JSSR: A Joint Synthesis, Segmentation, and Registration System for 3D Multi-Modal Image Alignment of Large-scale Pathological CT Scans

Multi-modal image registration is a challenging problem yet important clinical task in many real applications and scenarios. For medical imaging based diagnosis, deformable registration among different image modalities is often required in order to provide complementary visual information, as the first step. During the registration, the semantic information is the key to match homologous points and pixels. Nevertheless, many conventional registration methods are incapable to capture the high-level semantic anatomical dense correspondences. In this work, we propose a novel multi-task learning system, JSSR, based on an end-to-end 3D convolutional neural network that is composed of a generator, a register and a segmentor, for the tasks of synthesis, registration and segmentation, respectively. This system is optimized to satisfy the implicit constraints between different tasks unsupervisedly. It first synthesizes the source domain images into the target domain, then an intra-modal registration is applied on the synthesized images and target images. Then we can get the semantic segmentation by applying segmentors on the synthesized images and target images, which are aligned by the same deformation field generated by the registers. The supervision from another fully-annotated dataset is used to regularize the segmentors. We extensively evaluate our JSSR system on a large-scale medical image dataset containing 1,485 patient CT imaging studies of four different phases (i.e., 5,940 3D CT scans with pathological livers) on the registration, segmentation and synthesis tasks. The performance is improved after joint training on the registration and segmentation tasks by 0.9% and 1.9% respectively from a highly competitive and accurate baseline. The registration part also consistently outperforms the conventional state-of-the-art multi-modal registration methods.

Robust Object Detection under Occlusion with \\Context-Aware CompositionalNets

Detecting partially occluded objects is a difficult task. Our experimental results show that deep learning approaches, such as Faster R-CNN, are not robust at object detection under occlusion. Compositional convolutional neural networks (CompositionalNets) have been shown to be robust at classifying occluded objects by explicitly representing the object as a composition of parts. In this work, we propose to overcome two limitations of CompositionalNets which will enable them to detect partially occluded objects: 1) CompositionalNets, as well as other DCNN architectures, do not explicitly separate the representation of the context from the object itself. Under strong object occlusion, the influence of the context is amplified which can have severe negative effects for detection at test time. In order to overcome this, we propose to segment the context during training via bounding box annotations. We then use the segmentation to learn a context-aware CompositionalNet that disentangles the representation of the context and the object. 2) We extend the part-based voting scheme in CompositionalNets to vote for the corners of the object's bounding box, which enables the model to reliably estimate bounding boxes for partially occluded objects. Our extensive experiments show that our proposed model can detect objects robustly, increasing the detection performance of strongly occluded vehicles from PASCAL3D+ and MS-COCO by 41\% and 35\% respectively in absolute performance relative to Faster R-CNN.

Domain Adaptive Relational Reasoning for 3D Multi-Organ Segmentation

In this paper, we present a novel unsupervised domain adaptation (UDA) method, named Domain Adaptive Relational Reasoning (DARR), to generalize 3D multi-organ segmentation models to medical data collected from different scanners and/or protocols (domains). Our method is inspired by the fact that the spatial relationship between internal structures in medical images is relatively fixed, e.g., a spleen is always located at the tail of a pancreas, which serves as a latent variable to transfer the knowledge shared across multiple domains. We formulate the spatial relationship by solving a jigsaw puzzle task, i.e., recovering a CT scan from its shuffled patches, and jointly train it with the organ segmentation task. To guarantee the transferability of the learned spatial relationship to multiple domains, we additionally introduce two schemes: 1) Employing a super-resolution network also jointly trained with the segmentation model to standardize medical images from different domain to a certain spatial resolution; 2) Adapting the spatial relationship for a test image by test-time jigsaw puzzle training. Experimental results show that our method improves the performance by 29.60\% DSC on target datasets on average without using any data from the target domain during training.

Organ at Risk Segmentation for Head and Neck Cancer using Stratified Learning and Neural Architecture Search

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.

PatchAttack: A Black-box Texture-based Attack with Reinforcement Learning

Patch-based attacks introduce a perceptible but localized change to the input that induces misclassification. A limitation of current patch-based black-box attacks is that they perform poorly for targeted attacks, and even for the less challenging non-targeted scenarios, they require a large number of queries. Our proposed PatchAttack is query efficient and can break models for both targeted and non-targeted attacks. PatchAttack induces misclassifications by superimposing small textured patches on the input image. We parametrize the appearance of these patches by a dictionary of class-specific textures. This texture dictionary is learned by clustering Gram matrices of feature activations from a VGG backbone. PatchAttack optimizes the position and texture parameters of each patch using reinforcement learning. Our experiments show that PatchAttack achieves > 99% success rate on ImageNet for a wide range of architectures, while only manipulating 3% of the image for non-targeted attacks and 10% on average for targeted attacks. Furthermore, we show that PatchAttack circumvents state-of-the-art adversarial defense methods successfully.

Context-Aware Group Captioning via Self-Attention and Contrastive Features

While image captioning has progressed rapidly, existing works focus mainly on describing single images. In this paper, we introduce a new task, context-aware group captioning, which aims to describe a group of target images in the context of another group of related reference images. Context-aware group captioning requires not only summarizing information from both the target and reference image group but also contrasting between them. To solve this problem, we propose a framework combining self-attention mechanism with contrastive feature construction to effectively summarize common information from each image group while capturing discriminative information between them. To build the dataset for this task, we propose to group the images and generate the group captions based on single image captions using scene graphs matching. Our datasets are constructed on top of the public Conceptual Captions dataset and our new Stock Captions dataset. Experiments on the two datasets show the effectiveness of our method on this new task. Related Datasets and code are released at https://lizw14.github.io/project/groupcap .

Neural Architecture Search for Lightweight Non-Local Networks

Non-Local (NL) blocks have been widely studied in various vision tasks. However, it has been rarely explored to embed the NL blocks in mobile neural networks, mainly due to the following challenges: 1) NL blocks generally have heavy computation cost which makes it difficult to be applied in applications where computational resources are limited, and 2) it is an open problem to discover an optimal configuration to embed NL blocks into mobile neural networks. We propose AutoNL to overcome the above two obstacles. Firstly, we propose a Lightweight Non-Local (LightNL) block by squeezing the transformation operations and incorporating compact features. With the novel design choices, the proposed LightNL block is 400x computationally cheaper} than its conventional counterpart without sacrificing the performance. Secondly, by relaxing the structure of the LightNL block to be differentiable during training, we propose an efficient neural architecture search algorithm to learn an optimal configuration of LightNL blocks in an end-to-end manner. Notably, using only 32 GPU hours, the searched AutoNL model achieves 77.7% top-1 accuracy on ImageNet under a typical mobile setting (350M FLOPs), significantly outperforming previous mobile models including MobileNetV2 (+5.7%), FBNet (+2.8%) and MnasNet (+2.1%). Code and models are available at https://github.com/LiYingwei/AutoNL.

Compositional Convolutional Neural Networks: A Deep Architecture with Innate Robustness to Partial Occlusion

Recent findings show that deep convolutional neural networks (DCNNs) do not generalize well under partial occlusion. Inspired by the success of compositional models at classifying partially occluded objects, we propose to integrate compositional models and DCNNs into a unified deep model with innate robustness to partial occlusion. We term this architecture Compositional Convolutional Neural Network. In particular, we propose to replace the fully connected classification head of a DCNN with a differentiable compositional model. The generative nature of the compositional model enables it to localize occluders and subsequently focus on the non-occluded parts of the object. We conduct classification experiments on artificially occluded images as well as real images of partially occluded objects from the MS-COCO dataset. The results show that DCNNs do not classify occluded objects robustly, even when trained with data that is strongly augmented with partial occlusions. Our proposed model outperforms standard DCNNs by a large margin at classifying partially occluded objects, even when it has not been exposed to occluded objects during training. Additional experiments demonstrate that CompositionalNets can also localize the occluders accurately, despite being trained with class labels only. The code used in this work is publicly available.

Are Labels Necessary for Neural Architecture Search?

Existing neural network architectures in computer vision --- whether designed by humans or by machines --- were typically found using both images and their associated labels. In this paper, we ask the question: can we find high-quality neural architectures using only images, but no human-annotated labels? To answer this question, we first define a new setup called Unsupervised Neural Architecture Search (UnNAS). We then conduct two sets of experiments. In sample-based experiments, we train a large number (500) of diverse architectures with either supervised or unsupervised objectives, and find that the architecture rankings produced with and without labels are highly correlated. In search-based experiments, we run a well-established NAS algorithm (DARTS) using various unsupervised objectives, and report that the architectures searched without labels can be competitive to their counterparts searched with labels. Together, these results reveal the potentially surprising finding that labels are not necessary, and the image statistics alone may be sufficient to identify good neural architectures.

Synthesize then Compare: Detecting Failures and Anomalies for Semantic Segmentation

The ability to detect failures and anomalies are fundamental requirements for building reliable systems for computer vision applications, especially safety-critical applications of semantic segmentation, such as autonomous driving and medical image analysis. In this paper, we systematically study failure and anomaly detection for semantic segmentation and propose a unified framework, consisting of two modules, to address these two related problems. The first module is an image synthesis module, which generates a synthesized image from a segmentation layout map, and the second is a comparison module, which computes the difference between the synthesized image and the input image. We validate our framework on three challenging datasets and improve the state-of-the-arts by large margins, i.e., 6% AUPR-Error on Cityscapes, 10% DSC correlation on pancreatic tumor segmentation in MSD and 20% AUPR on StreetHazards anomaly segmentation.