Carlos-Francisco Méndez-Cruz / laigen-supervised-learning

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Carlos-Francisco Méndez-Cruz
b0fbb4dd 1 parent 28f7fff2

Classification binding thrombin data set

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Showing 3 changed files with 15 additions and 19 deletions
...@@ -46,13 +46,13 @@ __author__ = 'CMendezC' ...@@ -46,13 +46,13 @@ __author__ = 'CMendezC'
46 # Execution: 46 # Execution:
47 47
48 # python training-crossvalidation-testing-binding-thrombin.py 48 # python training-crossvalidation-testing-binding-thrombin.py
49 -# --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset 49 +# --inputPath /home/binding-thrombin-dataset
50 # --inputTrainingData thrombin.data 50 # --inputTrainingData thrombin.data
51 # --inputTestingData Thrombin.testset 51 # --inputTestingData Thrombin.testset
52 # --inputTestingClasses Thrombin.testset.class 52 # --inputTestingClasses Thrombin.testset.class
53 -# --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/models 53 +# --outputModelPath /home/binding-thrombin-dataset/models
54 # --outputModelFile SVM-lineal-model.mod 54 # --outputModelFile SVM-lineal-model.mod
55 -# --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports 55 +# --outputReportPath /home/binding-thrombin-dataset/reports
56 # --outputReportFile SVM-lineal.txt 56 # --outputReportFile SVM-lineal.txt
57 # --classifier SVM 57 # --classifier SVM
58 # --saveData 58 # --saveData
...@@ -60,7 +60,7 @@ __author__ = 'CMendezC' ...@@ -60,7 +60,7 @@ __author__ = 'CMendezC'
60 # --imbalanced RandomUS 60 # --imbalanced RandomUS
61 61
62 # source activate python3 62 # source activate python3
63 -# python training-crossvalidation-testing-binding-thrombin.py --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset --inputTrainingData thrombin.data --inputTestingData Thrombin.testset --inputTestingClasses Thrombin.testset.class --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/models --outputModelFile SVM-lineal-model.mod --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports --outputReportFile SVM-lineal.txt --classifier SVM --kernel linear --imbalanced RandomUS 63 +# python training-crossvalidation-testing-binding-thrombin.py --inputPath /home/binding-thrombin-dataset --inputTrainingData thrombin.data --inputTestingData Thrombin.testset --inputTestingClasses Thrombin.testset.class --outputModelPath /home/binding-thrombin-dataset/models --outputModelFile SVM-lineal-model.mod --outputReportPath /home/binding-thrombin-dataset/reports --outputReportFile SVM-lineal.txt --classifier SVM --kernel linear --imbalanced RandomUS
64 64
65 ########################################################### 65 ###########################################################
66 # MAIN PROGRAM # 66 # MAIN PROGRAM #
...@@ -258,10 +258,10 @@ if __name__ == "__main__": ...@@ -258,10 +258,10 @@ if __name__ == "__main__":
258 print(" Number of testing class I: {}".format(y_test.count('I'))) 258 print(" Number of testing class I: {}".format(y_test.count('I')))
259 print(" Shape of testing matrix: {}".format(X_test.shape)) 259 print(" Shape of testing matrix: {}".format(X_test.shape))
260 260
261 - jobs = -1 261 + jobs = 2
262 paramGrid = [] 262 paramGrid = []
263 - nIter = 20 263 + nIter = 5
264 - crossV = 10 264 + crossV = 5
265 print("Defining randomized grid search...") 265 print("Defining randomized grid search...")
266 if args.classifier == 'SVM': 266 if args.classifier == 'SVM':
267 # SVM 267 # SVM
......
...@@ -39,13 +39,13 @@ __author__ = 'CMendezC' ...@@ -39,13 +39,13 @@ __author__ = 'CMendezC'
39 # Execution: 39 # Execution:
40 40
41 # python imb-training-testing-binding-thrombin.py 41 # python imb-training-testing-binding-thrombin.py
42 -# --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset 42 +# --inputPath /home/binding-thrombin-dataset
43 # --inputTrainingData thrombin.data 43 # --inputTrainingData thrombin.data
44 # --inputTestingData Thrombin.testset 44 # --inputTestingData Thrombin.testset
45 # --inputTestingClasses Thrombin.testset.class 45 # --inputTestingClasses Thrombin.testset.class
46 -# --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/models 46 +# --outputModelPath /home/binding-thrombin-dataset/models
47 # --outputModelFile SVM-lineal-model.mod 47 # --outputModelFile SVM-lineal-model.mod
48 -# --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports 48 +# --outputReportPath /home/binding-thrombin-dataset/reports
49 # --outputReportFile SVM-lineal.txt 49 # --outputReportFile SVM-lineal.txt
50 # --classifier SVM 50 # --classifier SVM
51 # --saveData 51 # --saveData
...@@ -53,11 +53,7 @@ __author__ = 'CMendezC' ...@@ -53,11 +53,7 @@ __author__ = 'CMendezC'
53 # --imbalanced RandomUS 53 # --imbalanced RandomUS
54 54
55 # source activate python3 55 # source activate python3
56 -# python imb-training-testing-binding-thrombin.py --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset --inputTrainingData thrombin.data --inputTestingData Thrombin.testset --inputTestingClasses Thrombin.testset.class --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/models --outputModelFile SVM-lineal-model.mod --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports --outputReportFile SVM-lineal.txt --classifier SVM --kernel linear 56 +# python imb-training-testing-binding-thrombin.py --inputPath /home/binding-thrombin-dataset --inputTrainingData thrombin.data --inputTestingData Thrombin.testset --inputTestingClasses Thrombin.testset.class --outputModelPath /home/binding-thrombin-dataset/models --outputModelFile SVM-lineal-model.mod --outputReportPath /home/binding-thrombin-dataset/reports --outputReportFile SVM-lineal-RandomUS.txt --classifier SVM --kernel linear --imbalanced RandomUS
57 -# python imb-training-testing-binding-thrombin.py --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset --inputTrainingData thrombin.data --inputTestingData Thrombin.testset --inputTestingClasses Thrombin.testset.class --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/models --outputModelFile SVM-lineal-model.mod --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports --outputReportFile SVM-lineal-RandomUS.txt --classifier SVM --kernel linear --imbalanced RandomUS
58 -
59 -
60 -# --imbalanced RandomUS
61 57
62 ########################################################### 58 ###########################################################
63 # MAIN PROGRAM # 59 # MAIN PROGRAM #
......
...@@ -39,13 +39,13 @@ __author__ = 'CMendezC' ...@@ -39,13 +39,13 @@ __author__ = 'CMendezC'
39 # Execution: 39 # Execution:
40 40
41 # python training-crossvalidation-testing-binding-thrombin.py 41 # python training-crossvalidation-testing-binding-thrombin.py
42 -# --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset 42 +# --inputPath /home/binding-thrombin-dataset
43 # --inputTrainingData thrombin.data 43 # --inputTrainingData thrombin.data
44 # --inputTestingData Thrombin.testset 44 # --inputTestingData Thrombin.testset
45 # --inputTestingClasses Thrombin.testset.class 45 # --inputTestingClasses Thrombin.testset.class
46 -# --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/models 46 +# --outputModelPath /home/binding-thrombin-dataset/models
47 # --outputModelFile SVM-model.mod 47 # --outputModelFile SVM-model.mod
48 -# --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports 48 +# --outputReportPath /home/binding-thrombin-dataset/reports
49 # --outputReportFile SVM.txt 49 # --outputReportFile SVM.txt
50 # --classifier SVM 50 # --classifier SVM
51 # --saveData 51 # --saveData
...@@ -53,7 +53,7 @@ __author__ = 'CMendezC' ...@@ -53,7 +53,7 @@ __author__ = 'CMendezC'
53 # --reduction SVD200 53 # --reduction SVD200
54 54
55 # source activate python3 55 # source activate python3
56 -# python training-crossvalidation-testing-binding-thrombin.py --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset --inputTrainingData thrombin.data --inputTestingData Thrombin.testset --inputTestingClasses Thrombin.testset.class --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/models --outputModelFile SVM-linear-model.mod --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports --outputReportFile SVM-linear.txt --classifier SVM --kernel rbf 56 +# python training-crossvalidation-testing-binding-thrombin.py --inputPath /home/binding-thrombin-dataset --inputTrainingData thrombin.data --inputTestingData Thrombin.testset --inputTestingClasses Thrombin.testset.class --outputModelPath /home/binding-thrombin-dataset/models --outputModelFile SVM-linear-model.mod --outputReportPath /home/binding-thrombin-dataset/reports --outputReportFile SVM-linear.txt --classifier SVM --kernel rbf
57 57
58 ########################################################### 58 ###########################################################
59 # MAIN PROGRAM # 59 # MAIN PROGRAM #
......