Predicting Genetic Mutations from Single-Cell Bone Marrow Images in Acute Myeloid Leukemia Using Noise-Robust Deep Learning Models

TL;DR

This paper introduces a noise-robust deep learning approach for identifying leukemic cells and predicting genetic mutations from single-cell bone marrow images in AML, demonstrating high accuracy despite label noise.

Contribution

It presents a novel methodology that effectively handles label noise in single-cell image classification and mutation prediction for AML diagnostics.

Findings

Binary classifier achieved 90% accuracy in identifying leukemic cells.

Mutation classification model reached 85% accuracy despite label noise.

Model validated by haemato-pathologists with an approximate 20% error rate.

Abstract

In this study, we propose a robust methodology for identification of myeloid blasts followed by prediction of genetic mutation in single-cell images of blasts, tackling challenges associated with label accuracy and data noise. We trained an initial binary classifier to distinguish between leukemic (blasts) and non-leukemic cells images, achieving 90 percent accuracy. To evaluate the models generalization, we applied this model to a separate large unlabeled dataset and validated the predictions with two haemato-pathologists, finding an approximate error rate of 20 percent in the leukemic and non-leukemic labels. Assuming this level of label noise, we further trained a four-class model on images predicted as blasts to classify specific mutations. The mutation labels were known for only a bag of cell images extracted from a single slide. Despite the tumor label noise, our mutation classification model achieved 85 percent accuracy across four mutation classes, demonstrating resilience to label inconsistencies. This study highlights the capability of machine learning models to work with noisy labels effectively while providing accurate, clinically relevant mutation predictions, which is promising for diagnostic applications in areas such as haemato-pathology.