OAR segmentation is a critical step in radiotherapy of head and neck (H&N) cancer, where inconsistencies across radiation oncologists and prohibitive labor costs motivate automated approaches. However, leading methods using standard fully convolutional network workflows that are challenged when the number of OARs becomes large, e.g. > 40. For such scenarios, insights can be gained from the stratification approaches seen in manual clinical OAR delineation. This is the goal of our work, where we introduce stratified organ at risk segmentation (SOARS), an approach that stratifies OARs into anchor, mid-level, and small & hard (S&H) categories. SOARS stratifies across two dimensions. The first dimension is that distinct processing pipelines are used for each OAR category. In particular, inspired by clinical practices, anchor OARs are used to guide the mid-level and S&H categories. The second dimension is that distinct network architectures are used to manage the significant contrast, size, and anatomy variations between different OARs. We use differentiable neural architecture search (NAS), allowing the network to choose among 2D, 3D or Pseudo-3D convolutions. Extensive 4-fold cross-validation on 142 H&N cancer patients with 42 manually labeled OARs, the most comprehensive OAR dataset to date, demonstrates that both pipeline- and NAS-stratification significantly improves quantitative performance over the state-of-the-art (from 69.52% to 73.68% in absolute Dice scores). Thus, SOARS provides a powerful and principled means to manage the highly complex segmentation space of OARs.

While making a tremendous impact in various fields, deep neural networks usually require large amounts of labeled data for training which are expensive to collect in many applications, especially in the medical domain. Un-labeled data, on the other hand, is much more abundant. Semi-supervised learning techniques, such as co-training, could provide a powerful tool to leverage unlabeled data. In this paper, we propose a novel framework, uncertainty-aware multi-view co-training (UMCT), to address semi-supervised learning on 3D data, such as volumetric data from medical imaging. In our work, co-training is achieved by exploiting multi-viewpoint consistency of 3D data. We generate different views by rotating or permuting the 3D data and utilize asymmetrical 3D kernels to encourage diversified features in different sub-networks. In addition, we propose an uncertainty-weighted label fusion mechanism to estimate the reliability of each view's prediction with Bayesian deep learning. As one view requires the supervision from other views in co-training, our self-adaptive approach computes a confidence score for the prediction of each unlabeled sample in order to assign a reliable pseudo label. Thus, our approach can take advantage of unlabeled data during training. We show the effectiveness of our proposed semi-supervised method on several public datasets from medical image segmentation tasks (NIH pancreas & LiTS liver tumor dataset). Meanwhile, a fully-supervised method based on our approach achieved state-of-the-art performances on both the LiTS liver tumor segmentation and the Medical Segmentation Decathlon (MSD) challenge, demonstrating the robustness and value of our framework, even when fully supervised training is feasible.

Deep learning algorithms, in particular 2D and 3D fully convolutional neural networks (FCNs), have rapidly become the mainstream methodology for volumetric medical image segmentation. However, 2D convolutions cannot fully leverage the rich spatial information along the third axis, while 3D convolutions suffer from the demanding computation and high GPU memory consumption. In this paper, we propose to automatically search the network architecture tailoring to volumetric medical image segmentation problem. Concretely, we formulate the structure learning as differentiable neural architecture search, and let the network itself choose between 2D, 3D or Pseudo-3D (P3D) convolutions at each layer. We evaluate our method on 3 public datasets, i.e., the NIH Pancreas dataset, the Lung and Pancreas dataset from the Medical Segmentation Decathlon (MSD) Challenge. Our method, named V-NAS, consistently outperforms other state-of-the-arts on the segmentation tasks of both normal organ (NIH Pancreas) and abnormal organs (MSD Lung tumors and MSD Pancreas tumors), which shows the power of chosen architecture. Moreover, the searched architecture on one dataset can be well generalized to other datasets, which demonstrates the robustness and practical use of our proposed method.

In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial information along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-Sørensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.

While recent deep neural networks have achieved a promising performance on object recognition, they rely implicitly on the visual contents of the whole image. In this paper, we train deep neural networks on the foreground (object) and background (context) regions of images respectively. Considering human recognition in the same situations, networks trained on the pure background without objects achieves highly reasonable recognition performance that beats humans by a large margin if only given context. However, humans still outperform networks with pure object available, which indicates networks and human beings have different mechanisms in understanding an image. Furthermore, we straightforwardly combine multiple trained networks to explore different visual cues learned by different networks. Experiments show that useful visual hints can be explicitly learned separately and then combined to achieve higher performance, which verifies the advantages of the proposed framework.

Multiple-instance learning (MIL) has served as an important tool for a wide range of vision applications, for instance, image classification, object detection, and visual tracking. In this paper, we propose a novel method to solve the classical MIL problem, named relaxed multiple-instance SVM (RMI-SVM). We treat the positiveness of instance as a continuous variable, use Noisy-OR model to enforce the MIL constraints, and optimize them jointly in a unified framework. The optimization problem can be efficiently solved using stochastic gradient decent. The extensive experiments demonstrate that RMI-SVM consistently achieves superior performance on various benchmarks for MIL. Moreover, we simply applied RMI-SVM to a challenging vision task, common object discovery. The state-of-the arts results of object discovery on PASCAL VOC datasets further confirm the advantages of the proposed method.

View-based 3D shape retrieval is a popular branch in 3D shape analysis owing to the high discriminative property of 2D views. However, many previous works do not scale up to large 3D shape databases. We propose a two layer coding (TLC) framework to conduct shape matching much more efficiently. The first layer coding is applied to pairs of views represented as depth images. The spatial relationship of each view pair is captured with so-called eigen-angle, which is the planar angle between the two views measured at the center of the 3D shape. Prior to the second layer coding, the view pairs are divided into subsets according to their eigen-angles. Consequently, view pairs that differ significantly in their eigen-angles are encoded with different codewords, which implies that spatial arrangement of views is preserved in the second layer coding. The final feature vector of a 3D shape is the concatenation of all the encoded features from different subsets, which is used for efficient indexing directly. TLC is not limited to encode the local features from 2D views, but can be also applied to encoding 3D features. Exhaustive experimental results confirm that TLC achieves state-of-the-art performance in both retrieval accuracy and efficiency.