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Revisiting the Risk Factors for Endometriosis: A Machine Learning Approach.

ABSTRACT: Endometriosis is a condition characterized by implants of endometrial tissues into extrauterine sites, mostly within the pelvic peritoneum. The prevalence of endometriosis is under-diagnosed and is estimated to account for 5-10% of all women of reproductive age. The goal of this study was to develop a model for endometriosis based on the UK-biobank (UKB) and re-assess the contribution of known risk factors to endometriosis. We partitioned the data into those diagnosed with endometriosis (5924; ICD-10: N80) and a control group (142,723). We included over 1000 variables from the UKB covering personal information about female health, lifestyle, self-reported data, genetic variants, and medical history prior to endometriosis diagnosis. We applied machine learning algorithms to train an endometriosis prediction model. The optimal prediction was achieved with the gradient boosting algorithms of CatBoost for the data-combined model with an area under the ROC curve (ROC-AUC) of 0.81. The same results were obtained for women from a mixed ethnicity population of the UKB (7112; ICD-10: N80). We discovered that, prior to being diagnosed with endometriosis, affected women had significantly more ICD-10 diagnoses than the average unaffected woman. We used SHAP, an explainable AI tool, to estimate the marginal impact of a feature, given all other features. The informative features ranked by SHAP values included irritable bowel syndrome (IBS) and the length of the menstrual cycle. We conclude that the rich population-based retrospective data from the UKB are valuable for developing unified machine learning endometriosis models despite the limitations of missing data, noisy medical input, and participant age. The informative features of the model may improve clinical utility for endometriosis diagnosis.

SUBMITTER: Blass I

PROVIDER: S-EPMC9317820 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundCOVID-19 is a major public health concern. Given the extent of the pandemic, it is urgent to identify risk factors associated with disease severity. More accurate prediction of those at risk of developing severe infections is of high clinical importance.ObjectiveBased on the UK Biobank (UKBB), we aimed to build machine learning models to predict the risk of developing severe or fatal infections, and uncover major risk factors involved.MethodsWe first restricted the analysis to infected individuals (n=7846), then performed analysis at a population level, considering those with no known infection as controls (ncontrols=465,728). Hospitalization was used as a proxy for severity. A total of 97 clinical variables (collected prior to the COVID-19 outbreak) covering demographic variables, comorbidities, blood measurements (eg, hematological/liver/renal function/metabolic parameters), anthropometric measures, and other risk factors (eg, smoking/drinking) were included as predictors. We also constructed a simplified (lite) prediction model using 27 covariates that can be more easily obtained (demographic and comorbidity data). XGboost (gradient-boosted trees) was used for prediction and predictive performance was assessed by cross-validation. Variable importance was quantified by Shapley values (ShapVal), permutation importance (PermImp), and accuracy gain. Shapley dependency and interaction plots were used to evaluate the pattern of relationships between risk factors and outcomes.ResultsA total of 2386 severe and 477 fatal cases were identified. For analyses within infected individuals (n=7846), our prediction model achieved area under the receiving-operating characteristic curve (AUC-ROC) of 0.723 (95% CI 0.711-0.736) and 0.814 (95% CI 0.791-0.838) for severe and fatal infections, respectively. The top 5 contributing factors (sorted by ShapVal) for severity were age, number of drugs taken (cnt_tx), cystatin C (reflecting renal function), waist-to-hip ratio (WHR), and Townsend deprivation index (TDI). For mortality, the top features were age, testosterone, cnt_tx, waist circumference (WC), and red cell distribution width. For analyses involving the whole UKBB population, AUCs for severity and fatality were 0.696 (95% CI 0.684-0.708) and 0.825 (95% CI 0.802-0.848), respectively. The same top 5 risk factors were identified for both outcomes, namely, age, cnt_tx, WC, WHR, and TDI. Apart from the above, age, cystatin C, TDI, and cnt_tx were among the top 10 across all 4 analyses. Other diseases top ranked by ShapVal or PermImp were type 2 diabetes mellitus (T2DM), coronary artery disease, atrial fibrillation, and dementia, among others. For the "lite" models, predictive performances were broadly similar, with estimated AUCs of 0.716, 0.818, 0.696, and 0.830, respectively. The top ranked variables were similar to above, including age, cnt_tx, WC, sex (male), and T2DM.ConclusionsWe identified numerous baseline clinical risk factors for severe/fatal infection by XGboost. For example, age, central obesity, impaired renal function, multiple comorbidities, and cardiometabolic abnormalities may predispose to poorer outcomes. The prediction models may be useful at a population level to identify those susceptible to developing severe/fatal infections, facilitating targeted prevention strategies. A risk-prediction tool is also available online. Further replications in independent cohorts are required to verify our findings.

Project description:Introduction: Tetralogy of Fallot (TOF) repair is associated with excellent operative survival. However, a subset of patients experiences post-operative complications, which can significantly alter the early and late post-operative course. We utilized a machine learning approach to identify risk factors for post-operative complications after TOF repair. Methods: We conducted a single-center prospective cohort study of children <2 years of age with TOF undergoing surgical repair. The outcome was occurrence of post-operative cardiac complications, measured between TOF repair and hospital discharge or death. Predictors included patient, operative, and echocardiographic variables, including pre-operative right ventricular strain and fractional area change as measures of right ventricular function. Gradient-boosted quantile regression models (GBM) determined predictors of post-operative complications. Cross-validated GBMs were implemented with and without a filtering stage non-parametric regression model to select a subset of clinically meaningful predictors. Sensitivity analysis with gradient-boosted Poisson regression models was used to examine if the same predictors were identified in the subset of patients with at least one complication. Results: Of the 162 subjects enrolled between March 2012 and May 2018, 43 (26.5%) had at least one post-operative cardiac complication. The most frequent complications were arrhythmia requiring treatment (N = 22, 13.6%), cardiac catheterization (N = 17, 10.5%), and extracorporeal membrane oxygenation (ECMO) (N = 11, 6.8%). Fifty-six variables were used in the machine learning analysis, of which there were 21 predictors that were already identified from the first-stage regression. Duration of cardiopulmonary bypass (CPB) was the highest ranked predictor in all models. Other predictors included gestational age, pre-operative right ventricular (RV) global longitudinal strain, pulmonary valve Z-score, and immediate post-operative arterial oxygen level. Sensitivity analysis identified similar predictors, confirming the robustness of these findings across models. Conclusions: Cardiac complications after TOF repair are prevalent in a quarter of patients. A prolonged surgery remains an important predictor of post-operative complications; however, other perioperative factors are likewise important, including pre-operative right ventricular remodeling. This study identifies potential opportunities to optimize the surgical repair for TOF to diminish post-operative complications and secure improved clinical outcomes. Efforts toward optimizing pre-operative ventricular remodeling might mitigate post-operative complications and help reduce future morbidity.

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Revisiting the Risk Factors for Endometriosis: A Machine Learning Approach.

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