Survival prediction of glioblastoma patients using modern deep learning and machine learning techniques

In this study, we utilized data from the Surveillance, Epidemiology, and End Results (SEER) database to predict the glioblastoma patients' survival outcomes. To assess dataset skewness and detect feature importance, we applied Pearson's second coefficient test of skewness and the Ordinary Least Squares method, respectively. Using two sampling strategies, holdout and five-fold cross-validation, we developed five machine learning (ML) models alongside a feed-forward deep neural network (DNN) for the multiclass classification and regression prediction of glioblastoma patient survival. After balancing the classification and regression datasets, we obtained 46,340 and 28,573 samples, respectively. Shapley additive explanations (SHAP) were then used to explain the decision-making process of the best model. In both classification and regression tasks, as well as across holdout and cross-validation sampling strategies, the DNN consistently outperformed the ML models. Notably, the accuracy were 90.25% and 90.22% for holdout and five-fold cross-validation, respectively, while the corresponding R2 values were 0.6565 and 0.6622. SHAP analysis revealed the importance of age at diagnosis as the most influential feature in the DNN's survival predictions. These findings suggest that the DNN holds promise as a practical auxiliary tool for clinicians, aiding them in optimal decision-making concerning the treatment and care trajectories for glioblastoma patients.

Monkeypox detection using deep neural networks

BACKGROUND

In May 2022, the World Health Organization (WHO) European Region announced an atypical Monkeypox epidemic in response to reports of numerous cases in some member countries unrelated to those where the illness is endemic. This issue has raised concerns about the widespread nature of this disease around the world. The experience with Coronavirus Disease 2019 (COVID-19) has increased awareness about pandemics among researchers and health authorities.

METHODS

Deep Neural Networks (DNNs) have shown promising performance in detecting COVID-19 and predicting its outcomes. As a result, researchers have begun applying similar methods to detect Monkeypox disease. In this study, we utilize a dataset comprising skin images of three diseases: Monkeypox, Chickenpox, Measles, and Normal cases. We develop seven DNN models to identify Monkeypox from these images. Two scenarios of including two classes and four classes are implemented.

RESULTS

The results show that our proposed DenseNet201-based architecture has the best performance, with Accuracy = 97.63%, F1-Score = 90.51%, and Area Under Curve (AUC) = 94.27% in two-class scenario; and Accuracy = 95.18%, F1-Score = 89.61%, AUC = 92.06% for four-class scenario. Comparing our study with previous studies with similar scenarios, shows that our proposed model demonstrates superior performance, particularly in terms of the F1-Score metric. For the sake of transparency and explainability, Local Interpretable Model-Agnostic Explanations (LIME) and Gradient-weighted Class Activation Mapping (Grad-Cam) were developed to interpret the results. These techniques aim to provide insights into the decision-making process, thereby increasing the trust of clinicians.

CONCLUSION

The DenseNet201 model outperforms the other models in terms of the confusion metrics, regardless of the scenario. One significant accomplishment of this study is the utilization of LIME and Grad-Cam to identify the affected areas and assess their significance in diagnosing diseases based on skin images. By incorporating these techniques, we enhance our understanding of the infected regions and their relevance in distinguishing Monkeypox from other similar diseases. Our proposed model can serve as a valuable auxiliary tool for diagnosing Monkeypox and distinguishing it from other related conditions.

Application of machine learning techniques for predicting survival in ovarian cancer

BACKGROUND

Ovarian cancer is the fifth leading cause of mortality among women in the United States. Ovarian cancer is also known as forgotten cancer or silent disease. The survival of ovarian cancer patients depends on several factors, including the treatment process and the prognosis.

METHODS

The ovarian cancer patients' dataset is compiled from the Surveillance, Epidemiology, and End Results (SEER) database. With the help of a clinician, the dataset is curated, and the most relevant features are selected. Pearson's second coefficient of skewness test is used to evaluate the skewness of the dataset. Pearson correlation coefficient is also used to investigate the associations between features. Statistical test is utilized to evaluate the significance of the features. Six Machine Learning (ML) models, including K-Nearest Neighbors , Support Vector Machine (SVM), Decision Tree (DT), Random Forest (RF), Adaptive Boosting (AdaBoost), and Extreme Gradient Boosting (XGBoost), are implemented for survival prediction in both classification and regression approaches. An interpretable method, Shapley Additive Explanations (SHAP), is applied to clarify the decision-making process and determine the importance of each feature in prediction. Additionally, DTs of the RF model are displayed to show how the model predicts the survival intervals.

RESULTS

Our results show that RF (Accuracy = 88.72%, AUC = 82.38%) and XGBoost (Root Mean Squad Error (RMSE)) = 20.61%, R² = 0.4667) have the best performance for classification and regression approaches, respectively. Furthermore, using the SHAP method along with extracted DTs of the RF model, the most important features in the dataset are identified. Histologic type ICD-O-3, chemotherapy recode, year of diagnosis, age at diagnosis, tumor stage, and grade are the most important determinant factors in survival prediction.

CONCLUSION

To the best of our knowledge, our study is the first study that develops various ML models to predict ovarian cancer patients' survival on the SEER database in both classification and regression approaches. These ML algorithms also achieve more accurate results and outperform statistical methods. Furthermore, our study is the first study to use the SHAP method to increase confidence and transparency of the proposed models' prediction for clinicians. Moreover, our developed models, as an automated auxiliary tool, can help clinicians to have a better understanding of the estimated survival as well as important features that affect survival.

Identification of clinical factors related to prediction of alcohol use disorder from electronic health records using feature selection methods

BACKGROUND

High dimensionality in electronic health records (EHR) causes a significant computational problem for any systematic search for predictive, diagnostic, or prognostic patterns. Feature selection (FS) methods have been indicated to be effective in feature reduction as well as in identifying risk factors related to prediction of clinical disorders. This paper examines the prediction of patients with alcohol use disorder (AUD) using machine learning (ML) and attempts to identify risk factors related to the diagnosis of AUD.

METHODS

A FS framework consisting of two operational levels, base selectors and ensemble selectors. The first level consists of five FS methods: three filter methods, one wrapper method, and one embedded method. Base selector outputs are aggregated to develop four ensemble FS methods. The outputs of FS method were then fed into three ML algorithms: support vector machine (SVM), K-nearest neighbor (KNN), and random forest (RF) to compare and identify the best feature subset for the prediction of AUD from EHRs.

RESULTS

In terms of feature reduction, the embedded FS method could significantly reduce the number of features from 361 to 131. In terms of classification performance, RF based on 272 features selected by our proposed ensemble method (Union FS) with the highest accuracy in predicting patients with AUD, 96%, outperformed all other models in terms of AUROC, AUPRC, Precision, Recall, and F1-Score. Considering the limitations of embedded and wrapper methods, the best overall performance was achieved by our proposed Union Filter FS, which reduced the number of features to 223 and improved Precision, Recall, and F1-Score in RF from 0.77, 0.65, and 0.71 to 0.87, 0.81, and 0.84, respectively. Our findings indicate that, besides gender, age, and length of stay at the hospital, diagnosis related to digestive organs, bones, muscles and connective tissue, and the nervous systems are important clinical factors related to the prediction of patients with AUD.

CONCLUSION

Our proposed FS method could improve the classification performance significantly. It could identify clinical factors related to prediction of AUD from EHRs, thereby effectively helping clinical staff to identify and treat AUD patients and improving medical knowledge of the AUD condition. Moreover, the diversity of features among female and male patients as well as gender disparity were investigated using FS methods and ML techniques.

Machine learning techniques for mortality prediction in emergency departments: a systematic review

OBJECTIVES

This systematic review aimed to assess the performance and clinical feasibility of machine learning (ML) algorithms in prediction of in-hospital mortality for medical patients using vital signs at emergency departments (EDs).

DESIGN

A systematic review was performed.

SETTING

The databases including Medline (PubMed), Scopus and Embase (Ovid) were searched between 2010 and 2021, to extract published articles in English, describing ML-based models utilising vital sign variables to predict in-hospital mortality for patients admitted at EDs. Critical appraisal and data extraction for systematic reviews of prediction modelling studies checklist was used for study planning and data extraction. The risk of bias for included papers was assessed using the prediction risk of bias assessment tool.

PARTICIPANTS

Admitted patients to the ED.

MAIN OUTCOME MEASURE

In-hospital mortality.

RESULTS

Fifteen articles were included in the final review. We found that eight models including logistic regression, decision tree, K-nearest neighbours, support vector machine, gradient boosting, random forest, artificial neural networks and deep neural networks have been applied in this domain. Most studies failed to report essential main analysis steps such as data preprocessing and handling missing values. Fourteen included studies had a high risk of bias in the statistical analysis part, which could lead to poor performance in practice. Although the main aim of all studies was developing a predictive model for mortality, nine articles did not provide a time horizon for the prediction.

CONCLUSION

This review provided an updated overview of the state-of-the-art and revealed research gaps; based on these, we provide eight recommendations for future studies to make the use of ML more feasible in practice. By following these recommendations, we expect to see more robust ML models applied in the future to help clinicians identify patient deterioration earlier.

Quantifying the impact of addressing data challenges in prediction of length of stay

BACKGROUND

Prediction of length of stay (LOS) at admission time can provide physicians and nurses insight into the illness severity of patients and aid them in avoiding adverse events and clinical deterioration. It also assists hospitals with more effectively managing their resources and manpower.

METHODS

In this field of research, there are some important challenges, such as missing values and LOS data skewness. Moreover, various studies use a binary classification which puts a wide range of patients with different conditions into one category. To address these shortcomings, first multivariate imputation techniques are applied to fill incomplete records, then two proper resampling techniques, namely Borderline-SMOTE and SMOGN, are applied to address data skewness in the classification and regression domains, respectively. Finally, machine learning (ML) techniques including neural networks, extreme gradient boosting, random forest, support vector machine, and decision tree are implemented for both approaches to predict LOS of patients admitted to the Emergency Department of Odense University Hospital between June 2018 and April 2019. The ML models are developed based on data obtained from patients at admission time, including pulse rate, arterial blood oxygen saturation, respiratory rate, systolic blood pressure, triage category, arrival ICD-10 codes, age, and gender.

RESULTS

The performance of predictive models before and after addressing missing values and data skewness is evaluated using four evaluation metrics namely receiver operating characteristic, area under the curve (AUC), R-squared score (R2), and normalized root mean square error (NRMSE). Results show that the performance of predictive models is improved on average by 15.75% for AUC, 32.19% for R2 score, and 11.32% for NRMSE after addressing the mentioned challenges. Moreover, our results indicate that there is a relationship between the missing values rate, data skewness, and illness severity of patients, so it is clinically essential to take incomplete records of patients into account and apply proper solutions for interpolation of missing values.

CONCLUSION

We propose a new method comprised of three stages: missing values imputation, data skewness handling, and building predictive models based on classification and regression approaches. Our results indicated that addressing these challenges in a proper way enhanced the performance of models significantly, which led to a more valid prediction of LOS.

Data Vizualization Dashboards in Robotic Rehabilitation

Robotic rehabilitation can offer effective solutions, facilitating physiotherapist work, and helping patients regain their strength. Visualizing results of rehabilitative training could give a better insight into the factors that contribute to progress and measure the exact progress by every session. This paper aims to present a set of prototype dashboards to analyze and visualize data from robotic rehabilitation in order to help the patients measure their exerted force progress throughout the training period. The created visualization dashboards which proved helpful and essential to present achieved measurements, the progress of the patient, and the maximum force in a timeline presentation. The proposed prototypes could give a personalized overview to each patient, fed with the corresponding datasets.

Personalized Predictive Models for Identifying Clinical Deterioration Using LSTM in Emergency Departments

Early detection of deterioration at hospitals could be beneficial in terms of reducing mortality and morbidity rates and costs. In this paper, we present a model based on Long Short-Term Memory (LSTM) neural network used in deep learning to predict the illness severity of patients in advance. Hence, by predicting health severity, this model can be used to identify deteriorating patients. Our proposed model utilizes continuous monitored vital signs, including heart rate, respiratory rate, oxygen saturation, and blood pressure automatically collected from patients during hospitalization. In this study, a short-time prediction using a sliding window approach is applied. The performance of the proposed model was compared with the Multi-Layer Perceptron (MLP) neural network, a feedforward class of neural network, based on R2 score and Root Mean Square Error (RMSE) metrics. The results showed that the LSTM has a better performance and could predict the illness severity of patients more accurately.