Edmund H Wilkes 1 , Erin Emmett 2 , Luisa Beltran 2 , Gary M Woodward 3 , Rachel S Carling 2,4 Show Affiliations »
Abstract
BACKGROUND: Plasma amino acid (PAA) profiles are used in routine clinical practice for the diagnosis and monitoring of inherited disorders of amino acid metabolism, organic acidemias, and urea cycle defects. Interpretation of PAA profiles is complex and requires substantial training and expertise to perform. Given previous demonstrations of the ability of machine learning (ML) algorithms to interpret complex clinical biochemistry data, we sought to determine if ML-derived classifiers could interpret PAA profiles with high predictive performance. METHODS: We collected PAA profiling data routinely performed within a clinical biochemistry laboratory (2084 profiles) and developed decision support classifiers with several ML algorithms. We tested the generalization performance of each classifier using a nested cross-validation (CV) procedure and examined the effect of various subsampling, feature selection, and ensemble learning strategies. RESULTS: The classifiers demonstrated excellent predictive performance, with the 3 ML algorithms tested producing comparable results. The best-performing ensemble binary classifier achieved a mean precision-recall (PR) AUC of 0.957 (95% CI 0.952, 0.962) and the best-performing ensemble multiclass classifier achieved a mean F4 score of 0.788 (0.773, 0.803). CONCLUSIONS: This work builds upon previous demonstrations of the utility of ML-derived decision support tools in clinical biochemistry laboratories. Our findings suggest that, pending additional validation studies, such tools could potentially be used in routine clinical practice to streamline and aid the interpretation of PAA profiles. This would be particularly useful in laboratories with limited resources and large workloads. We provide the necessary code for other laboratories to develop their own decision support tools. © American Association for Clinical Chemistry 2020. All rights reserved. For permissions, please email: journals.permissions@oup.com.
BACKGROUND: Plasma amino acid (PAA) profiles are used in routine clinical practice for the diagnosis and monitoring of inherited disorders of amino acid metabolism , organic acidemias, and urea cycle defects. Interpretation of PAA profiles is complex and requires substantial training and expertise to perform. Given previous demonstrations of the ability of machine learning (ML) algorithms to interpret complex clinical biochemistry data, we sought to determine if ML-derived classifiers could interpret PAA profiles with high predictive performance. METHODS: We collected PAA profiling data routinely performed within a clinical biochemistry laboratory (2084 profiles) and developed decision support classifiers with several ML algorithms . We tested the generalization performance of each classifier using a nested cross-validation (CV) procedure and examined the effect of various subsampling, feature selection, and ensemble learning strategies. RESULTS: The classifiers demonstrated excellent predictive performance, with the 3 ML algorithms tested producing comparable results. The best-performing ensemble binary classifier achieved a mean precision-recall (PR) AUC of 0.957 (95% CI 0.952, 0.962) and the best-performing ensemble multiclass classifier achieved a mean F4 score of 0.788 (0.773, 0.803). CONCLUSIONS: This work builds upon previous demonstrations of the utility of ML-derived decision support tools in clinical biochemistry laboratories. Our findings suggest that, pending additional validation studies, such tools could potentially be used in routine clinical practice to streamline and aid the interpretation of PAA profiles. This would be particularly useful in laboratories with limited resources and large workloads. We provide the necessary code for other laboratories to develop their own decision support tools. © American Association for Clinical Chemistry 2020. All rights reserved. For permissions, please email: journals.permissions@oup.com.
Entities: Chemical
Disease
Keywords:
Machine learning; inherited metabolic disease; plasma amino acids
Year: 2020
PMID： 32870990 DOI： 10.1093/clinchem/hvaa134
Source DB: PubMed Journal: Clin Chem ISSN： 0009-9147 Impact factor: 8.327