Classifying 2-year recurrence in patients with dlbcl using clinical variables with imbalanced data and machine learning methods

Disability risk prediction model based on machine learning among Chinese healthy older adults: results from the China Health and Retirement Longitudinal Study

Background

Predicting disability risk in healthy older adults in China is essential for timely preventive interventions, improving their quality of life, and providing scientific evidence for disability prevention. Therefore, developing a machine learning model capable of evaluating disability risk based on longitudinal research data is crucial.

Methods

We conducted a prospective cohort study of 2,175 older adults enrolled in the China Health and Retirement Longitudinal Study (CHARLS) between 2015 and 2018 to develop and validate this prediction model. Several machine learning algorithms (logistic regression, k-nearest neighbors, naive Bayes, multilayer perceptron, random forest, and XGBoost) were used to assess the 3-year risk of developing disability. The optimal cutoff points and adjustment parameters are explored in the training set, the prediction accuracy of the models is compared in the testing set, and the best-performing models are further interpreted.

Results

During a 3-year follow-up period, a total of 505 (23.22%) healthy older adult individuals developed disabilities. Among the 43 features examined, the LASSO regression identified 11 features as significant for model establishment. When comparing six different machine learning models on the testing set, the XGBoost model demonstrated the best performance across various evaluation metrics, including the highest area under the ROC curve (0.803), accuracy (0.757), sensitivity (0.790), and F1 score (0.789), while its specificity was 0.712. The decision curve analysis (DCA) indicated showed that XGBoost had the highest net benefit in most of the threshold ranges. Based on the importance of features determined by SHAP (model interpretation method), the top five important features were identified as right-hand grip strength, depressive symptoms, marital status, respiratory function, and age. Moreover, the SHAP summary plot was used to illustrate the positive or negative effects attributed to the features influenced by XGBoost. The SHAP dependence plot explained how individual features affected the output of the predictive model.

Conclusion

Machine learning-based prediction models can accurately evaluate the likelihood of disability in healthy older adults over a period of 3 years. A combination of XGBoost and SHAP can provide clear explanations for personalized risk prediction and offer a more intuitive understanding of the effect of key features in the model.

Identification and Validation of Cuproptosis-Related LncRNA Signatures in the Prognosis and Immunotherapy of Clear Cell Renal Cell Carcinoma Using Machine Learning

(1) Objective: We aimed to mine cuproptosis-related LncRNAs with prognostic value and construct a corresponding prognostic model using machine learning. External validation of the model was performed in the ICGC database and in multiple renal cancer cell lines via qPCR. (2) Methods: TCGA and ICGC cohorts related to renal clear cell carcinoma were included. GO and KEGG analyses were conducted to determine the biological significance of differentially expressed cuproptosis-related LncRNAs (CRLRs). Machine learning (LASSO), Kaplan-Meier, and Cox analyses were conducted to determine the prognostic genes. The tumor microenvironment and tumor mutation load were further studied. TIDE and IC50 were used to evaluate the response to immunotherapy, a risk model of LncRNAs related to the cuproptosis genes was established, and the ability of this model was verified in an external independent ICGC cohort. LncRNAs were identified in normal HK-2 cells and verified in four renal cell lines via qPCR. (3) Results: We obtained 280 CRLRs and identified 66 LncRNAs included in the TCGA-KIRC cohort. Then, three hub LncRNAs (AC026401.3, FOXD2-AS1, and LASTR), which were over-expressed in the four ccRCC cell lines compared with the human renal cortex proximal tubule epithelial cell line HK-2, were identified. In the ICGC database, the expression of FOXD2-AS1 and LASTR was consistent with the qPCR and TCGA-KIRC. The results also indicated that patients with low-risk ccRCC-stratified by tumor-node metastasis stage, sex, and tumor grade-had significantly better overall survival than those with high-risk ccRCC. The predictive algorithm showed that, according to the three CRLR models, the low-risk group was more sensitive to nine target drugs (A.443654, A.770041, ABT.888, AG.014699, AMG.706, ATRA, AP.24534, axitinib, and AZ628), based on the estimated half-maximal inhibitory concentrations. In contrast, the high-risk group was more sensitive to ABT.263 and AKT inhibitors VIII and AS601245. Using the CRLR models, the correlation between the tumor immune microenvironment and cancer immunotherapy response revealed that high-risk patients are more likely to respond to immunotherapy than low-risk patients. In terms of immune marker levels, there were significant differences between the high- and low-risk groups. A high TMB score in the high-risk CRLR group was associated with worse survival, which could be a prognostic factor for KIRC. (4) Conclusions: This study elucidates the core cuproptosis-related LncRNAs, FOXD2-AS1, AC026401.3, and LASTR, in terms of potential predictive value, immunotherapeutic strategy, and outcome of ccRCC.

Predict DLBCL patients' recurrence within two years with Gaussian mixture model cluster oversampling and multi-kernel learning

BACKGROUND AND OBJECTIVE

Diffuse large B-cell lymphoma (DLBCL) is common in adults' non-Hodgkin's lymphoma. Relapse mainly occurs within two years after diagnosis and has a poor prognosis. Relapse after two years is less frequent and has a better prognosis. In this work, we constructed a relapse prediction model for diffuse large B-cell lymphoma patients within two years, expecting to provide a reference for Clinicians to implement individualized treatment.

METHOD

We propose a secondary-level class imbalance method based on Gaussian mixture model (GMM) clustering resampling to balance the data. Then use a multi-kernel support vector machine(SVM) to inscribe heterogeneous clinical data. Finally, merging them to identify recurrence patients within two years.

RESULTS

Among all the class imbalance methods in this work, Inverse Weighted -GMM +SMOTEENN has the best performance. Compared with NO-GMM (Directl use the SMOTEENN without the GMM clustering process), its Area Under the ROC Curve(AUC) increases by 8.75%, and ECE and brier scores decrease 2.07% and 3.09%, respectively. Among the four classification algorithms in this work, Multiple kernel learning (MKL) has the most minimized brier scores and expected calibration error(ECE), the largest AUC, accuracy, Recall, precision and F1, has the best discrimination and calibration.

CONCLUSION

Our inverse weighted -GMM+SMOTEENN+MKL (GMM-SENN-MKL) method can handle data class imbalance and clinical heterogeneity data well and can be used to predict recurrence in DLBCL patients.

LASSO Model Better Predicted the Prognosis of DLBCL than Random Forest Model: A Retrospective Multicenter Analysis of HHLWG

Background. Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous non-Hodgkin’s lymphoma with great clinical challenge. Machine learning (ML) has attracted substantial attention in diagnosis, prognosis, and treatment of diseases. This study is aimed at exploring the prognostic factors of DLBCL by ML. Methods. In total, 1211 DLBCL patients were retrieved from Huaihai Lymphoma Working Group (HHLWG). The least absolute shrinkage and selection operator (LASSO) and random forest algorithm were used to identify prognostic factors for the overall survival (OS) rate of DLBCL among twenty-five variables. Receiver operating characteristic (ROC) curve and decision curve analysis (DCA) were utilized to compare the predictive performance and clinical effectiveness of the two models, respectively. Results. The median follow-up time was 43.4 months, and the 5-year OS was 58.5%. The LASSO model achieved an Area under the curve (AUC) of 75.8% for the prognosis of DLBCL, which was higher than that of the random forest model (AUC: 71.6%). DCA analysis also revealed that the LASSO model could augment net benefits and exhibited a wider range of threshold probabilities by risk stratification than the random forest model. In addition, multivariable analysis demonstrated that age, white blood cell count, hemoglobin, central nervous system involvement, gender, and Ann Arbor stage were independent prognostic factors for DLBCL. The LASSO model showed better discrimination of outcomes compared with the IPI and NCCN-IPI models and identified three groups of patients: low risk, high-intermediate risk, and high risk. Conclusions. The prognostic model of DLBCL based on the LASSO regression was more accurate than the random forest, IPI, and NCCN-IPI models.

Selective oversampling approach for strongly imbalanced data

Challenges posed by imbalanced data are encountered in many real-world applications. One of the possible approaches to improve the classifier performance on imbalanced data is oversampling. In this paper, we propose the new selective oversampling approach (SOA) that first isolates the most representative samples from minority classes by using an outlier detection technique and then utilizes these samples for synthetic oversampling. We show that the proposed approach improves the performance of two state-of-the-art oversampling methods, namely, the synthetic minority oversampling technique and adaptive synthetic sampling. The prediction performance is evaluated on four synthetic datasets and four real-world datasets, and the proposed SOA methods always achieved the same or better performance than other considered existing oversampling methods.