Ensembling Unets for Rare Chromosomal Aberration Detection in Metaphase Images, Uncertainty Quantification, and...

In biological dosimetry a radiation dose is estimated using the average number of chromosomal aberrations per peripheral blood lymphocytes. This analysis is still manually performed on 2D metaphase images depicting the 23 pairs of chromosomes because the false discovery rate of current automated detection systems is too high and variable because of sensitivity to small variations in image quality (chromosome spread, illumination variations …). Therefore, the current systems are only used to assist human experts. Designing more performant automatic and reliable chromosomal aberration detection systems has become of paramount importance to improve diagnosis speed and reduce human expertise time. Here, we propose a novel deep-learning method for automatic rare chromosomal aberration detection and uncertainty quantification. We formulate the problem as a unique regression problem requiring the minimization of a sparsity-promoting loss to reduce the false alarm rate. Furthermore, we select checkpoints at the end of each epoch during training to form a model ensemble. The resulting artificial experts are further analyzed to derive a consensus voting, similar to an agreement of human annotator rating, to provide trustworthy aberration detections and confidence intervals. A radiation dose curve is finally derived from deep learning-assisted counting of dicentrics and fragments in metaphase images, in high agreement with the reference hand-crafted curve in biological dosimetry with a promising dose estimation validation.