Breast cancer risk prediction in African women using Random Forest Classifier

Brain tumor classification utilizing pixel distribution and spatial dependencies higher-order statistical measurements through explainable ML models

Brain tumors are among the most fatal and devastating diseases, and they often result in a significant reduction in life expectancy. The devising of treatment plans that can extend the lives of affected individuals hinges on an accurate diagnosis of these tumors. Identifying and analyzing large volumes of magnetic resonance imaging (MRI) data manually proves to be both challenging and time-consuming. As a result, there exists a pressing need for a reliable machine-learning approach to accurately diagnose brain tumors, and numerous methods have already been proposed over the last decade. In this paper, a novel, comprehensive approach is proposed for identifying and classifying a given MR brain image as abnormal. Three common brain diseases, namely glioma, meningioma, and pituitary tumor, are chosen as abnormal brains, and the Figshare MRI brain image dataset was collected from the Kaggle and IEEE websites. The proposed method is initiated by employing 1st-order statistics, 2nd-order statistics, and higher-order transformed (DWT) feature extraction to extract features from images. Then missing data is addressed and handled using KNNImputer, followed by the application of the ExtratreesClassifier and PCA feature selection methods to identify the most relevant features and reduce the dimensions of these features. Subsequently, the reduced features are submitted to seven machine learning models, namely RF, GB, CB, SVM, LGBM, DT, and LR. The strategy of k-fold cross-validation is utilized to enhance the performance of those models. Finally, the models are evaluated using XAI approaches, which ensure transparent decision-making processes and provide insights into the model's predictions. Remarkably, our approach achieves the highest accuracy, precision, recall, F1 score, MCC, Kappa, AUC-ROC, and R2, as well as the lowest loss, among the seven models evaluated, proving its effectiveness and applicability in multiple analytic applications relying on publicly available datasets.

Utilizing radiomics and dosiomics with AI for precision prediction of radiation dermatitis in breast cancer patients

PURPOSE

This study explores integrating clinical features with radiomic and dosiomic characteristics into AI models to enhance the prediction accuracy of radiation dermatitis (RD) in breast cancer patients undergoing volumetric modulated arc therapy (VMAT).

MATERIALS AND METHODS

This study involved a retrospective analysis of 120 breast cancer patients treated with VMAT at Kaohsiung Veterans General Hospital from 2018 to 2023. Patient data included CT images, radiation doses, Dose-Volume Histogram (DVH) data, and clinical information. Using a Treatment Planning System (TPS), we segmented CT images into Regions of Interest (ROIs) to extract radiomic and dosiomic features, focusing on intensity, shape, texture, and dose distribution characteristics. Features significantly associated with the development of RD were identified using ANOVA and LASSO regression (p-value < 0.05). These features were then employed to train and evaluate Logistic Regression (LR) and Random Forest (RF) models, using tenfold cross-validation to ensure robust assessment of model efficacy.

RESULTS

In this study, 102 out of 120 VMAT-treated breast cancer patients were included in the detailed analysis. Thirty-two percent of these patients developed Grade 2+ RD. Age and BMI were identified as significant clinical predictors. Through feature selection, we narrowed down the vast pool of radiomic and dosiomic data to 689 features, distributed across 10 feature subsets for model construction. In the LR model, the J subset, comprising DVH, Radiomics, and Dosiomics features, demonstrated the highest predictive performance with an AUC of 0.82. The RF model showed that subset I, which includes clinical, radiomic, and dosiomic features, achieved the best predictive accuracy with an AUC of 0.83. These results emphasize that integrating radiomic and dosiomic features significantly enhances the prediction of Grade 2+ RD.

CONCLUSION

Integrating clinical, radiomic, and dosiomic characteristics into AI models significantly improves the prediction of Grade 2+ RD risk in breast cancer patients post-VMAT. The RF model analysis demonstrates that a comprehensive feature set maximizes predictive efficacy, marking a promising step towards utilizing AI in radiation therapy risk assessment and enhancing patient care outcomes.

Development and validation of colorectal cancer risk prediction tools: A comparison of models

BACKGROUND

Identification of individuals at elevated risk can improve cancer screening programmes by permitting risk-adjusted screening intensities. Previous work introduced a prognostic model using sex, age and two preceding faecal haemoglobin concentrations to predict the risk of colorectal cancer (CRC) in the next screening round. Using data of 3 screening rounds, this model attained an area under the receiver-operating-characteristic curve (AUC) of 0.78 for predicting advanced neoplasia (AN). We validated this existing logistic regression (LR) model and attempted to improve it by applying a more flexible machine-learning approach.

METHODS

We trained an existing LR and a newly developed random forest (RF) model using updated data from 219,257 third-round participants of the Dutch CRC screening programme until 2018. For both models, we performed two separate out-of-sample validations using 1,137,599 third-round participants after 2018 and 192,793 fourth-round participants from 2020 onwards. We evaluated the AUC and relative risks of the predicted high-risk groups for the outcomes AN and CRC.

RESULTS

For third-round participants after 2018, the AUC for predicting AN was 0.77 (95% CI: 0.76-0.77) using LR and 0.77 (95% CI: 0.77-0.77) using RF. For fourth-round participants, the AUCs were 0.73 (95% CI: 0.72-0.74) and 0.73 (95% CI: 0.72-0.74) for the LR and RF models, respectively. For both models, the 5% with the highest predicted risk had a 7-fold risk of AN compared to average, whereas the lowest 80% had a risk below the population average for third-round participants.

CONCLUSION

The LR is a valid risk prediction method in stool-based screening programmes. Although predictive performance declined marginally, the LR model still effectively predicted risk in subsequent screening rounds. An RF did not improve CRC risk prediction compared to an LR, probably due to the limited number of available explanatory variables. The LR remains the preferred prediction tool because of its interpretability.

Disulfidptosis-associated lncRNAs predict breast cancer subtypes

Disulfidptosis is a newly discovered mode of cell death. However, its relationship with breast cancer subtypes remains unclear. In this study, we aimed to construct a disulfidptosis-associated breast cancer subtype prediction model. We obtained 19 disulfidptosis-related genes from published articles and performed correlation analysis with lncRNAs differentially expressed in breast cancer. We then used the random forest algorithm to select important lncRNAs and establish a breast cancer subtype prediction model. We identified 132 lncRNAs significantly associated with disulfidptosis (FDR < 0.01, |R|> 0.15) and selected the first four important lncRNAs to build a prediction model (training set AUC = 0.992). The model accurately predicted breast cancer subtypes (test set AUC = 0.842). Among the key lncRNAs, LINC02188 had the highest expression in the Basal subtype, while LINC01488 and GATA3-AS1 had the lowest expression in Basal. In the Her2 subtype, LINC00511 had the highest expression level compared to other key lncRNAs. GATA3-AS1 had the highest expression in LumA and LumB subtypes, while LINC00511 had the lowest expression in these subtypes. In the Normal subtype, GATA3-AS1 had the highest expression level compared to other key lncRNAs. Our study also found that key lncRNAs were closely related to RNA methylation modification and angiogenesis (FDR < 0.05, |R|> 0.1), as well as immune infiltrating cells (P.adj < 0.01, |R|> 0.1). Our random forest model based on disulfidptosis-related lncRNAs can accurately predict breast cancer subtypes and provide a new direction for research on clinical therapeutic targets for breast cancer.

Comparative study of convolutional neural network architectures for gastrointestinal lesions classification

The gastrointestinal (GI) tract can be affected by different diseases or lesions such as esophagitis, ulcers, hemorrhoids, and polyps, among others. Some of them can be precursors of cancer such as polyps. Endoscopy is the standard procedure for the detection of these lesions. The main drawback of this procedure is that the diagnosis depends on the expertise of the doctor. This means that some important findings may be missed. In recent years, this problem has been addressed by deep learning (DL) techniques. Endoscopic studies use digital images. The most widely used DL technique for image processing is the convolutional neural network (CNN) due to its high accuracy for modeling complex phenomena. There are different CNNs that are characterized by their architecture. In this article, four architectures are compared: AlexNet, DenseNet-201, Inception-v3, and ResNet-101. To determine which architecture best classifies GI tract lesions, a set of metrics; accuracy, precision, sensitivity, specificity, F1-score, and area under the curve (AUC) were used. These architectures were trained and tested on the HyperKvasir dataset. From this dataset, a total of 6,792 images corresponding to 10 findings were used. A transfer learning approach and a data augmentation technique were applied. The best performing architecture was DenseNet-201, whose results were: 97.11% of accuracy, 96.3% sensitivity, 99.67% specificity, and 95% AUC.

Construction of machine learning-based models for cancer outcomes in low and lower-middle income countries: A scoping review

Background

The impact and utility of machine learning (ML)-based prediction tools for cancer outcomes including assistive diagnosis, risk stratification, and adjunctive decision-making have been largely described and realized in the high income and upper-middle-income countries. However, statistical projections have estimated higher cancer incidence and mortality risks in low and lower-middle-income countries (LLMICs). Therefore, this review aimed to evaluate the utilization, model construction methods, and degree of implementation of ML-based models for cancer outcomes in LLMICs.

Methods

PubMed/Medline, Scopus, and Web of Science databases were searched and articles describing the use of ML-based models for cancer among local populations in LLMICs between 2002 and 2022 were included. A total of 140 articles from 22,516 citations that met the eligibility criteria were included in this study.

Results

ML-based models from LLMICs were often based on traditional ML algorithms than deep or deep hybrid learning. We found that the construction of ML-based models was skewed to particular LLMICs such as India, Iran, Pakistan, and Egypt with a paucity of applications in sub-Saharan Africa. Moreover, models for breast, head and neck, and brain cancer outcomes were frequently explored. Many models were deemed suboptimal according to the Prediction model Risk of Bias Assessment tool (PROBAST) due to sample size constraints and technical flaws in ML modeling even though their performance accuracy ranged from 0.65 to 1.00. While the development and internal validation were described for all models included (n=137), only 4.4% (6/137) have been validated in independent cohorts and 0.7% (1/137) have been assessed for clinical impact and efficacy.

Conclusion

Overall, the application of ML for modeling cancer outcomes in LLMICs is increasing. However, model development is largely unsatisfactory. We recommend model retraining using larger sample sizes, intensified external validation practices, and increased impact assessment studies using randomized controlled trial designs.

Systematic review registration

https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=308345, identifier CRD42022308345.

A hybrid breast cancer classification algorithm based on meta-learning and artificial neural networks

The incidence of breast cancer in women has surpassed that of lung cancer as the world’s leading new cancer case. Regular screening and measures become an effective way to prevent breast cancer and also provide a good foundation for later treatment. Women should receive regular checkups in the hospital after reaching a certain age. The use of computer-aided technology can improve the accuracy and efficiency of physicians’ decision-making. Data pre-processing is required before data analysis, and 16 features are selected using a correlation-based feature selection method. In this paper, meta-learning and Artificial Neural Networks (ANN) are combined to create a hybrid algorithm. The proposed hybrid algorithm for predicting breast cancer was attempted to achieve 98.74% accuracy and 98.02% F1-score by creating a combination of various meta-learning models whose output was used as input features for creating ANN models. Therefore, the hybrid algorithm proposed in this paper can obtain better prediction results than a single model.