4 research outputs found
Uncertainty quantification in medical image segmentation with normalizing flows
Medical image segmentation is inherently an ambiguous task due to factors
such as partial volumes and variations in anatomical definitions. While in most
cases the segmentation uncertainty is around the border of structures of
interest, there can also be considerable inter-rater differences. The class of
conditional variational autoencoders (cVAE) offers a principled approach to
inferring distributions over plausible segmentations that are conditioned on
input images. Segmentation uncertainty estimated from samples of such
distributions can be more informative than using pixel level probability
scores. In this work, we propose a novel conditional generative model that is
based on conditional Normalizing Flow (cFlow). The basic idea is to increase
the expressivity of the cVAE by introducing a cFlow transformation step after
the encoder. This yields improved approximations of the latent posterior
distribution, allowing the model to capture richer segmentation variations.
With this we show that the quality and diversity of samples obtained from our
conditional generative model is enhanced. Performance of our model, which we
call cFlow Net, is evaluated on two medical imaging datasets demonstrating
substantial improvements in both qualitative and quantitative measures when
compared to a recent cVAE based model.Comment: 12 pages. Accepted to be presented at 11th International Workshop on
Machine Learning in Medical Imaging. Source code will be updated at
https://github.com/raghavian/cFlo
SoftSeg: Advantages of soft versus binary training for image segmentation
Most image segmentation algorithms are trained on binary masks formulated as
a classification task per pixel. However, in applications such as medical
imaging, this "black-and-white" approach is too constraining because the
contrast between two tissues is often ill-defined, i.e., the voxels located on
objects' edges contain a mixture of tissues. Consequently, assigning a single
"hard" label can result in a detrimental approximation. Instead, a soft
prediction containing non-binary values would overcome that limitation. We
introduce SoftSeg, a deep learning training approach that takes advantage of
soft ground truth labels, and is not bound to binary predictions. SoftSeg aims
at solving a regression instead of a classification problem. This is achieved
by using (i) no binarization after preprocessing and data augmentation, (ii) a
normalized ReLU final activation layer (instead of sigmoid), and (iii) a
regression loss function (instead of the traditional Dice loss). We assess the
impact of these three features on three open-source MRI segmentation datasets
from the spinal cord gray matter, the multiple sclerosis brain lesion, and the
multimodal brain tumor segmentation challenges. Across multiple
cross-validation iterations, SoftSeg outperformed the conventional approach,
leading to an increase in Dice score of 2.0% on the gray matter dataset
(p=0.001), 3.3% for the MS lesions, and 6.5% for the brain tumors. SoftSeg
produces consistent soft predictions at tissues' interfaces and shows an
increased sensitivity for small objects. The richness of soft labels could
represent the inter-expert variability, the partial volume effect, and
complement the model uncertainty estimation. The developed training pipeline
can easily be incorporated into most of the existing deep learning
architectures. It is already implemented in the freely-available deep learning
toolbox ivadomed (https://ivadomed.org)