 3: 0 (0.0) | | | | | | BLAST_proks = 4: 0 (0.0) | | | | | | BLAST_proks = 5: 0 (0.0) | | | | | EXPT_vacuole = 1: 0 (2.0) | | | EXPT_cytoplam = 1 | | | | EXPT_nucleus = 0: 0 (123.0/11.0) | | | | EXPT_nucleus = 1 | | | | | INTXN_PARTNERS <= 17: 0 (155.0/20.0) | | | | | INTXN_PARTNERS > 17 | | | | | | EXPT_other = 0 | | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | | | | BLAST_closeyeast = 2: 0 (0.0) | | | | | | | BLAST_closeyeast = 3 | | | | | | | | BLAST_yeast <= 1 | | | | | | | | | INTXN_PARTNERS <= 71 | | | | | | | | | | CLOSE_STOP_RATIO <= 0.044507: 0 (11.0) | | | | | | | | | | CLOSE_STOP_RATIO > 0.044507 | | | | | | | | | | | CHR <= 10: 1 (6.0/1.0) | | | | | | | | | | | CHR > 10: 0 (3.0) | | | | | | | | | INTXN_PARTNERS > 71: 1 (3.0) | | | | | | | | BLAST_yeast > 1: 1 (2.0) | | | | | | | BLAST_closeyeast = 4 | | | | | | | | mRNA_EXPR <= 0.3: 0 (8.0) | | | | | | | | mRNA_EXPR > 0.3 | | | | | | | | | mRNA_EXPR <= 0.7 | | | | | | | | | | CLOSE_STOP_RATIO <= 0.050142: 1 (7.0) | | | | | | | | | | CLOSE_STOP_RATIO > 0.050142: 0 (3.0) | | | | | | | | | mRNA_EXPR > 0.7 | | | | | | | | | | mRNA_EXPR <= 1.2: 0 (13.0) | | | | | | | | | | mRNA_EXPR > 1.2 | | | | | | | | | | | INTXN_PARTNERS <= 34: 1 (5.0) | | | | | | | | | | | INTXN_PARTNERS > 34: 0 (9.0/1.0) | | | | | | | BLAST_closeyeast = 5 | | | | | | | | BLAST_yeast <= 0 | | | | | | | | | INTXN_PARTNERS <= 47: 1 (7.0/1.0) | | | | | | | | | INTXN_PARTNERS > 47: 0 (6.0/1.0) | | | | | | | | BLAST_yeast > 0: 1 (2.0) | | | | | | | BLAST_closeyeast = 6: 0 (4.0/1.0) | | | | | | EXPT_other = 1: 1 (5.0/1.0) | PRED_vacuole = 1: 0 (57.0) INTXN_PARTNERS > 82 | EXPT_mitochondria = 0 | | GC <= 0.428 | | | EXPT_nucleus = 0 | | | | EXPT_other = 0 | | | | | PRED_mitochondria = 0 | | | | | | INTRON = 0 | | | | | | | Hydro <= -0.204669 | | | | | | | | Nc <= 41.8 | | | | | | | | | mRNA_EXPR <= 6.7: 1 (9.0/1.0) | | | | | | | | | mRNA_EXPR > 6.7 | | | | | | | | | | RARE_AA_RATIO <= 0.062176: 0 (7.0/1.0) | | | | | | | | | | RARE_AA_RATIO > 0.062176: 1 (4.0) | | | | | | | | Nc > 41.8: 0 (31.0/5.0) | | | | | | | Hydro > -0.204669: 0 (14.0/1.0) | | | | | | INTRON = 1: 0 (3.0) | | | | | PRED_mitochondria = 1: 1 (2.0) | | | | EXPT_other = 1 | | | | | PRED_nucleus = 0 | | | | | | mRNA_EXPR <= 0.6: 0 (7.0) | | | | | | mRNA_EXPR > 0.6 | | | | | | | CLOSE_STOP_RATIO <= 0.046924: 1 (30.0/9.0) | | | | | | | CLOSE_STOP_RATIO > 0.046924: 0 (6.0) | | | | | PRED_nucleus = 1 | | | | | | CLOSE_STOP_RATIO <= 0.025245 | | | | | | | RARE_AA_RATIO <= 0.037445: 0 (3.0) | | | | | | | RARE_AA_RATIO > 0.037445: 1 (2.0) | | | | | | CLOSE_STOP_RATIO > 0.025245: 1 (20.0) | | | EXPT_nucleus = 1 | | | | BLAST_yeast <= 2 | | | | | EXPT_other = 0 | | | | | | INTXN_PARTNERS <= 213 | | | | | | | CHR <= 10 | | | | | | | | CHR <= 7 | | | | | | | | | BLAST_yeast <= 0 | | | | | | | | | | CAI <= 0.121 | | | | | | | | | | | Nc <= 50.47: 1 (2.0) | | | | | | | | | | | Nc > 50.47: 0 (7.0) | | | | | | | | | | CAI > 0.121 | | | | | | | | | | | L_aa <= 1208: 1 (47.0/6.0) | | | | | | | | | | | L_aa > 1208: 0 (2.0) | | | | | | | | | BLAST_yeast > 0 | | | | | | | | | | GC <= 0.413: 1 (3.0) | | | | | | | | | | GC > 0.413: 0 (3.0) | | | | | | | | CHR > 7 | | | | | | | | | PRED_cytoplasm = 0: 0 (8.0/1.0) | | | | | | | | | PRED_cytoplasm = 1: 1 (4.0/1.0) | | | | | | | CHR > 10: 1 (57.0/9.0) | | | | | | INTXN_PARTNERS > 213: 0 (7.0/1.0) | | | | | EXPT_other = 1 | | | | | | PRED_cytoplasm = 0 | | | | | | | CLOSE_STOP_RATIO <= 0.018391: 0 (2.0) | | | | | | | CLOSE_STOP_RATIO > 0.018391: 1 (28.0/1.0) | | | | | | PRED_cytoplasm = 1: 0 (2.0) | | | | BLAST_yeast > 2 | | | | | EXPT_cytoplam = 0: 0 (5.0) | | | | | EXPT_cytoplam = 1 | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | | | BLAST_closeyeast = 2: 0 (0.0) | | | | | | BLAST_closeyeast = 3: 0 (0.0) | | | | | | BLAST_closeyeast = 4: 0 (0.0) | | | | | | BLAST_closeyeast = 5: 1 (2.0) | | | | | | BLAST_closeyeast = 6: 0 (3.0) | | GC > 0.428 | | | BLAST_yeast <= 0 | | | | PRED_vacuole = 0 | | | | | CHR <= 14 | | | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | | | BLAST_closeyeast = 1: 0 (0.0) | | | | | | BLAST_closeyeast = 2: 0 (0.0) | | | | | | BLAST_closeyeast = 3 | | | | | | | Hydro <= -0.209585: 1 (6.0) | | | | | | | Hydro > -0.209585: 0 (4.0) | | | | | | BLAST_closeyeast = 4 | | | | | | | EXPT_nucleus = 0: 0 (7.0) | | | | | | | EXPT_nucleus = 1 | | | | | | | | RARE_AA_RATIO <= 0.041379: 1 (2.0) | | | | | | | | RARE_AA_RATIO > 0.041379: 0 (9.0/1.0) | | | | | | BLAST_closeyeast = 5: 0 (6.0/1.0) | | | | | | BLAST_closeyeast = 6 | | | | | | | L_aa <= 404: 0 (4.0) | | | | | | | L_aa > 404: 1 (2.0) | | | | | CHR > 14: 1 (4.0) | | | | PRED_vacuole = 1: 0 (2.0) | | | BLAST_yeast > 0: 0 (22.0) | EXPT_mitochondria = 1: 0 (28.0/1.0) Number of Leaves : 207 Size of the tree : 370 Time taken to build model: 0.83 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 2359 76.3678 % Incorrectly Classified Instances 730 23.6322 % Kappa statistic 0.2767 Mean absolute error 0.2848 Root mean squared error 0.4517 Relative absolute error 79.7246 % Root relative squared error 106.8861 % Total Number of Instances 3089 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.883 0.63 0.822 0.883 0.852 0 0.37 0.117 0.49 0.37 0.422 1 === Confusion Matrix === a b <-- classified as 2093 277 | a = 0 453 266 | b = 1 -------------- Evaluation of Information Gain Ratio ------------------------------------ === Run information === Evaluator: weka.attributeSelection.GainRatioAttributeEval Search: weka.attributeSelection.Ranker -T -1.7976931348623157E308 -N -1 Relation: cerevisiae_SET_ABC Instances: 3089 Attributes: 29 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON Hydro TM_HELIX PRED_mitochondria PRED_cytoplasm PRED_er PRED_nucleus PRED_vacuole PRED_other mRNA_EXPR INTXN_PARTNERS EXPT_mitochondria EXPT_cytoplam EXPT_er EXPT_nucleus EXPT_vacuole EXPT_other SGD-ess Evaluation mode: evaluate on all training data === Attribute Selection on all input data === Search Method: Attribute ranking. Attribute Evaluator (supervised, Class (nominal): 29 SGD-ess): Gain Ratio feature evaluator Ranked attributes: 0.038887 18 PRED_nucleus 0.037404 22 INTXN_PARTNERS 0.034023 19 PRED_vacuole 0.027664 26 EXPT_nucleus 0.025542 23 EXPT_mitochondria 0.025036 27 EXPT_vacuole 0.023299 15 PRED_mitochondria 0.019481 7 BLAST_yeast 0.017345 14 TM_HELIX 0.014788 13 Hydro 0.012899 20 PRED_other 0.010809 1 CAI 0.010497 21 mRNA_EXPR 0.010153 2 Nc 0.007776 3 GC 0.006421 24 EXPT_cytoplam 0.005974 28 EXPT_other 0.005178 8 BLAST_closeyeast 0.003949 9 BLAST_proks 0.002706 16 PRED_cytoplasm 0.00137 17 PRED_er 0.001031 12 INTRON 0.000231 25 EXPT_er 0 4 L_aa 0 10 CHR 0 11 CHR_POSN 0 5 CLOSE_STOP_RATIO 0 6 RARE_AA_RATIO Selected attributes: 18,22,19,26,23,27,15,7,14,13,20,1,21,2,3,24,28,8,9,16,17,12,25,4,10,11,5,6 : 28 ========================================================== SET LARGE A ========================================================== WITH 0.25 CONFIDENCE LEVEL PRUNING === Run information === Scheme: weka.classifiers.trees.J48 -C 0.25 -M 2 Relation: cerevisiae_SET_A_LARGE Instances: 5548 Attributes: 13 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ : 0 (5548.0/1030.0) Number of Leaves : 1 Size of the tree : 1 Time taken to build model: 0.42 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 4472 80.6056 % Incorrectly Classified Instances 1076 19.3944 % Kappa statistic 0.0556 Mean absolute error 0.2893 Root mean squared error 0.3916 Relative absolute error 95.6673 % Root relative squared error 100.7218 % Total Number of Instances 5548 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.976 0.938 0.82 0.976 0.891 0 0.062 0.024 0.368 0.062 0.106 1 === Confusion Matrix === a b <-- classified as 4408 110 | a = 0 966 64 | b = 1 WITH 0.275 CONFIDENCE LEVEL PRUNING === Run information === Scheme: weka.classifiers.trees.J48 -C 0.275 -M 2 Relation: cerevisiae_SET_A_LARGE Instances: 5548 Attributes: 13 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON SGD-ess Test mode: 10-fold cross-validation === Classifier model (full training set) === J48 pruned tree ------------------ BLAST_yeast <= 0 | CAI <= 0.146: 0 (2538.0/387.0) | CAI > 0.146 | | BLAST_closeyeast = 0 | | | L_aa <= 93: 0 (3.0) | | | L_aa > 93: 1 (2.0) | | BLAST_closeyeast = 1: 0 (15.0) | | BLAST_closeyeast = 2 | | | GC <= 0.354: 1 (2.0) | | | GC > 0.354 | | | | CLOSE_STOP_RATIO <= 0.02818: 1 (4.0/1.0) | | | | CLOSE_STOP_RATIO > 0.02818: 0 (26.0) | | BLAST_closeyeast = 3 | | | INTRON = 0: 0 (333.0/67.0) | | | INTRON = 1 | | | | CHR_POSN <= 0.437883: 1 (13.0/4.0) | | | | CHR_POSN > 0.437883 | | | | | CAI <= 0.239: 0 (7.0) | | | | | CAI > 0.239 | | | | | | CAI <= 0.415: 1 (2.0) | | | | | | CAI > 0.415: 0 (2.0) | | BLAST_closeyeast = 4: 0 (874.0/229.0) | | BLAST_closeyeast = 5 | | | BLAST_proks = 0 | | | | INTRON = 0 | | | | | CLOSE_STOP_RATIO <= 0.049696: 1 (200.0/98.0) | | | | | CLOSE_STOP_RATIO > 0.049696: 0 (108.0/33.0) | | | | INTRON = 1 | | | | | GC <= 0.411: 0 (3.0) | | | | | GC > 0.411: 1 (5.0) | | | BLAST_proks = 1: 0 (4.0/1.0) | | | BLAST_proks = 2: 0 (0.0) | | | BLAST_proks = 3: 0 (1.0) | | | BLAST_proks = 4: 0 (0.0) | | | BLAST_proks = 5: 0 (0.0) | | BLAST_closeyeast = 6 | | | GC <= 0.419 | | | | BLAST_proks = 0: 1 (84.0/34.0) | | | | BLAST_proks = 1 | | | | | RARE_AA_RATIO <= 0.05303: 0 (2.0) | | | | | RARE_AA_RATIO > 0.05303: 1 (2.0) | | | | BLAST_proks = 2: 1 (0.0) | | | | BLAST_proks = 3: 1 (0.0) | | | | BLAST_proks = 4: 1 (0.0) | | | | BLAST_proks = 5: 1 (0.0) | | | GC > 0.419 | | | | CAI <= 0.597 | | | | | CHR <= 8: 0 (18.0) | | | | | CHR > 8 | | | | | | CAI <= 0.21 | | | | | | | Nc <= 45.84: 1 (3.0) | | | | | | | Nc > 45.84: 0 (5.0/1.0) | | | | | | CAI > 0.21: 0 (6.0) | | | | CAI > 0.597 | | | | | L_aa <= 203: 0 (3.0/1.0) | | | | | L_aa > 203: 1 (8.0) BLAST_yeast > 0 | CLOSE_STOP_RATIO <= 0.05178 | | L_aa <= 454 | | | CLOSE_STOP_RATIO <= 0.015 | | | | GC <= 0.398: 1 (3.0) | | | | GC > 0.398: 0 (31.0/2.0) | | | CLOSE_STOP_RATIO > 0.015: 0 (339.0/18.0) | | L_aa > 454 | | | Nc <= 50.67 | | | | BLAST_closeyeast = 0: 0 (0.0) | | | | BLAST_closeyeast = 1: 0 (1.0) | | | | BLAST_closeyeast = 2: 0 (1.0) | | | | BLAST_closeyeast = 3 | | | | | CLOSE_STOP_RATIO <= 0.028939 | | | | | | BLAST_yeast <= 24 | | | | | | | CAI <= 0.136: 1 (2.0) | | | | | | | CAI > 0.136: 0 (8.0/1.0) | | | | | | BLAST_yeast > 24: 1 (4.0) | | | | | CLOSE_STOP_RATIO > 0.028939 | | | | | | CLOSE_STOP_RATIO <= 0.047389: 0 (32.0/1.0) | | | | | | CLOSE_STOP_RATIO > 0.047389: 1 (3.0/1.0) | | | | BLAST_closeyeast = 4: 0 (53.0/18.0) | | | | BLAST_closeyeast = 5 | | | | | BLAST_proks = 0 | | | | | | CHR <= 12 | | | | | | | CHR_POSN <= 0.662441 | | | | | | | | BLAST_yeast <= 3 | | | | | | | | | Nc <= 42.06: 1 (6.0) | | | | | | | | | Nc > 42.06 | | | | | | | | | | CAI <= 0.189 | | | | | | | | | | | L_aa <= 1038: 1 (8.0/2.0) | | | | | | | | | | | L_aa > 1038: 0 (2.0) | | | | | | | | | | CAI > 0.189: 0 (6.0) | | | | | | | | BLAST_yeast > 3: 1 (5.0) | | | | | | | CHR_POSN > 0.662441 | | | | | | | | BLAST_yeast <= 1: 1 (3.0/1.0) | | | | | | | | BLAST_yeast > 1: 0 (9.0) | | | | | | CHR > 12: 0 (17.0/2.0) | | | | | BLAST_proks = 1 | | | | | | BLAST_yeast <= 17: 0 (3.0) | | | | | | BLAST_yeast > 17: 1 (3.0) | | | | | BLAST_proks = 2: 0 (3.0) | | | | | BLAST_proks = 3: 0 (0.0) | | | | | BLAST_proks = 4: 0 (0.0) | | | | | BLAST_proks = 5: 0 (0.0) | | | | BLAST_closeyeast = 6 | | | | | GC <= 0.38: 1 (3.0) | | | | | GC > 0.38: 0 (49.0/7.0) | | | Nc > 50.67: 0 (220.0/20.0) | CLOSE_STOP_RATIO > 0.05178: 0 (461.0/18.0) Number of Leaves : 65 Size of the tree : 107 Time taken to build model: 0.41 seconds === Stratified cross-validation === === Summary === Correctly Classified Instances 4461 80.4074 % Incorrectly Classified Instances 1087 19.5926 % Kappa statistic 0.0651 Mean absolute error 0.2831 Root mean squared error 0.3912 Relative absolute error 93.6181 % Root relative squared error 100.6229 % Total Number of Instances 5548 === Detailed Accuracy By Class === TP Rate FP Rate Precision Recall F-Measure Class 0.97 0.925 0.821 0.97 0.89 0 0.075 0.03 0.365 0.075 0.124 1 === Confusion Matrix === a b <-- classified as 4384 134 | a = 0 953 77 | b = 1 -------------- Evaluation of Information Gain Ratio ------------------------------------ === Run information === Evaluator: weka.attributeSelection.GainRatioAttributeEval Search: weka.attributeSelection.Ranker -T -1.7976931348623157E308 -N -1 Relation: cerevisiae_SET_A_LARGE Instances: 5548 Attributes: 13 CAI Nc GC L_aa CLOSE_STOP_RATIO RARE_AA_RATIO BLAST_yeast BLAST_closeyeast BLAST_proks CHR CHR_POSN INTRON SGD-ess Evaluation mode: evaluate on all training data === Attribute Selection on all input data === Search Method: Attribute ranking. Attribute Evaluator (supervised, Class (nominal): 13 SGD-ess): Gain Ratio feature evaluator Ranked attributes: 0.026896 11 CHR_POSN 0.016338 7 BLAST_yeast 0.012817 1 CAI 0.012165 2 Nc 0.011747 8 BLAST_closeyeast 0.01089 3 GC 0.009157 5 CLOSE_STOP_RATIO 0.008187 6 RARE_AA_RATIO 0.001356 9 BLAST_proks 0.000555 12 INTRON 0 4 L_aa 0 10 CHR Selected attributes: 11,7,1,2,8,3,5,6,9,12,4,10 : 12