Emerging Semantic Segmentation from Positive and Negative Coarse Label Learning

Large annotated datasets are vital for training segmentation models, but pixel-level labeling is time-consuming, error-prone, and often requires scarce expert annotators, especially in medical imaging. In contrast, coarse annotations are quicker, cheaper, and easier to produce, even by non-experts. In this paper, we propose to use coarse drawings from both positive (target) and negative (background) classes in the image, even with noisy pixels, to train a convolutional neural network (CNN) for semantic segmentation. We present a method for learning the true segmentation label distributions from purely noisy coarse annotations using two coupled CNNs. The separation of the two CNNs is achieved by high fidelity with the characters of the noisy training annotations. We propose to add a complementary label learning that encourages estimating negative label distribution. To illustrate the properties of our method, we first use a toy segmentation dataset based on MNIST. We then present the quantitative results of experiments using publicly available datasets: Cityscapes dataset for multi-class segmentation, and retinal images for medical applications. In all experiments, our method outperforms state-of-the-art methods, particularly in the cases where the ratio of coarse annotations is small compared to the given dense annotations.

An Algorithm for Learning Shape and Appearance Models without Annotations

This paper presents a framework for automatically learning shape and appearance models for medical (and certain other) images. It is based on the idea that having a more accurate shape and appearance model leads to more accurate image registration, which in turn leads to a more accurate shape and appearance model. This leads naturally to an iterative scheme, which is based on a probabilistic generative model that is fit using Gauss-Newton updates within an EM-like framework. It was developed with the aim of enabling distributed privacy-preserving analysis of brain image data, such that shared information (shape and appearance basis functions) may be passed across sites, whereas latent variables that encode individual images remain secure within each site. These latent variables are proposed as features for privacy-preserving data mining applications. The approach is demonstrated qualitatively on the KDEF dataset of 2D face images, showing that it can align images that traditionally require shape and appearance models trained using manually annotated data (manually defined landmarks etc.). It is applied to MNIST dataset of handwritten digits to show its potential for machine learning applications, particularly when training data is limited. The model is able to handle ``missing data'', which allows it to be cross-validated according to how well it can predict left-out voxels. The suitability of the derived features for classifying individuals into patient groups was assessed by applying it to a dataset of over 1,900 segmented T1-weighted MR images, which included images from the COBRE and ABIDE datasets.

Diffeomorphic brain shape modelling using Gauss-Newton optimisation

Shape modelling describes methods aimed at capturing the natural variability of shapes and commonly relies on probabilistic interpretations of dimensionality reduction techniques such as principal component analysis. Due to their computational complexity when dealing with dense deformation models such as diffeomorphisms, previous attempts have focused on explicitly reducing their dimension, diminishing de facto their flexibility and ability to model complex shapes such as brains. In this paper, we present a generative model of shape that allows the covariance structure of deformations to be captured without squashing their domain, resulting in better normalisation. An efficient inference scheme based on Gauss-Newton optimisation is used, which enables processing of 3D neuroimaging data. We trained this algorithm on segmented brains from the OASIS database, generating physiologically meaningful deformation trajectories. To prove the model's robustness, we applied it to unseen data, which resulted in equivalent fitting scores.