Active label cleaning for improved dataset quality under resource constraints

Mélanie Bernhardt, Daniel C Castro, Ryutaro Tanno, Anton Schwaighofer, Kerem C Tezcan, Miguel Monteiro, Shruthi Bannur, Matthew P Lungren, Aditya Nori, Ben Glocker, Javier Alvarez-Valle, Ozan Oktay

Published in Nature communications, 2022

[paper] [cite]

Abstract

Imperfections in data annotation, known as label noise, are detrimental to the training of machine learning models and have a confounding effect on the assessment of model performance. Nevertheless, employing experts to remove label noise by fully re-annotating large datasets is infeasible in resource-constrained settings, such as healthcare. This work advocates for a data-driven approach to prioritising samples for re-annotation—which we term “active label cleaning”. We propose to rank instances according to estimated label correctness and labelling difficulty of each sample, and introduce a simulation framework to evaluate relabelling efficacy. Our experiments on natural images and on a specifically-devised medical imaging benchmark show that cleaning noisy labels mitigates their negative impact on model training, evaluation, and selection. Crucially, the proposed approach enables correcting labels up to 4 × more effectively than typical random selection in realistic conditions, making better use of experts’ valuable time for improving dataset quality.