Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation

We consider the problem of segmenting a biomedical image into anatomical regions of interest. We specifically address the frequent scenario where we have no paired training data that contains images and their manual segmentations. Instead, we employ unpaired segmentation images to build an anatomical prior. Critically these segmentations can be derived from imaging data from a different dataset and imaging modality than the current task. We introduce a generative probabilistic model that employs the learned prior through a convolutional neural network to compute segmentations in an unsupervised setting. We conducted an empirical analysis of the proposed approach in the context of structural brain MRI segmentation, using a multi-study dataset of more than 14,000 scans. Our results show that an anatomical prior can enable fast unsupervised segmentation which is typically not possible using standard convolutional networks. The integration of anatomical priors can facilitate CNN-based anatomical segmentation in a range of novel clinical problems, where few or no annotations are available and thus standard networks are not trainable. The code is freely available at http://github.com/adalca/neuron.Comment: Presented at CVPR 2018. IEEE CVPR proceedings pp. 9290-929

An Inhomogeneous Bayesian Texture Model for Spatially Varying Parameter Estimation

In statistical model based texture feature extraction, features based on spatially varying parameters achievehigher discriminative performances compared to spatially constant parameters. In this paper we formulate anovel Bayesian framework which achieves texture characterization by spatially varying parameters based onGaussian Markov random fields. The parameter estimation is carried out by Metropolis-Hastings algorithm.The distributions of estimated spatially varying parameters are then used as successful discriminant texturefeatures in classification and segmentation. Results show that novel features outperform traditional GaussianMarkov random field texture features which use spatially constant parameters. These features capture bothpixel spatial dependencies and structural properties of a texture giving improved texture features for effectivetexture classification and segmentation

Learning Human Pose Estimation Features with Convolutional Networks

This paper introduces a new architecture for human pose estimation using a multi- layer convolutional network architecture and a modified learning technique that learns low-level features and higher-level weak spatial models. Unconstrained human pose estimation is one of the hardest problems in computer vision, and our new architecture and learning schema shows significant improvement over the current state-of-the-art results. The main contribution of this paper is showing, for the first time, that a specific variation of deep learning is able to outperform all existing traditional architectures on this task. The paper also discusses several lessons learned while researching alternatives, most notably, that it is possible to learn strong low-level feature detectors on features that might even just cover a few pixels in the image. Higher-level spatial models improve somewhat the overall result, but to a much lesser extent then expected. Many researchers previously argued that the kinematic structure and top-down information is crucial for this domain, but with our purely bottom up, and weak spatial model, we could improve other more complicated architectures that currently produce the best results. This mirrors what many other researchers, like those in the speech recognition, object recognition, and other domains have experienced

Bayesian orthogonal component analysis for sparse representation

This paper addresses the problem of identifying a lower dimensional space where observed data can be sparsely represented. This under-complete dictionary learning task can be formulated as a blind separation problem of sparse sources linearly mixed with an unknown orthogonal mixing matrix. This issue is formulated in a Bayesian framework. First, the unknown sparse sources are modeled as Bernoulli-Gaussian processes. To promote sparsity, a weighted mixture of an atom at zero and a Gaussian distribution is proposed as prior distribution for the unobserved sources. A non-informative prior distribution defined on an appropriate Stiefel manifold is elected for the mixing matrix. The Bayesian inference on the unknown parameters is conducted using a Markov chain Monte Carlo (MCMC) method. A partially collapsed Gibbs sampler is designed to generate samples asymptotically distributed according to the joint posterior distribution of the unknown model parameters and hyperparameters. These samples are then used to approximate the joint maximum a posteriori estimator of the sources and mixing matrix. Simulations conducted on synthetic data are reported to illustrate the performance of the method for recovering sparse representations. An application to sparse coding on under-complete dictionary is finally investigated.Comment: Revised version. Accepted to IEEE Trans. Signal Processin