Completeness of reporting of clinical prediction models developed using supervised machine learning: A systematic review

ABSTRACTObjectiveWhile many studies have consistently found incomplete reporting of regression-based prediction model studies, evidence is lacking for machine learning-based prediction model studies. We aim to systematically review the adherence of Machine Learning (ML)-based prediction model studies to the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD) Statement.Study design and settingWe included articles reporting on development or external validation of a multivariable prediction model (either diagnostic or prognostic) developed using supervised ML for individualized predictions across all medical fields (PROSPERO, CRD42019161764). We searched PubMed from 1 January 2018 to 31 December 2019. Data extraction was performed using the 22-item checklist for reporting of prediction model studies (www.TRIPOD-statement.org). We measured the overall adherence per article and per TRIPOD item.ResultsOur search identified 24 814 articles, of which 152 articles were included: 94 (61.8%) prognostic and 58 (38.2%) diagnostic prediction model studies. Overall, articles adhered to a median of 38.7% (IQR 31.0-46.4) of TRIPOD items. No articles fully adhered to complete reporting of the abstract and very few reported the flow of participants (3.9%, 95% CI 1.8 to 8.3), appropriate title (4.6%, 95% CI 2.2 to 9.2), blinding of predictors (4.6%, 95% CI 2.2 to 9.2), model specification (5.2%, 95% CI 2.4 to 10.8), and model’s predictive performance (5.9%, 95% CI 3.1 to 10.9). There was often complete reporting of source of data (98.0%, 95% CI 94.4 to 99.3) and interpretation of the results (94.7%, 95% CI 90.0 to 97.3).ConclusionSimilar to prediction model studies developed using conventional regression-based techniques, the completeness of reporting is poor. Essential information to decide to use the model (i.e. model specification and its performance) is rarely reported. However, some items and sub-items of TRIPOD might be less suitable for ML-based prediction model studies and thus, TRIPOD requires extensions. Overall, there is an urgent need to improve the reporting quality and usability of research to avoid research waste.What is new?Key findings: Similar to prediction model studies developed using regression techniques, machine learning (ML)-based prediction model studies adhered poorly to the TRIPOD statement, the current standard reporting guideline.What this adds to what is known? In addition to efforts to improve the completeness of reporting in ML-based prediction model studies, an extension of TRIPOD for these type of studies is needed.What is the implication, what should change now? While TRIPOD-AI is under development, we urge authors to follow the recommendations of the TRIPOD statement to improve the completeness of reporting and reduce potential research waste of ML-based prediction model studies.</jats:sec

Risk of bias assessments in individual participant data meta-analyses of test accuracy and prediction models:a review shows improvements are needed

OBJECTIVES: Risk of bias assessments are important in meta-analyses of both aggregate and individual participant data (IPD). There is limited evidence on whether and how risk of bias of included studies or datasets in IPD meta-analyses (IPDMAs) is assessed. We review how risk of bias is currently assessed, reported, and incorporated in IPDMAs of test accuracy and clinical prediction model studies and provide recommendations for improvement.STUDY DESIGN AND SETTING: We searched PubMed (January 2018-May 2020) to identify IPDMAs of test accuracy and prediction models, then elicited whether each IPDMA assessed risk of bias of included studies and, if so, how assessments were reported and subsequently incorporated into the IPDMAs.RESULTS: Forty-nine IPDMAs were included. Nineteen of 27 (70%) test accuracy IPDMAs assessed risk of bias, compared to 5 of 22 (23%) prediction model IPDMAs. Seventeen of 19 (89%) test accuracy IPDMAs used Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2), but no tool was used consistently among prediction model IPDMAs. Of IPDMAs assessing risk of bias, 7 (37%) test accuracy IPDMAs and 1 (20%) prediction model IPDMA provided details on the information sources (e.g., the original manuscript, IPD, primary investigators) used to inform judgments, and 4 (21%) test accuracy IPDMAs and 1 (20%) prediction model IPDMA provided information or whether assessments were done before or after obtaining the IPD of the included studies or datasets. Of all included IPDMAs, only seven test accuracy IPDMAs (26%) and one prediction model IPDMA (5%) incorporated risk of bias assessments into their meta-analyses. For future IPDMA projects, we provide guidance on how to adapt tools such as Prediction model Risk Of Bias ASsessment Tool (for prediction models) and QUADAS-2 (for test accuracy) to assess risk of bias of included primary studies and their IPD.CONCLUSION: Risk of bias assessments and their reporting need to be improved in IPDMAs of test accuracy and, especially, prediction model studies. Using recommended tools, both before and after IPD are obtained, will address this.</p

Prediction models for diagnosis and prognosis of covid-19: : systematic review and critical appraisal

Readers’ note This article is a living systematic review that will be updated to reflect emerging evidence. Updates may occur for up to two years from the date of original publication. This version is update 3 of the original article published on 7 April 2020 (BMJ 2020;369:m1328). Previous updates can be found as data supplements (https://www.bmj.com/content/369/bmj.m1328/related#datasupp). When citing this paper please consider adding the update number and date of access for clarity. Funding: LW, BVC, LH, and MDV acknowledge specific funding for this work from Internal Funds KU Leuven, KOOR, and the COVID-19 Fund. LW is a postdoctoral fellow of Research Foundation-Flanders (FWO) and receives support from ZonMw (grant 10430012010001). BVC received support from FWO (grant G0B4716N) and Internal Funds KU Leuven (grant C24/15/037). TPAD acknowledges financial support from the Netherlands Organisation for Health Research and Development (grant 91617050). VMTdJ was supported by the European Union Horizon 2020 Research and Innovation Programme under ReCoDID grant agreement 825746. KGMM and JAAD acknowledge financial support from Cochrane Collaboration (SMF 2018). KIES is funded by the National Institute for Health Research (NIHR) School for Primary Care Research. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care. GSC was supported by the NIHR Biomedical Research Centre, Oxford, and Cancer Research UK (programme grant C49297/A27294). JM was supported by the Cancer Research UK (programme grant C49297/A27294). PD was supported by the NIHR Biomedical Research Centre, Oxford. MOH is supported by the National Heart, Lung, and Blood Institute of the United States National Institutes of Health (grant R00 HL141678). ICCvDH and BCTvB received funding from Euregio Meuse-Rhine (grant Covid Data Platform (coDaP) interref EMR187). The funders played no role in study design, data collection, data analysis, data interpretation, or reporting.Peer reviewedPublisher PD

Dementia prediction in the general population using clinically accessible variables: a proof-of-concept study using machine learning. The AGES-Reykjavik study

Abstract Background Early identification of dementia is crucial for prompt intervention for high-risk individuals in the general population. External validation studies on prognostic models for dementia have highlighted the need for updated models. The use of machine learning in dementia prediction is in its infancy and may improve predictive performance. The current study aimed to explore the difference in performance of machine learning algorithms compared to traditional statistical techniques, such as logistic and Cox regression, for prediction of all-cause dementia. Our secondary aim was to assess the feasibility of only using clinically accessible predictors rather than MRI predictors. Methods Data are from 4,793 participants in the population-based AGES-Reykjavik Study without dementia or mild cognitive impairment at baseline (mean age: 76 years, % female: 59%). Cognitive, biometric, and MRI assessments (total: 59 variables) were collected at baseline, with follow-up of incident dementia diagnoses for a maximum of 12 years. Machine learning algorithms included elastic net regression, random forest, support vector machine, and elastic net Cox regression. Traditional statistical methods for comparison were logistic and Cox regression. Model 1 was fit using all variables and model 2 was after feature selection using the Boruta package. A third model explored performance when leaving out neuroimaging markers (clinically accessible model). Ten-fold cross-validation, repeated ten times, was implemented during training. Upsampling was used to account for imbalanced data. Tuning parameters were optimized for recalibration automatically using the caret package in R. Results 19% of participants developed all-cause dementia. Machine learning algorithms were comparable in performance to logistic regression in all three models. However, a slight added performance was observed in the elastic net Cox regression in the third model (c = 0.78, 95% CI: 0.78–0.78) compared to the traditional Cox regression (c = 0.75, 95% CI: 0.74–0.77). Conclusions Supervised machine learning only showed added benefit when using survival techniques. Removing MRI markers did not significantly worsen our model’s performance. Further, we presented the use of a nomogram using machine learning methods, showing transportability for the use of machine learning models in clinical practice. External validation is needed to assess the use of this model in other populations. Identifying high-risk individuals will amplify prevention efforts and selection for clinical trials

Protocol for a systematic review on the methodological and reporting quality of prediction model studies using machine learning techniques

Introduction Studies addressing the development and/or validation of diagnostic and prognostic prediction models are abundant in most clinical domains. Systematic reviews have shown that the methodological and reporting quality of prediction model studies is suboptimal. Due to the increasing availability of larger, routinely collected and complex medical data, and the rising application of Artificial Intelligence (AI) or machine learning (ML) techniques, the number of prediction model studies is expected to increase even further. Prediction models developed using AI or ML techniques are often labelled as a ‘black box’ and little is known about their methodological and reporting quality. Therefore, this comprehensive systematic review aims to evaluate the reporting quality, the methodological conduct, and the risk of bias of prediction model studies that applied ML techniques for model development and/or validation.Methods and analysis A search will be performed in PubMed to identify studies developing and/or validating prediction models using any ML methodology and across all medical fields. Studies will be included if they were published between January 2018 and December 2019, predict patient-related outcomes, use any study design or data source, and available in English. Screening of search results and data extraction from included articles will be performed by two independent reviewers. The primary outcomes of this systematic review are: (1) the adherence of ML-based prediction model studies to the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD), and (2) the risk of bias in such studies as assessed using the Prediction model Risk Of Bias ASsessment Tool (PROBAST). A narrative synthesis will be conducted for all included studies. Findings will be stratified by study type, medical field and prevalent ML methods, and will inform necessary extensions or updates of TRIPOD and PROBAST to better address prediction model studies that used AI or ML techniques.Ethics and dissemination Ethical approval is not required for this study because only available published data will be analysed. Findings will be disseminated through peer-reviewed publications and scientific conferences.Systematic review registration PROSPERO, CRD42019161764