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'
# Execution:
# python training-crossvalidation-testing-binding-thrombin.py
# --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset
# --inputPath /home/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
# --outputModelPath /home/binding-thrombin-dataset/models
# --outputModelFile SVM-lineal-model.mod
# --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports
# --outputReportPath /home/binding-thrombin-dataset/reports
# --outputReportFile SVM-lineal.txt
# --classifier SVM
# --saveData
......@@ -60,7 +60,7 @@ __author__ = 'CMendezC'
# --imbalanced RandomUS
# source activate python3
# 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
# 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
###########################################################
# MAIN PROGRAM #
......@@ -258,10 +258,10 @@ if __name__ == "__main__":
print(" Number of testing class I: {}".format(y_test.count('I')))
print(" Shape of testing matrix: {}".format(X_test.shape))
jobs = -1
jobs = 2
paramGrid = []
nIter = 20
crossV = 10
nIter = 5
crossV = 5
print("Defining randomized grid search...")
if args.classifier == 'SVM':
# SVM
......
......@@ -39,13 +39,13 @@ __author__ = 'CMendezC'
# Execution:
# python imb-training-testing-binding-thrombin.py
# --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset
# --inputPath /home/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
# --outputModelPath /home/binding-thrombin-dataset/models
# --outputModelFile SVM-lineal-model.mod
# --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports
# --outputReportPath /home/binding-thrombin-dataset/reports
# --outputReportFile SVM-lineal.txt
# --classifier SVM
# --saveData
......@@ -53,11 +53,7 @@ __author__ = 'CMendezC'
# --imbalanced RandomUS
# source activate python3
# 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
# 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
# --imbalanced RandomUS
# 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
###########################################################
# MAIN PROGRAM #
......
......@@ -39,13 +39,13 @@ __author__ = 'CMendezC'
# Execution:
# python training-crossvalidation-testing-binding-thrombin.py
# --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset
# --inputPath /home/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
# --outputModelPath /home/binding-thrombin-dataset/models
# --outputModelFile SVM-model.mod
# --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports
# --outputReportPath /home/binding-thrombin-dataset/reports
# --outputReportFile SVM.txt
# --classifier SVM
# --saveData
......@@ -53,7 +53,7 @@ __author__ = 'CMendezC'
# --reduction SVD200
# source activate python3
# 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
# 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
###########################################################
# MAIN PROGRAM #
......