Machine learning analysis of multispectral imaging and clinical risk factors to predict amputation wound healing

2021 ◽  
Author(s):  
John J. Squiers ◽  
Jeffrey E. Thatcher ◽  
David Bastawros ◽  
Andrew J. Applewhite ◽  
Ronald D. Baxter ◽  
...  
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Wound Healing ◽  
Multispectral Imaging ◽  
Clinical Risk Factors ◽  
Clinical Risk ◽  
Learning Analysis

scholarly journals Machine Learning Analysis of Multispectral Imaging and Clinical Risk Factors to Predict Amputation Wound Healing

2021 ◽  
Vol 73 (1) ◽  
pp. e15-e16
Author(s):  
John J. Squiers ◽  
David Bastawros ◽  
Andrew J. Applewhite ◽  
Ronald D. Baxter ◽  
Faliu Yi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Wound Healing ◽  
Multispectral Imaging ◽  
Clinical Risk Factors ◽  
Clinical Risk ◽  
Learning Analysis

scholarly journals Machine Learning Based on a Multiparametric and Multiregional Radiomics Signature Predicts Radiotherapeutic Response in Patients with Glioblastoma

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Zi-Qi Pan ◽  
Shu-Jun Zhang ◽  
Xiang-Lian Wang ◽  
Yu-Xin Jiao ◽  
Jian-Jian Qiu
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Cox Regression ◽  
Clinical Risk Factors ◽  
Cox Regression Analysis ◽  
Clinical Risk ◽  
Independent Test ◽  
Independent Test Dataset ◽  
Multiple Regions ◽  
Radiomics Signature

Background and Objective. Although radiotherapy has become one of the main treatment methods for cancer, there is no noninvasive method to predict the radiotherapeutic response of individual glioblastoma (GBM) patients before surgery. The purpose of this study is to develop and validate a machine learning-based radiomics signature to predict the radiotherapeutic response of GBM patients. Methods. The MRI images, genetic data, and clinical data of 152 patients with GBM were analyzed. 122 patients from the TCIA dataset (training set: n = 82 ; validation set: n = 40 ) and 30 patients from local hospitals were used as an independent test dataset. Radiomics features were extracted from multiple regions of multiparameter MRI. Kaplan-Meier survival analysis was used to verify the ability of the imaging signature to predict the response of GBM patients to radiotherapy before an operation. Multivariate Cox regression including radiomics signature and preoperative clinical risk factors was used to further improve the ability to predict the overall survival (OS) of individual GBM patients, which was presented in the form of a nomogram. Results. The radiomics signature was built by eight selected features. The C -index of the radiomics signature in the TCIA and independent test cohorts was 0.703 ( P < 0.001 ) and 0.757 ( P = 0.001 ), respectively. Multivariate Cox regression analysis confirmed that the radiomics signature (HR: 0.290, P < 0.001 ), age (HR: 1.023, P = 0.01 ), and KPS (HR: 0.968, P < 0.001 ) were independent risk factors for OS in GBM patients before surgery. When the radiomics signature and preoperative clinical risk factors were combined, the radiomics nomogram further improved the performance of OS prediction in individual patients ( C ‐ index = 0.764 and 0.758 in the TCIA and test cohorts, respectively). Conclusion. This study developed a radiomics signature that can predict the response of individual GBM patients to radiotherapy and may be a new supplement for precise GBM radiotherapy.

scholarly journals Uncovering clinical risk factors and prediction of severe COVID-19: A machine learning approach based on UK Biobank data

2020 ◽  
Author(s):  
Kenneth C.Y. WONG ◽  
Hon-Cheong So
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Renal Function ◽  
Population Level ◽  
Clinical Risk Factors ◽  
Health Concern ◽  
Targeted Prevention ◽  
Uk Biobank ◽  
Clinical Risk ◽  
Glutamyl Transferase

Background: COVID-19 is a major public health concern. Given the extent of the pandemic, it is urgent to identify risk factors associated with severe disease. Accurate prediction of those at risk of developing severe infections is also important clinically. Methods: Based on the UK Biobank (UKBB data), we built machine learning(ML) models to predict the risk of developing severe or fatal infections, and to evaluate the major risk factors involved. We first restricted the analysis to infected subjects, then performed analysis at a population level, considering those with no known infections as controls. Hospitalization was used as a proxy for severity. Totally 93 clinical variables (collected prior to the COVID-19 outbreak) covering demographic variables, comorbidities, blood measurements (e.g. hematological/liver and renal function/metabolic parameters etc.), anthropometric measures and other risk factors (e.g. smoking/drinking habits) were included as predictors. XGboost (gradient boosted trees) was used for prediction and predictive performance was assessed by cross-validation. Variable importance was quantified by Shapley values and accuracy gain. Shapley dependency and interaction plots were used to evaluate the pattern of relationship between risk factors and outcomes. Results: A total of 1191 severe and 358 fatal cases were identified. For the analysis among infected individuals (N=1747), our prediction model achieved AUCs of 0.668 and 0.712 for severe and fatal infections respectively. Since only pre-diagnostic clinical data were available, the main objective of this analysis was to identify baseline risk factors. The top five contributing factors for severity were age, waist-hip ratio(WHR), HbA1c, number of drugs taken(cnt_tx) and gamma-glutamyl transferase levels. For prediction of mortality, the top features were age, systolic blood pressure, waist circumference (WC), urea and WHR. In subsequent analyses involving the whole UKBB population (N for controls=489987), the corresponding AUCs for severity and fatality were 0.669 and 0.749. The same top five risk factors were identified for both outcomes, namely age, cnt_tx, WC, WHR and cystatin C. We also uncovered other features of potential relevance, including testosterone, IGF-1 levels, red cell distribution width (RDW) and lymphocyte percentage. Conclusions: We identified a number of baseline clinical risk factors for severe/fatal infection by an ML approach. For example, age, central obesity, impaired renal function, multi-comorbidities and cardiometabolic abnormalities may predispose to poorer outcomes. The presented prediction models may be useful at a population level to help identify those susceptible to developing severe/fatal infections, hence facilitating targeted prevention strategies. Further replications in independent cohorts are required to verify our findings.

scholarly journals Uncovering Clinical Risk Factors and Predicting Severe COVID-19 Cases Using UK Biobank Data: Machine Learning Approach (Preprint)

2021 ◽  
Author(s):  
Kenneth Chi-Yin Wong ◽  
Yong Xiang ◽  
Liangying Yin ◽  
Hon-Cheong So
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Renal Function ◽  
Prediction Model ◽  
Cystatin C ◽  
Population Level ◽  
Clinical Risk Factors ◽  
Health Concern ◽  
Uk Biobank ◽  
Clinical Risk

BACKGROUND COVID-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. OBJECTIVE Based 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. METHODS We 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. RESULTS A 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. CONCLUSIONS We 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.

scholarly journals A Machine Learning Approach to Predict 5-year Risk for Complications in Type 1 Diabetes

2021 ◽  
Author(s):  
Naba Al-Sari ◽  
Svetlana Kutuzova ◽  
Tommi Suvitaival ◽  
Peter Henriksen ◽  
Flemming Pociot ◽  
...  
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Type 1 Diabetes ◽  
Diabetic Retinopathy ◽  
Kidney Disease ◽  
Diabetic Kidney Disease ◽  
Clinical Risk Factors ◽  
Diabetic Kidney ◽  
Clinical Risk

OBJECTIVE: Our aim was to apply state-of-the-art machine learning algorithms to predict the risk of future progression to diabetes complications, including diabetic kidney disease (≥30% decline in eGFR) and diabetic retinopathy (mild, moderate or severe). RESEARCH DESIGN AND METHODS: Using data in a cohort of 537 adults with type 1 diabetes we predicted diabetes complications emerging during a median follow-up of 5.4 years. Prediction models were computed first with clinical risk factors at baseline (17 measures) and then with clinical risk factors and blood-derived metabolomics and lipidomics data (965 molecular features) at baseline. Participants were first classified into two groups: type 1 diabetes stable (n=195) or type 1 diabetes with progression to diabetes complications (n=190). Furthermore, progression of diabetic kidney disease (≥30% decline in eGFR; n=79) and diabetic retinopathy (mild, moderate or severe; n=111) were predicted in two complication-specific models. Models were compared by 5-fold cross-validated area under the receiver operating characteristic (AUROC) curves. The Shapley additive explanations algorithm was used for feature selection and for interpreting the models. Accuracy, precision, recall, and F-score were used to evaluate clinical utility. RESULTS: During a median follow-up of 5.4 years, 79 (21 %) of the participants (mean+-SD: age 54.8 +- 13.7 years) progressed in diabetic kidney disease and 111 (29 %) of the participants progressed to diabetic retinopathy. The predictive models for diabetic kidney disease progression were highly accurate with clinical risk factors: the accuracy of 0.95 and AUROC of 0.92 (95% CI 0.857;0.995) was achieved, further improved to the accuracy of 0.98 and AUROC of 0.99 (95% CI 0.876;0.997) when omics-based predictors were included. The predictive panel composition was: albuminuria, retinopathy, estimated glomerular filtration rate, hemoglobin A1c, and six metabolites (five identified as ribitol, ribonic acid, myo-inositol, 2,4- and 3,4-dihydroxybutanoic acids). Models for diabetic retinopathy progression were less predictive with clinical risk predictors at, AUROC of 0.81 (95% CI 0.754;0.958) and with omics included at AUROC of 0.87 (95% CI 0.781;0.996) curve. The final retinopathy-panel included: hemoglobin A1c, albuminuria, mild degree of retinopathy, and seven metabolites, including one ceramide and the 3,4-dihydroxybutanoic acid). CONCLUSIONS: Here we demonstrate the application of machine learning to effectively predict five-year progression of complications, in particular diabetic kidney disease, using a panel of known clinical risk factors in combination with blood small molecules. Further replication of this machine learning tool in a real-world context or a clinical trial will facilitate its implementation in the clinic.

scholarly journals Uncovering Clinical Risk Factors and Predicting Severe COVID-19 Cases Using UK Biobank Data: Machine Learning Approach

10.2196/29544 ◽  
2021 ◽  
Vol 7 (9) ◽  
pp. e29544
Author(s):  
Kenneth Chi-Yin Wong ◽  
Yong Xiang ◽  
Liangying Yin ◽  
Hon-Cheong So
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Renal Function ◽  
Prediction Model ◽  
Cystatin C ◽  
Population Level ◽  
Clinical Risk Factors ◽  
Health Concern ◽  
Uk Biobank ◽  
Clinical Risk

Background COVID-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. Objective Based 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. Methods We 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. Results A 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. Conclusions We 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.

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