Many real-world vision problems suffer from inherent ambiguities. In clinical applications for example, it might not be clear from a CT scan alone which particular region is cancer tissue. Therefore a group of graders typically produces a set of diverse but plausible segmentations.

Neural Information Processing Systems http://nips.cc/

Climate models are limited by heavy computational costs, often producing outputs at coarse spatial resolutions, while many climate change impact studies require finer scales. Statistical downscaling bridges this gap, and we adapt the probabilistic U-Net for this task, combining a deterministic U-Net backbone with a variational latent space to capture aleatoric uncertainty. We evaluate four training objectives, afCRPS and WMSE-MS-SSIM with three settings for downscaling precipitation and temperature from $16\times$ coarser resolution. Our main finding is that WMSE-MS-SSIM performs well for extremes under certain settings, whereas afCRPS better captures spatial variability across scales.

Post rebuttal: Authors have responded well to the issues raised, and I champion publication of this work. Main idea: Use a conditional variational auto-encoder to produce well-calibrated segmentation hypotheses for a given input. Strengths: The application is well motivated and experiments are convincing and state of the art. Possibly in response, the manuscript is a little vague in its positioning relative to prior work. While relevant prior work is cited, the reader is left with some ambiguity and, if not familiar with this prior work, might be misled to think that there is methodological innovation beyond the specifics of architecture and application.

In the domain of medical imaging, many supervised learning based methods for segmentation face several challenges such as high variability in annotations from multiple experts, paucity of labelled data and class imbalanced datasets. These issues may result in segmentations that lack the requisite precision for clinical analysis and can be misleadingly overconfident without associated uncertainty quantification. We propose the PULASki for biomedical image segmentation that accurately captures variability in expert annotations, even in small datasets. Our approach makes use of an improved loss function based on statistical distances in a conditional variational autoencoder structure (Probabilistic UNet), which improves learning of the conditional decoder compared to the standard cross-entropy particularly in class imbalanced problems. We analyse our method for two structurally different segmentation tasks (intracranial vessel and multiple sclerosis (MS) lesion) and compare our results to four well-established baselines in terms of quantitative metrics and qualitative output. Empirical results demonstrate the PULASKi method outperforms all baselines at the 5\% significance level. The generated segmentations are shown to be much more anatomically plausible than in the 2D case, particularly for the vessel task. Our method can also be applied to a wide range of multi-label segmentation tasks and and is useful for downstream tasks such as hemodynamic modelling (computational fluid dynamics and data assimilation), clinical decision making, and treatment planning.

Uncertainty quantification in medical images has become an essential addition to segmentation models for practical application in the real world. Although there are valuable developments in accurate uncertainty quantification methods using 2D images and slices of 3D volumes, in clinical practice, the complete 3D volumes (such as CT and MRI scans) are used to evaluate and plan the medical procedure. As a result, the existing 2D methods miss the rich 3D spatial information when resolving the uncertainty. A popular approach for quantifying the ambiguity in the data is to learn a distribution over the possible hypotheses. In recent work, this ambiguity has been modeled to be strictly Gaussian. Normalizing Flows (NFs) are capable of modelling more complex distributions and thus, better fit the embedding space of the data. To this end, we have developed a 3D probabilistic segmentation framework augmented with NFs, to enable capturing the distributions of various complexity. To test the proposed approach, we evaluate the model on the LIDC-IDRI dataset for lung nodule segmentation and quantify the aleatoric uncertainty introduced by the multi-annotator setting and inherent ambiguity in the CT data. Following this approach, we are the first to present a 3D Squared Generalized Energy Distance (GED) of 0.401 and a high 0.468 Hungarian-matched 3D IoU. The obtained results reveal the value in capturing the 3D uncertainty, using a flexible posterior distribution augmented with a Normalizing Flow. Finally, we present the aleatoric uncertainty in a visual manner with the aim to provide clinicians with additional insight into data ambiguity and facilitating more informed decision-making.

We propose the Generalized Probabilistic U-Net, which extends the Probabilistic U-Net by allowing more general forms of the Gaussian distribution as the latent space distribution that can better approximate the uncertainty in the reference segmentations. We study the effect the choice of latent space distribution has on capturing the variation in the reference segmentations for lung tumors and white matter hyperintensities in the brain. We show that the choice of distribution affects the sample diversity of the predictions and their overlap with respect to the reference segmentations.

We propose the Generalized Probabilistic U-Net, which extends the Probabilistic U-Net by allowing more general forms of the Gaussian distribution as the latent space distribution that can better approximate the uncertainty in the reference segmentations. We study the effect the choice of latent space distribution has on capturing the uncertainty in the reference segmentations using the LIDC-IDRI dataset. We show that the choice of distribution affects the sample diversity of the predictions and their overlap with respect to the reference segmentations. For the LIDC-IDRI dataset, we show that using a mixture of Gaussians results in a statistically significant improvement in the generalized energy distance (GED) metric with respect to the standard Probabilistic U-Net. We have made our implementation available at https://github.com/ishaanb92/GeneralizedProbabilisticUNet

Many important problems in the real world don't have unique solutions. It is thus important for machine learning models to be capable of proposing different plausible solutions with meaningful probability measures. In this work we introduce such a deep learning framework that learns the one-to-many mappings between the inputs and outputs, together with faithful uncertainty measures. We call our framework {\it modal uncertainty estimation} since we model the one-to-many mappings to be generated through a set of discrete latent variables, each representing a latent mode hypothesis that explains the corresponding type of input-output relationship. The discrete nature of the latent representations thus allows us to estimate for any input the conditional probability distribution of the outputs very effectively. Both the discrete latent space and its uncertainty estimation are jointly learned during training. We motivate our use of discrete latent space through the multi-modal posterior collapse problem in current conditional generative models, then develop the theoretical background, and extensively validate our method on both synthetic and realistic tasks. Our framework demonstrates significantly more accurate uncertainty estimation than the current state-of-the-art methods, and is informative and convenient for practical use.

Many real-world vision problems suffer from inherent ambiguities. In clinical applications for example, it might not be clear from a CT scan alone which particular region is cancer tissue. Therefore a group of graders typically produces a set of diverse but plausible segmentations. We consider the task of learning a distribution over segmentations given an input. To this end we propose a generative segmentation model based on a combination of a U-Net with a conditional variational autoencoder that is capable of efficiently producing an unlimited number of plausible hypotheses.