Merge branch 'release/v0.1.5'

.gitignore

@@ -24,3 +24,7 @@ __pycache__
 
 # simulate models .csv file
 simulate_models*.csv
+
+# log file if used
+logs
+*.log

custom_config.py

@@ -4,6 +4,8 @@ from modules.config.attributes_config import *
 context_vars = vars()
 
 # folders
+logs_folder                        = 'logs'
+
 ## min_max_custom_folder           = 'custom_norm'
 ## correlation_indices_folder      = 'corr_indices'
 

find_best_attributes.py

@@ -0,0 +1,146 @@
+# main imports
+import os
+import sys
+import argparse
+import pandas as pd
+import numpy as np
+import logging
+
+# model imports
+from sklearn.model_selection import train_test_split
+from sklearn.model_selection import GridSearchCV
+from sklearn.linear_model import LogisticRegression
+from sklearn.ensemble import RandomForestClassifier, VotingClassifier
+
+import sklearn.svm as svm
+from sklearn.utils import shuffle
+from sklearn.externals import joblib
+from sklearn.metrics import roc_auc_score
+from sklearn.model_selection import cross_val_score
+
+# modules and config imports
+sys.path.insert(0, '') # trick to enable import of main folder module
+
+import custom_config as cfg
+import models as mdl
+
+from optimization.algorithms.IteratedLocalSearch import IteratedLocalSearch as ILS
+from optimization.solutions.BinarySolution import BinarySolution
+
+from optimization.operators.mutators.SimpleMutation import SimpleMutation
+from optimization.operators.mutators.SimpleBinaryMutation import SimpleBinaryMutation
+from optimization.operators.crossovers.SimpleCrossover import SimpleCrossover
+
+from optimization.operators.policies.RandomPolicy import RandomPolicy
+
+# variables and parameters
+models_list         = cfg.models_names_list
+number_of_values    = 26
+
+# default validator
+def validator(solution):
+
+    if list(solution.data).count(1) < 5:
+        return False
+
+    return True
+
+# init solution (13 filters)
+def init():
+    return BinarySolution([], 13).random(validator)
+
+def loadDataset(filename):
+
+    ########################
+    # 1. Get and prepare data
+    ########################
+    dataset_train = pd.read_csv(filename + '.train', header=None, sep=";")
+    dataset_test = pd.read_csv(filename + '.test', header=None, sep=";")
+
+    # default first shuffle of data
+    dataset_train = shuffle(dataset_train)
+    dataset_test = shuffle(dataset_test)
+
+    # get dataset with equal number of classes occurences
+    noisy_df_train = dataset_train[dataset_train.iloc[:, 0] == 1]
+    not_noisy_df_train = dataset_train[dataset_train.iloc[:, 0] == 0]
+    nb_noisy_train = len(noisy_df_train.index)
+
+    noisy_df_test = dataset_test[dataset_test.iloc[:, 0] == 1]
+    not_noisy_df_test = dataset_test[dataset_test.iloc[:, 0] == 0]
+    nb_noisy_test = len(noisy_df_test.index)
+
+    final_df_train = pd.concat([not_noisy_df_train[0:nb_noisy_train], noisy_df_train])
+    final_df_test = pd.concat([not_noisy_df_test[0:nb_noisy_test], noisy_df_test])
+
+    # shuffle data another time
+    final_df_train = shuffle(final_df_train)
+    final_df_test = shuffle(final_df_test)
+
+    # use of the whole data set for training
+    x_dataset_train = final_df_train.iloc[:,1:]
+    x_dataset_test = final_df_test.iloc[:,1:]
+
+    y_dataset_train = final_df_train.iloc[:,0]
+    y_dataset_test = final_df_test.iloc[:,0]
+
+    return x_dataset_train, y_dataset_train, x_dataset_test, y_dataset_test
+
+def main():
+
+    parser = argparse.ArgumentParser(description="Train and find best filters to use for model")
+
+    parser.add_argument('--data', type=str, help='dataset filename prefix (without .train and .test)')
+    parser.add_argument('--choice', type=str, help='model choice from list of choices', choices=models_list)
+
+    args = parser.parse_args()
+
+    p_data_file = args.data
+    p_choice    = args.choice
+
+    # load data from file
+    x_train, y_train, x_test, y_test = loadDataset(p_data_file)
+
+    # create `logs` folder if necessary
+    if not os.path.exists(cfg.logs_folder):
+        os.makedirs(cfg.logs_folder)
+
+    logging.basicConfig(format='%(asctime)s %(message)s', filename='logs/%s.log' % p_data_file.split('/')[-1], level=logging.DEBUG)
+
+    # define evaluate function here (need of data information)
+    def evaluate(solution):
+
+        # get indices of filters data to use (filters selection from solution)
+        indices = []
+
+        for index, value in enumerate(solution.data): 
+            if value == 1: 
+                indices.append(index*2) 
+                indices.append(index*2+1) 
+
+        # keep only selected filters from solution
+        x_train_filters = x_train.iloc[:, indices]
+        y_train_filters = y_train
+        x_test_filters = x_test.iloc[:, indices]
+
+        model = mdl.get_trained_model(p_choice, x_train_filters, y_train_filters)
+        
+        y_test_model = model.predict(x_test_filters)
+        test_roc_auc = roc_auc_score(y_test, y_test_model)
+
+        return test_roc_auc
+
+    # prepare optimization algorithm
+    updators = [SimpleBinaryMutation(), SimpleMutation(), SimpleCrossover()]
+    policy = RandomPolicy(updators)
+
+    algo = ILS(init, evaluate, updators, policy, validator, True)
+
+    bestSol = algo.run(100, 10)
+
+    # print best solution found
+    print("Found ", bestSol)
+
+
+if __name__ == "__main__":
+    main()

models.py

@@ -14,7 +14,7 @@ def _get_best_model(X_train, y_train):
     param_grid = {'kernel':['rbf'], 'C': Cs, 'gamma' : gammas}
 
     svc = svm.SVC(probability=True)
-    clf = GridSearchCV(svc, param_grid, cv=10, scoring='accuracy', verbose=10)
+    clf = GridSearchCV(svc, param_grid, cv=10, scoring='accuracy', verbose=0)
 
     clf.fit(X_train, y_train)
 

optimization

@@ -1 +1 @@
-Subproject commit 5b9dac1062e899e121c19335e15cfd2125402045
+Subproject commit 6dcd32014ae07124470a2428bddbb05c7fee2a1d