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Improving the accuracy of medical diagnosis with causal machine learning.

ABSTRACT: Machine learning promises to revolutionize clinical decision making and diagnosis. In medical diagnosis a doctor aims to explain a patient's symptoms by determining the diseases causing them. However, existing machine learning approaches to diagnosis are purely associative, identifying diseases that are strongly correlated with a patients symptoms. We show that this inability to disentangle correlation from causation can result in sub-optimal or dangerous diagnoses. To overcome this, we reformulate diagnosis as a counterfactual inference task and derive counterfactual diagnostic algorithms. We compare our counterfactual algorithms to the standard associative algorithm and 44 doctors using a test set of clinical vignettes. While the associative algorithm achieves an accuracy placing in the top 48% of doctors in our cohort, our counterfactual algorithm places in the top 25% of doctors, achieving expert clinical accuracy. Our results show that causal reasoning is a vital missing ingredient for applying machine learning to medical diagnosis.

SUBMITTER: Richens JG

PROVIDER: S-EPMC7419549 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Improving the accuracy of medical diagnosis with causal machine learning.

Richens Jonathan G JG Lee Ciarán M CM Johri Saurabh S

Nature communications 20200811 1

Machine learning promises to revolutionize clinical decision making and diagnosis. In medical diagnosis a doctor aims to explain a patient's symptoms by determining the diseases causing them. However, existing machine learning approaches to diagnosis are purely associative, identifying diseases that are strongly correlated with a patients symptoms. We show that this inability to disentangle correlation from causation can result in sub-optimal or dangerous diagnoses. To overcome this, we reformul ...[more]

PMID: 32782264

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Project description:AimsWe conducted a systematic review assessing the reporting quality of studies validating models based on machine learning (ML) for clinical diagnosis, with a specific focus on the reporting of information concerning the participants on which the diagnostic task was evaluated on.MethodMedline Core Clinical Journals were searched for studies published between July 2015 and July 2018. Two reviewers independently screened the retrieved articles, a third reviewer resolved any discrepancies. An extraction list was developed from the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis guideline. Two reviewers independently extracted the data from the eligible articles. Third and fourth reviewers checked, verified the extracted data as well as resolved any discrepancies between the reviewers.ResultsThe search results yielded 161 papers, of which 28 conformed to the eligibility criteria. Detail of data source was reported in 24 of the 28 papers. For all of the papers, the set of patients on which the ML-based diagnostic system was evaluated was partitioned from a larger dataset, and the method for deriving such set was always reported. Information on the diagnostic/non-diagnostic classification was reported well (23/28). The least reported items were the use of reporting guideline (0/28), distribution of disease severity (8/28 patient flow diagram (10/28) and distribution of alternative diagnosis (10/28). A large proportion of studies (23/28) had a delay between the conduct of the reference standard and ML tests, while one study did not and four studies were unclear. For 15 studies, it was unclear whether the evaluation group corresponded to the setting in which the ML test will be applied to.ConclusionAll studies in this review failed to use reporting guidelines, and a large proportion of them lacked adequate detail on participants, making it difficult to replicate, assess and interpret study findings.Prospero registration numberCRD42018099167.

Project description:ObjectiveTo assess both the feasibility and potential impact of predicting preventable hospital readmissions using causal machine learning applied to data from the implementation of a readmissions prevention intervention (the Transitions Program).Data sourcesElectronic health records maintained by Kaiser Permanente Northern California (KPNC).Study designRetrospective causal forest analysis of postdischarge outcomes among KPNC inpatients. Using data from both before and after implementation, we apply causal forests to estimate individual-level treatment effects of the Transitions Program intervention on 30-day readmission. These estimates are used to characterize treatment effect heterogeneity and to assess the notional impacts of alternative targeting strategies in terms of the number of readmissions prevented.Data collection1 539 285 index hospitalizations meeting the inclusion criteria and occurring between June 2010 and December 2018 at 21 KPNC hospitals.Principal findingsThere appears to be substantial heterogeneity in patients' responses to the intervention (omnibus test for heterogeneity p = 2.23 × 10-7 ), particularly across levels of predicted risk. Notably, predicted treatment effects become more positive as predicted risk increases; patients at somewhat lower risk appear to have the largest predicted effects. Moreover, these estimates appear to be well calibrated, yielding the same estimate of annual readmissions prevented in the actual treatment subgroup (1246, 95% confidence interval [CI] 1110-1381) as did a formal evaluation of the Transitions Program (1210, 95% CI 990-1430). Estimates of the impacts of alternative targeting strategies suggest that as many as 4458 (95% CI 3925-4990) readmissions could be prevented annually, while decreasing the number needed to treat from 33 to 23, by targeting patients with the largest predicted effects rather than those at highest risk.ConclusionsCausal machine learning can be used to identify preventable hospital readmissions, if the requisite interventional data are available. Moreover, our results suggest a mismatch between risk and treatment effects.

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Improving the accuracy of medical diagnosis with causal machine learning.

Publications

Improving the accuracy of medical diagnosis with causal machine learning.

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