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tried pca

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Tanushree Tunstall 2022-07-05 23:05:37 +01:00
parent 8d831f3613
commit a15d801c2a
2 changed files with 35 additions and 28 deletions
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61
scripts/ml/ml_functions/MultClfs.py
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@ -74,6 +74,7 @@ from sklearn.impute import KNNImputer as KNN
import json import json
import argparse import argparse
import re import re
from sklearn.decomposition import PCA
#%% GLOBALS #%% GLOBALS
rs = {'random_state': 42} rs = {'random_state': 42}
njobs = {'n_jobs': os.cpu_count() } # the number of jobs should equal the number of CPU cores njobs = {'n_jobs': os.cpu_count() } # the number of jobs should equal the number of CPU cores
@ -232,33 +233,33 @@ def MultModelsCl(input_df, target
models = [('AdaBoost Classifier' , AdaBoostClassifier(**rs) ) models = [('AdaBoost Classifier' , AdaBoostClassifier(**rs) )
, ('Bagging Classifier' , BaggingClassifier(**rs, **njobs, bootstrap = True, oob_score = True, verbose = 3, n_estimators = 100) ) , ('Bagging Classifier' , BaggingClassifier(**rs, **njobs, bootstrap = True, oob_score = True, verbose = 3, n_estimators = 100) )
, ('Decision Tree' , DecisionTreeClassifier(**rs) ) , ('Decision Tree' , DecisionTreeClassifier(**rs) )
, ('Extra Tree' , ExtraTreeClassifier(**rs) ) , ('Extra Tree' , ExtraTreeClassifier(**rs) )
, ('Extra Trees' , ExtraTreesClassifier(**rs) ) , ('Extra Trees' , ExtraTreesClassifier(**rs) )
, ('Gradient Boosting' , GradientBoostingClassifier(**rs) ) , ('Gradient Boosting' , GradientBoostingClassifier(**rs) )
, ('Gaussian NB' , GaussianNB() ) , ('Gaussian NB' , GaussianNB() )
, ('Gaussian Process' , GaussianProcessClassifier(**rs) ) , ('Gaussian Process' , GaussianProcessClassifier(**rs) )
, ('K-Nearest Neighbors' , KNeighborsClassifier() ) , ('K-Nearest Neighbors' , KNeighborsClassifier() )
, ('LDA' , LinearDiscriminantAnalysis() ) , ('LDA' , LinearDiscriminantAnalysis() )
, ('Logistic Regression' , LogisticRegression(**rs) ) , ('Logistic Regression' , LogisticRegression(**rs) )
, ('Logistic RegressionCV' , LogisticRegressionCV(cv = 3, **rs)) , ('Logistic RegressionCV' , LogisticRegressionCV(cv = 3, **rs))
, ('MLP' , MLPClassifier(max_iter = 500, **rs) ) , ('MLP' , MLPClassifier(max_iter = 500, **rs) )
#, ('Multinomial' , MultinomialNB() ) #, ('Multinomial' , MultinomialNB() )
, ('Naive Bayes' , BernoulliNB() ) , ('Naive Bayes' , BernoulliNB() )
, ('Passive Aggresive' , PassiveAggressiveClassifier(**rs, **njobs) ) , ('Passive Aggresive' , PassiveAggressiveClassifier(**rs, **njobs) )
, ('QDA' , QuadraticDiscriminantAnalysis() ) , ('QDA' , QuadraticDiscriminantAnalysis() )
, ('Random Forest' , RandomForestClassifier(**rs, n_estimators = 1000, **njobs ) ) , ('Random Forest' , RandomForestClassifier(**rs, n_estimators = 1000, **njobs ) )
# , ('Random Forest2' , RandomForestClassifier(min_samples_leaf = 5 # , ('Random Forest2' , RandomForestClassifier(min_samples_leaf = 5
# , n_estimators = 1000 # , n_estimators = 1000
# , bootstrap = True # , bootstrap = True
# , oob_score = True # , oob_score = True
# , **njobs # , **njobs
# , **rs # , **rs
# , max_features = 'auto') ) # , max_features = 'auto') )
, ('Ridge Classifier' , RidgeClassifier(**rs) ) , ('Ridge Classifier' , RidgeClassifier(**rs) )
, ('Ridge ClassifierCV' , RidgeClassifierCV(cv = 3) ) , ('Ridge ClassifierCV' , RidgeClassifierCV(cv = 3) )
, ('SVC' , SVC(**rs) ) , ('SVC' , SVC(**rs) )
, ('Stochastic GDescent' , SGDClassifier(**rs, **njobs) ) , ('Stochastic GDescent' , SGDClassifier(**rs, **njobs) )
, ('XGBoost' , XGBClassifier(**rs, verbosity = 0, use_label_encoder =False, **njobs) ) , ('XGBoost' , XGBClassifier(**rs, verbosity = 0, use_label_encoder =False, **njobs) )
] ]
mm_skf_scoresD = {} mm_skf_scoresD = {}
@ -280,6 +281,12 @@ def MultModelsCl(input_df, target
model_pipeline = Pipeline([ model_pipeline = Pipeline([
('prep' , col_transform) ('prep' , col_transform)
, ('model' , model_fn)]) , ('model' , model_fn)])
# model_pipeline = Pipeline([
# ('prep' , col_transform)
# , ('pca' , PCA(n_components = 2))
# , ('model' , model_fn)])
print('\nRunning model pipeline:', model_pipeline) print('\nRunning model pipeline:', model_pipeline)
skf_cv_modD = cross_validate(model_pipeline skf_cv_modD = cross_validate(model_pipeline

2
scripts/ml/ml_functions/test_func_singlegene.py
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@ -82,7 +82,7 @@ fooD = MultModelsCl(input_df = df2['X']
, tts_split_type = spl_type , tts_split_type = spl_type
, resampling_type = 'none' # default , resampling_type = 'none' # default
, var_type = ['mixed'] , var_type = ['mixed']
, scale_numeric = ['min_max_neg'] , scale_numeric = ['min_max']
, return_formatted_output = False , return_formatted_output = False
) )