A Machine Learning Approach to Predict Stress Hormones and Inflammatory Markers Using Illness Perception and Quality of Life in Breast Cancer Patients
Abstract
:1. Introduction
2. Materials and Methods
2.1. Participants
2.2. Measures
2.3. Procedure
2.4. Data Analysis
3. Results
3.1. Data Analysis Using SPSS
3.1.1. Characteristics of Breast Cancer Patients
3.1.2. Quality of Life and Illness Perception
3.1.3. Stress Hormones and Psychosocial Factors
3.1.4. Inflammatory Markers and Psychosocial Factors
3.2. Data Analysis with Artificial Intelligence (AI) Methods
3.2.1. Comparing Consistently the Machine Learning Algorithms
3.2.2. Gradient Boosting for Classification
Grid Search for Hyperparameters
3.2.3. Feature Selection for Machine Learning in Python
Feature Selection
Feature Selection for Machine Learning
Univariate Selection
Recursive Feature Elimination
Principal Component Analysis
Feature Importance
3.2.4. Machine Learning Results
4. Discussion
4.1. Illness Perception and Quality of Life
4.2. Ilness Perception, Quality of Life and Stress Hormones
4.3. Quality of Life, Illness Perception and Inflammatory Markers
5. Limitations and Future Directions
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
Appendix A.1. Comparing the Machine Learning Algorithms in Python with Scikit-Learn
Appendix A.2. Choosing the Best Machine Learning Model
Appendix A.3. Careful Comparison of Machine Learning Models
Appendix B
# compare algorithms |
import pandas |
import matplotlib.pyplot as plt |
from sklearn import model_selection |
from sklearn.linear_model import LogisticRegression |
from sklearn.tree import DecisionTreeClassifier |
from sklearn.neighbors import KNeighborsClassifier |
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis |
from sklearn.naive_bayes import GaussianNB |
from sklearn.svm import SVC |
# load dataset |
dataframe = pandas.read_csv(‘ACTH.csv’) |
array = dataframe.values |
X = array[:,0:12] |
Y = array[:,12] |
# prepare models |
models = [] |
models.append((‘LR’, LogisticRegression())) |
models.append((‘LDA’, LinearDiscriminantAnalysis())) |
models.append((‘KNN’, KNeighborsClassifier())) |
models.append((‘CART’, DecisionTreeClassifier())) |
models.append((‘NB’, GaussianNB())) |
models.append((‘SVM’, SVC())) |
# evaluate each model in turn |
results = [] |
names = [] |
scoring = ‘accuracy’ |
for name, model in models: |
kfold = model_selection.KFold(n_splits = 10, shuffle = True) |
cv_results = model_selection.cross_val_score(model, X, Y, cv = kfold, scoring = scoring) |
results.append(cv_results) |
names.append(name) |
msg = “%s: %f (%f)” % (name, cv_results.mean(), cv_results.std()) |
print(msg) |
# boxplot algorithm comparison |
fig = plt.figure() |
fig.suptitle(‘Algorithm Comparison’) |
ax = fig.add_subplot(111) |
plt.boxplot(results) |
ax.set_xticklabels(names) |
plt.show() |
Appendix C
Appendix C.1. Developing a Gradient Boosting Machine Ensemble in Python
Appendix C.2. Gradient Boosting Machines Algorithm
- Tree constraints: such as the depth of the trees and the number of trees used in the ensemble.
- Weighted updates: such as a learning rate used to limit how much each tree contributes to the ensemble.
- Random sampling: such as fitting trees to random subsets of features and samples. The use of random sampling often leads to a change in the name of the algorithm in “stochastic gradient boosting”.
Appendix C.3. Interface (API) Scikit-Learn Gradient Boosting (API)
# check scikit-learn version |
import sklearn |
print(sklearn.__version__) |
OUT |
0.22.2.post1 |
Appendix D
# evaluate gradient boosting algorithm for classification |
from numpy import mean |
from numpy import std |
from sklearn.datasets import make_classification |
from sklearn.model_selection import cross_val_score |
from sklearn.model_selection import RepeatedStratifiedKFold |
from sklearn.ensemble import GradientBoostingClassifier |
# define the model |
model = GradientBoostingClassifier() |
# define the evaluation method |
cv = RepeaedStratifiedKFold(n_splits = 10, n_repeats = 3, random_state = 1) |
# evaluate the model on the dataset |
n_scores = cross_val_score(model, X, y, scoring = ‘accuracy’, cv = cv, n_jobs = −1) |
# report performance |
print(‘Mean Accuracy: %.3f (%.3f)’ % (mean(n_scores), std(n_scores))) |
Appendix E
# example of grid searching key hyperparameters for gradient boosting on a classification dataset |
from sklearn.datasets import make_classification |
from sklearn.model_selection import RepeatedStratifiedKFold |
from sklearn.model_selection import GridSearchCV |
from sklearn.ensemble import GradientBoostingClassifier |
# define the model with default hyperparameters |
model = GradientBoostingClassifier() |
# define the grid of values to search |
grid = dict() |
grid[‘n_estimators’] = [10, 50, 100, 500] |
grid[‘learning_rate’] = [0.0001, 0.001, 0.01, 0.1, 1.0] |
grid[‘subsample’] = [0.5, 0.7, 1.0] |
grid[‘max_depth’] = [3, 7, 9] |
# define the evaluation procedure |
cv = RepeatedStratifiedKFold(n_splits = 10, n_repeats = 3, random_state = 1) |
# define the grid search procedure |
grid_search = GridSearchCV(estimator = model, param_grid = grid, n_jobs = −1, cv = cv, scoring = ‘accuracy’) |
# execute the grid search |
grid_result = grid_search.fit(X, Y) |
# summarize the best score and configuration |
print(“Best: %f using %s” % (grid_result.best_score_, grid_result.best_params_)) |
# summarize all scores that were evaluated |
means = grid_result.cv_results_[‘mean_test_score’] |
stds = grid_result.cv_results_[‘std_test_score’] |
params = grid_result.cv_results_[‘params’] |
for mean, stdev, param in zip(means, stds, params): |
print(“%f (%f) with: %r” % (mean, stdev, param)) |
Appendix F
# make predictions using gradient boosting for classification |
from sklearn.datasets import make_classification |
from sklearn.ensemble import GradientBoostingClassifier |
# define the model |
model = GradientBoostingClassifier() |
# fit the model on the whole dataset |
model.fit(X, y) |
# make a single prediction |
row = [13, 15, 23, 24, 21, 14, 20, 156, 11.62, 23.79, 24, 25.2] |
yhat = model.predict([row]) |
# summarize prediction |
print(‘Predicted Class: %d’ % yhat[0]) |
Appendix G
# feature selection with univariate statistical tests |
from pandas import read_csv |
from numpy import set_printoptions |
from sklearn.feature_selection import SelectKBest |
from sklearn.feature_selection import f_classif |
# feature extraction |
test = SelectKBest(score_func = f_classif, k = 4) |
fit = test.fit(X, Y) |
# summarize scores |
set_printoptions(precision = 3) |
print(fit.scores_) |
features = fit.transform(X) |
# summarize selected features |
print(features[0:5,:]) |
Appendix H
# feature extraction with RFE |
from pandas import read_csv |
from sklearn.feature_selection import RFE |
from sklearn.linear_model import LogisticRegression |
# feature extraction |
model = LogisticRegression(solver = ‘lbfgs’) |
rfe = RFE(model, 3) |
fit = rfe.fit(X, Y) |
print(“Num Features: %d” % fit.n_features_) |
print(“Selected Features: %s” % fit.support_) |
print(“Feature Ranking: %s” % fit.ranking_) |
Appendix I
# feature extraction with PCA |
import numpy |
from pandas import read_csv |
from sklearn.decomposition import PCA |
# feature extraction |
pca = PCA(n_components = 3) |
fit = pca.fit(X) |
# summarize components |
print(“Explained Variance: %s” % fit.explained_variance_ratio_) |
print(fit.components_) |
Appendix J
# feature importance with extra trees classifier |
from pandas import read_csv |
from sklearn.ensemble import ExtraTreesClassifier |
# feature extraction |
model = ExtraTreesClassifier(n_estimators = 10) |
model.fit(X, Y) |
print(model.feature_importances_) |
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Mean (SD) | N | % | |
---|---|---|---|
Age (mean) | 53(11.6) | ||
Years since treatment | 4.7(5.01) | ||
6 months–1 year | 23 | 32.8 | |
1–5 years | 22 | 31.4 | |
5–10 years | 13 | 18.5 | |
10–20 years | 12 | 17.1 | |
Type of intervention | |||
Conservative intervention | 22 | 31 | |
Mastectomy | 48 | 69 | |
Type of treatment | |||
Radiotherapy | 11 | 15.7 | |
Chemotherapy | 16 | 22.8 | |
Radio + Chemotherapy | 38 | 54.2 | |
Other treatments | 5 | 7.14 | |
Relationship status | |||
Married/in a relationship | 50 | 71.4 | |
Single/divorced | 20 | 28.5 | |
Education level | |||
At least high school | 63 | 90 | |
Cancer stage | |||
Stage I | 27 | 38.5 | |
Stage II | 30 | 42.8 | |
Stage III | 13 | 18.5 |
Health | Social | Psychological | Family | |
---|---|---|---|---|
Timeline | −0.17 | −0.21 | −0.30 * | −0.14 |
Time cyclical | −0.25 * | 0.22 | −0.15 | −0.17 |
Consequences | −0.44 ** | −0.36 ** | −0.38 ** | −0.20 |
Personal control | −0.01 | 0.08 | 0.006 | −0.02 |
Treatment control | 0.16 | 0.15 | 0.26 * | 0.16 |
Coherence | 0.40 ** | 0.33 ** | 0.36 ** | 0.27 * |
Emotions | −0.51 ** | −0.54 ** | −58 ** | −0.35 ** |
Identity | 0.08 | 0.04 | 0.05 | −0.09 |
Variables | Quality of Life | ||
---|---|---|---|
ΔR2 | ΔF | Β | |
Time cyclical | 0.06 | 4.11 * | −0.02 |
Consequences | 0.14 | 11.57 *** | −0.19 |
Coherence | 0.11 | 9.93 ** | 0.22* |
Emotions | 0.10 | 11.36 *** | −0.40 *** |
First Assessment | Second Assessment | t-Test | |||
---|---|---|---|---|---|
M | SD | M | SD | ||
ESR (mm/1 h) | 6.63 | 5.208 | 5.04 | 2.87 | 1.45 |
Fibrinogen (mg/dL) | 385.53 | 62.81 | 360.38 | 61.200 | 3.24 ** |
CRP (mg/dL) | 0.67 | 2.26 | 0.17 | 1.37 | 0.81 |
ACTH (pg/mL) | 26.76 | 26.01 | 20.34 | 32.29 | 1.45 |
Cortisol | 121 | 56.83 | 105.09 | 57.26 | 0.99 |
qolH | qolS | qolP | qolF | ipT | ipCy | ipCo | ipP | ipT | Ipcoh | ipE | ipI | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Cortisol | 0.09 | −0.04 | −0.06 | 0.007 | 0.09 | −0.12 | −0.22 | 0.06 | −0.08 | 0.06 | 0.01 | −0.21 |
ACTH | −0.13 | −0.12 | −0.06 | −0.57 ** | 0.08 | −0.01 | −0.04 | −0.11 | −0.24 ^ | −0.06 | 0.05 | 0.06 |
Variables | ACTH | |||
---|---|---|---|---|
ΔR2 | ΔF | Β | Β | |
Step 1 | Step 2 | |||
Step 1 | 0.02 | 0.16 | ||
Age | 0.07 | 0.09 | ||
Years since diagnosis | −0.12 | −0.09 | ||
Cancer stage | −0.02 | −0.04 | ||
Step 2 | 0.48 | 10.13 *** | ||
Family quality of life | −0.66 *** | |||
Treatment control | −0.07 |
qolH | qolS | qolP | qolF | ipT | ipCy | ipCo | ipP | ipT | ipcoh | ipE | ipI | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ESR | −0.18 | −0.10 | −0.13 | −0.08 | 0.34 * | 0.07 | 0.08 | −0.06 | 0.06 | 0.01 | 0.23 | −0.06 |
CRP | −0.21 | −0.02 | 0.07 | −0.04 | −0.08 | 0.12 | −0.07 | 0.04 | 0.13 | −0.03 | −0.01 | −0.25 |
FBG | 0.09 | 0.03 | 0.10 | −0.05 | 0.26 ^ | −0.02 | −0.06 | 0.09 | 0.09 | 0.03 | 0.02 | −0.01 |
Data Bases | Targets = 0 (Decrease or Stagnation) = 1 (growth) | Features | ||
---|---|---|---|---|
Stress Hormones | Inflammatory markers | Illness perception | Quality of life | |
ACTH.csv | ACTH | CRP | 0 IPQtimeline (−) | 8 hfsub (health QL) |
CLU.csv | CLU | ESR | 1 IPQticyclical (−) | 9 socsub (social QL) |
CRP.csv | FBG | 2 IPQconsequences (−) | 10 pspsub (psychological QL) | |
ESR.csv | 3 IPQpersonal control (+) | 11 famsub (family QL) | ||
FBG.csv | 4 IPQtreatment control (+) | |||
5 IPQillness coherence (+) | ||||
6 IPQemotional (−) | ||||
7 IPQidentity (−) |
LR | LDA | KNN | CART | NB | SVM | |
---|---|---|---|---|---|---|
M (SD) | 0.738 (0.109) | 0.771 (0.171) | 0.778 (0.157) | 0.623 (0.128) | 0.740 (0.188) | 0.809 (0.132) |
Selected Features | All Features |
---|---|
LR: 0.800000 (0.159079) | LR: 0.754762 (0.180089) |
LDA: 0.800000 (0.182946) | LDA: 0.752381 (0.213809) |
KNN: 0.811905 (0.090633) | KNN: 0.795238 (0.100000) |
CART: 0.680952 (0.139728) | CART: 0.638095 (0.203373) |
NB: 0.769048 (0.092857) | NB: 0.695238 (0.118952) |
SVM: 0.814286 (0.169633) | SVM: 0.811905 (0.127975) |
LR | LDA | KNN | CART | NB | SVM | GBM | |
---|---|---|---|---|---|---|---|
ACTH | 0.738095 | 0.771429 | 0.778571 | 0.623810 | 0.740476 | 0.809524 | 0.811905 |
CLU | 0.385714 | 0.304762 | 0.390476 | 0.523810 | 0.461905 | 0.376190 | 0.521429 |
CRP | 0.626190 | 0.590476 | 0.404762 | 0.452381 | 0.550000 | 0.364286 | 0.616667 |
ESR | 0.578571 | 0.535714 | 0.466667 | 0.566667 | 0.664286 | 0.664286 | 0.700000 |
FBG | 0.552381 | 0.609524 | 0.595238 | 0.464286 | 0.628571 | 0.680952 | 0.680952 |
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Crumpei-Tanasă, I.; Crumpei, I. A Machine Learning Approach to Predict Stress Hormones and Inflammatory Markers Using Illness Perception and Quality of Life in Breast Cancer Patients. Curr. Oncol. 2021, 28, 3150-3171. https://doi.org/10.3390/curroncol28040275
Crumpei-Tanasă I, Crumpei I. A Machine Learning Approach to Predict Stress Hormones and Inflammatory Markers Using Illness Perception and Quality of Life in Breast Cancer Patients. Current Oncology. 2021; 28(4):3150-3171. https://doi.org/10.3390/curroncol28040275
Chicago/Turabian StyleCrumpei-Tanasă, Irina, and Iulia Crumpei. 2021. "A Machine Learning Approach to Predict Stress Hormones and Inflammatory Markers Using Illness Perception and Quality of Life in Breast Cancer Patients" Current Oncology 28, no. 4: 3150-3171. https://doi.org/10.3390/curroncol28040275
APA StyleCrumpei-Tanasă, I., & Crumpei, I. (2021). A Machine Learning Approach to Predict Stress Hormones and Inflammatory Markers Using Illness Perception and Quality of Life in Breast Cancer Patients. Current Oncology, 28(4), 3150-3171. https://doi.org/10.3390/curroncol28040275