A Machine Learning-Based Predictive Model for Predicting Lymph Node Metastasis in Patients With Ewing's Sarcoma

Predictive factors of chemotherapy‑induced nausea and vomiting in elderly patients with gynecological cancer undergoing paclitaxel and carboplatin therapy: A retrospective study

Chemotherapy-induced nausea and vomiting (CINV) is a common and distressing adverse effect in elderly patients with gynecological cancer undergoing paclitaxel and carboplatin therapy. The present study aimed to identify predictors of CINV in this population. A retrospective analysis was conducted of 209 elderly patients with gynecological cancer treated with paclitaxel and carboplatin chemotherapy at The Affiliated Hospital, Southwest Medical University (Luzhou, China) between May 2019 and July 2023. The Multinational Association of Supportive Care in Cancer Antiemesis Tool (MAT) was used to assess the presence, frequency, and severity of CINV. Patients were categorized into the CINV group (n=76) and non-CINV group (n=133) based on the MAT results. Age, hypertension, pre-chemotherapy sleep duration and pre-chemotherapy anxiety level were identified as significant predictors of CINV in the univariate analysis. In the multivariate analysis, age, pre-chemotherapy sleep duration and pre-chemotherapy anxiety level remained significant predictors. In conclusion, age, pre-chemotherapy sleep duration and pre-chemotherapy anxiety level are significant predictors of CINV in elderly patients with gynecological cancer undergoing paclitaxel and carboplatin therapy. These findings could help in tailoring preventative strategies for CINV in this population.

Enhancing Clinical Decision Making by Predicting Readmission Risk in Patients With Heart Failure Using Machine Learning: Predictive Model Development Study

Background

Patients with heart failure frequently face the possibility of rehospitalization following an initial hospital stay, placing a significant burden on both patients and health care systems. Accurate predictive tools are crucial for guiding clinical decision-making and optimizing patient care. However, the effectiveness of existing models tailored specifically to the Chinese population is still limited.

Objective

This study aimed to formulate a predictive model for assessing the likelihood of readmission among patients diagnosed with heart failure.

Methods

In this study, we analyzed data from 1948 patients with heart failure in a hospital in Sichuan Province between 2016 and 2019. By applying 3 variable selection strategies, 29 relevant variables were identified. Subsequently, we constructed 6 predictive models using different algorithms: logistic regression, support vector machine, gradient boosting machine, Extreme Gradient Boosting, multilayer perception, and graph convolutional networks.

Results

The graph convolutional network model showed the highest prediction accuracy with an area under the receiver operating characteristic curve of 0.831, accuracy of 75%, sensitivity of 52.12%, and specificity of 90.25%.

Conclusions

The model crafted in this study proves its effectiveness in forecasting the likelihood of readmission among patients with heart failure, thus serving as a crucial reference for clinical decision-making.

Machine learning algorithms to predict treatment success for patients with pulmonary tuberculosis

Despite advancements in detection and treatment, tuberculosis (TB), an infectious illness caused by the Mycobacterium TB bacteria, continues to pose a serious threat to world health. The TB diagnosis phase includes a patient's medical history, physical examination, chest X-rays, and laboratory procedures, such as molecular testing and sputum culture. In artificial intelligence (AI), machine learning (ML) is an advanced study of statistical algorithms that can learn from historical data and generalize the results to unseen data. There are not many studies done on the ML algorithm that enables the prediction of treatment success for patients with pulmonary TB (PTB). The objective of this study is to identify an effective and predictive ML algorithm to evaluate the detection of treatment success in PTB patients and to compare the predictive performance of the ML models. In this retrospective study, a total of 1236 PTB patients who were given treatment under a randomized controlled clinical trial at the ICMR-National Institute for Research in Tuberculosis, Chennai, India were considered for data analysis. The multiple ML models were developed and tested to identify the best algorithm to predict the sputum culture conversion of TB patients during the treatment period. In this study, decision tree (DT), random forest (RF), support vector machine (SVM) and naïve bayes (NB) models were validated with high performance by achieving an area under the curve (AUC) of receiver operating characteristic (ROC) greater than 80%. The salient finding of the study is that the DT model was produced as a better algorithm with the highest accuracy (92.72%), an AUC (0.909), precision (95.90%), recall (95.60%) and F1-score (95.75%) among the ML models. This methodology may be used to study the precise ML model classification for predicting the treatment success of TB patients during the treatment period.

Machine learning-based individualized survival prediction model for prognosis in osteosarcoma: Data from the SEER database

Patient outcomes of osteosarcoma vary because of tumor heterogeneity and treatment strategies. This study aimed to compare the performance of multiple machine learning (ML) models with the traditional Cox proportional hazards (CoxPH) model in predicting prognosis and explored the potential of ML models in clinical decision-making. From 2000 to 2018, 1243 patients with osteosarcoma were collected from the Surveillance, Epidemiology, and End Results (SEER) database. Three ML methods were chosen for model development (DeepSurv, neural multi-task logistic regression [NMTLR]) and random survival forest [RSF]) and compared them with the traditional CoxPH model and TNM staging systems. 871 samples were used for model training, and the rest were used for model validation. The models' overall performance and predictive accuracy for 3- and 5-year survival were assessed by several metrics, including the concordance index (C-index), the Integrated Brier Score (IBS), receiver operating characteristic curves (ROC), area under the ROC curves (AUC), calibration curves, and decision curve analysis. The efficacy of personalized recommendations by ML models was evaluated by the survival curves. The performance was highest in the DeepSurv model (C-index, 0.77; IBS, 0.14; 3-year AUC, 0.80; 5-year AUC, 0.78) compared with other methods (C-index, 0.73-0.74; IBS, 0.16-0.17; 3-year AUC, 0.73-0.78; 5-year AUC, 0.72-0.78). There are also significant differences in survival outcomes between patients who align with the treatment option recommended by the DeepSurv model and those who do not (hazard ratio, 1.88; P < .05). The DeepSurv model is available in an approachable web app format at https://survivalofosteosarcoma.streamlit.app/. We developed ML models capable of accurately predicting the survival of osteosarcoma, which can provide useful information for decision-making regarding the appropriate treatment.

Bibliometric analysis of scientific outputs on psychobiotics: Strengthening the food and mood connection

The role of human microbiota in mental health and the underlying mechanisms of psychobiotics, which can modulate mood and behavior through the microbiota-gut-brain axis, has been a focus of scientific scrutiny. This work presents a bibliometric analysis to uncover research trends and insights in psychobiotics literature. The Clarivate Analytics Web of Science database served as the source for articles and reviews on psychobiotics spanning the years 2012 to 2023. Bibliometric network visualization and graphing were conducted using VOSviewer, Microsoft Excel for Windows 10, and Datawrapper software. A total of 348 publications were included, and it has been determined that the number of publications and citations shows an increasing trend from 2012 to 2023. The most active authors on psychobiotics, in order, were Dinan TG, Cryan JF, and Tsai YC. The most active organizations have been identified as University College Cork, National Yang Ming Chiao Tung University, and Bened Biomedical Co. Ltd. The most active countries in psychobiotic research were China, Ireland, and United States of America, while the most active journals were Nutrients, International Journal of Molecular Sciences, and Probiotics and Antimicrobial Proteins. The most commonly used keywords were "psychobiotics," "probiotics," and "gut-brain axis." This bibliometric analysis has revealed the growing academic interest in psychobiotics, indicating that the relationship between gut microbiota and mental health will increasingly be supported by scientific evidence in the years ahead.

Using machine learning techniques to predict the risk of osteoporosis based on nationwide chronic disease data

Osteoporosis is a major public health concern that significantly increases the risk of fractures. The aim of this study was to develop a Machine Learning based predictive model to screen individuals at high risk of osteoporosis based on chronic disease data, thus facilitating early detection and personalized management. A total of 10,000 complete patient records of primary healthcare data in the German Disease Analyzer database (IMS HEALTH) were included, of which 1293 diagnosed with osteoporosis and 8707 without the condition. The demographic characteristics and chronic disease data, including age, gender, lipid disorder, cancer, COPD, hypertension, heart failure, CHD, diabetes, chronic kidney disease, and stroke were collected from electronic health records. Ten different machine learning algorithms were employed to construct the predictive mode. The performance of the model was further validated and the relative importance of features in the model was analyzed. Out of the ten machine learning algorithms, the Stacker model based on Logistic Regression, AdaBoost Classifier, and Gradient Boosting Classifier demonstrated superior performance. The Stacker model demonstrated excellent performance through ten-fold cross-validation on the training set and ROC curve analysis on the test set. The confusion matrix, lift curve and calibration curves indicated that the Stacker model had optimal clinical utility. Further analysis on feature importance highlighted age, gender, lipid metabolism disorders, cancer, and COPD as the top five influential variables. In this study, a predictive model for osteoporosis based on chronic disease data was developed using machine learning. The model shows great potential in early detection and risk stratification of osteoporosis, ultimately facilitating personalized prevention and management strategies.

A machine learning-based online web calculator to aid in the diagnosis of sarcopenia in the US community

Background

Sarcopenia places a heavy healthcare burden on individuals and society. Recognizing sarcopenia and intervening at an early stage is critical. However, there is no simple and easy-to-use prediction tool for diagnosing sarcopenia. The aim of this study was to construct a well-performing online web calculator based on a machine learning approach to predict the risk of low lean body mass (LBM) to assist in the diagnosis of sarcopenia.

Methods

Data from the National Health and Nutritional Examination Surveys 1999-2004 were selected for model construction, and the included data were randomly divided into training and validation sets in the ratio of 75:25. Six machine learning methods- Classification and Regression Trees, Logistic Regression, Neural Network, Random Forest, Support Vector Machine, and Extreme Gradient Boosting (XGBoost)-were used to develop the model. They are screened for features and evaluated for performance. The best-performing models were further developed as an online web calculator for clinical applications.

Results

There were 3046 participants enrolled in the study and 815 (26.8%) participants with LBM. Through feature screening, height, waist circumference, race, and age were used as machine learning features to construct the model. After performance evaluation and sensitivity analysis, the XGBoost-based model was determined to be the best model with better discriminative performance, clinical utility, and robustness.

Conclusion

The XGBoost-based model in this study has excellent performance, and the online web calculator based on it can easily and quickly predict the risk of LBM to aid in the diagnosis of sarcopenia in adults over the age of 60.

Application of machine learning algorithm in prediction of lymph node metastasis in patients with intermediate and high-risk prostate cancer

PURPOSE

This study aims to establish the best prediction model of lymph node metastasis (LNM) in patients with intermediate- and high-risk prostate cancer (PCa) through machine learning (ML), and provide the guideline of accurate clinical diagnosis and precise treatment for clinicals.

METHODS

A total of 24,470 patients with intermediate- and high-risk PCa were included in this study. Multivariate logistic regression model was used to screen the independent risk factors of LNM. At the same time, six algorithms, namely random forest (RF), naive Bayesian classifier (NBC), xgboost (XGB), gradient boosting machine (GBM), logistic regression (LR) and decision tree (DT) are used to establish risk prediction models. Based on the best prediction performance of ML algorithm, a prediction model is established, and the performance of the model is evaluated from three aspects: area under curve (AUC), sensitivity and specificity.

RESULTS

In multivariate logistic regression analysis, T stage, PSA, Gleason score and bone metastasis were independent predictors of LNM in patients with intermediate- and high-risk PCa. By comprehensively comparing the prediction model performance of training set and test set, GBM model has the best prediction performance (F1 score = 0.838, AUROC = 0.804). Finally, we developed a preliminary calculator model that can quickly and accurately calculate the regional LNM in patients with intermediate- and high-risk PCa.

CONCLUSION

T stage, PSA, Gleason and bone metastasis were independent risk factors for predicting LNM in patients with intermediate- and high-risk PCa. The prediction model established in this study performs well; however, the GBM model is the best one.

A decision tree model to predict liver cirrhosis in hepatocellular carcinoma patients: a retrospective study

BACKGROUND

The severity of liver cirrhosis in hepatocellular carcinoma (HCC) patients is essential for determining the scope of surgical resection. It also affects the long-term efficacy of systemic anti-tumor therapy and transcatheter arterial chemoembolization (TACE). Non-invasive tools, including aspartate aminotransferase to platelet ratio index (APRI), fibrosis-4 (FIB-4), and γ-glutamyl transferase to platelet ratio (GPR), are less accurate in predicting cirrhosis in HCC patients. We aimed to build a novel decision tree model to improve diagnostic accuracy of liver cirrhosis.

PATIENTS AND METHODS

The Mann-Whitney U test, χ2 test, and multivariate logistic regression analysis were used to identify independent cirrhosis predictors. A decision tree model was developed using machine learning algorithms in a training cohort of 141 HCC patients. Internal validation was conducted in 99 HCC patients. The diagnostic accuracy and calibration of the established model were evaluated using receiver operating characteristic (ROC) and calibration curves, respectively.

RESULTS

Sex and platelet count were identified as independent cirrhosis predictors. A decision tree model integrating imaging-reported cirrhosis, APRI, FIB-4, and GPR was established. The novel model had an excellent diagnostic performance in the training and validation cohorts, with area under the curve (AUC) values of 0.853 and 0.817, respectively. Calibration curves and the Hosmer-Lemeshow test showed good calibration of the novel model. The decision curve analysis (DCA) indicated that the decision tree model could provide a larger net benefit to predict liver cirrhosis.

CONCLUSION

Our developed decision tree model could successfully predict liver cirrhosis in HCC patients, which may be helpful in clinical decision-making.

A machine learning-based model for predicting the risk of early-stage inguinal lymph node metastases in patients with squamous cell carcinoma of the penis

Objective

Inguinal lymph node metastasis (ILNM) is significantly associated with poor prognosis in patients with squamous cell carcinoma of the penis (SCCP). Patient prognosis could be improved if the probability of ILNM incidence could be accurately predicted at an early stage. We developed a predictive model based on machine learning combined with big data to achieve this.

Methods

Data of patients diagnosed with SCCP were obtained from the Surveillance, Epidemiology, and End Results Program Research Data. By combing variables that represented the patients' clinical characteristics, we applied five machine learning algorithms to create predictive models based on logistic regression, eXtreme Gradient Boosting, Random Forest, Support Vector Machine, and k-Nearest Neighbor. Model performance was evaluated by ten-fold cross-validation receiver operating characteristic curves, which were used to calculate the area under the curve of the five models for predictive accuracy. Decision curve analysis was conducted to estimate the clinical utility of the models. An external validation cohort of 74 SCCP patients was selected from the Affiliated Hospital of Xuzhou Medical University (February 2008 to March 2021).

Results

A total of 1,056 patients with SCCP from the SEER database were enrolled as the training cohort, of which 164 (15.5%) developed early-stage ILNM. In the external validation cohort, 16.2% of patients developed early-stage ILNM. Multivariate logistic regression showed that tumor grade, inguinal lymph node dissection, radiotherapy, and chemotherapy were independent predictors of early-stage ILNM risk. The model based on the eXtreme Gradient Boosting algorithm showed stable and efficient prediction performance in both the training and external validation groups.

Conclusion

The ML model based on the XGB algorithm has high predictive effectiveness and may be used to predict early-stage ILNM risk in SCCP patients. Therefore, it may show promise in clinical decision-making.

A practical dynamic nomogram model for predicting bone metastasis in patients with thyroid cancer

PURPOSE

The aim of this study was to established a dynamic nomogram for assessing the risk of bone metastasis in patients with thyroid cancer (TC) and assist physicians to make accurate clinical decisions.

METHODS

The clinical data of patients with TC admitted to the First Affiliated hospital of Nanchang University from January 2006 to November 2016 were included in this study. Demographic and clinicopathological parameters of all patients at primary diagnosis were analyzed. Univariate and multivariate logistic regression analysis was applied to build a predictive model incorporating parameters. The discrimination, calibration, and clinical usefulness of the nomogram were evaluated using the C-index, ROC curve, calibration plot, and decision curve analysis. Internal validation was evaluated using the bootstrapping method.

RESULTS

A total of 565 patients were enrolled in this study, of whom 25 (4.21%) developed bone metastases. Based on logistic regression analysis, age (OR=1.040, P=0.019), hemoglobin (HB) (OR=0.947, P<0.001) and alkaline phosphatase (ALP) (OR=1.006, P=0.002) levels were used to construct the nomogram. The model exhibited good discrimination, with a C-index of 0.825 and good calibration. A C-index value of 0.815 was achieved on interval validation analysis. Decision curve analysis showed that the nomogram was clinically useful when intervention was decided at a bone metastases possibility threshold of 1%.

CONCLUSIONS

This dynamic nomogram, with relatively good accuracy, incorporating age, HB, and ALP, could be conveniently used to facilitate the prediction of bone metastasis risk in patients with TC.

Comparison of the effectiveness of different machine learning algorithms in predicting new fractures after PKP for osteoporotic vertebral compression fractures

BACKGROUND

The use of machine learning has the potential to estimate the probability of a second classification event more accurately than traditional statistical methods, and few previous studies on predicting new fractures after osteoporotic vertebral compression fractures (OVCFs) have focussed on this point. The aim of this study was to explore whether several different machine learning models could produce better predictions than logistic regression models and to select an optimal model.

METHODS

A retrospective analysis of 529 patients who underwent percutaneous kyphoplasty (PKP) for OVCFs at our institution between June 2017 and June 2020 was performed. The patient data were used to create machine learning (including decision trees (DT), random forests (RF), support vector machines (SVM), gradient boosting machines (GBM), neural networks (NNET), and regularized discriminant analysis (RDA)) and logistic regression models (LR) to estimate the probability of new fractures occurring after surgery. The dataset was divided into a training set (75%) and a test set (25%), and machine learning models were built in the training set after ten cross-validations, after which each model was evaluated in the test set, and model performance was assessed by comparing the area under the curve (AUC) of each model.

RESULTS

Among the six machine learning algorithms, except that the AUC of DT [0.775 (95% CI 0.728-0.822)] was lower than that of LR [0.831 (95% CI 0.783-0.878)], RA [0.953 (95% CI 0.927-0.980)], GBM [0.941 (95% CI 0.911-0.971)], SVM [0.869 (95% CI 0.827-0.910), NNET [0.869 (95% CI 0.826-0.912)], and RDA [0.890 (95% CI 0.851-0.929)] were all better than LR.

CONCLUSIONS

For prediction of the probability of new fracture after PKP, machine learning algorithms outperformed logistic regression, with random forest having the strongest predictive power.

Stmol: A component for building interactive molecular visualizations within streamlit web-applications

Streamlit is an open-source Python coding framework for building web-applications or "web-apps" and is now being used by researchers to share large data sets from published studies and other resources. Here we present Stmol, an easy-to-use component for rendering interactive 3D molecular visualizations of protein and ligand structures within Streamlit web-apps. Stmol can render protein and ligand structures with just a few lines of Python code by utilizing popular visualization libraries, currently Py3DMol and Speck. On the user-end, Stmol does not require expertise to interactively navigate. On the developer-end, Stmol can be easily integrated within structural bioinformatic and cheminformatic pipelines to provide a simple means for user-end researchers to advance biological studies and drug discovery efforts. In this paper, we highlight a few examples of how Stmol has already been utilized by scientific communities to share interactive molecular visualizations of protein and ligand structures from known open databases. We hope Stmol will be used by researchers to build additional open-sourced web-apps to benefit current and future generations of scientists.

A Machine Learning Algorithm for Predicting the Risk of Developing to M1b Stage of Patients With Germ Cell Testicular Cancer

Objective

Distant metastasis other than non-regional lymph nodes and lung (i.e., M1b stage) significantly contributes to the poor survival prognosis of patients with germ cell testicular cancer (GCTC). The aim of this study was to develop a machine learning (ML) algorithm model to predict the risk of patients with GCTC developing the M1b stage, which can be used to assist in early intervention of patients.

Methods

The clinical and pathological data of patients with GCTC were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. Combing the patient's characteristic variables, we applied six machine learning (ML) algorithms to develop the predictive models, including logistic regression(LR), eXtreme Gradient Boosting (XGBoost), light Gradient Boosting Machine (lightGBM), random forest (RF), multilayer perceptron (MLP), and k-nearest neighbor (kNN). Model performances were evaluated by 10-fold cross-receiver operating characteristic (ROC) curves, which calculated the area under the curve (AUC) of models for predictive accuracy. A total of 54 patients from our own center (October 2006 to June 2021) were collected as the external validation cohort.

Results

A total of 4,323 patients eligible for inclusion were screened for enrollment from the SEER database, of which 178 (4.12%) developing M1b stage. Multivariate logistic regression showed that lymph node dissection (LND), T stage, N stage, lung metastases, and distant lymph node metastases were the independent predictors of developing M1b stage risk. The models based on both the XGBoost and RF algorithms showed stable and efficient prediction performance in the training and external validation groups.

Conclusion

S-stage is not an independent factor for predicting the risk of developing the M1b stage of patients with GCTC. The ML models based on both XGBoost and RF algorithms have high predictive effectiveness and may be used to predict the risk of developing the M1b stage of patients with GCTC, which is of promising value in clinical decision-making. Models still need to be tested with a larger sample of real-world data.