Cancer Classification with a Cost-Sensitive Naive Bayes Stacking Ensemble

Image segmentation of mouse eye in vivo with optical coherence tomography based on Bayesian classification

OBJECTIVES

Optical coherence tomography (OCT) is a new imaging technology that uses an optical analog of ultrasound imaging for biological tissues. Image segmentation plays an important role in dealing with quantitative analysis of medical images.

METHODS

We have proposed a novel framework to deal with the low intensity problem, based on the labeled patches and Bayesian classification (LPBC) model. The proposed method includes training and testing phases. During the training phase, firstly, we manually select the sub-images of background and Region of Interest (ROI) from the training image, and then extract features by patches. Finally, we train the Bayesian model with the features. The segmentation threshold of each patch is computed by the learned Bayesian model.

RESULTS

In addition, we have collected a new dataset of mouse eyes in vivo with OCT, named MEVOCT, which can be found at URL https://17861318579.github.io/LPBC. MEVOCT consists of 20 high-resolution images. The resolution of every image is 2048 × 2048 pixels.

CONCLUSIONS

The experimental results demonstrate the effectiveness of the LPBC method on the new MEVOCT dataset. The ROI segmentation is of great importance for the distortion correction.

The Application of Artificial Intelligence to Cancer Research: A Comprehensive Guide

Advancements in AI have notably changed cancer research, improving patient care by enhancing detection, survival prediction, and treatment efficacy. This review covers the role of Machine Learning, Soft Computing, and Deep Learning in oncology, explaining key concepts and algorithms (like SVM, Naïve Bayes, and CNN) in a clear, accessible manner. It aims to make AI advancements understandable to a broad audience, focusing on their application in diagnosing, classifying, and predicting various cancer types, thereby underlining AI's potential to better patient outcomes. Moreover, we present a tabular summary of the most significant advances from the literature, offering a time-saving resource for readers to grasp each study's main contributions. The remarkable benefits of AI-powered algorithms in cancer care underscore their potential for advancing cancer research and clinical practice. This review is a valuable resource for researchers and clinicians interested in the transformative implications of AI in cancer care.

Machine learning (ML) techniques to predict breast cancer in imbalanced datasets: a systematic review

Knowledge discovery in databases (KDD) is crucial in analyzing data to extract valuable insights. In medical outcome prediction, KDD is increasingly applied, particularly in diseases with high incidence, mortality, and costs, like cancer. ML techniques can develop more accurate predictive models for cancer patients' clinical outcomes, aiding informed healthcare decision-making. However, cancer prediction modeling faces challenges because of the unbalanced nature of the datasets, where there is a small minority category of patients with a cancer diagnosis compared to a majority category of cancer-free patients. Imbalanced datasets pose statistical hurdles like bias and overfitting when developing accurate prediction models. This systematic review focuses on breast cancer prediction articles published from 2008 to 2023. The objective is to examine ML methods used in three critical steps of KDD: preprocessing, data mining, and interpretation which address the imbalanced data problem in breast cancer prediction. This work synthesizes prior research in ML methods for breast cancer prediction. The findings help identify effective preprocessing strategies, including balancing and feature selection methods, robust predictive models, and evaluation metrics of those models. The study aims to inform healthcare providers and researchers about effective techniques for accurate breast cancer prediction.

A Bayesian optimization tunning integrated multi-stacking classifier framework for the prediction of radiodermatitis from 4D-CT of patients underwent breast cancer radiotherapy

Purpose

In this study, we aimed to develop a novel Bayesian optimization based multi-stacking deep learning platform for the prediction of radiation-induced dermatitis (grade ≥ two) (RD 2+) before radiotherapy, by using multi-region dose-gradient-related radiomics features extracted from pre-treatment planning four-dimensional computed tomography (4D-CT) images, as well as clinical and dosimetric characteristics of breast cancer patients who underwent radiotherapy.

Materials and methods

The study retrospectively included 214 patients with breast cancer who received radiotherapy after breast surgeries. Six regions of interest (ROIs) were delineated based on three PTV dose -gradient-related and three skin dose-gradient-related parameters (i.e., isodose). A total of 4309 radiomics features extracted from these six ROIs, as well as clinical and dosimetric characteristics, were used to train and validate the prediction model using nine mainstream deep machine learning algorithms and three stacking classifiers (i.e., meta-learners). To achieve the best prediction performance, a Bayesian optimization based multi-parameter tuning technology was adopted for the AdaBoost, random forest (RF), decision tree (DT), gradient boosting (GB) and extra tree (XTree) five machine learning models. The five parameter -tuned learners and the other four learners (i.e., logistic regression (LR), K-nearest neighbors (KNN), linear discriminant analysis (LDA), Bagging) whose parameters cannot be tuned, all as the primary week learners, were fed into the subsequent meta-learners for training and learning the final prediction model.

Results

The final prediction model included 20 radiomics features and eight clinical and dosimetric characteristics. At the primary learner level, on base of Bayesian parameter tuning optimization, the RF, XGBoost, AdaBoost, GBDT, and LGBM models with the best parameter combinations achieved AUC of 0.82, 0.82, 0.77, 0.80, and 0.80 prediction performance in the verification data set, respectively. In the secondary meta-learner lever, compared with LR and MLP meta-learner, the best predictor of symptomatic RD 2+ for stacked classifiers was the GB meta-learner with an area under the curve (AUC) of 0.97 [95% CI: 0.91-1.0] and an AUC of 0.93 [95% CI: 0.87-0.97] in the training and validation datasets, respectively and the 10 top predictive characteristics were identified.

Conclusion

A novel multi-region dose-gradient-based Bayesian optimization tunning integrated multi-stacking classifier framework can achieve a high-accuracy prediction of symptomatic RD 2+ in breast cancer patients than any other single deep machine learning algorithm.

Brain Tumor Classification based on Improved Stacked Ensemble Deep Learning Methods

OBJECTIVE

Brain Tumor diagnostic prediction is essential for assisting radiologists and other healthcare professionals in identifying and classifying brain tumors. For the diagnosis and treatment of cancer diseases, prediction and classification accuracy are crucial. The aim of this study was to improve ensemble deep learning models for classifing brain tumor and increase the performance of structure models by combining different model of deep learning to develop a model with more accurate predictions than the individual models.

METHODS

Convolutional neural networks (CNNs), which are made up of a single algorithm called CNN model, are the foundation of most current methods for classifying cancer illness images. The model CNN is combined with other models to create other methods of classification called ensemble method. However, compared to a single machine learning algorithm, ensemble machine learning models are more accurate. This study used stacked ensemble deep learning technology. The data set used in this study was obtained from Kaggle and included two categories: abnormal & normal brains. The data set was trained with three models: VGG19, Inception v3, and Resnet 10.

RESULT

The 96.6% accuracy for binary classification (0,1) have been achieved by stacked ensemble deep learning model with Loss binary cross entropy, and Adam optimizer take into consideration with stacking models.

CONCLUSION

The stacked ensemble deep learning model can be improved over a single framework.

A Risk Prediction Model for Physical Restraints Among Older Chinese Adults in Long-term Care Facilities: Machine Learning Study

BACKGROUND

Numerous studies have identified risk factors for physical restraint (PR) use in older adults in long-term care facilities. Nevertheless, there is a lack of predictive tools to identify high-risk individuals.

OBJECTIVE

We aimed to develop machine learning (ML)-based models to predict the risk of PR in older adults.

METHODS

This study conducted a cross-sectional secondary data analysis based on 1026 older adults from 6 long-term care facilities in Chongqing, China, from July 2019 to November 2019. The primary outcome was the use of PR (yes or no), identified by 2 collectors' direct observation. A total of 15 candidate predictors (older adults' demographic and clinical factors) that could be commonly and easily collected from clinical practice were used to build 9 independent ML models: Gaussian Naïve Bayesian (GNB), k-nearest neighbor (KNN), decision tree (DT), logistic regression (LR), support vector machine (SVM), random forest (RF), multilayer perceptron (MLP), extreme gradient boosting (XGBoost), and light gradient boosting machine (Lightgbm), as well as stacking ensemble ML. Performance was evaluated using accuracy, precision, recall, an F score, a comprehensive evaluation indicator (CEI) weighed by the above indicators, and the area under the receiver operating characteristic curve (AUC). A net benefit approach using the decision curve analysis (DCA) was performed to evaluate the clinical utility of the best model. Models were tested via 10-fold cross-validation. Feature importance was interpreted using Shapley Additive Explanations (SHAP).

RESULTS

A total of 1026 older adults (mean 83.5, SD 7.6 years; n=586, 57.1% male older adults) and 265 restrained older adults were included in the study. All ML models performed well, with an AUC above 0.905 and an F score above 0.900. The 2 best independent models are RF (AUC 0.938, 95% CI 0.914-0.947) and SVM (AUC 0.949, 95% CI 0.911-0.953). The DCA demonstrated that the RF model displayed better clinical utility than other models. The stacking model combined with SVM, RF, and MLP performed best with AUC (0.950) and CEI (0.943) values, as well as the DCA curve indicated the best clinical utility. The SHAP plots demonstrated that the significant contributors to model performance were related to cognitive impairment, care dependency, mobility decline, physical agitation, and an indwelling tube.

CONCLUSIONS

The RF and stacking models had high performance and clinical utility. ML prediction models for predicting the probability of PR in older adults could offer clinical screening and decision support, which could help medical staff in the early identification and PR management of older adults.

Non-Fatal Drowning Risk Prediction Based on Stacking Ensemble Algorithm

Drowning is a major public health problem and a leading cause of death in children living in developing countries. We seek better machine learning (ML) algorithms to provide a novel risk-assessment insight on non-fatal drowning prediction. The data on non-fatal drowning were collected in Qingyuan city, Guangdong Province, China. We developed four ML models to predict the non-fatal drowning risk, including a logistic regression model (LR), random forest model (RF), support vector machine model (SVM), and stacking-based model, on three primary learners (LR, RF, SVM). The area under the curve (AUC), F1 value, accuracy, sensitivity, and specificity were calculated to evaluate the predictive ability of the different learning algorithms. This study included a total of 8390 children. Of those, 12.07% (1013) had experienced non-fatal drowning. We found the following risk factors are closely associated with the risk of non-fatal drowning: the frequency of swimming in open water, distance between the school and the surrounding open waters, swimming skills, personality (introvert) and relationality with family members. Compared to the other three base models, the stacking generalization model achieved a superior performance in the non-fatal drowning dataset (AUC = 0.741, sensitivity = 0.625, F1 value = 0.359, accuracy = 0.739 and specificity = 0.754). This study indicates that applying stacking ensemble algorithms in the non-fatal drowning dataset may outperform other ML models.

Bias and Class Imbalance in Oncologic Data-Towards Inclusive and Transferrable AI in Large Scale Oncology Data Sets

Recent technological developments have led to an increase in the size and types of data in the medical field derived from multiple platforms such as proteomic, genomic, imaging, and clinical data. Many machine learning models have been developed to support precision/personalized medicine initiatives such as computer-aided detection, diagnosis, prognosis, and treatment planning by using large-scale medical data. Bias and class imbalance represent two of the most pressing challenges for machine learning-based problems, particularly in medical (e.g., oncologic) data sets, due to the limitations in patient numbers, cost, privacy, and security of data sharing, and the complexity of generated data. Depending on the data set and the research question, the methods applied to address class imbalance problems can provide more effective, successful, and meaningful results. This review discusses the essential strategies for addressing and mitigating the class imbalance problems for different medical data types in the oncologic domain.

Tumor Nonimmune-Microenvironment-Related Gene Expression Signature Predicts Brain Metastasis in Lung Adenocarcinoma Patients after Surgery: A Machine Learning Approach Using Gene Expression Profiling

Simple Summary

It is important to be able to predict brain metastasis in lung adenocarcinoma patients; however, research in this area is still lacking. Much of the previous work on tumor microenvironments in lung adenocarcinoma with brain metastasis concerns the tumor immune microenvironment. The importance of the tumor nonimmune microenvironment (extracellular matrix (ECM), epithelial–mesenchymal transition (EMT) feature, and angiogenesis) has been overlooked with regard to brain metastasis. We evaluated tumor nonimmune-microenvironment-related gene expression signatures that could predict brain metastasis after the surgical resection of lung adenocarcinoma using a machine learning approach. We identified a tumor nonimmune-microenvironment-related 17-gene expression signature, and this signature showed high brain metastasis predictive power in four machine learning classifiers. The immunohistochemical expression of the top three genes of the 17-gene expression signature yielded similar results to NanoString tests. Our tumor nonimmune-microenvironment-related gene expression signatures are important biological markers that can predict brain metastasis and provide patient-specific treatment options.

Abstract

Using a machine learning approach with a gene expression profile, we discovered a tumor nonimmune-microenvironment-related gene expression signature, including extracellular matrix (ECM) remodeling, epithelial–mesenchymal transition (EMT), and angiogenesis, that could predict brain metastasis (BM) after the surgical resection of 64 lung adenocarcinomas (LUAD). Gene expression profiling identified a tumor nonimmune-microenvironment-related 17-gene expression signature that significantly correlated with BM. Of the 17 genes, 11 were ECM-remodeling-related genes. The 17-gene expression signature showed high BM predictive power in four machine learning classifiers (areas under the receiver operating characteristic curve = 0.845 for naïve Bayes, 0.849 for support vector machine, 0.858 for random forest, and 0.839 for neural network). Subgroup analysis revealed that the BM predictive power of the 17-gene signature was higher in the early-stage LUAD than in the late-stage LUAD. Pathway enrichment analysis showed that the upregulated differentially expressed genes were mainly enriched in the ECM–receptor interaction pathway. The immunohistochemical expression of the top three genes of the 17-gene expression signature yielded similar results to NanoString tests. The tumor nonimmune-microenvironment-related gene expression signatures found in this study are important biological markers that can predict BM and provide patient-specific treatment options.

Intelligent Decision Support System for Predicting Student’s E-Learning Performance Using Ensemble Machine Learning

Electronic learning management systems provide live environments for students and faculty members to connect with their institutional online portals and perform educational activities virtually. Although modern technologies proactively support these online sessions, students’ active participation remains a challenge that has been discussed in previous research. Additionally, one concern for both parents and teachers is how to accurately measure student performance using different attributes collected during online sessions. Therefore, the research idea undertaken in this study is to understand and predict the performance of the students based on features extracted from electronic learning management systems. The dataset chosen in this study belongs to one of the learning management systems providing a number of features predicting student’s performance. The integrated machine learning model proposed in this research can be useful to make proactive and intelligent decisions according to student performance evaluated through the electronic system’s data. The proposed model consists of five traditional machine learning algorithms, which are further enhanced by applying four ensemble techniques: bagging, boosting, stacking, and voting. The overall F1 scores of the single models are as follows: DT (0.675), RF (0.777), GBT (0.714), NB (0.654), and KNN (0.664). The model performance has shown remarkable improvement using ensemble approaches. The stacking model by combining all five classifiers has outperformed and recorded the highest F1 score (0.8195) among other ensemble methods. The integration of the ML models has improved the prediction ratio and performed better than all other ensemble approaches. The proposed model can be useful for predicting student performance and helping educators to make informed decisions by proactively notifying the students.