Accurate multi-organ abdominal CT segmentation is essential to many clinical applications such as computer-aided intervention. As data annotation requires massive human labor from experienced radiologists, it is common that training data are partially labeled, e.g., pancreas datasets only have the pancreas labeled while leaving the rest marked as background. However, these background labels can be misleading in multi-organ segmentation since the "background" usually contains some other organs of interest. To address the background ambiguity in these partially-labeled datasets, we propose Prior-aware Neural Network (PaNN) via explicitly incorporating anatomical priors on abdominal organ sizes, guiding the training process with domain-specific knowledge. More specifically, PaNN assumes that the average organ size distributions in the abdomen should approximate their empirical distributions, a prior statistics obtained from the fully-labeled dataset. As our training objective is difficult to be directly optimized using stochastic gradient descent [20], we propose to reformulate it in a min-max form and optimize it via the stochastic primal-dual gradient algorithm. PaNN achieves state-of-the-art performance on the MICCAI2015 challenge "Multi-Atlas Labeling Beyond the Cranial Vault", a competition on organ segmentation in the abdomen. We report an average Dice score of 84.97 , surpassing the prior art by a large margin of 3.27 .
In the medical imaging domain, it becomes more intractable to acquire sufficient labeled data due to the difficulty of annotation, as the annotation has to be done by experts. Although fully-supervised methods ( , UNet @cite_45 , VoxResNet @cite_40 , DeepMedic @cite_4 , 3D-DSN @cite_55 , HNN @cite_23 ) have achieved remarkable performance improvement in tasks such as brain MR segmentation, abdominal single-organ segmentation and multi-organ segmentation, semi- or weakly- supervised learning is still a far more realistic solution. For example, Bai al @cite_15 proposed an EM-based iterative method, where a CNN is alternately trained on labeled and post-processed unlabeled sets. @cite_18 , supervised and unsupervised adversarial costs are involved to address semi-supervised gland segmentation. DeepCut @cite_43 shows that weak annotations such as bounding-boxes in medical image segmentation can also be utilized by performing an iterative optimization scheme like @cite_57 .
@cite_18 @cite_4 @cite_55 @cite_57 @cite_43 @cite_40 @cite_45 @cite_23 @cite_15
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We present an adversarial domain adaptation based deep learning approach for automatic tumor segmentation from T2-weighted MRI. Our approach is composed of two steps: (i) a tumor-aware unsupervised cross-domain adaptation (CT to MRI), followed by (ii) semi-supervised tumor segmentation using Unet trained with synthesized and limited number of original MRIs. We introduced a novel target specific loss, called tumor-aware loss, for unsupervised cross-domain adaptation that helps to preserve tumors on synthesized MRIs produced from CT images. In comparison, state-of-the art adversarial networks trained without our tumor-aware loss produced MRIs with ill-preserved or missing tumors. All networks were trained using labeled CT images from 377 patients with non-small cell lung cancer obtained from the Cancer Imaging Archive and unlabeled T2w MRIs from a completely unrelated cohort of 6 patients with pre-treatment and 36 on-treatment scans. Next, we combined 6 labeled pre-treatment MRI scans with the synthesized MRIs to boost tumor segmentation accuracy through semi-supervised learning. Semi-supervised training of cycle-GAN produced a segmentation accuracy of 0.66 computed using Dice Score Coefficient (DSC). Our method trained with only synthesized MRIs produced an accuracy of 0.74 while the same method trained in semi-supervised setting produced the best accuracy of 0.80 on test. Our results show that tumor-aware adversarial domain adaptation helps to achieve reasonably accurate cancer segmentation from limited MRI data by leveraging large CT datasets. Deep learning algorithms require large amounts of labeled data which is difficult to attain for medical imaging. Even if a particular dataset is accessible, a learned classifier struggles to maintain the same level of performance on a different medical imaging dataset from a new or never-seen data source domain. Utilizing generative adversarial networks in a semi-supervised learning architecture, we address both problems of labeled data scarcity and data domain overfitting. For cardiac abnormality classification in chest X-rays, we demonstrate that an order of magnitude less data is required with semi-supervised learning generative adversarial networks than with conventional supervised learning convolutional neural networks. In addition, we demonstrate its robustness across different datasets for similar classification tasks. Learning representative computational models from medical imaging data requires large training data sets. Often, voxel-level annotation is unfeasible for sufficient amounts of data. An alternative to manual annotation, is to use the enormous amount of knowledge encoded in imaging data and corresponding reports generated during clinical routine. Weakly supervised learning approaches can link volume-level labels to image content but suffer from the typical label distributions in medical imaging data where only a small part consists of clinically relevant abnormal structures. In this paper we propose to use a semantic representation of clinical reports as a learning target that is predicted from imaging data by a convolutional neural network. We demonstrate how we can learn accurate voxel-level classifiers based on weak volume-level semantic descriptions on a set of 157 optical coherence tomography (OCT) volumes. We specifically show how semantic information increases classification accuracy for intraretinal cystoid fluid (IRC), subretinal fluid (SRF) and normal retinal tissue, and how the learning algorithm links semantic concepts to image content and geometry. While deep convolutional neural networks (CNNs) have achieved remarkable success in 2D medical image segmentation, it is still a difficult task for CNNs to segment important organs or structures from 3D medical images owing to several mutually affected challenges, including the complicated anatomical environments in volumetric images, optimization difficulties of 3D networks and inadequacy of training samples. In this paper, we present a novel and efficient 3D fully convolutional network equipped with a 3D deep supervision mechanism to comprehensively address these challenges; we call it 3D DSN. Our proposed 3D DSN is capable of conducting volume-to-volume learning and inference, which can eliminate redundant computations and alleviate the risk of over-fitting on limited training data. More importantly, the 3D deep supervision mechanism can effectively cope with the optimization problem of gradients vanishing or exploding when training a 3D deep model, accelerating the convergence speed and simultaneously improving the discrimination capability. Such a mechanism is developed by deriving an objective function that directly guides the training of both lower and upper layers in the network, so that the adverse effects of unstable gradient changes can be counteracted during the training procedure. We also employ a fully connected conditional random field model as a post-processing step to refine the segmentation results. We have extensively validated the proposed 3D DSN on two typical yet challenging volumetric medical image segmentation tasks: (i) liver segmentation from 3D CT scans and (ii) whole heart and great vessels segmentation from 3D MR images, by participating two grand challenges held in conjunction with MICCAI. We have achieved competitive segmentation results to state-of-the-art approaches in both challenges with a much faster speed, corroborating the effectiveness of our proposed 3D DSN.