Unsupervised Lesion Detection via Image Restoration with a Normative Prior

Unsupervised lesion detection is a challenging problem that requires accurately estimating normative distributions of healthy anatomy and detecting lesions as outliers without training examples. Recently, this problem has received increased attention from the research community following the advances in unsupervised learning with deep learning. Such advances allow the estimation of high-dimensional distributions, such as normative distributions, with higher accuracy than previous methods.The main approach of the recently proposed methods is to learn a latent-variable model parameterized with networks to approximate the normative distribution using example images showing healthy anatomy, perform prior-projection, i.e. reconstruct the image with lesions using the latent-variable model, and determine lesions based on the differences between the reconstructed and original images. While being promising, the prior-projection step often leads to a large number of false positives. In this work, we approach unsupervised lesion detection as an image restoration problem and propose a probabilistic model that uses a network-based prior as the normative distribution and detect lesions pixel-wise using MAP estimation. The probabilistic model punishes large deviations between restored and original images, reducing false positives in pixel-wise detections. Experiments with gliomas and stroke lesions in brain MRI using publicly available datasets show that the proposed approach outperforms the state-of-the-art unsupervised methods by a substantial margin, +0.13 (AUC), for both glioma and stroke detection. Extensive model analysis confirms the effectiveness of MAP-based image restoration.Comment: Extended version of 'Unsupervised Lesion Detection via Image Restoration with a Normative Prior' (MIDL2019

Semantic labeling of places using information extracted from laser and vision sensor data

Indoor environments can typically be divided into places with different functionalities like corridors, kitchens, offices, or seminar rooms. The ability to learn such semantic categories from sensor data enables a mobile robot to extend the representation of the environment facilitating the interaction withhumans. As an example, natural language terms like corridor or room can be used to communicate the position of the robot in a map in a more intuitive way. In this work, we firrst propose an approach based on supervised learning to classify the pose of a mobile robot into semantic classes. Our method uses AdaBoost to boost simple features extracted from range data and vision into a strong classifier. We present two main applications of this approach. Firstly, we show how our approach can be utilized by a moving robot for an online classification of the poses traversed along its path using a hidden Markov model. Secondly, we introduce an approach to learn topological maps from geometric maps by applying our semantic classification procedure in combination with a probabilistic relaxation procedure. We finally show how to apply associative Markov networks (AMNs) together with AdaBoost for classifying complete geometric maps. Experimental results obtained in simulation and with real robots demonstrate the effectiveness of our approach in various indoor environments

Graph Refinement based Airway Extraction using Mean-Field Networks and Graph Neural Networks

Graph refinement, or the task of obtaining subgraphs of interest from over-complete graphs, can have many varied applications. In this work, we extract trees or collection of sub-trees from image data by, first deriving a graph-based representation of the volumetric data and then, posing the tree extraction as a graph refinement task. We present two methods to perform graph refinement. First, we use mean-field approximation (MFA) to approximate the posterior density over the subgraphs from which the optimal subgraph of interest can be estimated. Mean field networks (MFNs) are used for inference based on the interpretation that iterations of MFA can be seen as feed-forward operations in a neural network. This allows us to learn the model parameters using gradient descent. Second, we present a supervised learning approach using graph neural networks (GNNs) which can be seen as generalisations of MFNs. Subgraphs are obtained by training a GNN-based graph refinement model to directly predict edge probabilities. We discuss connections between the two classes of methods and compare them for the task of extracting airways from 3D, low-dose, chest CT data. We show that both the MFN and GNN models show significant improvement when compared to one baseline method, that is similar to a top performing method in the EXACT'09 Challenge, and a 3D U-Net based airway segmentation model, in detecting more branches with fewer false positives.Comment: Accepted for publication at Medical Image Analysis. 14 page

Unsupervised robust nonparametric learning of hidden community properties

We consider learning of fundamental properties of communities in large noisy networks, in the prototypical situation where the nodes or users are split into two classes according to a binary property, e.g., according to their opinions or preferences on a topic. For learning these properties, we propose a nonparametric, unsupervised, and scalable graph scan procedure that is, in addition, robust against a class of powerful adversaries. In our setup, one of the communities can fall under the influence of a knowledgeable adversarial leader, who knows the full network structure, has unlimited computational resources and can completely foresee our planned actions on the network. We prove strong consistency of our results in this setup with minimal assumptions. In particular, the learning procedure estimates the baseline activity of normal users asymptotically correctly with probability 1; the only assumption being the existence of a single implicit community of asymptotically negligible logarithmic size. We provide experiments on real and synthetic data to illustrate the performance of our method, including examples with adversaries.Comment: Experiments with new types of adversaries adde

Recurrent Saliency Transformation Network: Incorporating Multi-Stage Visual Cues for Small Organ Segmentation

We aim at segmenting small organs (e.g., the pancreas) from abdominal CT scans. As the target often occupies a relatively small region in the input image, deep neural networks can be easily confused by the complex and variable background. To alleviate this, researchers proposed a coarse-to-fine approach, which used prediction from the first (coarse) stage to indicate a smaller input region for the second (fine) stage. Despite its effectiveness, this algorithm dealt with two stages individually, which lacked optimizing a global energy function, and limited its ability to incorporate multi-stage visual cues. Missing contextual information led to unsatisfying convergence in iterations, and that the fine stage sometimes produced even lower segmentation accuracy than the coarse stage. This paper presents a Recurrent Saliency Transformation Network. The key innovation is a saliency transformation module, which repeatedly converts the segmentation probability map from the previous iteration as spatial weights and applies these weights to the current iteration. This brings us two-fold benefits. In training, it allows joint optimization over the deep networks dealing with different input scales. In testing, it propagates multi-stage visual information throughout iterations to improve segmentation accuracy. Experiments in the NIH pancreas segmentation dataset demonstrate the state-of-the-art accuracy, which outperforms the previous best by an average of over 2%. Much higher accuracies are also reported on several small organs in a larger dataset collected by ourselves. In addition, our approach enjoys better convergence properties, making it more efficient and reliable in practice.Comment: Accepted to CVPR 2018 (10 pages, 6 figures