#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Fri Mar 4 15:25:33 2022 @author: tanu """ #%% import os, sys import pandas as pd import numpy as np import pprint as pp from copy import deepcopy from sklearn import linear_model from sklearn import datasets from collections import Counter from sklearn.linear_model import LogisticRegression, LogisticRegressionCV from sklearn.linear_model import RidgeClassifier, RidgeClassifierCV, SGDClassifier, PassiveAggressiveClassifier from sklearn.naive_bayes import BernoulliNB from sklearn.neighbors import KNeighborsClassifier from sklearn.svm import SVC from sklearn.tree import DecisionTreeClassifier, ExtraTreeClassifier from sklearn.ensemble import RandomForestClassifier, ExtraTreesClassifier, AdaBoostClassifier, GradientBoostingClassifier, BaggingClassifier from sklearn.naive_bayes import GaussianNB from sklearn.gaussian_process import GaussianProcessClassifier, kernels from sklearn.gaussian_process.kernels import RBF, DotProduct, Matern, RationalQuadratic, WhiteKernel from sklearn.discriminant_analysis import LinearDiscriminantAnalysis, QuadraticDiscriminantAnalysis from sklearn.neural_network import MLPClassifier from sklearn.svm import SVC from xgboost import XGBClassifier from sklearn.naive_bayes import MultinomialNB from sklearn.preprocessing import StandardScaler, MinMaxScaler, OneHotEncoder from sklearn.compose import ColumnTransformer from sklearn.compose import make_column_transformer from sklearn.metrics import make_scorer, confusion_matrix, accuracy_score, balanced_accuracy_score, precision_score, average_precision_score, recall_score from sklearn.metrics import roc_auc_score, roc_curve, f1_score, matthews_corrcoef, jaccard_score, classification_report # added from sklearn.model_selection import train_test_split, cross_validate, cross_val_score, LeaveOneOut, KFold, RepeatedKFold, cross_val_predict from sklearn.model_selection import train_test_split, cross_validate, cross_val_score from sklearn.model_selection import StratifiedKFold,RepeatedStratifiedKFold, RepeatedKFold from sklearn.pipeline import Pipeline, make_pipeline from sklearn.feature_selection import RFE, RFECV import itertools import seaborn as sns import matplotlib.pyplot as plt from statistics import mean, stdev, median, mode from imblearn.over_sampling import RandomOverSampler from imblearn.under_sampling import RandomUnderSampler from imblearn.over_sampling import SMOTE from sklearn.datasets import make_classification from imblearn.combine import SMOTEENN from imblearn.combine import SMOTETomek from imblearn.over_sampling import SMOTENC from imblearn.under_sampling import EditedNearestNeighbours from imblearn.under_sampling import RepeatedEditedNearestNeighbours from sklearn.model_selection import GridSearchCV from sklearn.base import BaseEstimator from sklearn.impute import KNNImputer as KNN import json import argparse import re import itertools from sklearn.model_selection import LeaveOneGroupOut from sklearn.decomposition import PCA from sklearn.naive_bayes import ComplementNB from sklearn.dummy import DummyClassifier #%% GLOBALS #rs = {'random_state': 42} # INSIDE FUNCTION CALL NOW #njobs = {'n_jobs': os.cpu_count() } # the number of jobs should equal the number of CPU cores scoring_fn = ({ 'mcc' : make_scorer(matthews_corrcoef) , 'fscore' : make_scorer(f1_score) , 'precision' : make_scorer(precision_score) , 'recall' : make_scorer(recall_score) , 'accuracy' : make_scorer(accuracy_score) , 'roc_auc' : make_scorer(roc_auc_score) , 'jcc' : make_scorer(jaccard_score) }) # for sel_cv INSIDE FUNCTION CALL NOW #skf_cv = StratifiedKFold(n_splits = 10 # #, shuffle = False, random_state= None) # , shuffle = True, **rs) #rskf_cv = RepeatedStratifiedKFold(n_splits = 10 # , n_repeats = 3 # , **rs) mcc_score_fn = {'mcc': make_scorer(matthews_corrcoef)} jacc_score_fn = {'jcc': make_scorer(jaccard_score)} ############################################################################### score_type_ordermapD = { 'mcc' : 1 , 'fscore' : 2 , 'jcc' : 3 , 'precision' : 4 , 'recall' : 5 , 'accuracy' : 6 , 'roc_auc' : 7 , 'TN' : 8 , 'FP' : 9 , 'FN' : 10 , 'TP' : 11 , 'trainingY_neg': 12 , 'trainingY_pos': 13 , 'blindY_neg' : 14 , 'blindY_pos' : 15 , 'fit_time' : 16 , 'score_time' : 17 } scoreCV_mapD = {'test_mcc' : 'MCC' , 'test_fscore' : 'F1' , 'test_precision' : 'Precision' , 'test_recall' : 'Recall' , 'test_accuracy' : 'Accuracy' , 'test_roc_auc' : 'ROC_AUC' , 'test_jcc' : 'JCC' } scoreBT_mapD = {'bts_mcc' : 'MCC' , 'bts_fscore' : 'F1' , 'bts_precision' : 'Precision' , 'bts_recall' : 'Recall' , 'bts_accuracy' : 'Accuracy' , 'bts_roc_auc' : 'ROC_AUC' , 'bts_jcc' : 'JCC' } #gene_group = 'gene_name' #%%############################################################################ ############################ # MultModelsCl() # Run Multiple Classifiers ############################ # Multiple Classification - Model Pipeline def MultModelsCl(input_df , target , sel_cv , tts_split_type , resampling_type #, group = None , add_cm = True # adds confusion matrix based on cross_val_predict , add_yn = True # adds target var class numbers , var_type = ['numerical', 'categorical','mixed'] , scale_numeric = ['min_max', 'std', 'min_max_neg', 'none'] , run_blind_test = True , blind_test_df = pd.DataFrame() , blind_test_target = pd.Series(dtype = int) , return_formatted_output = True , random_state = 42 , n_jobs = os.cpu_count() # the number of jobs should equal the number of CPU cores ): ''' @ param input_df: input features @ type: df with input features WITHOUT the target variable @param target: target (or output) feature @type: df or np.array or Series @param skv_cv: stratifiedK fold int or object to allow shuffle and random state to pass @type: int or StratifiedKfold() @var_type: numerical, categorical and mixed to determine what col_transform to apply (MinMaxScalar and/or one-hot encoder) @type: list returns Dict containing multiple classification scores for each model and mean of each Stratified Kfold including training ''' #%% Func globals rs = {'random_state': random_state} njobs = {'n_jobs': n_jobs} skf_cv = StratifiedKFold(n_splits = 10 #, shuffle = False, random_state= None) , shuffle = True,**rs) rskf_cv = RepeatedStratifiedKFold(n_splits = 10 , n_repeats = 3 , **rs) logo = LeaveOneGroupOut() # select CV type: # if group == None: # sel_cv = skf_cv # else: # sel_cv = logo #====================================================== # Determine categorical and numerical features #====================================================== numerical_ix = input_df.select_dtypes(include=['int64', 'float64']).columns numerical_ix categorical_ix = input_df.select_dtypes(include=['object', 'bool']).columns categorical_ix #====================================================== # Determine preprocessing steps ~ var_type #====================================================== # if var_type == 'numerical': # t = [('num', MinMaxScaler(), numerical_ix)] # if var_type == 'categorical': # t = [('cat', OneHotEncoder(), categorical_ix)] # # if var_type == 'mixed': # # t = [('num', MinMaxScaler(), numerical_ix) # # , ('cat', OneHotEncoder(), categorical_ix) ] # col_transform = ColumnTransformer(transformers = t # , remainder='passthrough') if type(var_type) == list: var_type = str(var_type[0]) else: var_type = var_type if var_type in ['numerical','mixed']: if scale_numeric == ['none']: t = [('cat', OneHotEncoder(), categorical_ix)] if scale_numeric != ['none']: if scale_numeric == ['min_max']: scaler = MinMaxScaler() if scale_numeric == ['min_max_neg']: scaler = MinMaxScaler(feature_range=(-1, 1)) if scale_numeric == ['std']: scaler = StandardScaler() t = [('num', scaler, numerical_ix) , ('cat', OneHotEncoder(), categorical_ix)] if var_type == 'categorical': t = [('cat', OneHotEncoder(), categorical_ix)] col_transform = ColumnTransformer(transformers = t , remainder='passthrough') #====================================================== # Specify multiple Classification Models #====================================================== models = [('AdaBoost Classifier' , AdaBoostClassifier(**rs) ) , ('Bagging Classifier' , BaggingClassifier(**rs, **njobs, bootstrap = True, oob_score = True, verbose = 3, n_estimators = 100) ) ##, ('Bernoulli NB' , BernoulliNB() ) # pks Naive Bayes, CAUTION , ('Complement NB' , ComplementNB() ) , ('Decision Tree' , DecisionTreeClassifier(**rs) ) , ('Extra Tree' , ExtraTreeClassifier(**rs) ) , ('Extra Trees' , ExtraTreesClassifier(**rs) ) , ('Gradient Boosting' , GradientBoostingClassifier(**rs) ) , ('Gaussian NB' , GaussianNB() ) , ('Gaussian Process' , GaussianProcessClassifier(**rs) ) , ('K-Nearest Neighbors' , KNeighborsClassifier() ) , ('LDA' , LinearDiscriminantAnalysis() ) , ('Logistic Regression' , LogisticRegression(**rs) ) , ('Logistic RegressionCV' , LogisticRegressionCV(cv = 3, **rs)) , ('MLP' , MLPClassifier(max_iter = 500, **rs) ) , ('Multinomial NB' , MultinomialNB() ) , ('Passive Aggresive' , PassiveAggressiveClassifier(**rs, **njobs) ) , ('QDA' , QuadraticDiscriminantAnalysis() ) , ('Random Forest' , RandomForestClassifier(**rs, n_estimators = 1000, **njobs ) ) , ('Random Forest2' , RandomForestClassifier(min_samples_leaf = 5 , n_estimators = 1000 , bootstrap = True , oob_score = True , **njobs , **rs , max_features = 'auto') ) , ('Ridge Classifier' , RidgeClassifier(**rs) ) , ('Ridge ClassifierCV' , RidgeClassifierCV(cv = 3) ) , ('SVC' , SVC(**rs) ) , ('Stochastic GDescent' , SGDClassifier(**rs, **njobs) ) , ('XGBoost' , XGBClassifier(**rs, verbosity = 0, use_label_encoder = False, **njobs) ) #, ('Dummy Classifier' , DummyClassifier(strategy = 'most_frequent') ) , ('Dummy Classifier' , DummyClassifier(constant = 1) ) ] mm_skf_scoresD = {} print('\n==============================================================\n' , '\nRunning several classification models (n):', len(models) ,'\nList of models:') for m in models: print(m) print('\n================================================================\n') index = 1 for model_name, model_fn in models: print('\nRunning classifier:', index , '\nModel_name:' , model_name , '\nModel func:' , model_fn) index = index+1 model_pipeline = Pipeline([ ('prep' , col_transform) , ('model' , model_fn)]) # model_pipeline = Pipeline([ # ('prep' , col_transform) # , ('pca' , PCA(n_components = 2)) # , ('model' , model_fn)]) print('\nRunning model pipeline:', model_pipeline) cv_modD = cross_validate(model_pipeline , input_df , target , cv = sel_cv #, groups = group , scoring = scoring_fn , return_train_score = True) #============================== # Extract mean values for CV #============================== mm_skf_scoresD[model_name] = {} for key, value in cv_modD.items(): print('\nkey:', key, '\nvalue:', value) print('\nmean value:', np.mean(value)) mm_skf_scoresD[model_name][key] = round(np.mean(value),2) # ADD more info: meta data related to input df mm_skf_scoresD[model_name]['resampling'] = resampling_type mm_skf_scoresD[model_name]['n_training_size'] = len(input_df) mm_skf_scoresD[model_name]['n_trainingY_ratio'] = round(Counter(target)[0]/Counter(target)[1], 2) mm_skf_scoresD[model_name]['n_features'] = len(input_df.columns) mm_skf_scoresD[model_name]['tts_split'] = tts_split_type ####################################################################### #====================================================== # Option: Add confusion matrix from cross_val_predict # Understand and USE with caution #====================================================== if add_cm: cmD = {} # Calculate cm y_pred = cross_val_predict(model_pipeline , input_df , target , cv = sel_cv #, groups = group , **njobs) #_tn, _fp, _fn, _tp = confusion_matrix(y_pred, y).ravel() # internally tn, fp, fn, tp = confusion_matrix(y_pred, target).ravel() # Build cm dict cmD = {'TN' : tn , 'FP': fp , 'FN': fn , 'TP': tp} # Update cv dict cmD mm_skf_scoresD[model_name].update(cmD) #============================================= # Option: Add targety numbers for data #============================================= if add_yn: tnD = {} # Build tn numbers dict tnD = {'n_trainingY_neg' : Counter(target)[0] , 'n_trainingY_pos' : Counter(target)[1] } # Update cv dict with cmD and tnD mm_skf_scoresD[model_name].update(tnD) #%% #========================= # Option: Blind test (bts) #========================= if run_blind_test: btD = {} # Build bts numbers dict btD = {'n_blindY_neg' : Counter(blind_test_target)[0] , 'n_blindY_pos' : Counter(blind_test_target)[1] , 'n_testY_ratio' : round(Counter(blind_test_target)[0]/Counter(blind_test_target)[1], 2) , 'n_test_size' : len(blind_test_df) } # Update cmD+tnD dicts with btD mm_skf_scoresD[model_name].update(btD) #-------------------------------------------------------- # Build the final results with all scores for the model #-------------------------------------------------------- #bts_predict = gscv_fs.predict(blind_test_df) model_pipeline.fit(input_df, target) bts_predict = model_pipeline.predict(blind_test_df) bts_mcc_score = round(matthews_corrcoef(blind_test_target, bts_predict),2) print('\nMCC on Blind test:' , bts_mcc_score) #print('\nAccuracy on Blind test:', round(accuracy_score(blind_test_target, bts_predict),2)) print('\nMCC on Training:' , mm_skf_scoresD[model_name]['test_mcc'] ) mm_skf_scoresD[model_name]['bts_mcc'] = bts_mcc_score mm_skf_scoresD[model_name]['bts_fscore'] = round(f1_score(blind_test_target, bts_predict),2) mm_skf_scoresD[model_name]['bts_precision'] = round(precision_score(blind_test_target, bts_predict),2) mm_skf_scoresD[model_name]['bts_recall'] = round(recall_score(blind_test_target, bts_predict),2) mm_skf_scoresD[model_name]['bts_accuracy'] = round(accuracy_score(blind_test_target, bts_predict),2) mm_skf_scoresD[model_name]['bts_roc_auc'] = round(roc_auc_score(blind_test_target, bts_predict),2) mm_skf_scoresD[model_name]['bts_jcc'] = round(jaccard_score(blind_test_target, bts_predict),2) #mm_skf_scoresD[model_name]['diff_mcc'] = train_test_diff_MCC #return(mm_skf_scoresD) #============================ # Process the dict to have WF #============================ if return_formatted_output: CV_BT_metaDF = ProcessMultModelsCl(mm_skf_scoresD) return(CV_BT_metaDF) else: return(mm_skf_scoresD) #%% Process output function ################################################### ############################ # ProcessMultModelsCl() ############################ #Processes the dict from above if use_formatted_output = True def ProcessMultModelsCl(inputD = {}, blind_test_data = True): scoresDF = pd.DataFrame(inputD) #------------------------ # Extracting split_name #----------------------- tts_split_nameL = [] for k,v in inputD.items(): tts_split_nameL = tts_split_nameL + [v['tts_split']] if len(set(tts_split_nameL)) == 1: tts_split_name = str(list(set(tts_split_nameL))[0]) print('\nExtracting tts_split_name:', tts_split_name) #---------------------- # WF: CV results #---------------------- scoresDFT = scoresDF.T scoresDF_CV = scoresDFT.filter(regex='^test_.*$', axis = 1); scoresDF_CV.columns # map colnames for consistency to allow concatenting scoresDF_CV.columns = scoresDF_CV.columns.map(scoreCV_mapD); scoresDF_CV.columns scoresDF_CV['source_data'] = 'CV' #---------------------- # WF: Meta data #---------------------- metaDF = scoresDFT.filter(regex='^(?!test_.*$|bts_.*$|train_.*$).*'); metaDF.columns print('\nTotal cols in each df:' , '\nCV df:', len(scoresDF_CV.columns) , '\nmetaDF:', len(metaDF.columns)) #------------------------------------- # Combine WF: CV + Metadata #------------------------------------- combDF = pd.merge(scoresDF_CV, metaDF, left_index = True, right_index = True) print('\nAdding column: Model_name') combDF['Model_name'] = combDF.index #---------------------- # WF: BTS results #---------------------- if blind_test_data: scoresDF_BT = scoresDFT.filter(regex='^bts_.*$', axis = 1); scoresDF_BT.columns # map colnames for consistency to allow concatenting scoresDF_BT.columns = scoresDF_BT.columns.map(scoreBT_mapD); scoresDF_BT.columns scoresDF_BT['source_data'] = 'BT' print('\nTotal cols in bts df:' , '\nBT_df:', len(scoresDF_BT.columns)) if len(scoresDF_CV.columns) == len(scoresDF_BT.columns): print('\nFirst proceeding to rowbind CV and BT dfs:') expected_ncols_out = len(scoresDF_BT.columns) + len(metaDF.columns) print('\nFinal output should have:', expected_ncols_out, 'columns' ) #----------------- # Combine WF #----------------- dfs_combine_wf = [scoresDF_CV, scoresDF_BT] print('\nCombinig', len(dfs_combine_wf), 'using pd.concat by row ~ rowbind' , '\nChecking Dims of df to combine:' , '\nDim of CV:', scoresDF_CV.shape , '\nDim of BT:', scoresDF_BT.shape) #print(scoresDF_CV) #print(scoresDF_BT) dfs_nrows_wf = [] for df in dfs_combine_wf: dfs_nrows_wf = dfs_nrows_wf + [len(df)] dfs_nrows_wf = max(dfs_nrows_wf) dfs_ncols_wf = [] for df in dfs_combine_wf: dfs_ncols_wf = dfs_ncols_wf + [len(df.columns)] dfs_ncols_wf = max(dfs_ncols_wf) print(dfs_ncols_wf) expected_nrows_wf = len(dfs_combine_wf) * dfs_nrows_wf expected_ncols_wf = dfs_ncols_wf common_cols_wf = list(set.intersection(*(set(df.columns) for df in dfs_combine_wf))) print('\nNumber of Common columns:', dfs_ncols_wf , '\nThese are:', common_cols_wf) if len(common_cols_wf) == dfs_ncols_wf : combined_baseline_wf = pd.concat([df[common_cols_wf] for df in dfs_combine_wf], ignore_index=False) print('\nConcatenating dfs with different resampling methods [WF]:' , '\nSplit type:', tts_split_name , '\nNo. of dfs combining:', len(dfs_combine_wf)) #print('\n================================================^^^^^^^^^^^^') if len(combined_baseline_wf) == expected_nrows_wf and len(combined_baseline_wf.columns) == expected_ncols_wf: #print('\n================================================^^^^^^^^^^^^') print('\nPASS:', len(dfs_combine_wf), 'dfs successfully combined' , '\nnrows in combined_df_wf:', len(combined_baseline_wf) , '\nncols in combined_df_wf:', len(combined_baseline_wf.columns)) else: print('\nFAIL: concatenating failed' , '\nExpected nrows:', expected_nrows_wf , '\nGot:', len(combined_baseline_wf) , '\nExpected ncols:', expected_ncols_wf , '\nGot:', len(combined_baseline_wf.columns)) sys.exit('\nFIRST IF FAILS') ## c1L = list(set(combined_baseline_wf.index)) c2L = list(metaDF.index) #if set(c1L) == set(c2L): if set(c1L) == set(c2L) and all(x in c2L for x in c1L) and all(x in c1L for x in c2L): print('\nPASS: proceeding to merge metadata with CV and BT dfs') combDF = pd.merge(combined_baseline_wf, metaDF, left_index = True, right_index = True) print('\nAdding column: Model_name') combDF['Model_name'] = combDF.index else: sys.exit('\nFAIL: Could not merge metadata with CV and BT dfs') else: # print('\nConcatenting dfs not possible [WF],check numbers ') print('\nOnly combining CV and metadata') #------------------------------------- # Combine WF+Metadata: Final output #------------------------------------- # if len(combDF.columns) == expected_ncols_out: # print('\nPASS: Combined df has expected ncols') # else: # sys.exit('\nFAIL: Length mismatch for combined_df') # print('\nAdding column: Model_name') # combDF['Model_name'] = combDF.index print('\n=========================================================' , '\nSUCCESS: Ran multiple classifiers' , '\n=======================================================') #resampling_methods_wf = combined_baseline_wf[['resampling']] #resampling_methods_wf = resampling_methods_wf.drop_duplicates() #, '\n', resampling_methods_wf) return combDF ###############################################################################