Therapeutic Decision Making in Prevascular Mediastinal Tumors Using CT Radiomics and Clinical Features: Upfront Surgery or Pretreatment Needle Biopsy?

The study aimed to develop machine learning (ML) classification models for differentiating patients who needed direct surgery from patients who needed core needle biopsy among patients with prevascular mediastinal tumor (PMT). Patients with PMT who received a contrast-enhanced computed tomography (CECT) scan and initial management for PMT between January 2010 and December 2020 were included in this retrospective study. Fourteen ML algorithms were used to construct candidate classification models via the voting ensemble approach, based on preoperative clinical data and radiomic features extracted from the CECT. The classification accuracy of clinical diagnosis was 86.1%. The first ensemble learning model was built by randomly choosing seven ML models from a set of fourteen ML models and had a classification accuracy of 88.0% (95% CI = 85.8 to 90.3%). The second ensemble learning model was the combination of five ML models, including NeuralNetFastAI, NeuralNetTorch, RandomForest with Entropy, RandomForest with Gini, and XGBoost, and had a classification accuracy of 90.4% (95% CI = 87.9 to 93.0%), which significantly outperformed clinical diagnosis (p < 0.05). Due to the superior performance, the voting ensemble learning clinical-radiomic classification model may be used as a clinical decision support system to facilitate the selection of the initial management of PMT.

Interpretable machine learning model for prediction of overall survival in laryngeal cancer.

Background: The mortality rates of laryngeal squamous cell carcinoma cancer (LSCC) have not significantly decreased in the last decades.Objectives: We primarily aimed to compare the predictive performance of DeepTables with the state-of-the-art machine learning (ML) algorithms (Voting ensemble, Stack ensemble, and XGBoost) to stratify patients with LSCC into chance of overall survival (OS). In addition, we complemented the developed model by providing interpretability using both global and local model-agnostic techniques.Methods: A total of 2792 patients in the Surveillance, Epidemiology, and End Results (SEER) database diagnosed with LSCC were reviewed. The global model-agnostic interpretability was examined using SHapley Additive exPlanations (SHAP) technique. Likewise, individual interpretation of the prediction was made using Local Interpretable Model Agnostic Explanations (LIME).Results: The state-of-the-art ML ensemble algorithms outperformed DeepTables. Specifically, the examined ensemble algorithms showed comparable weighted area under receiving curve of 76.9, 76.8, and 76.1 with an accuracy of 71.2%, 70.2%, and 71.8%, respectively. The global methods of interpretability (SHAP) demonstrated that the age of the patient at diagnosis, N-stage, T-stage, tumor grade, and marital status are among the prominent parameters.Conclusions: A ML model for OS prediction may serve as an ancillary tool for treatment planning of LSCC patients.

Improved detection of dry age-related macular degeneration from optical coherence tomography images using adaptive window based feature extraction and weighted ensemble based classification approach.

BACKGROUND: Dry Age-related macular degeneration (AMD), which affects the older population, can lead to blindness when left untreated. Preventing vision loss in elderly needs early identification. Dry-AMD diagnosis is still time-consuming and very subjective, depending on the ophthalmologist. Setting up a thorough eye-screening system to find Dry-AMD is a very difficult task. METHODOLOGY: This study aims to develop a weighted majority voting (WMV) ensemble-based prediction model to diagnose Dry-AMD. The WMV approach combines the predictions from base-classifiers and chooses the class with greatest vote based on assigned weights to each classifier. A novel feature extraction method is used along the retinal pigment epithelium (RPE) layer, with the number of windows calculated for each picture playing an important part in identifying Dry-AMD/normal images using the WMV methodology. Pre-processing using hybrid-median filter followed by scale-invariant feature transform based segmentation of RPE layer and curvature flattening of retina is employed to measure exact thickness of RPE layer. RESULT: The proposed model is trained on 70% of the OCT image database (OCTID) and evaluated on remaining OCTID and SD-OCT Noor dataset. Model has achieved accuracy of 96.15% and 96.94%, respectively. The suggested algorithm's effectiveness in Dry-AMD identification is demonstrated by comparison with alternative approaches. Even though the suggested model is only trained on the OCTID, it has performed well when tested on additional dataset. CONCLUSION: The suggested architecture can be used for quick eye-screening for early identification of Dry-AMD. The recommended method may be applied in real-time since it requires fewer complexity and learning-variables.

A Machine Learning-Based Applied Prediction Model for Identification of Acute Coronary Syndrome (ACS) Outcomes and Mortality in Patients during the Hospital Stay.

Nowadays, machine learning (ML) is a revolutionary and cutting-edge technology widely used in the medical domain and health informatics in the diagnosis and prognosis of cardiovascular diseases especially. Therefore, we propose a ML-based soft-voting ensemble classifier (SVEC) for the predictive modeling of acute coronary syndrome (ACS) outcomes such as STEMI and NSTEMI, discharge reasons for the patients admitted in the hospitals, and death types for the affected patients during the hospital stay. We used the Korea Acute Myocardial Infarction Registry (KAMIR-NIH) dataset, which has 13,104 patients' data containing 551 features. After data extraction and preprocessing, we used the 125 useful features and applied the SMOTETomek hybrid sampling technique to oversample the data imbalance of minority classes. Our proposed SVEC applied three ML algorithms, such as random forest, extra tree, and the gradient-boosting machine for predictive modeling of our target variables, and compared with the performances of all base classifiers. The experiments showed that the SVEC outperformed other ML-based predictive models in accuracy (99.0733%), precision (99.0742%), recall (99.0734%), F1-score (99.9719%), and the area under the ROC curve (AUC) (99.9702%). Overall, the performance of the SVEC was better than other applied models, but the AUC was slightly lower than the extra tree classifier for the predictive modeling of ACS outcomes. The proposed predictive model outperformed other ML-based models; hence it can be used practically in hospitals for the diagnosis and prediction of heart problems so that timely detection of proper treatments can be chosen, and the occurrence of disease predicted more accurately.

Effectiveness of Federated Learning and CNN Ensemble Architectures for Identifying Brain Tumors Using MRI Images.

Medical institutions often revoke data access due to the privacy concern of patients. Federated Learning (FL) is a collaborative learning paradigm that can generate an unbiased global model based on collecting updates from local models trained by client's data while keeping the local data private. This study aims to address the centralized data collection issue through the application of FL on brain tumor identification from MRI images. At first, several CNN models were trained using the MRI data and the best three performing CNN models were selected to form different variants of ensemble classifiers. Afterward, the FL model was constructed using the ensemble architecture. It was trained using model weights from the local model without sharing the client's data (MRI images) using the FL approach. Experimental results show only a slight decline in the performance of the FL approach as it achieved 91.05% accuracy compared to the 96.68% accuracy of the base ensemble model. Additionally, same approach was taken for another slightly larger dataset to prove the scalability of the method. This study shows that the FL approach can achieve privacy-protected tumor classification from MRI images without compromising much accuracy compared to the traditional deep learning approach.

Inspection of Underwater Hull Surface Condition Using the Soft Voting Ensemble of the Transfer-Learned Models.

In this study, we propose a method for inspecting the condition of hull surfaces using underwater images acquired from the camera of a remotely controlled underwater vehicle (ROUV). To this end, a soft voting ensemble classifier comprising six well-known convolutional neural network models was used. Using the transfer learning technique, the images of the hull surfaces were used to retrain the six models. The proposed method exhibited an accuracy of 98.13%, a precision of 98.73%, a recall of 97.50%, and an F1-score of 98.11% for the classification of the test set. Furthermore, the time taken for the classification of one image was verified to be approximately 56.25 ms, which is applicable to ROUVs that require real-time inspection.

Differential diagnosis between Parkinson's disease and atypical parkinsonism based on gait and postural instability: Artificial intelligence using an enhanced weight voting ensemble model.

BACKGROUND: Parkinsonian diseases and cerebellar ataxia among movement disorders, are representative diseases which present with distinct pathological gaits. We proposed a machine learning system that can differentiate Parkinson's disease (PD), cerebellar ataxia and progressive supranuclear palsy Richardson syndrome (PSP-RS) based on postural instability and gait analysis. METHODS: We screened 1467 gait (GAITRite) and postural instability (Pedoscan) analyses performed in Samsung Medical Center from January 2019 to December 2020. PD, probable PSP-RS, and cerebellar ataxia (i.e., probable MSA-C, hereditary ataxia, and sporadic adult-onset ataxia) were included in the study. The gated recurrent units for GaitRite and the deep neural network for Pedoscan were applied. The enhanced weight voting ensemble (EWVE) method was applied to incorporate the two modalities. RESULTS: We included 551 PD, 38 PSP-RS, 113 cerebellar ataxia and among them, 71 were MSA-C. Pedoscan-based and Gait-based model showed high sensitivity but low specificity in differentiating atypical parkinsonism from PD. The EWVE showed significantly improved specificity and reliable performance in differentiation between PD vs. ataxia patients (AUC 0.974 ± 0.036, sensitivity 0.829 ± 0.217, specificity 0.969 ± 0.038), PD vs. MSA-C (AUC 0.975 ± 0.020, sensitivity 0.823 ± 0.162, specificity 0.932 ± 0.030) and PD vs. PSP-RS (AUC 0.963 ± 0.028, sensitivity 0.555 ± 0.157, specificity 0.936 ± 0.031). CONCLUSION: We proposed reliable Pedoscan-based, Gait-based and EWVE model in differentiating gait disorders by integrating information from gait and postural instability. This model can provide diagnosis guidelines to primary caregivers and assist in differential diagnosis of PD from atypical parkinsonism for neurologists.

Ensemble Machine Learning Model to Predict SARS-CoV-2 T-Cell Epitopes as Potential Vaccine Targets.

An ongoing outbreak of coronavirus disease 2019 (COVID-19), caused by a single-stranded RNA virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a worldwide pandemic that continues to date. Vaccination has proven to be the most effective technique, by far, for the treatment of COVID-19 and to combat the outbreak. Among all vaccine types, epitope-based peptide vaccines have received less attention and hold a large untapped potential for boosting vaccine safety and immunogenicity. Peptides used in such vaccine technology are chemically synthesized based on the amino acid sequences of antigenic proteins (T-cell epitopes) of the target pathogen. Using wet-lab experiments to identify antigenic proteins is very difficult, expensive, and time-consuming. We hereby propose an ensemble machine learning (ML) model for the prediction of T-cell epitopes (also known as immune relevant determinants or antigenic determinants) against SARS-CoV-2, utilizing physicochemical properties of amino acids. To train the model, we retrieved the experimentally determined SARS-CoV-2 T-cell epitopes from Immune Epitope Database and Analysis Resource (IEDB) repository. The model so developed achieved accuracy, AUC (Area under the ROC curve), Gini, specificity, sensitivity, F-score, and precision of 98.20%, 0.991, 0.994, 0.971, 0.982, 0.990, and 0.981, respectively, using a test set consisting of SARS-CoV-2 peptides (T-cell epitopes and non-epitopes) obtained from IEDB. The average accuracy of 97.98% was recorded in repeated 5-fold cross validation. Its comparison with 05 robust machine learning classifiers and existing T-cell epitope prediction techniques, such as NetMHC and CTLpred, suggest the proposed work as a better model. The predicted epitopes from the current model could possess a high probability to act as potential peptide vaccine candidates subjected to in vitro and in vivo scientific assessments. The model developed would help scientific community working in vaccine development save time to screen the active T-cell epitope candidates of SARS-CoV-2 against the inactive ones.

Performance of Machine Learning-Based Multi-Model Voting Ensemble Methods for Network Threat Detection in Agriculture 4.0.

The upcoming agricultural revolution, known as Agriculture 4.0, integrates cutting-edge Information and Communication Technologies in existing operations. Various cyber threats related to the aforementioned integration have attracted increasing interest from security researchers. Network traffic analysis and classification based on Machine Learning (ML) methodologies can play a vital role in tackling such threats. Towards this direction, this research work presents and evaluates different ML classifiers for network traffic classification, i.e., K-Nearest Neighbors (KNN), Support Vector Classification (SVC), Decision Tree (DT), Random Forest (RF) and Stochastic Gradient Descent (SGD), as well as a hard voting and a soft voting ensemble model of these classifiers. In the context of this research work, three variations of the NSL-KDD dataset were utilized, i.e., initial dataset, undersampled dataset and oversampled dataset. The performance of the individual ML algorithms was evaluated in all three dataset variations and was compared to the performance of the voting ensemble methods. In most cases, both the hard and the soft voting models were found to perform better in terms of accuracy compared to the individual models.

An Automated System for ECG Arrhythmia Detection Using Machine Learning Techniques.

The new advances in multiple types of devices and machine learning models provide opportunities for practical automatic computer-aided diagnosis (CAD) systems for ECG classification methods to be practicable in an actual clinical environment. This imposes the requirements for the ECG arrhythmia classification methods that are inter-patient. We aim in this paper to design and investigate an automatic classification system using a new comprehensive ECG database inter-patient paradigm separation to improve the minority arrhythmical classes detection without performing any features extraction. We investigated four supervised machine learning models: support vector machine (SVM), k-nearest neighbors (KNN), Random Forest (RF), and the ensemble of these three methods. We test the performance of these techniques in classifying: Normal beat (NOR), Left Bundle Branch Block Beat (LBBB), Right Bundle Branch Block Beat (RBBB), Premature Atrial Contraction (PAC), and Premature Ventricular Contraction (PVC), using inter-patient real ECG records from MIT-DB after segmentation and normalization of the data, and measuring four metrics: accuracy, precision, recall, and f1-score. The experimental results emphasized that with applying no complicated data pre-processing or feature engineering methods, the SVM classifier outperforms the other methods using our proposed inter-patient paradigm, in terms of all metrics used in experiments, achieving an accuracy of 0.83 and in terms of computational cost, which remains a very important factor in implementing classification models for ECG arrhythmia. This method is more realistic in a clinical environment, where varieties of ECG signals are collected from different patients.

A Soft Voting Ensemble-Based Model for the Early Prediction of Idiopathic Pulmonary Fibrosis (IPF) Disease Severity in Lungs Disease Patients.

Idiopathic pulmonary fibrosis, which is one of the lung diseases, is quite rare but fatal in nature. The disease is progressive, and detection of severity takes a long time as well as being quite tedious. With the advent of intelligent machine learning techniques, and also the effectiveness of these techniques, it was possible to detect many lung diseases. So, in this paper, we have proposed a model that could be able to detect the severity of IPF at the early stage so that fatal situations can be controlled. For the development of this model, we used the IPF dataset of the Korean interstitial lung disease cohort data. First, we preprocessed the data while applying different preprocessing techniques and selected 26 highly relevant features from a total of 502 features for 2424 subjects. Second, we split the data into 80% training and 20% testing sets and applied oversampling on the training dataset. Third, we trained three state-of-the-art machine learning models and combined the results to develop a new soft voting ensemble-based model for the prediction of severity of IPF disease in patients with this chronic lung disease. Hyperparameter tuning was also performed to get the optimal performance of the model. Fourth, the performance of the proposed model was evaluated by calculating the accuracy, AUC, confusion matrix, precision, recall, and F1-score. Lastly, our proposed soft voting ensemble-based model achieved the accuracy of 0.7100, precision 0.6400, recall 0.7100, and F1-scores 0.6600. This proposed model will help the doctors, IPF patients, and physicians to diagnose the severity of the IPF disease in its early stages and assist them to take proactive measures to overcome this disease by enabling the doctors to take necessary decisions pertaining to the treatment of IPF disease.

An Ensemble Matrix Completion Model for Predicting Potential Drugs Against SARS-CoV-2.

Because of the catastrophic outbreak of global coronavirus disease 2019 (COVID-19) and its strong infectivity and possible persistence, computational repurposing of existing approved drugs will be a promising strategy that facilitates rapid clinical treatment decisions and provides reasonable justification for subsequent clinical trials and regulatory reviews. Since the effects of a small number of conditionally marketed vaccines need further clinical observation, there is still an urgent need to quickly and effectively repurpose potentially available drugs before the next disease peak. In this work, we have manually collected a set of experimentally confirmed virus-drug associations through the publicly published database and literature, consisting of 175 drugs and 95 viruses, as well as 933 virus-drug associations. Then, because the samples are extremely sparse and unbalanced, negative samples cannot be easily obtained. We have developed an ensemble model, EMC-Voting, based on matrix completion and weighted soft voting, a semi-supervised machine learning model for computational drug repurposing. Finally, we have evaluated the prediction performance of EMC-Voting by fivefold crossing-validation and compared it with other baseline classifiers and prediction models. The case study for the virus SARS-COV-2 included in the dataset demonstrates that our model achieves the outperforming AUPR value of 0.934 in virus-drug association's prediction.

Novel Feature Selection and Voting Classifier Algorithms for COVID-19 Classification in CT Images.

Diagnosis is a critical preventive step in Coronavirus research which has similar manifestations with other types of pneumonia. CT scans and X-rays play an important role in that direction. However, processing chest CT images and using them to accurately diagnose COVID-19 is a computationally expensive task. Machine Learning techniques have the potential to overcome this challenge. This article proposes two optimization algorithms for feature selection and classification of COVID-19. The proposed framework has three cascaded phases. Firstly, the features are extracted from the CT scans using a Convolutional Neural Network (CNN) named AlexNet. Secondly, a proposed features selection algorithm, Guided Whale Optimization Algorithm (Guided WOA) based on Stochastic Fractal Search (SFS), is then applied followed by balancing the selected features. Finally, a proposed voting classifier, Guided WOA based on Particle Swarm Optimization (PSO), aggregates different classifiers' predictions to choose the most voted class. This increases the chance that individual classifiers, e.g. Support Vector Machine (SVM), Neural Networks (NN), k-Nearest Neighbor (KNN), and Decision Trees (DT), to show significant discrepancies. Two datasets are used to test the proposed model: CT images containing clinical findings of positive COVID-19 and CT images negative COVID-19. The proposed feature selection algorithm (SFS-Guided WOA) is compared with other optimization algorithms widely used in recent literature to validate its efficiency. The proposed voting classifier (PSO-Guided-WOA) achieved AUC (area under the curve) of 0.995 that is superior to other voting classifiers in terms of performance metrics. Wilcoxon rank-sum, ANOVA, and T-test statistical tests are applied to statistically assess the quality of the proposed algorithms as well.

Prediction and molecular insights into fungal adhesins and adhesin like proteins.

Adhesion is the foremost step in pathogenesis and biofilm formation and is facilitated by a special class of cell wall proteins known as adhesins. Formation of biofilms in catheters and other medical devices subsequently leads to infections. As compared to bacterial adhesins, there is relatively less work for the characterization and identification of fungal adhesins. Understanding the sequence characterization of fungal adhesins may facilitate a better understanding of its role in pathogenesis. Experimental methods for investigation and characterization of fungal adhesins are labor intensive and expensive. Therefore, there is a need for fast and efficient computational methods for the identification and characterization of fungal adhesins. The aim of the current study is twofold: (i) to develop an accurate predictor for fungal adhesins, (ii) to sieve out the prominent molecular signatures present in fungal adhesins. Of the many supervised learning algorithms implemented in the current study, voting ensembles resulted in enhanced prediction accuracy. The best voting-ensemble consisting of three support vector machines with three different kernels (PolyK, RBF, PuK) achieved an accuracy of 94.9% on leave one out cross validation and 98.0% accuracy on blind testing set. A preference/avoidance list of molecular features as well as human interpretable rules are also extracted giving insights into the general sequence features of fungal adhesins. Fungal adhesins are characterized by high Threonine and Cysteine and avoidance for Phenylalanine and Methionine. They also have avoidance for average hydrophilicity. The current analysis possibly will facilitate the understanding of the mechanism of fungal adhesin function which may further help in designing methods for restricting adhesin mediated pathogenesis.