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Optimizing sample size for supervised machine learning with bulk transcriptomic sequencing: a learning curve approach

Y. Qi,Xinyi Wang,L. Qin

Published 2024 in Briefings Bioinform.

ABSTRACT

Abstract Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determining a suitable sample size that ensures adequate classification accuracy without undue resource allocation. Current sample size calculation methods rely on assumptions and algorithms that may not align with supervised machine learning techniques for sample classification. Addressing this critical methodological gap, we present a novel computational approach that establishes the accuracy-versus-sample size relationship by employing a data augmentation strategy followed by fitting a learning curve. We comprehensively evaluated its performance for microRNA and RNA sequencing data, considering diverse data characteristics and algorithm configurations, based on a spectrum of evaluation metrics. To foster accessibility and reproducibility, the Python and R code for implementing our approach is available on GitHub. Its deployment will significantly facilitate the adoption of machine learning in transcriptomics studies and accelerate their translation into clinically useful classifiers for personalized treatment.

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