Atlas Based Segmentations via Semi-Supervised Diffeomorphic Registrations

Purpose: Segmentation of organs-at-risk (OARs) is a bottleneck in current radiation oncology pipelines and is often time consuming and labor intensive. In this paper, we propose an atlas-based semi-supervised registration algorithm to generate accurate segmentations of OARs for which there are ground truth contours and rough segmentations of all other OARs in the atlas. To the best of our knowledge, this is the first study to use learning-based registration methods for the segmentation of head and neck patients and demonstrate its utility in clinical applications. Methods: Our algorithm cascades rigid and deformable deformation blocks, and takes on an atlas image (M), set of atlas-space segmentations (S_A), and a patient image (F) as inputs, while outputting patient-space segmentations of all OARs defined on the atlas. We train our model on 475 CT images taken from public archives and Stanford RadOnc Clinic (SROC), validate on 5 CT images from SROC, and test our model on 20 CT images from SROC. Results: Our method outperforms current state of the art learning-based registration algorithms and achieves an overall dice score of 0.789 on our test set. Moreover, our method yields a performance comparable to manual segmentation and supervised segmentation, while solving a much more complex registration problem. Whereas supervised segmentation methods only automate the segmentation process for a select few number of OARs, we demonstrate that our methods can achieve similar performance for OARs of interest, while also providing segmentations for every other OAR on the provided atlas. Conclusions: Our proposed algorithm has significant clinical applications and could help reduce the bottleneck for segmentation of head and neck OARs. Further, our results demonstrate that semi-supervised diffeomorphic registration can be accurately applied to both registration and segmentation problems.

Machine Learning Techniques for Biomedical Image Segmentation: An Overview of Technical Aspects and Introduction to State-of-Art Applications

In recent years, significant progress has been made in developing more accurate and efficient machine learning algorithms for segmentation of medical and natural images. In this review article, we highlight the imperative role of machine learning algorithms in enabling efficient and accurate segmentation in the field of medical imaging. We specifically focus on several key studies pertaining to the application of machine learning methods to biomedical image segmentation. We review classical machine learning algorithms such as Markov random fields, k-means clustering, random forest, etc. Although such classical learning models are often less accurate compared to the deep learning techniques, they are often more sample efficient and have a less complex structure. We also review different deep learning architectures, such as the artificial neural networks (ANNs), the convolutional neural networks (CNNs), and the recurrent neural networks (RNNs), and present the segmentation results attained by those learning models that were published in the past three years. We highlight the successes and limitations of each machine learning paradigm. In addition, we discuss several challenges related to the training of different machine learning models, and we present some heuristics to address those challenges.

Modified U-Net (mU-Net) with Incorporation of Object-Dependent High Level Features for Improved Liver and Liver-Tumor Segmentation in CT Images

Segmentation of livers and liver tumors is one of the most important steps in radiation therapy of hepatocellular carcinoma. The segmentation task is often done manually, making it tedious, labor intensive, and subject to intra-/inter- operator variations. While various algorithms for delineating organ-at-risks (OARs) and tumor targets have been proposed, automatic segmentation of livers and liver tumors remains intractable due to their low tissue contrast with respect to the surrounding organs and their deformable shape in CT images. The U-Net has gained increasing popularity recently for image analysis tasks and has shown promising results. Conventional U-Net architectures, however, suffer from three major drawbacks. To cope with these problems, we added a residual path with deconvolution and activation operations to the skip connection of the U-Net to avoid duplication of low resolution information of features. In the case of small object inputs, features in the skip connection are not incorporated with features in the residual path. Furthermore, the proposed architecture has additional convolution layers in the skip connection in order to extract high level global features of small object inputs as well as high level features of high resolution edge information of large object inputs. Efficacy of the modified U-Net (mU-Net) was demonstrated using the public dataset of Liver tumor segmentation (LiTS) challenge 2017. The proposed mU-Net outperformed existing state-of-art networks.

A Mean-Field Theory for Kernel Alignment with Random Features in Generative Adversarial Networks

We propose a novel supervised learning method to optimize the kernel in maximum mean discrepancy generative adversarial networks (MMD GANs). Specifically, we characterize a distributionally robust optimization problem to compute a good distribution for the random feature model of Rahimi and Recht to approximate a good kernel function. Due to the fact that the distributional optimization is infinite dimensional, we consider a Monte-Carlo sample average approximation (SAA) to obtain a more tractable finite dimensional optimization problem. We subsequently leverage a particle stochastic gradient descent (SGD) method to solve finite dimensional optimization problems. Based on a mean-field analysis, we then prove that the empirical distribution of the interactive particles system at each iteration of the SGD follows the path of the gradient descent flow on the Wasserstein manifold. We also establish the non-asymptotic consistency of the finite sample estimator. Our empirical evaluation on synthetic data-set as well as MNIST and CIFAR-10 benchmark data-sets indicates that our proposed MMD GAN model with kernel learning indeed attains higher inception scores well as Fr\`{e}chet inception distances and generates better images compared to the generative moment matching network (GMMN) and MMD GAN with untrained kernels.

On Sample Complexity of Projection-Free Primal-Dual Methods for Learning Mixture Policies in Markov Decision Processes

We study the problem of learning policy of an infinite-horizon, discounted cost, Markov decision process (MDP) with a large number of states. We compute the actions of a policy that is nearly as good as a policy chosen by a suitable oracle from a given mixture policy class characterized by the convex hull of a set of known base policies. To learn the coefficients of the mixture model, we recast the problem as an approximate linear programming (ALP) formulation for MDPs, where the feature vectors correspond to the occupation measures of the base policies defined on the state-action space. We then propose a projection-free stochastic primal-dual method with the Bregman divergence to solve the characterized ALP. Furthermore, we analyze the probably approximately correct (PAC) sample complexity of the proposed stochastic algorithm, namely the number of queries required to achieve near optimal objective value. We also propose a modification of our proposed algorithm with the polytope constraint sampling for the smoothed ALP, where the restriction to lower bounding approximations are relaxed. In addition, we apply the proposed algorithms to a queuing problem, and compare their performance with a penalty function algorithm. The numerical results illustrates that the primal-dual achieves better efficiency and low variance across different trials compared to the penalty function method.

Multiple Kernel Learning from $U$-Statistics of Empirical Measures in the Feature Space

We propose a novel data-driven method to learn multiple kernels in kernel methods of statistical machine learning from training samples. The proposed kernel learning algorithm is based on a $U$-statistics of the empirical marginal distributions of features in the feature space given their class labels. We prove the consistency of the $U$-statistic estimate using the empirical distributions for kernel learning. In particular, we show that the empirical estimate of $U$-statistic converges to its population value with respect to all admissible distributions as the number of the training samples increase. We also prove the sample optimality of the estimate by establishing a minimax lower bound via Fano's method. In addition, we establish the generalization bounds of the proposed kernel learning approach by computing novel upper bounds on the Rademacher and Gaussian complexities using the concentration of measures for the quadratic matrix forms.We apply the proposed kernel learning approach to classification of the real-world data-sets using the kernel SVM and compare the results with $5$-fold cross-validation for the kernel model selection problem. We also apply the proposed kernel learning approach to devise novel architectures for the semantic segmentation of biomedical images. The proposed segmentation networks are suited for training on small data-sets and employ new mechanisms to generate representations from input images.

Robustness of Maximum Correntropy Estimation Against Large Outliers

The maximum correntropy criterion (MCC) has recently been successfully applied in robust regression, classification and adaptive filtering, where the correntropy is maximized instead of minimizing the well-known mean square error (MSE) to improve the robustness with respect to outliers (or impulsive noises). Considerable efforts have been devoted to develop various robust adaptive algorithms under MCC, but so far little insight has been gained as to how the optimal solution will be affected by outliers. In this work, we study this problem in the context of parameter estimation for a simple linear errors-in-variables (EIV) model where all variables are scalar. Under certain conditions, we derive an upper bound on the absolute value of the estimation error and show that the optimal solution under MCC can be very close to the true value of the unknown parameter even with outliers (whose values can be arbitrarily large) in both input and output variables. Illustrative examples are presented to verify and clarify the theory.

Quantized Minimum Error Entropy Criterion

Comparing with traditional learning criteria, such as mean square error (MSE), the minimum error entropy (MEE) criterion is superior in nonlinear and non-Gaussian signal processing and machine learning. The argument of the logarithm in Renyis entropy estimator, called information potential (IP), is a popular MEE cost in information theoretic learning (ITL). The computational complexity of IP is however quadratic in terms of sample number due to double summation. This creates computational bottlenecks especially for large-scale datasets. To address this problem, in this work we propose an efficient quantization approach to reduce the computational burden of IP, which decreases the complexity from O(N*N) to O (MN) with M << N. The new learning criterion is called the quantized MEE (QMEE). Some basic properties of QMEE are presented. Illustrative examples are provided to verify the excellent performance of QMEE.

Deep Generative Adversarial Networks for Compressed Sensing Automates MRI

Magnetic resonance image (MRI) reconstruction is a severely ill-posed linear inverse task demanding time and resource intensive computations that can substantially trade off {\it accuracy} for {\it speed} in real-time imaging. In addition, state-of-the-art compressed sensing (CS) analytics are not cognizant of the image {\it diagnostic quality}. To cope with these challenges we put forth a novel CS framework that permeates benefits from generative adversarial networks (GAN) to train a (low-dimensional) manifold of diagnostic-quality MR images from historical patients. Leveraging a mixture of least-squares (LS) GANs and pixel-wise $\ell_1$ cost, a deep residual network with skip connections is trained as the generator that learns to remove the {\it aliasing} artifacts by projecting onto the manifold. LSGAN learns the texture details, while $\ell_1$ controls the high-frequency noise. A multilayer convolutional neural network is then jointly trained based on diagnostic quality images to discriminate the projection quality. The test phase performs feed-forward propagation over the generator network that demands a very low computational overhead. Extensive evaluations are performed on a large contrast-enhanced MR dataset of pediatric patients. In particular, images rated based on expert radiologists corroborate that GANCS retrieves high contrast images with detailed texture relative to conventional CS, and pixel-wise schemes. In addition, it offers reconstruction under a few milliseconds, two orders of magnitude faster than state-of-the-art CS-MRI schemes.

Robust Learning with Kernel Mean p-Power Error Loss

Correntropy is a second order statistical measure in kernel space, which has been successfully applied in robust learning and signal processing. In this paper, we define a nonsecond order statistical measure in kernel space, called the kernel mean-p power error (KMPE), including the correntropic loss (CLoss) as a special case. Some basic properties of KMPE are presented. In particular, we apply the KMPE to extreme learning machine (ELM) and principal component analysis (PCA), and develop two robust learning algorithms, namely ELM-KMPE and PCA-KMPE. Experimental results on synthetic and benchmark data show that the developed algorithms can achieve consistently better performance when compared with some existing methods.