scholarly journals Predicting Kidney Graft Survival using Machine Learning Methods: Prediction Model Development and Feature Significance Analysis Study (Preprint)

2021 ◽  
Author(s):  
Syed Asil Ali Naqvi ◽  
Karthik Tennankore ◽  
Amanda Vinson ◽  
Patrice C. Roy ◽  
Syed Sibte Raza Abidi
Keyword(s):  
Machine Learning ◽  
Kidney Transplantation ◽  
Graft Survival ◽  
Graft Failure ◽  
Prediction Models ◽  
Model Development ◽  
Area Under The Curve ◽  
Kidney Graft ◽  
Applied Machine Learning ◽  
Importance Analysis

BACKGROUND Kidney transplantation is the optimal treatment for patients with end-stage kidney disease. Short and long term kidney graft survival is influenced by a number of donor-and recipient factors. Predicting the success of kidney transplantation is important to optimize kidney allocation. OBJECTIVE To predict the risk of kidney graft failure across three temporal cohorts – within 1 year, 5 years, and more than 5 years after transplantation, based on donor and recipient characteristics. We analyzed a large dataset comprising over 50000 kidney transplants covering an approximate 20-year period. METHODS We applied machine learning based classification algorithms to develop prediction models to predict the risk of graft failure for the three different temporal cohorts. Deep learning based autoencoders were applied for data dimensionality reduction, which improved the prediction performance. Feature influence towards graft survival for each cohort was studied by investigating a new non-overlapping patient stratification approach. RESULTS Our models predicted graft survival with area under the curve (AUC) scores of 82% within 1 year, 69% within 5 years, and 81% within 17 years. The feature importance analysis elucidated the varying influence of clinical features towards graft survival across the three different temporal cohorts. CONCLUSIONS We developed machine learning models to predict kidney graft survival for three temporal cohorts and analyzed the changing relevance of features over time.

scholarly journals Using machine learning techniques to develop risk prediction models to predict graft failure following kidney transplantation: protocol for a retrospective cohort study

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 1810
Author(s):  
Sameera Senanayake ◽  
Adrian Barnett ◽  
Nicholas Graves ◽  
Helen Healy ◽  
Keshwar Baboolal ◽  
...  
Keyword(s):  
Machine Learning ◽  
Kidney Transplant ◽  
Predictive Models ◽  
Graft Failure ◽  
Prediction Models ◽  
Deceased Donor ◽  
Machine Learning Techniques ◽  
Kidney Graft ◽  
Learning Techniques ◽  
Deceased Donor Kidney Transplant

Background: A mechanism to predict graft failure before the actual kidney transplantation occurs is crucial to clinical management of chronic kidney disease patients.  Several kidney graft outcome prediction models, developed using machine learning methods, are available in the literature.  However, most of those models used small datasets and none of the machine learning-based prediction models available in the medical literature modelled time-to-event (survival) information, but instead used the binary outcome of failure or not. The objective of this study is to develop two separate machine learning-based predictive models to predict graft failure following live and deceased donor kidney transplant, using time-to-event data in a large national dataset from Australia.   Methods: The dataset provided by the Australia and New Zealand Dialysis and Transplant Registry will be used for the analysis. This retrospective dataset contains the cohort of patients who underwent a kidney transplant in Australia from January 1 st, 2007, to December 31 st, 2017. This included 3,758 live donor transplants and 7,365 deceased donor transplants. Three machine learning methods (survival tree, random survival forest and survival support vector machine) and one traditional regression method, Cox proportional regression, will be used to develop the two predictive models (for live donor and deceased donor transplants). The best predictive model will be selected based on the model’s performance. Discussion: This protocol describes the development of two separate machine learning-based predictive models to predict graft failure following live and deceased donor kidney transplant, using a large national dataset from Australia. Furthermore, these two models will be the most comprehensive kidney graft failure predictive models that have used survival data to model using machine learning techniques. Thus, these models are expected to provide valuable insight into the complex interactions between graft failure and donor and recipient characteristics.

scholarly journals Using machine learning techniques to develop risk prediction models to predict graft failure following kidney transplantation: protocol for a retrospective cohort study

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1810 ◽  
Author(s):  
Sameera Senanayake ◽  
Adrian Barnett ◽  
Nicholas Graves ◽  
Helen Healy ◽  
Keshwar Baboolal ◽  
...  
Keyword(s):  
Machine Learning ◽  
Kidney Transplant ◽  
Predictive Models ◽  
Graft Failure ◽  
Prediction Models ◽  
Deceased Donor ◽  
Machine Learning Techniques ◽  
Kidney Graft ◽  
Learning Techniques ◽  
Deceased Donor Kidney Transplant

Background: A mechanism to predict graft failure before the actual kidney transplantation occurs is crucial to clinical management of chronic kidney disease patients.  Several kidney graft outcome prediction models, developed using machine learning methods, are available in the literature.  However, most of those models used small datasets and none of the machine learning-based prediction models available in the medical literature modelled time-to-event (survival) information, but instead used the binary outcome of failure or not. The objective of this study is to develop two separate machine learning-based predictive models to predict graft failure following live and deceased donor kidney transplant, using time-to-event data in a large national dataset from Australia.   Methods: The dataset provided by the Australia and New Zealand Dialysis and Transplant Registry will be used for the analysis. This retrospective dataset contains the cohort of patients who underwent a kidney transplant in Australia from January 1st, 2007, to December 31st, 2017.  This included 3,758 live donor transplants and 7,365 deceased donor transplants.  Three machine learning methods (survival tree, random survival forest and survival support vector machine) and one traditional regression method, Cox proportional regression, will be used to develop the two predictive models.  The best predictive model will be selected based on the model’s performance. Discussion: This protocol describes the development of two separate machine learning-based predictive models to predict graft failure following live and deceased donor kidney transplant, using a large national dataset from Australia.   Furthermore, these two models will be the most comprehensive kidney graft failure predictive models that have used survival data to model using machine learning techniques.  Thus, these models are expected to provide valuable insight into the complex interactions between graft failure and donor and recipient characteristics.

scholarly journals Impact of Early Pancreatic Graft Loss on Outcome after Simultaneous Pancreas–Kidney Transplantation (SPKT)—A Landmark Analysis

2021 ◽  
Vol 10 (15) ◽  
pp. 3237
Author(s):  
Lukas Johannes Lehner ◽  
Robert Öllinger ◽  
Brigitta Globke ◽  
Marcel G. Naik ◽  
Klemens Budde ◽  
...  
Keyword(s):  
Kidney Transplantation ◽  
Graft Survival ◽  
Graft Loss ◽  
Type I ◽  
Kidney Graft ◽  
Landmark Analysis ◽  
Pancreas Kidney Transplantation ◽  
Simultaneous Pancreas Kidney ◽  
Simultaneous Pancreas Kidney Transplantation ◽  
Pancreas Graft

(1) Background: Simultaneous pancreas–kidney transplantation (SPKT) is a standard therapeutic option for patients with diabetes mellitus type I and kidney failure. Early pancreas allograft failure is a complication potentially associated with worse outcomes. (2) Methods: We performed a landmark analysis to assess the impact of early pancreas graft loss within 3 months on mortality and kidney graft survival over 10 years. This retrospective single-center study included 114 adult patients who underwent an SPKT between 2005 and 2018. (3) Results: Pancreas graft survival rate was 85.1% at 3 months. The main causes of early pancreas graft loss were thrombosis (6.1%), necrosis (2.6%), and pancreatitis (2.6%). Early pancreas graft loss was not associated with reduced patient survival (p = 0.168) or major adverse cerebral or cardiovascular events over 10 years (p = 0.741) compared to patients with functioning pancreas, after 3 months. Moreover, kidney graft function (p = 0.494) and survival (p = 0.461) were not significantly influenced by early pancreas graft loss. (4) Conclusion: In this study, using the landmark analysis technique, early pancreas graft loss within 3 months did not significantly impact patient or kidney graft survival over 10 years.

scholarly journals Predicting and elucidating the etiology of fatty liver disease using a machine learning-based approach: an IMI DIRECT study

2020 ◽  
Author(s):  
Naeimeh Atabaki-Pasdar ◽  
Mattias Ohlsson ◽  
Ana Viñuela ◽  
Francesca Frau ◽  
Hugo Pomares-Millan ◽  
...  
Keyword(s):  
Machine Learning ◽  
Liver Disease ◽  
Fatty Liver ◽  
Fatty Liver Disease ◽  
Prediction Models ◽  
Cell Function ◽  
Area Under The Curve ◽  
Liver Fat ◽  
Irreversible Damage ◽  
Alcoholic Fatty Liver

ABSTRACTBackgroundNon-alcoholic fatty liver disease (NAFLD) is highly prevalent and causes serious health complications in type 2 diabetes (T2D) and beyond. Early diagnosis of NAFLD is important, as this can help prevent irreversible damage to the liver and ultimately hepatocellular carcinomas.Methods and FindingsUtilizing the baseline data from the IMI DIRECT participants (n=1514) we sought to expand etiological understanding and develop a diagnostic tool for NAFLD using machine learning. Multi-omic (genetic, transcriptomic, proteomic, and metabolomic) and clinical (liver enzymes and other serological biomarkers, anthropometry, and measures of beta-cell function, insulin sensitivity, and lifestyle) data comprised the key input variables. The models were trained on MRI image-derived liver fat content (<5% or ≥5%). We applied LASSO (least absolute shrinkage and selection operator) to select features from the different layers of omics data and Random Forest analysis to develop the models. The prediction models included clinical and omics variables separately or in combination. A model including all omics and clinical variables yielded a cross-validated receiver operator characteristic area under the curve (ROCAUC) of 0.84 (95% confidence interval (CI)=0.82, 0.86), which compared with a ROCAUC of 0.82 (95% CI=0.81, 0.83) for a model including nine clinically-accessible variables. The IMI DIRECT prediction models out-performed existing non-invasive NAFLD prediction tools.ConclusionsWe have developed clinically useful liver fat prediction models (see: www.predictliverfat.org) and identified biological features that appear to affect liver fat accumulation.

scholarly journals The Comparison and Interpretation of Machine-Learning Models in Post-Stroke Functional Outcome Prediction

Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1784
Author(s):  
Shih-Chieh Chang ◽  
Chan-Lin Chu ◽  
Chih-Kuang Chen ◽  
Hsiang-Ning Chang ◽  
Alice M. K. Wong ◽  
...  
Keyword(s):  
Machine Learning ◽  
Area Under The Curve ◽  
Superior Performance ◽  
Support Vector ◽  
Balance Test ◽  
Post Stroke ◽  
Feature Importance ◽  
Value Range ◽  
Importance Analysis ◽  
Partial Dependence

Prediction of post-stroke functional outcomes is crucial for allocating medical resources. In this study, a total of 577 patients were enrolled in the Post-Acute Care-Cerebrovascular Disease (PAC-CVD) program, and 77 predictors were collected at admission. The outcome was whether a patient could achieve a Barthel Index (BI) score of >60 upon discharge. Eight machine-learning (ML) methods were applied, and their results were integrated by stacking method. The area under the curve (AUC) of the eight ML models ranged from 0.83 to 0.887, with random forest, stacking, logistic regression, and support vector machine demonstrating superior performance. The feature importance analysis indicated that the initial Berg Balance Test (BBS-I), initial BI (BI-I), and initial Concise Chinese Aphasia Test (CCAT-I) were the top three predictors of BI scores at discharge. The partial dependence plot (PDP) and individual conditional expectation (ICE) plot indicated that the predictors’ ability to predict outcomes was the most pronounced within a specific value range (e.g., BBS-I < 40 and BI-I < 60). BI at discharge could be predicted by information collected at admission with the aid of various ML models, and the PDP and ICE plots indicated that the predictors could predict outcomes at a certain value range.

scholarly journals A Survey of Domain Knowledge Elicitation in Applied Machine Learning

2021 ◽  
Vol 5 (12) ◽  
pp. 73
Author(s):  
Daniel Kerrigan ◽  
Jessica Hullman ◽  
Enrico Bertini
Keyword(s):  
Machine Learning ◽  
Domain Knowledge ◽  
Development Process ◽  
Model Development ◽  
Knowledge Elicitation ◽  
Future Directions ◽  
Domain Experts ◽  
Applied Machine Learning ◽  
Elicitation Process ◽  
Model Development Process

Eliciting knowledge from domain experts can play an important role throughout the machine learning process, from correctly specifying the task to evaluating model results. However, knowledge elicitation is also fraught with challenges. In this work, we consider why and how machine learning researchers elicit knowledge from experts in the model development process. We develop a taxonomy to characterize elicitation approaches according to the elicitation goal, elicitation target, elicitation process, and use of elicited knowledge. We analyze the elicitation trends observed in 28 papers with this taxonomy and identify opportunities for adding rigor to these elicitation approaches. We suggest future directions for research in elicitation for machine learning by highlighting avenues for further exploration and drawing on what we can learn from elicitation research in other fields.

The Influence of Inhomogeneous Input Data from Different Waves on Predictive Model Development for COVID-19 ICU Patients (Preprint)

2021 ◽  
Author(s):  
Sebastian Johannes Fritsch ◽  
Konstantin Sharafutdinov ◽  
Moein Einollahzadeh Samadi ◽  
Gernot Marx ◽  
Andreas Schuppert ◽  
...  
Keyword(s):  
Machine Learning ◽  
Convex Hull ◽  
Prediction Models ◽  
Model Development ◽  
Predictive Performance ◽  
Support Vector ◽  
Good Prediction ◽  
The Impact ◽  
Second Wave ◽  
Over Time

BACKGROUND During the course of the COVID-19 pandemic, a variety of machine learning models were developed to predict different aspects of the disease, such as long-term causes, organ dysfunction or ICU mortality. The number of training datasets used has increased significantly over time. However, these data now come from different waves of the pandemic, not always addressing the same therapeutic approaches over time as well as changing outcomes between two waves. The impact of these changes on model development has not yet been studied. OBJECTIVE The aim of the investigation was to examine the predictive performance of several models trained with data from one wave predicting the second wave´s data and the impact of a pooling of these data sets. Finally, a method for comparison of different datasets for heterogeneity is introduced. METHODS We used two datasets from wave one and two to develop several predictive models for mortality of the patients. Four classification algorithms were used: logistic regression (LR), support vector machine (SVM), random forest classifier (RF) and AdaBoost classifier (ADA). We also performed a mutual prediction on the data of that wave which was not used for training. Then, we compared the performance of models when a pooled dataset from two waves was used. The populations from the different waves were checked for heterogeneity using a convex hull analysis. RESULTS 63 patients from wave one (03-06/2020) and 54 from wave two (08/2020-01/2021) were evaluated. For both waves separately, we found models reaching sufficient accuracies up to 0.79 AUROC (95%-CI 0.76-0.81) for SVM on the first wave and up 0.88 AUROC (95%-CI 0.86-0.89) for RF on the second wave. After the pooling of the data, the AUROC decreased relevantly. In the mutual prediction, models trained on second wave´s data showed, when applied on first wave´s data, a good prediction for non-survivors but an insufficient classification for survivors. The opposite situation (training: first wave, test: second wave) revealed the inverse behaviour with models correctly classifying survivors and incorrectly predicting non-survivors. The convex hull analysis for the first and second wave populations showed a more inhomogeneous distribution of underlying data when compared to randomly selected sets of patients of the same size. CONCLUSIONS Our work demonstrates that a larger dataset is not a universal solution to all machine learning problems in clinical settings. Rather, it shows that inhomogeneous data used to develop models can lead to serious problems. With the convex hull analysis, we offer a solution for this problem. The outcome of such an analysis can raise concerns if the pooling of different datasets would cause inhomogeneous patterns preventing a better predictive performance.

scholarly journals Prediction of Adverse Events in Stable Non-Variceal Gastrointestinal Bleeding Using Machine Learning

2020 ◽  
Vol 9 (8) ◽  
pp. 2603 ◽  
Author(s):  
Dong-Woo Seo ◽  
Hahn Yi ◽  
Beomhee Park ◽  
Youn-Jung Kim ◽  
Dae Ho Jung ◽  
...  
Keyword(s):  
Machine Learning ◽  
High Risk ◽  
Adverse Events ◽  
Gastrointestinal Bleeding ◽  
Area Under The Curve ◽  
Scoring Systems ◽  
Hemodynamic Instability ◽  
Machine Learning Algorithms ◽  
Gradient Boosting ◽  
Importance Analysis

Clinical risk-scoring systems are important for identifying patients with upper gastrointestinal bleeding (UGIB) who are at a high risk of hemodynamic instability. We developed an algorithm that predicts adverse events in patients with initially stable non-variceal UGIB using machine learning (ML). Using prospective observational registry, 1439 out of 3363 consecutive patients were enrolled. Primary outcomes included adverse events such as mortality, hypotension, and rebleeding within 7 days. Four machine learning algorithms, namely, logistic regression with regularization (LR), random forest classifier (RF), gradient boosting classifier (GB), and voting classifier (VC), were compared with the Glasgow–Blatchford score (GBS) and Rockall scores. The RF model showed the highest accuracies and significant improvement over conventional methods for predicting mortality (area under the curve: RF 0.917 vs. GBS 0.710), but the performance of the VC model was best in hypotension (VC 0.757 vs. GBS 0.668) and rebleeding within 7 days (VC 0.733 vs. GBS 0.694). Clinically significant variables including blood urea nitrogen, albumin, hemoglobin, platelet, prothrombin time, age, and lactate were identified by the global feature importance analysis. These results suggest that ML models will be useful early predictive tools for identifying high-risk patients with initially stable non-variceal UGIB admitted at an emergency department.

scholarly journals Predicting mortality in hemodialysis patients using machine learning analysis

2020 ◽  
Author(s):  
Victoria Garcia-Montemayor ◽  
Alejandro Martin-Malo ◽  
Carlo Barbieri ◽  
Francesco Bellocchio ◽  
Sagrario Soriano ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Random Forest ◽  
Prediction Models ◽  
Initial Period ◽  
Area Under The Curve ◽  
Mortality Prediction ◽  
Machine Learning Techniques ◽  
Prediction Of Mortality ◽  
Mortality Prediction Models

Abstract Background Besides the classic logistic regression analysis, non-parametric methods based on machine learning techniques such as random forest are presently used to generate predictive models. The aim of this study was to evaluate random forest mortality prediction models in haemodialysis patients. Methods Data were acquired from incident haemodialysis patients between 1995 and 2015. Prediction of mortality at 6 months, 1 year and 2 years of haemodialysis was calculated using random forest and the accuracy was compared with logistic regression. Baseline data were constructed with the information obtained during the initial period of regular haemodialysis. Aiming to increase accuracy concerning baseline information of each patient, the period of time used to collect data was set at 30, 60 and 90 days after the first haemodialysis session. Results There were 1571 incident haemodialysis patients included. The mean age was 62.3 years and the average Charlson comorbidity index was 5.99. The mortality prediction models obtained by random forest appear to be adequate in terms of accuracy [area under the curve (AUC) 0.68–0.73] and superior to logistic regression models (ΔAUC 0.007–0.046). Results indicate that both random forest and logistic regression develop mortality prediction models using different variables. Conclusions Random forest is an adequate method, and superior to logistic regression, to generate mortality prediction models in haemodialysis patients.

Sign in / Sign up

Export Citation Format

Share Document