Uncovering waterlogging-responsive genes in cucumber through machine learning and differential gene correlation analysis

Background Machine learning (ML) algorithm support vector machine (SVM) performed better than Thrombolysis in Myocardial Infarction (TIMI) score for ASIAN STEMI patients. However, Deep Learning (DL) effectiveness in the multiethnic ASIAN population has yet to be determined. DL has automatic learning of the feature from a given dataset without the need to conduct feature selection. However, the selected features by the algorithm is black box. Identifying features associated with mortality is essential to recognize characteristics of patients with high risk for better patient management. Purpose To develop a DL algorithm for in-hospital mortality in multiethnic STEMI patients using predictors identified from the SVM algorithm. To investigate DL performance constructed using predictors from SVM feature extraction and expert-recommended predictors. Methods We constructed four algorithms; a) DL and SVM algorithms with predictors identified from the SVM variable importance b) DL and SVM using predictors based on expert recommendation. We used registry data from the National Cardiovascular Disease Database of 11397 patient's. Fifty parameters including demographics, cardiovascular risk, medications and clinical variables were considered. The Area under the curve (AUC) is the performance evaluation metric. Algorithms were validated against the TIMI and tested using the same validation data. SVM variable importance with backward elimination was used to select and rank important variables. Results DL algorithms outperform SVM and TIMI on the validation dataset; i) DL with SVM selected predictors (15 predictors, AUC = 0.97), ii) DL with expert-recommended predictors (16 predictors, AUC = 0.96), iii) SVM with selected predictors (15 predictors, AUC = 0.92), iv) SVM with expert-recommended predictors (AUC = 0.89) and TIMI (AUC = 0.82). Common predictors across SVM feature selection, expert-recommendation and TIMI are: age, heart rate, Killip class, fasting blood glucose, systolic blood pressure, comorbid diseases and ST-elevation. SVM feature selection also identified diuretics, PCI and pharmacotherapy drugs as predictors that improve mortality prediction in STEMI patients. Our findings suggest that the TIMI score underestimates patients risk of mortality. DL algorithm using selected predictors classified 35% of nonsurvival patients as high risk (risk probabilities >50%) compared to only 12.7% nonsurvival patients by TIMI (score >5) (Figure below). Conclusions In the ASIAN population, patients with STEMI can be better classified using the DL algorithm compared to the ML and TIMI score. Combining ML feature selection with DL allows the identification of distinct factors in a unique ASIAN population for better mortality prediction than relying solely on an expert recommendation as it is a very subjective approach. Continuous validation on population-specific algorithms using DL and ML is needed before implementing in a real clinical setting. Funding Acknowledgement Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Technology Development Fund 1 TIMI performance on validation setDL performance on validation set

Background:This study aimed to develop and validate a predictive model for major adverse cardiovascular events (MACE) following percutaneous coronary intervention (PCI) in patients with new-onset ST-segment elevation myocardial infarction (STEMI) using four machine learning (ML) algorithms.Methods:Data from 250 new-onset STEMI patients were retrospectively collected. Feature selection was performed using the Boruta algorithm. Four ML algorithms—K-nearest neighbors (KNN), support vector machine (SVM), Complement Naive Bayes (CNB), and logistic regression—were applied to predict MACE risk. Model performance was evaluated using area under the curve (AUC), sensitivity, and specificity. Shapley Additive Explanations (SHAP) analysis was used to rank feature importance, and a nomogram was constructed for risk visualization.Results:Logistic regression showed the best performance (AUC = 0.814 in training, 0.776 in validation) compared to KNN, SVM, and CNB. SHAP analysis identified seven key predictors, including Killip classification, Gensini score, blood urea nitrogen (BUN), heart rate (HR), creatinine (CR), glutamine transferase (GLT), and platelet count (PCT). The nomogram provided accurate risk predictions with strong agreement between predicted and observed outcomes.Conclusions:The logistic regression model effectively predicts MACE risk after PCI in STEMI patients. The nomogram serves as a practical tool for clinicians, supporting personalized risk assessment and improving clinical decision-making.

BackgroundMachine learning (ML) algorithm support vector machine (SVM) performed better than Thrombolysis in Myocardial Infarction (TIMI) score for ASIAN STEMI patients. However, Deep Learning (DL) effectiveness in the multiethnic ASIAN population has yet to be determined. DL has automatic learning of the feature from a given dataset without the need to conduct feature selection. However, the selected features by the algorithm is black box. Identifying features associated with mortality is essential to recognize characteristics of patients with high risk for better patient management.PurposeTo develop a DL algorithm for in-hospital mortality in multiethnic STEMI patients using predictors identified from the SVM algorithm. To investigate DL performance constructed using predictors from SVM feature extraction and expert-recommended predictors.MethodsWe constructed four algorithms; a) DL and SVM algorithms with predictors identified from the SVM variable importance b) DL and SVM using predictors based on expert recommendation. We used registry data from the National Cardiovascular Disease Database of 11397 patient's. Fifty parameters including demographics, cardiovascular risk, medications and clinical variables were considered. The Area under the curve (AUC) is the performance evaluation metric. Algorithms were validated against the TIMI and tested using the same validation data. SVM variable importance with backward elimination was used to select and rank important variables.ResultsDL algorithms outperform SVM and TIMI on the validation dataset; i) DL with SVM selected predictors (15 predictors, AUC = 0.97), ii) DL with expert-recommended predictors (16 predictors, AUC = 0.96), iii) SVM with selected predictors (15 predictors, AUC = 0.92), iv) SVM with expert-recommended predictors (AUC = 0.89) and TIMI (AUC = 0.82). Common predictors across SVM feature selection, expert-recommendation and TIMI are: age, heart rate, Killip class, fasting blood glucose, systolic blood pressure, comorbid diseases and ST-elevation. SVM feature selection also identified diuretics, PCI and pharmacotherapy drugs as predictors that improve mortality prediction in STEMI patients. Our findings suggest that the TIMI score underestimates patients risk of mortality. DL algorithm using selected predictors classified 35% of nonsurvival patients as high risk (risk probabilities >50%) compared to only 12.7% nonsurvival patients by TIMI (score >5) (Figure below).ConclusionsIn the ASIAN population, patients with STEMI can be better classified using the DL algorithm compared to the ML and TIMI score. Combining ML feature selection with DL allows the identification of distinct factors in a unique ASIAN population for better mortality prediction than relying solely on an expert recommendation as it is a very subjective approach. Continuous validation on population-specific algorithms using DL and ML is needed before implementing in a real clinical setting.Funding AcknowledgementType of funding sources: Public grant(s) – National budget only. Main funding source(s): Technology Development Fund 1TIMI performance on validation setDL performance on validation set

Complete mesocolic excision (CME) is a technically complex and highly invasive surgical approach, and patients undergoing CME are consequently at elevated risk of postoperative acute kidney injury (AKI). Despite this vulnerability, reliable tools for individualized AKI risk prediction in this population remain unavailable. Moreover, the contributions of perioperative inflammatory responses and blood transfusion to AKI pathogenesis have not been comprehensively examined. Here, we sought to develop and validate a multicenter, machine learning-based model to predict AKI following CME and to delineate the relative impact of inflammation- and transfusion-related determinants. We retrospectively enrolled patients with colon cancer who underwent CME between 2010 and 2020 at five tertiary referral centers. Patients were allocated to an internal cohort or an external validation cohort according to hospital of origin. The internal cohort was randomly divided into training and validation subsets in a 7:3 ratio. Feature selection and model construction were performed using multivariable analyses and five machine learning algorithms: Extreme Gradient Boosting (XGBoost), Random Forest, Support Vector Machine, k-Nearest Neighbors (KNN), and Multilayer Perceptron (MLP). Model performance was assessed using receiver operating characteristic (ROC) curves, calibration plots, decision curve analysis (DCA), and k-fold cross-validation, followed by independent external validation. Model interpretability and the quantitative contribution of inflammatory and transfusion variables were evaluated using SHapley Additive exPlanations (SHAP). Among the evaluated models, XGBoost achieved the most favorable performance, exhibiting superior discrimination, calibration, clinical utility, and generalizability, with area under the curve (AUC) values of 0.92 in the training set, 0.88 in the validation set, and 0.922 in the external cohort. SHAP analysis highlighted tumor size, operative duration, preoperative anemia, postoperative neutrophil-to-lymphocyte ratio (NLR), intraoperative blood loss, C-reactive protein (CRP), intraoperative hypoxemia, and perioperative blood transfusion as the dominant predictors of AKI. Notably, inflammation-related markers (NLR and CRP) and transfusion-related factors exerted a substantial influence on AKI risk. We established an interpretable, multicenter machine learning-based model with high predictive accuracy, robustness, and clinical relevance for AKI following CME. Our findings identify perioperative inflammation and blood transfusion as key drivers of postoperative AKI, offering mechanistic insight and a foundation for early risk stratification and targeted preventive strategies in high-risk patients.

To investigate the value of multimodal MRI radiomics model in predicting Neoadjuvant chemotherapy (NAC) response in Nasopharyngeal carcinoma (NPC) and assess the performance differences between machine learning and deep learning models. 370 NPC patients were retrospectively enrolled, with 126 patients receiving additional Dynamic contrast-enhanced Magnetic Resonance Imaging (DCE-MRI). Radiomics features were extracted from T1WI, PDWI, CE-T1WI and DCE-MRI sequences. Feature selection was performed through Mutual Information Criterion (MIC), Least Absolute Shrinkage and Selection Operator (LASSO) algorithms, and feature selection network. Machine learning models based on logistic regression, support vector machines, random forests, and extreme gradient boosting, as well as deep learning prediction models of multi-layer perceptrons were established. Model performance was evaluated using Receiver Operating Characteristic (ROC) curves and interpreted through SHapley Additive exPlanations (SHAP) values. The deep learning model incorporating DCE-MRI features showed superior performance with an Area under the curve(AUC) of 0.885, sensitivity of 79.6%, and specificity of 83.7%. SHAP analysis revealed that DCE-MRI features, particularly from late enhancement phases, contributed most significantly to model predictions. The multimodal MRI radiomics model, especially when combined with DCE-MRI, can effectively predict NAC response in NPC patients. The model's interpretability through SHAP analysis demonstrates its potential for clinical application.

Objective:The aim of this study was to develop and validate a machine learning model to predict the risk of comorbid depression in asthma patients.Methods:We conducted a retrospective study of 2464 asthma patients with comorbid depression using National Health and Nutrition Examination Survey (NHANES) data. Feature selection was conducted using the Boruta algorithm and the Least Absolute Shrinkage and Selection Operator (LASSO). Eight machine learning algorithms, namely Decision Tree (DT), k-Nearest Neighbors (KNN), Light Gradient Booster Machine (LGBM), Logistic Regression (LR), Random Forest (RF), Support Vector Machine (SVM), eXtreme Gradient Boosting (XGBoost), and Multilayer Perceptron (MLP), were trained using 5-fold cross-validation methodology. Model performance was evaluated through various metrics such as area under the curve (AUC), accuracy, sensitivity, specificity, F1 score, and decision curve analysis (DCA). Interpretation was conducted using SHapley Additive exPlanations (SHAP) analysis, highlighting feature importance.Results:The training set comprised 1724 participants, while the validation set included 740 participants, with a depression prevalence of 14.45%. Significant predictors identified included hypertension, chronic obstructive pulmonary disease (COPD), stroke, sleep questionnaire (SLQ) scores, smoking status, Poverty Index Ratio (PIR), and educational level. The XGBoost model demonstrated superior performance compared with alternative machine learning (ML) algorithms, achieving an AUC of 0.750, an accuracy of 69.1%, a sensitivity of 68.2%, a specificity of 73.8%, and an F1 score of 79%. The SHAP method identified SLQ, PIR, and education level as the primary decision factors influencing the ML model’s predictions.Conclusion:The XGBoost model effectively predicts the risk of depression in asthma patients, serving as a valuable reference for early clinical identification and intervention.

This study aimed to develop and validate a machine learning (ML)-based model for predicting 6-month all-cause mortality in patients diagnosed with infective endocarditis (IE), using retrospective data from a single tertiary care center. Additionally, key prognostic features were identified through model interpretability analysis. A cohort of 444 patients with IE was retrospectively assessed and randomly divided into a training set (n = 310) and a test set (n = 134). Following feature selection, a Cox proportional hazards model and four ML-based survival models: Random Survival Forest, Extremely Randomized Survival Trees (EST), eXtreme Gradient Boosting, and Support Vector Machine were established. Model performance was assessed using the concordance index (C-index), time-dependent area under the curve (AUC), and Kaplan-Meier survival analysis. The model demonstrating optimal performance underwent interpretability analysis using Shapley additive explanations and an exploratory online tool was developed to demonstrate its functionality. Nine predictors were selected for model construction: hemoglobin concentration, presence of severe valvular regurgitation, occurrence of septic shock, New York Heart Association (NYHA) classification, serum albumin level, intracerebral hemorrhage, neutrophil percentage, history of coronary heart disease, and receipt of surgical intervention. The EST model demonstrated the highest predictive performance in the test set (C-index: 0.852), with the smallest discrepancy in performance between the training and test datasets, indicating favorable generalizability. Time-dependent AUCs at 30, 90, and 180 days were 0.957, 0.925, and 0.855, respectively. Surgical intervention was modeled as a protective factor, associated with lower mortality risk, while intracerebral hemorrhage, higher NYHA class, severe valvular regurgitation, and septic shock were associated with increased risk. The EST model demonstrated a high predictive accuracy for 6-month mortality in patients with IE, outperforming both conventional and other ML models. Its robust performance and interpretability suggest that, following rigorous external and multicenter validation, it may serve as a hypothesis-generating toolfor risk stratification. It is not yet validated for direct clinical application and should currently be considered exploratory.

A prognostic gene model with psychological stress-related genes captures immune activation in breast cancer

Machine learning for classifying chronic ankle instability based on ankle strength, range of motion, postural control and anatomical deformities in delivery service workers with a history of lateral ankle sprains.

Chronic Hepatitis B (CHB) is a leading cause of liver fibrosis. Accurate and non-invasive diagnosis of liver fibrosis in CHB patients is of critical clinical importance. This study aimed to develop and validate machine learning (ML)-based models for predicting significant liver fibrosis in CHB patients. This retrospective cohort study included 328 CHB patients (225 with non-significant liver fibrosis and 103 with significant liver fibrosis) from 2017 to 2022. Four ML models were constructed based on four selected features identified through the least absolute shrinkage and selection operator (LASSO) regression. Model performance was assessed using the receiver operating characteristic (ROC) curve, and the area under the curve (AUC), accuracy, sensitivity, specificity, and SHapley Additive exPlanations (SHAP) analysis. The random forest (RF) model demonstrated the highest predictive performance, with an AUC of 0.874 (95% CI: 0.813-0.934) in the training set and 0.863 (95% CI: 0.772-0.955) in the test set, outperforming extreme gradient boosting (XGBoost), logistic regression (LR), and support vector machine (SVM). Compared with the traditional fibrosis indices such as aspartate aminotransferase to platelet ratio index (APRI) (AUC = 0.585) and fibrosis-4 (FIB-4) (AUC = 0.633), the RF model (AUC = 0.863) demonstrated significantly higher predictive accuracy. SHAP analysis identified platelet count (PLT) as the most influential predictor in the RF model. The ML-based RF model offers a highly accurate, non-invasive interpretable tool for predicting significant liver fibrosis in patients with CHB, offering potential for clinical application in routine fibrosis risk assessment.

Machine-learning prediction of treatment response to stereotactic body radiation therapy in oligometastatic gynecological cancer: A multi-institutional study

Text mining is a special case of data mining which explore unstructured or semi-structured text documents, to establish valuable patterns and rules that indicate trends and significant features about specific topics. Text mining has been in pattern recognition, predictive studies, sentiment analysis and statistical theories in many areas of research, medicine, financial analysis, social life analysis, and business intelligence. Text mining uses concept of natural language processing and machine learning. Machine learning algorithms have been used and reported to give great results, but their performance of machine learning algorithms is affected by factors such as dataset domain, number of classes, length of the corpus, and feature selection techniques used. Redundant attribute affects the performance of the classification algorithm, but this can be reduced by using different feature selection techniques and dimensionality reduction techniques. Feature selection is a data preprocessing step that chooses a subset of input variable while eliminating features with little or no predictive information. Feature selection techniques are Information gain, Term Frequency, Term Frequency-Inverse document frequency, Mutual Information, and Chi-Square, which can use a filters, wrappers, or embedded approaches. To get the most value from machine learning, pairing the best algorithms with the right tools and processes is necessary. Little research has been done on the effect of feature selection techniques on classification accuracy for pairing of these algorithms with the best feature selection techniques for optimal results. In this research, a text classification experiment was conducted using incident management dataset, where incidents were classified into their resolver groups. Support vector machine (SVM), K-Nearest Neighbors (KNN), Naïve Bayes (NB) and Decision tree (DT) machine learning algorithms were examined. Filtering approach was used on the feature selection techniques, with different ranking indices applied for optimal feature set and classification accuracy results analyzed. The classification accuracy results obtained using TF were, 88% for SVM, 70% for NB, 79% for Decision tree, and KNN had 55%, while Boolean registered 90%, 83%, 82% and 75%, for SVM, NB, DT, and KNN respectively. TF-IDF, had 91%, 83%, 76%, and 56% for SVM, NB, DT, and KNN respectively. The results showed that algorithm performance is affected by feature selection technique applied. SVM performed best, followed by DT, KNN and finally NB. In conclusion, presence of noisy data leads to poor learning performance and increases the computational time. The classifiers performed differently depending on the feature selection technique applied. For optimal results, the classifier that performed best together with the feature selection technique with the best feature subset should be applied for all types of data for accurate classification performance. Keywords: Text Classification, Supervised Machine Learning, Feature Selection DOI : 10.7176/JIEA/9-3-06 Publication date :May 31 st 2019

ObjectiveTo develop an interpretable stacking ensemble model for predicting in-hospital mortality in intensive care unit (ICU) patients with CKD and sepsis and to deploy it as a web-based tool for bedside clinical use.MethodsData were extracted from the MIMIC-IV 3.0 database and split into training and test sets at a 7:3 ratio. Feature selection was performed by combining the least absolute shrinkage and selection operator (LASSO) regression with the Boruta algorithm. Eight machine learning (ML) models were trained and optimized via ten-fold cross-validation and grid search. The two models with the highest area under the curve (AUC) in the training set were combined using a stacking ensemble strategy. SHapley Additive exPlanations (SHAP) were applied to improve interpretability. Model performance was compared with the SOFA score.ResultsA total of 5344 ICU patients with CKD and sepsis were included, with an in-hospital mortality rate of 19.1%. After feature selection, 16 variables were retained. In the training set, XGBoost and LightGBM performed best. The stacking model achieved an AUC of 0.757 on the test set, outperforming SOFA (AUC = 0.668). SHAP analysis identified age, Acute Physiology Score III, Simplified Acute Physiology Score II, and respiratory rate as the top predictors. The model was also deployed as a publicly accessible web application.ConclusionThe stacking ensemble model demonstrated good discriminatory performance and interpretability for predicting in-hospital mortality in ICU patients with CKD and sepsis. Its web-based deployment provides a convenient platform for early risk assessment, although external validation is needed to confirm its broader applicability.

BackgroundThe subjective assessment of Breast Imaging Reporting and Data System (BI-RADS) 4A lesions leads to a high number of unnecessary biopsies, highlighting the need for more objective and accurate diagnostic tools. This study aimed to construct and validate a novel multimodal framework that integrates deep learning (DL), radiomics, and clinical and breast ultrasound (US) features to distinguish between benign and malignant breast lesions classified as BI-RADS 4A.MethodsA total of 935 patients with pathologically confirmed BI-RADS 4A lesions were retrospectively enrolled and randomly divided into a training cohort (n=654) and an internal validation cohort (n=281). An additional 488 patients were enrolled as the external validation cohort. DL and radiomics models were developed with the light gradient boosting machine (LightGBM) algorithm, a machine learning technique known for its efficiency in handling high-dimensional data. Univariate and multivariate logistic regression (LR) analyses identified significant clinical and US features. After handcrafted radiomics features, DL features, and clinical/breast US features were combined, dimensionality reduction and feature selection were performed. The integrated model was developed via LightGBM, and the SHapley Additive Explanations (SHAP) approach was applied to rank feature contributions.ResultsThe integrated model achieved robust discrimination between benign and malignant BI-RADS 4A lesions, with an area under the curve (AUC) of 0.938, 0.870, and 0.861 for the training cohort, internal validation cohort, and external validation cohort, respectively. Furthermore, in the external validation cohort, the integrated model significantly outperformed the handcrafted radiomics model (AUC =0.719; P<0.001) and the DL model (AUC =0.763; P=0.011). Decision curve analysis confirmed that the integrated model was the most clinically useful across the three cohorts.ConclusionsThe integrated model demonstrated high accuracy in differentiating between benign and malignant BI-RADS 4A lesions, exhibiting the ability to significantly reduce unnecessary biopsies while maintaining diagnostic accuracy.

IntroductionThis study aimed to develop a diabetic retinopathy (DR) Prediction model using various machine learning algorithms incorporating the novel predictor Triglyceride-glucose index (TyG). Furthermore, the model was interpreted using the SHapley Additive exPlanations (SHAP) method.MethodReal-world data were collected from a general hospital in a major city and a county clinic, then divided into the DR Group (1392) and non-DR group (2358). Baseline data were collected, and variables were selected using Recursive Feature Elimination with Cross-Validation (RFECV). The performance of five machine learning algorithms, including Logistic Regression model (LR), Decision Tree (DT), Random Forest (RF), Support Vector Machine (SVM), and XGBoost (XGB), was assessed based on accuracy, sensitivity, specificity, and Area Under the Curve (AUC) of the Receiver Operating characteristic Curve (ROC). The optimal model was interpreted using SHAP.ResultLVM and LR demonstrated superior performance in both the test set and training set (ROC, 0.85 and 0.82, respectively). The top five predictors identified by SHAP analysis included TyG, Insulin therapy, HbA1c, Diabetes Course, HDL. HDL was identified as a protective factor, while the remaining factors were associated with retinopathy.ConclusionLR and SVM demonstrated the best performance. To our knowledge, this is the first machine learning-based DR prediction model integrating the triglyceride-glucose index (TyG) as a core predictor, overcoming limitations of insulin resistance (IR) assessment in resource-limited settings. TyG provides a cost-effective alternative to conventional IR biomarkers (e.g., HOMA-IR), enabling practical DR risk stratification in primary care.