added combined model FS code and run script
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scripts/ml/combined_model/cm_logo_skf_FS.py
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scripts/ml/combined_model/cm_logo_skf_FS.py
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Wed Jun 29 19:44:06 2022
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@author: tanu
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"""
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import sys, os
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import pandas as pd
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import numpy as np
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import re
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from copy import deepcopy
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from sklearn import linear_model
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from sklearn import datasets
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from collections import Counter
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from sklearn.linear_model import LogisticRegression, LogisticRegressionCV
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from sklearn.linear_model import RidgeClassifier, RidgeClassifierCV, SGDClassifier, PassiveAggressiveClassifier
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from sklearn.naive_bayes import BernoulliNB
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from sklearn.neighbors import KNeighborsClassifier
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from sklearn.svm import SVC
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from sklearn.tree import DecisionTreeClassifier, ExtraTreeClassifier
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from sklearn.ensemble import RandomForestClassifier, ExtraTreesClassifier, AdaBoostClassifier, GradientBoostingClassifier, BaggingClassifier
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from sklearn.naive_bayes import GaussianNB
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from sklearn.gaussian_process import GaussianProcessClassifier, kernels
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from sklearn.gaussian_process.kernels import RBF, DotProduct, Matern, RationalQuadratic, WhiteKernel
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from sklearn.discriminant_analysis import LinearDiscriminantAnalysis, QuadraticDiscriminantAnalysis
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from sklearn.neural_network import MLPClassifier
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from sklearn.svm import SVC
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from xgboost import XGBClassifier
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from sklearn.naive_bayes import MultinomialNB
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from sklearn.preprocessing import StandardScaler, MinMaxScaler, OneHotEncoder
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from sklearn.compose import ColumnTransformer
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from sklearn.compose import make_column_transformer
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from sklearn.metrics import make_scorer, confusion_matrix, accuracy_score, balanced_accuracy_score, precision_score, average_precision_score, recall_score
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from sklearn.metrics import roc_auc_score, roc_curve, f1_score, matthews_corrcoef, jaccard_score, classification_report
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# added
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from sklearn.model_selection import train_test_split, cross_validate, cross_val_score, LeaveOneOut, KFold, RepeatedKFold, cross_val_predict
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from sklearn.model_selection import train_test_split, cross_validate, cross_val_score
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from sklearn.model_selection import StratifiedKFold,RepeatedStratifiedKFold, RepeatedKFold
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from sklearn.pipeline import Pipeline, make_pipeline
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from sklearn.feature_selection import RFE, RFECV
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import itertools
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import seaborn as sns
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import matplotlib.pyplot as plt
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from statistics import mean, stdev, median, mode
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from imblearn.over_sampling import RandomOverSampler
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from imblearn.under_sampling import RandomUnderSampler
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from imblearn.over_sampling import SMOTE
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from sklearn.datasets import make_classification
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from imblearn.combine import SMOTEENN
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from imblearn.combine import SMOTETomek
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from imblearn.over_sampling import SMOTENC
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from imblearn.under_sampling import EditedNearestNeighbours
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from imblearn.under_sampling import RepeatedEditedNearestNeighbours
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from sklearn.model_selection import GridSearchCV
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from sklearn.base import BaseEstimator
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from sklearn.impute import KNNImputer as KNN
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import json
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import argparse
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import re
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import itertools
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from sklearn.model_selection import LeaveOneGroupOut
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from boruta import BorutaPy
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###############################################################################
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# homedir = os.path.expanduser("~")
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# sys.path.append(homedir + '/git/LSHTM_analysis/scripts/ml/ml_functions')
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# sys.path
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###############################################################################
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#outdir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
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#====================
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# Import ML functions
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#====================
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#from ml_data_combined import *
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#from MultClfs import *
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#from GetMLData import *
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#from SplitTTS import *
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#skf_cv = StratifiedKFold(n_splits = 10 , shuffle = True, random_state = 42)
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#logo = LeaveOneGroupOut()
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########################################################################
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# COMPLETE data: No tts_split
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########################################################################
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#%%
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def CMLogoSkf_FS(cm_input_df
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, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
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, bts_genes = ["embb", "katg", "rpob", "pnca", "gid"]
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, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
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, target_var = 'dst_mode'
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, gene_group = 'gene_name'
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, std_gene_omit = []
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, var_type = ['numerical', 'categorical','mixed']
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):
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n_jobs = os.cpu_count()
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njobs = {'n_jobs': n_jobs }
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rs = {'random_state': 42}
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cm_gene_featuresD = {}
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for bts_gene in bts_genes:
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print('\n BTS gene:', bts_gene)
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if not std_gene_omit:
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training_genesL = ['alr']
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else:
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training_genesL = []
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tr_gene_omit = std_gene_omit + [bts_gene]
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n_tr_genes = (len(bts_genes) - (len(std_gene_omit)))
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#n_total_genes = (len(bts_genes) - len(std_gene_omit))
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n_total_genes = len(all_genes)
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training_genesL = training_genesL + list(set(bts_genes) - set(tr_gene_omit))
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#training_genesL = [element for element in bts_genes if element not in tr_gene_omit]
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print('\nTotal genes: ', n_total_genes
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,'\nTraining on:', n_tr_genes
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,'\nTraining on genes:', training_genesL
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, '\nOmitted genes:', tr_gene_omit
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, '\nBlind test gene:', bts_gene)
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print('\nDim of data:', cm_input_df.shape)
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tts_split_type = "logo_skf_BT_" + bts_gene
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#-------
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# training
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#------
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cm_training_df = cm_input_df[~cm_input_df['gene_name'].isin(tr_gene_omit)]
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cm_X = cm_training_df.drop(cols_to_drop, axis=1, inplace=False)
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#cm_y = cm_training_df.loc[:,'dst_mode']
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cm_y = cm_training_df.loc[:, target_var]
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gene_group = cm_training_df.loc[:,'gene_name']
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print('\nTraining data dim:', cm_X.shape
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, '\nTraining Target dim:', cm_y.shape)
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if all(cm_X.columns.isin(cols_to_drop) == False):
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print('\nChecked training df does NOT have Target var')
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else:
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sys.exit('\nFAIL: training data contains Target var')
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#---------------
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# BTS: genes
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#---------------
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cm_test_df = cm_input_df[cm_input_df['gene_name'].isin([bts_gene])]
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cm_bts_X = cm_test_df.drop(cols_to_drop, axis = 1, inplace = False)
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#cm_bts_y = cm_test_df.loc[:, 'dst_mode']
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cm_bts_y = cm_test_df.loc[:, target_var]
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print('\nTEST data dim:' , cm_bts_X.shape
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, '\nTEST Target dim:' , cm_bts_y.shape)
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print("Running Multiple models on LOGO with SKF")
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# REASSIGN for simplicity
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# X
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X_train = cm_X.copy()
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X_test = cm_bts_X.copy()
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X_train.shape
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X_test.shape
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# Y
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y_train = cm_y.copy()
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y_test = cm_bts_y.copy()
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y_train.shape
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y_test.shape
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##############################################################################
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#PREPROCESS
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numerical_ix = X_train.select_dtypes(include=['int64', 'float64']).columns
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numerical_ix
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print("\nNo. of numerical indices:", len(numerical_ix))
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categorical_ix = X_train.select_dtypes(include=['object', 'bool']).columns
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categorical_ix
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print("\nNo. of categorical indices:", len(categorical_ix))
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#======================================================
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# Determine preprocessing steps ~ var_type
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#======================================================
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if var_type == 'numerical':
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t = [('num', MinMaxScaler(), numerical_ix)]
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if var_type == 'categorical':
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t = [('cat', OneHotEncoder(), categorical_ix)]
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if var_type == 'mixed':
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t = [('num', MinMaxScaler(), numerical_ix)
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, ('cat', OneHotEncoder(), categorical_ix)]
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col_transform = ColumnTransformer(transformers = t
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, remainder='passthrough')
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col_transform.fit(X_train)
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col_transform.get_feature_names_out()
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var_type_colnames = col_transform.get_feature_names_out()
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var_type_colnames = pd.Index(var_type_colnames)
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if var_type == 'mixed':
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print('\nVariable type is:', var_type
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, '\nNo. of columns in input_df:', len(X_train.columns)
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, '\nNo. of columns post one hot encoder:', len(var_type_colnames))
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else:
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print('\nNo. of columns in input_df:', len(cm_input_df.columns))
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##############################################################################
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# FS: Random Forest + Boruta
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X_train = col_transform.fit_transform(X_train)
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X_test = col_transform.fit_transform(X_test)
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fs_clf = "RandomForestClassifier"
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rf_all_features = RandomForestClassifier(n_estimators=1000, max_depth=5
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, **rs, **njobs)
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# fit
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rf_all_features.fit(np.array(X_train), np.array(y_train))
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print("RF, baseline MCC:", matthews_corrcoef(y_test, rf_all_features.predict(X_test)))
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# BORUTA and fit
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boruta_selector = BorutaPy(rf_all_features,**rs, verbose = 3)
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boruta_selector.fit(np.array(X_train), np.array(y_train))
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# Get chosen features
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print("Ranking: ", boruta_selector.ranking_)
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print("No. of significant features: ", boruta_selector.n_features_)
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X_important_train = boruta_selector.transform(np.array(X_train))
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X_important_test = boruta_selector.transform(np.array(X_test))
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# just retesting with selected features on RF itselfs
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rf_all_features.fit(X_important_train, y_train)
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print("RF, Boruta MCC:", matthews_corrcoef(y_test, rf_all_features.predict(X_important_test)))
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selected_rf_features = pd.DataFrame({'Feature':list(var_type_colnames),
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'Ranking':boruta_selector.ranking_})
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sel_rf_features_sorted = selected_rf_features.sort_values(by='Ranking')
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sel_features = var_type_colnames[boruta_selector.support_]
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cm_gene_featuresD.update({bts_gene: {
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"sel_features": sel_features
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, "fs_ranking" : sel_rf_features_sorted
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, "fs_model_name": fs_clf
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}
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}
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)
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return(cm_gene_featuresD)
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32
scripts/ml/combined_model/run_cm_logo.py
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scripts/ml/combined_model/run_cm_logo.py
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Sat Sep 3 09:43:22 2022
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@author: tanu
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"""
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###############################################################################
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homedir = os.path.expanduser("~")
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sys.path.append(homedir + '/home/tanu/git/LSHTM_analysis/scripts/ml/combined_model')
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sys.path.append(homedir + '/home/tanu/git/LSHTM_analysis/scripts/ml/ml_functions')
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sys.path.append(homedir + '/home/tanu/git/LSHTM_analysis/scripts/ml')
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from MultClfs import *
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###############################################################################
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#%% RUN: Combined model Baseline
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outdir_cg = "/home/tanu/git/LSHTM_ML/output/combined/"
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#===============
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# Complete Data
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#===============
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CombinedModelML(cm_input_df = combined_df, outdir = outdir_cg, file_suffix = "complete")
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CombinedModelML(cm_input_df = combined_df, outdir = outdir_cg, std_gene_omit=['alr'], file_suffix = "complete")
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#===============
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# Actual Data
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#===============
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CombinedModelML(cm_input_df = combined_df_actual, outdir = outdir_cg, file_suffix = "actual")
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CombinedModelML(cm_input_df = combined_df_actual, outdir = outdir_cg, std_gene_omit=['alr'], file_suffix = "actual")
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scripts/ml/combined_model/run_cm_logo_FS.py
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scripts/ml/combined_model/run_cm_logo_FS.py
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Fri Sep 2 19:17:46 2022
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@author: tanu
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"""
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###############################################################################
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homedir = os.path.expanduser("~")
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sys.path.append(homedir + '/home/tanu/git/LSHTM_analysis/scripts/ml/combined_model')
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sys.path.append(homedir + '/home/tanu/git/LSHTM_analysis/scripts/ml/ml_functions')
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sys.path.append(homedir + '/home/tanu/git/LSHTM_analysis/scripts/ml')
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from MultClfs import *
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from cm_logo_skf_FS import *
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###############################################################################
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#%% FS with all genes in training
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###############################################################################
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# 1. Select Features
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boruta_features = CMLogoSkf_FS(cm_input_df = combined_df,var_type = 'mixed', file_suffix = "complete")
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# 2. Find original column names of features
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# if it starts with num__, get rid of num__
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# if it starts with cat__, get rid of cat__ and the _<number> at the end
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for i in boruta_features:
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print(i)
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boruta_features[i]['sel_features']=[re.sub('^num__|cat__(.*)_\d*$',r'\1', current_thing) for current_thing in boruta_features[i]['sel_features']]
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boruta_features[i]['sel_features'] = list(set(boruta_features[i]['sel_features']))
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# write json
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OutFile_6Tgenes = "/home/tanu/git/LSHTM_ML/output/feature_selection/boruta_features_6_Tgenes.json"
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pd.DataFrame(boruta_features).to_json(path_or_buf=OutFile_6Tgenes)
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# 3. Run all classification models using original column names from (2)
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combined_df_embb=combined_df[boruta_features['embb']['sel_features']+['dst', 'dst_mode', 'gene_name']]
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combined_df_katg=combined_df[boruta_features['katg']['sel_features']+['dst', 'dst_mode', 'gene_name']]
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combined_df_pnca=combined_df[boruta_features['pnca']['sel_features']+['dst', 'dst_mode', 'gene_name']]
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combined_df_gid= combined_df[boruta_features['gid' ]['sel_features']+['dst', 'dst_mode', 'gene_name']]
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combined_df_rpob= combined_df[boruta_features['rpob' ]['sel_features']+['dst', 'dst_mode', 'gene_name']]
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# from /home/tanu/git/LSHTM_analysis/scripts/ml/ml_functions/MultClf.py
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CombinedModelML(combined_df_embb
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, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
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, bts_genes = ["embb"]
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, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
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, target_var = 'dst_mode'
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, gene_group = 'gene_name'
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, std_gene_omit = []
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, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
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, file_suffix = "FS"
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)
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CombinedModelML(combined_df_katg
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, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
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, bts_genes = ["katg"]
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, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
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, target_var = 'dst_mode'
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, gene_group = 'gene_name'
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, std_gene_omit = []
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, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
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, file_suffix = "FS"
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)
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CombinedModelML(combined_df_pnca
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, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
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, bts_genes = ["pnca"]
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, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
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, target_var = 'dst_mode'
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, gene_group = 'gene_name'
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, std_gene_omit = []
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, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
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, file_suffix = "FS"
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)
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CombinedModelML(combined_df_gid
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, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
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, bts_genes = ["gid"]
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, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
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, target_var = 'dst_mode'
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, gene_group = 'gene_name'
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, std_gene_omit = []
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, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
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, file_suffix = "FS"
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)
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CombinedModelML(combined_df_rpob
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, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
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, bts_genes = ["rpob"]
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, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
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, target_var = 'dst_mode'
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, gene_group = 'gene_name'
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, std_gene_omit = []
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, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
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, file_suffix = "FS"
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)
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|
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|
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# write all feature rankings
|
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for i in boruta_features:
|
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print (i)
|
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gene_fs_ranking = boruta_features[i]['fs_ranking']
|
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gene_fs_ranking.to_csv("/home/tanu/git/LSHTM_ML/output/feature_selection/"+ i + "_boruta_featues_6Tgenes.csv")
|
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|
||||
|
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###############################################################################
|
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#%% FS withour training including ALR
|
||||
###############################################################################
|
||||
# With training omitting alr
|
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boruta_features_omit_alr = CMLogoSkf_FS(cm_input_df = combined_df
|
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, std_gene_omit = ['alr']
|
||||
, var_type = 'mixed')
|
||||
|
||||
# 2. Find original column names of features
|
||||
# if it starts with num__, get rid of num__
|
||||
# if it starts with cat__, get rid of cat__ and the _<number> at the end
|
||||
for i in boruta_features_omit_alr:
|
||||
print(i)
|
||||
boruta_features_omit_alr[i]['sel_features']=[re.sub('^num__|cat__(.*)_\d*$',r'\1', current_thing) for current_thing in boruta_features[i]['sel_features']]
|
||||
boruta_features_omit_alr[i]['sel_features'] = list(set(boruta_features_omit_alr[i]['sel_features']))
|
||||
|
||||
# write json
|
||||
OutFile_5Tgenes = "/home/tanu/git/LSHTM_ML/output/feature_selection/boruta_features_5_Tgenes.json"
|
||||
pd.DataFrame(boruta_features_omit_alr).to_json(path_or_buf=OutFile_5Tgenes)
|
||||
|
||||
# 3. Run all classification models using original column names from (2)
|
||||
cm_input_df5 = combined_df[~combined_df['gene_name'].isin(omit_gene_alr)]
|
||||
|
||||
combined_df_embb_no_alr = cm_input_df5[boruta_features_omit_alr['embb']['sel_features']+['dst', 'dst_mode', 'gene_name']]
|
||||
combined_df_katg_no_alr = cm_input_df5[boruta_features_omit_alr['katg']['sel_features']+['dst', 'dst_mode', 'gene_name']]
|
||||
combined_df_pnca_no_alr = cm_input_df5[boruta_features_omit_alr['pnca']['sel_features']+['dst', 'dst_mode', 'gene_name']]
|
||||
combined_df_gid_no_alr = cm_input_df5[boruta_features_omit_alr['gid' ]['sel_features']+['dst', 'dst_mode', 'gene_name']]
|
||||
combined_df_rpob_no_alr = cm_input_df5[boruta_features_omit_alr['rpob' ]['sel_features']+['dst', 'dst_mode', 'gene_name']]
|
||||
|
||||
|
||||
CombinedModelML(combined_df_embb_no_alr
|
||||
, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
|
||||
, bts_genes = ["embb"]
|
||||
, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
|
||||
, target_var = 'dst_mode'
|
||||
, gene_group = 'gene_name'
|
||||
, std_gene_omit = ["alr"]
|
||||
, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
|
||||
, file_suffix = "FS_no_Talr"
|
||||
)
|
||||
|
||||
|
||||
CombinedModelML(combined_df_katg_no_alr
|
||||
, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
|
||||
, bts_genes = ["katg"]
|
||||
, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
|
||||
, target_var = 'dst_mode'
|
||||
, gene_group = 'gene_name'
|
||||
, std_gene_omit = ["alr"]
|
||||
, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
|
||||
, file_suffix = "FS_no_Talr"
|
||||
)
|
||||
|
||||
|
||||
CombinedModelML(combined_df_pnca_no_alr
|
||||
, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
|
||||
, bts_genes = ["pnca"]
|
||||
, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
|
||||
, target_var = 'dst_mode'
|
||||
, gene_group = 'gene_name'
|
||||
, std_gene_omit = ["alr"]
|
||||
, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
|
||||
, file_suffix = "FS_no_Talr"
|
||||
)
|
||||
|
||||
CombinedModelML(combined_df_gid_no_alr
|
||||
, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
|
||||
, bts_genes = ["gid"]
|
||||
, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
|
||||
, target_var = 'dst_mode'
|
||||
, gene_group = 'gene_name'
|
||||
, std_gene_omit = ["alr"]
|
||||
, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
|
||||
, file_suffix = "FS_no_Talr"
|
||||
)
|
||||
|
||||
CombinedModelML(combined_df_rpob_no_alr
|
||||
, all_genes = ["embb", "katg", "rpob", "pnca", "gid", "alr"]
|
||||
, bts_genes = ["rpob"]
|
||||
, cols_to_drop = ['dst', 'dst_mode', 'gene_name']
|
||||
, target_var = 'dst_mode'
|
||||
, gene_group = 'gene_name'
|
||||
, std_gene_omit = ["alr"]
|
||||
, output_dir = "/home/tanu/git/LSHTM_ML/output/feature_selection/"
|
||||
, file_suffix = "FS_no_Talr"
|
||||
)
|
||||
|
||||
|
||||
# write all feature rankings
|
||||
for i in boruta_features_omit_alr:
|
||||
print (i)
|
||||
gene_fs_ranking_no_alr = boruta_features_omit_alr[i]['fs_ranking']
|
||||
gene_fs_ranking_no_alr.to_csv("/home/tanu/git/LSHTM_ML/output/feature_selection/"+ i + "_boruta_featues_5Tgenes.csv")
|
||||
|
||||
|
||||
Loading…
Add table
Add a link
Reference in a new issue