def print_results_get_mean_acc(ds1, ds2):
l1 = len(ds1)
l2 = len(ds2)
bias_acc = max(l1,l2) / (l1 + l2)
print(f"bias_accuracy: {bias_acc : .3f}")
X_set1, _ = prepare_full_dataset(ds1)
X_set2, _ = prepare_full_dataset(ds2)
y_set1 = np.zeros(l1)
y_set2 = np.ones(l2)
X_full = np.concatenate([X_set1, X_set2])
y_full = np.concatenate([y_set1, y_set2])
kf = RepeatedStratifiedKFold(n_splits=5, n_repeats=1)
rez = []
for i, (train_index, test_index) in enumerate(kf.split(X_full, y_full)):
X_train, X_test = X_full[train_index], X_full[test_index]
y_train, y_test = y_full[train_index], y_full[test_index]
rez.append(calc_results_simple(X_train, X_test, y_train, y_test, XGBClassifier()))
print(list2d_to_4g_str_pm(rez))
return np.mean(np.array(rez)[:,0])
def print_results(dataset, set1, set2):
genes_list = list(
dataset.drop(
columns=['study', 'patient_ID', 'pCR', 'RFS', 'DFS', 'posOutcome'
]))
X_set1, y_set1 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, y_set2 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set2)])
print("set1")
print_mean_fold_importance(X_set1, y_set1, genes_list)
# print("set2")
# print_mean_fold_importance(X_set2,y_set2,genes_list)
print("stack")
print_mean_fold_importance(np.concatenate([X_set1, X_set2]),
np.concatenate([y_set1, y_set2]), genes_list)
X_set1_wf = add_one_features_tail(X_set1, 0)
X_set2_wf = add_one_features_tail(X_set2, 1)
print("stack_with_set")
print_mean_fold_importance(np.concatenate([X_set1_wf, X_set2_wf]),
np.concatenate([y_set1, y_set2]), genes_list)
def print_results_baseline(dataset, set1, set2):
print("==> baseline: ")
X_set1, y_set1 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, y_set2 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set2)])
_print_results_set1set2(X_set1, y_set1, X_set2, y_set2)
print("")
def print_results(dataset, set1, set2):
X_set1, y_set1 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, y_set2 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set2)])
print("set1")
print_counter(X_set1[:, 0], y_set1)
print("set2")
print_counter(X_set2[:, 0], y_set2)
def print_results(dataset, set1, set2):
X_set1, y_set1 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, y_set2 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set2)])
# X_set1 = np.random.rand(*X_set1.shape)
# X_set2 = np.random.rand(*X_set2.shape)
X_set1_wf = add_one_features(X_set1, 0)
X_set2_wf = add_one_features(X_set2, 1)
X_genes = np.concatenate([X_set1, X_set2])
X_genes_wf = np.concatenate([X_set1_wf, X_set2_wf])
y_all = np.concatenate([y_set1, y_set2])
Xs = X_genes_wf[:, :1]
kf = RepeatedStratifiedKFold(n_splits=5, n_repeats=10)
print_order = [
"genes", "genes_set", "genes_biased", "genes_double", "study"
]
max_len_order = max(map(len, print_order))
rez = defaultdict(list)
for i, (train_index, test_index) in enumerate(kf.split(X_genes, y_all)):
rez["genes"].append(
calc_results_for_fold(X_genes, y_all, train_index, test_index,
XGBClassifier()))
rez["genes_set"].append(
calc_results_for_fold(X_genes_wf, y_all, train_index, test_index,
XGBClassifier()))
rez["genes_biased"].append(
calc_results_for_fold(X_genes_wf, y_all, train_index, test_index,
BiasedXgboost()))
rez["genes_double"].append(
calc_results_for_fold(X_genes_wf, y_all, train_index, test_index,
DoubleXgboost()))
rez["study"].append(
calc_results_for_fold(Xs, y_all, train_index, test_index,
XGBClassifier()))
for order in print_order:
print(order, " " * (max_len_order - len(order)),
" y, y_maxi, y_prob, y_prob_maxi : ",
list_to_4g_str(rez[order][-1]))
print("")
for order in print_order:
print("==> ", order, " " * (max_len_order - len(order)),
" y, y_maxi, y_prob, y_prob_maxi : ",
list_to_4g_str(np.mean(rez[order], axis=0)))
def print_results(dataset, set1, set2):
X_set1, y_set1 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, y_set2 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set2)])
X_set1_wf = add_one_features(X_set1, 0)
X_set2_wf = add_one_features(X_set2, 1)
X_full = np.concatenate([X_set1, X_set2])
X_full_wf = np.concatenate([X_set1_wf, X_set2_wf])
y_full = np.concatenate([y_set1, y_set2])
Xs = X_full_wf[:, :1]
kf = RepeatedStratifiedKFold(n_splits=5, n_repeats=1)
rez = []
rez_wf = []
rez_s = []
print_order = ["base", "studyf", "studyf_l", "only_study"]
max_len_order = max(map(len, print_order))
rez = defaultdict(list)
for i, (train_index, test_index) in enumerate(kf.split(X_full, y_full)):
rez["base"].append(
calc_results_for_fold(X_full, y_full, train_index, test_index,
XGBClassifier()))
rez["studyf"].append(
calc_results_for_fold(X_full_wf, y_full, train_index, test_index,
XGBClassifier()))
rez["studyf_l"].append(
calc_results_for_fold(X_full_wf, y_full, train_index, test_index,
XGBClassifier("binary:logistic")))
rez["only_study"].append(
calc_results_for_fold(Xs, y_full, train_index, test_index,
XGBClassifier()))
for order in print_order:
print(order, " " * (max_len_order - len(order)), ": ",
list_to_4g_str(rez[order][-1]))
print("")
for order in print_order:
print("==> ", order, " " * (max_len_order - len(order)), ": ",
list2d_to_4g_str_pm(rez[order]))
def print_results(dataset, set1, set2):
X_set1, y_set1 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, y_set2 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set2)])
print("set1")
clf = XGBClassifier()
clf.fit(X_set1, y_set1)
print(sorted(np.argsort(-1 * clf.feature_importances_)[:20]))
# print(np.sort(-1 * clf.feature_importances_)[:20])
set1_set20 = set(np.argsort(-1 * clf.feature_importances_)[:20])
print("set2")
clf = XGBClassifier()
clf.fit(X_set2, y_set2)
print(sorted(np.argsort(-1 * clf.feature_importances_)[:20]))
# print(np.sort(-1 * clf.feature_importances_)[:20])
set2_set20 = set(np.argsort(-1 * clf.feature_importances_)[:20])
print("intersection set1 set2", set1_set20.intersection(set2_set20))
print("stack")
clf = XGBClassifier()
clf.fit(np.concatenate([X_set1, X_set2]), np.concatenate([y_set1, y_set2]))
print(sorted(np.argsort(-1 * clf.feature_importances_)[:20]))
# print(np.sort(-1 * clf.feature_importances_)[:20])
stack_set20 = set(np.argsort(-1 * clf.feature_importances_)[:20])
print("intersection set1 stack", set1_set20.intersection(stack_set20))
print("intersection set2 stack", set2_set20.intersection(stack_set20))
X_set1_wf = add_one_features_tail(X_set1, 0)
X_set2_wf = add_one_features_tail(X_set2, 1)
print("stack_with_set")
clf = XGBClassifier()
clf.fit(np.concatenate([X_set1_wf, X_set2_wf]),
np.concatenate([y_set1, y_set2]))
print(sorted(np.argsort(-1 * clf.feature_importances_)[:20]))
def print_results(dataset, set1, set2):
bias_acc = max(len(set1), len(set2)) / (len(set1) + len(set2))
print(len(set1), len(set2))
print(f"bias_accuracy: {bias_acc : .3f}")
X_set1, _ = prepare_full_dataset(dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, _ = prepare_full_dataset(dataset.loc[dataset['patient_ID'].isin(set2)])
y_set1 = np.zeros(len(set1))
y_set2 = np.ones(len(set2))
X_full = np.concatenate([X_set1, X_set2])
y_full = np.concatenate([y_set1, y_set2])
kf = RepeatedStratifiedKFold(n_splits=5, n_repeats=10)
rez = []
for i, (train_index, test_index) in enumerate(kf.split(X_full, y_full)):
X_train, X_test = X_full[train_index], X_full[test_index]
y_train, y_test = y_full[train_index], y_full[test_index]
rez.append(calc_results_simple(X_train, X_test, y_train, y_test, XGBClassifier()))
print(list2d_to_4g_str_pm(rez))
def print_results(dataset, set1, set2):
bias_acc = max(len(set1), len(set2)) / (len(set1) + len(set2))
print(len(set1), len(set2))
print(f"bias_accuracy: {bias_acc : .3f}")
X_set1, _ = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, _ = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set2)])
y_set1 = np.zeros(len(set1))
y_set2 = np.ones(len(set2))
X_full = np.concatenate([X_set1, X_set2])
y_full = np.concatenate([y_set1, y_set2])
kf = RepeatedStratifiedKFold(n_splits=5, n_repeats=1)
rez = []
for i, (train_index, test_index) in enumerate(kf.split(X_full, y_full)):
X_train, X_test = X_full[train_index], X_full[test_index]
y_train, y_test = y_full[train_index], y_full[test_index]
clf = XGBClassifier()
rez.append(calc_results_simple(X_train, X_test, y_train, y_test, clf))
clf.fit(X_train, y_train)
print(np.argsort(-1 * clf.feature_importances_)[:20])
print(np.sort(-1 * clf.feature_importances_)[:20])
for i in np.argsort(-1 * clf.feature_importances_)[:20]:
print(
list(
dataset.drop(columns=[
'study', 'patient_ID', 'pCR', 'RFS', 'DFS',
'posOutcome'
]))[i])
print(list2d_to_4g_str_pm(rez))
import pandas as pd
import os
import numpy as np
import random
import math
from funs_common import read_mike_dataset, drop_trea, prepare_full_dataset
from sklearn.manifold import TSNE
import pickle
dataset = read_mike_dataset()
notrea_dataset = drop_trea(dataset)
X, y = prepare_full_dataset(notrea_dataset, y_field='study')
X_embedded = TSNE(n_components=2).fit_transform(X)
pickle.dump(X_embedded, open("experement24_studytest_tsne.p", "wb"))
def print_results(dataset, set1, set2):
X_set1, y_set1 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, y_set2 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set2)])
# X_set1 = np.random.rand(*X_set1.shape)
# X_set2 = np.random.rand(*X_set2.shape)
X_set1_wf = add_one_features(X_set1, 0)
X_set2_wf = add_one_features(X_set2, 1)
X_genes_wf = np.concatenate([X_set1_wf, X_set2_wf])
y_all = np.concatenate([y_set1, y_set2])
kf = RepeatedStratifiedKFold(n_splits=5, n_repeats=10)
print_order = [
"genes", "genes_set", "genes_biased", "genes_double", "study"
]
max_len_order = max(map(len, print_order))
rez = defaultdict(list)
for i, (train_index, test_index) in enumerate(kf.split(X_genes_wf, y_all)):
X_genes_wf_train, X_genes_wf_test = X_genes_wf[
train_index], X_genes_wf[test_index]
y_train, y_test = y_all[train_index], y_all[test_index]
print("before balanced")
print_count_two_sets(X_genes_wf_train[:, 0], y_train)
print_count_two_sets(X_genes_wf_test[:, 0], y_test)
# print("counter before balance", Counter(X_genes_wf_train[:,0]), Counter(X_genes_wf_test[:,0]), Counter(y_train), Counter(y_test))
X_genes_wf_train, y_train = random_upsample_balance(
X_genes_wf_train, y_train)
X_genes_wf_test, y_test = random_upsample_balance(
X_genes_wf_test, y_test)
# print("counter after balance", Counter(X_genes_wf_train[:,0]), Counter(X_genes_wf_test[:,0]), Counter(y_train), Counter(y_test))
print("after balanced")
print_count_two_sets(X_genes_wf_train[:, 0], y_train)
print_count_two_sets(X_genes_wf_test[:, 0], y_test)
X_genes_train = X_genes_wf_train[:, 1:]
X_genes_test = X_genes_wf_test[:, 1:]
Xs_train = X_genes_wf_train[:, :1]
Xs_test = X_genes_wf_test[:, :1]
rez["genes"].append(
calc_results_simple(X_genes_train, X_genes_test, y_train, y_test,
XGBClassifier()))
rez["genes_set"].append(
calc_results_simple(X_genes_wf_train, X_genes_wf_test, y_train,
y_test, XGBClassifier()))
rez["genes_biased"].append(
calc_results_simple(X_genes_wf_train, X_genes_wf_test, y_train,
y_test, BiasedXgboost()))
rez["genes_double"].append(
calc_results_simple(X_genes_wf_train, X_genes_wf_test, y_train,
y_test, DoubleXgboost()))
rez["study"].append(
calc_results_simple(Xs_train, Xs_test, y_train, y_test,
XGBClassifier()))
for order in print_order:
print(order, " " * (max_len_order - len(order)), ": ",
list_to_4g_str(rez[order][-1]))
print("")
for order in print_order:
print("==> ", order, " " * (max_len_order - len(order)), ": ",
list2d_to_4g_str_pm(rez[order]))
print("==> DFS", prefix)
print_results_for_field(dataset, Xt_full_dict, "DFS", prefix)
print("")
print("")
print("==> posOutcome", prefix)
print_results_for_field(dataset, Xt_full_dict, "posOutcome", prefix)
print("")
print("")
treat_dataset = read_treat_dataset()
combat_dataset = read_combat_dataset()
pam_types_cat_dataset = read_pam_types_cat_dataset()
X_full, _ = prepare_full_dataset(drop_trea(combat_dataset))
assert all(pam_types_cat_dataset['patient_ID'] == combat_dataset['patient_ID'])
#print(list(pam_types_cat_dataset))
#print_results(pam_types_cat_dataset, "old")
for n_cluster in [1, 5, 10, 20, 100, 200]:
lda = LatentDirichletAllocation(n_components=n_cluster)
Xt_full = lda.fit_transform(X_full - np.min(X_full))
Xt_full_dict = {
i: x
for i, x in zip(combat_dataset['patient_ID'], Xt_full)
}
print_results(pam_types_cat_dataset, Xt_full_dict, "nc" + str(n_cluster))
def print_set(dataset, set1, y_field):
X_set1, y_set1 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)], y_field)
print_counter(X_set1[:, 0], y_set1)
