Recently, increasing attention has been drawn to training semantic segmentation models using synthetic data and computer-generated annotation. However, domain gap remains a major barrier and prevents models learned from synthetic data from generalizing well to real-world applications. In this work, we take the advantage of additional geometric information from synthetic data, a powerful yet largely neglected cue, to bridge the domain gap. Such geometric information can be generated easily from synthetic data, and is proven to be closely coupled with semantic information. With the geometric information, we propose a model to reduce domain shift on two levels: on the input level, we augment the traditional image translation network with the additional geometric information to translate synthetic images into realistic styles; on the output level, we build a task network which simultaneously performs depth estimation and semantic segmentation on the synthetic data. Meanwhile, we encourage the network to preserve the correlation between depth and semantics by adversarial training on the output space. We then validate our method on two pairs of synthetic to real dataset: Virtual KITTI→KITTI, and SYNTHIA→Cityscapes, where we achieve a significant performance gain compared to the non-adaptive baseline and methods without using geometric information. This demonstrates the usefulness of geometric information from synthetic data for cross-domain semantic segmentation.

Lesion detection in brain Magnetic Resonance Images (MRI) remains a challenging task. State-of-the-art approaches are mostly based on supervised learning making use of large annotated datasets. Human beings, on the other hand, even nonexperts, can detect most abnormal lesions after seeing a handful of healthy brain images. Replicating this capability of using prior information on the appearance of healthy brain structure to detect lesions can help computers achieve human level abnormality detection, specifically reducing the need for numerous labeled examples and bettering generalization of previously unseen lesions. To this end, we study detection of lesion regions in an unsupervised manner by learning data distribution of brain MRI of healthy subjects using auto-encoder based methods. We hypothesize that one of the main limitations of the current models is the lack of consistency in latent representation. We propose a simple yet effective constraint that helps mapping of an image bearing lesion close to its corresponding healthy image in the latent space. We use the Human Connectome Project dataset to learn distribution of healthy-appearing brain MRI and report improved detection, in terms of AUC, of the lesions in the BRATS challenge dataset.

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Probabilistic modelling has been an essential tool in medical image analysis, especially for analyzing brain Magnetic Resonance Images (MRI). Recent deep learning techniques for estimating highdimensional distributions, in particular Variational Autoencoders (VAEs), opened up new avenues for probabilistic modeling. Modelling of volumetric data has remained a challenge, however, because constraints on available computation and training data make it difficult effectively leverage VAEs, which are well-developed for 2D images. We propose a method to model 3D MR brain volumes distribution by combining a 2D slice VAE with a Gaussian model that captures the relationships between slices. We do so by estimating the sample mean and covariance in the latent space of the 2D model over the slice direction. This combined model lets us sample new coherent stacks of latent variables to decode into slices of a volume. We also introduce a novel evaluation method for generated volumes that quantifies how well their segmentations match those of true brain anatomy. We demonstrate that our proposed model is competitive in generating high quality volumes at high resolutions according to both traditional metrics and our proposed evaluation. 1

Recent advances in deep learning led to novel generative modeling techniques that achieve unprecedented quality in generated samples and performance in learning complex distributions in imaging data. These new models in medical image computing have important applications that form clinically relevant and very challenging unsupervised learning problems. In this paper, we explore the feasibility of using state-of-the-art auto-encoder-based deep generative models, such as variational and adversarial auto-encoders, for one such task: abnormality detection in medical imaging. We utilize typical, publicly available datasets with brain scans from healthy subjects and patients with stroke lesions and brain tumors. We use the data from healthy subjects to train different auto-encoder based models to learn the distribution of healthy images and detect pathologies as outliers. Models that can better learn the data distribution should be able to detect outliers more accurately. We evaluate the detection performance of deep generative models and compare them with non-deep learning based approaches to provide a benchmark of the current state of research. We conclude that abnormality detection is a challenging task for deep generative models and large room exists for improvement. In order to facilitate further research, we aim to provide carefully pre-processed imaging data available to the research community.