Reliability-based cleaning of noisy training labels with inductive
  conformal prediction in multi-modal biomedical data mining
Xianghao Zhan Qinmei Xu Yuanning Zheng Guangming Lu Olivier Gevaert
Accurately labeling biomedical data presents a challenge. Traditional
semi-supervised learning methods often under-utilize available unlabeled data.
To address this, we propose a novel reliability-based training data cleaning
method employing inductive conformal prediction (ICP). This method capitalizes
on a small set of accurately labeled training data and leverages ICP-calculated
reliability metrics to rectify mislabeled data and outliers within vast
quantities of noisy training data. The efficacy of the method is validated
across three classification tasks within distinct modalities: filtering
drug-induced-liver-injury (DILI) literature with title and abstract, predicting
ICU admission of COVID-19 patients through CT radiomics and electronic health
records, and subtyping breast cancer using RNA-sequencing data. Varying levels
of noise to the training labels were introduced through label permutation.
Results show significant enhancements in classification performance: accuracy
enhancement in 86 out of 96 DILI experiments (up to 11.4%), AUROC and AUPRC
enhancements in all 48 COVID-19 experiments (up to 23.8% and 69.8%), and
accuracy and macro-average F1 score improvements in 47 out of 48 RNA-sequencing
experiments (up to 74.6% and 89.0%). Our method offers the potential to
substantially boost classification performance in multi-modal biomedical
machine learning tasks. Importantly, it accomplishes this without necessitating
an excessive volume of meticulously curated training data.