Deep 3D Vessel Segmentation based on Cross Transformer Network

The coronary microvascular disease poses a great threat to human health. Computer-aided analysis/diagnosis systems help physicians intervene in the disease at early stages, where 3D vessel segmentation is a fundamental step. However, there is a lack of carefully annotated dataset to support algorithm development and evaluation. On the other hand, the commonly-used U-Net structures often yield disconnected and inaccurate segmentation results, especially for small vessel structures. In this paper, motivated by the data scarcity, we first construct two large-scale vessel segmentation datasets consisting of 100 and 500 computed tomography (CT) volumes with pixel-level annotations by experienced radiologists. To enhance the U-Net, we further propose the cross transformer network (CTN) for fine-grained vessel segmentation. In CTN, a transformer module is constructed in parallel to a U-Net to learn long-distance dependencies between different anatomical regions; and these dependencies are communicated to the U-Net at multiple stages to endow it with global awareness. Experimental results on the two in-house datasets indicate that this hybrid model alleviates unexpected disconnections by considering topological information across regions. Our codes, together with the trained models are made publicly available at https://github.com/qibaolian/ctn.

Computer-aided Tuberculosis Diagnosis with Attribute Reasoning Assistance

Although deep learning algorithms have been intensively developed for computer-aided tuberculosis diagnosis (CTD), they mainly depend on carefully annotated datasets, leading to much time and resource consumption. Weakly supervised learning (WSL), which leverages coarse-grained labels to accomplish fine-grained tasks, has the potential to solve this problem. In this paper, we first propose a new large-scale tuberculosis (TB) chest X-ray dataset, namely the tuberculosis chest X-ray attribute dataset (TBX-Att), and then establish an attribute-assisted weakly-supervised framework to classify and localize TB by leveraging the attribute information to overcome the insufficiency of supervision in WSL scenarios. Specifically, first, the TBX-Att dataset contains 2000 X-ray images with seven kinds of attributes for TB relational reasoning, which are annotated by experienced radiologists. It also includes the public TBX11K dataset with 11200 X-ray images to facilitate weakly supervised detection. Second, we exploit a multi-scale feature interaction model for TB area classification and detection with attribute relational reasoning. The proposed model is evaluated on the TBX-Att dataset and will serve as a solid baseline for future research. The code and data will be available at https://github.com/GangmingZhao/tb-attribute-weak-localization.

Cross-Modality High-Frequency Transformer for MR Image Super-Resolution

Improving the resolution of magnetic resonance (MR) image data is critical to computer-aided diagnosis and brain function analysis. Higher resolution helps to capture more detailed content, but typically induces to lower signal-to-noise ratio and longer scanning time. To this end, MR image super-resolution has become a widely-interested topic in recent times. Existing works establish extensive deep models with the conventional architectures based on convolutional neural networks (CNN). In this work, to further advance this research field, we make an early effort to build a Transformer-based MR image super-resolution framework, with careful designs on exploring valuable domain prior knowledge. Specifically, we consider two-fold domain priors including the high-frequency structure prior and the inter-modality context prior, and establish a novel Transformer architecture, called Cross-modality high-frequency Transformer (Cohf-T), to introduce such priors into super-resolving the low-resolution (LR) MR images. Comprehensive experiments on two datasets indicate that Cohf-T achieves new state-of-the-art performance.

Cross-level Contrastive Learning and Consistency Constraint for Semi-supervised Medical Image Segmentation

Semi-supervised learning (SSL), which aims at leveraging a few labeled images and a large number of unlabeled images for network training, is beneficial for relieving the burden of data annotation in medical image segmentation. According to the experience of medical imaging experts, local attributes such as texture, luster and smoothness are very important factors for identifying target objects like lesions and polyps in medical images. Motivated by this, we propose a cross-level contrastive learning scheme to enhance representation capacity for local features in semi-supervised medical image segmentation. Compared to existing image-wise, patch-wise and point-wise contrastive learning algorithms, our devised method is capable of exploring more complex similarity cues, namely the relational characteristics between global and local patch-wise representations. Additionally, for fully making use of cross-level semantic relations, we devise a novel consistency constraint that compares the predictions of patches against those of the full image. With the help of the cross-level contrastive learning and consistency constraint, the unlabelled data can be effectively explored to improve segmentation performance on two medical image datasets for polyp and skin lesion segmentation respectively. Code of our approach is available.

Incremental Cross-view Mutual Distillation for Self-supervised Medical CT Synthesis

Due to the constraints of the imaging device and high cost in operation time, computer tomography (CT) scans are usually acquired with low intra-slice resolution. Improving the intra-slice resolution is beneficial to the disease diagnosis for both human experts and computer-aided systems. To this end, this paper builds a novel medical slice synthesis to increase the between-slice resolution. Considering that the ground-truth intermediate medical slices are always absent in clinical practice, we introduce the incremental cross-view mutual distillation strategy to accomplish this task in the self-supervised learning manner. Specifically, we model this problem from three different views: slice-wise interpolation from axial view and pixel-wise interpolation from coronal and sagittal views. Under this circumstance, the models learned from different views can distill valuable knowledge to guide the learning processes of each other. We can repeat this process to make the models synthesize intermediate slice data with increasing inter-slice resolution. To demonstrate the effectiveness of the proposed approach, we conduct comprehensive experiments on a large-scale CT dataset. Quantitative and qualitative comparison results show that our method outperforms state-of-the-art algorithms by clear margins.

Weakly Supervised Semantic Segmentation via Alternative Self-Dual Teaching

Current weakly supervised semantic segmentation (WSSS) frameworks usually contain the separated mask-refinement model and the main semantic region mining model. These approaches would contain redundant feature extraction backbones and biased learning objectives, making them computational complex yet sub-optimal to addressing the WSSS task. To solve this problem, this paper establishes a compact learning framework that embeds the classification and mask-refinement components into a unified deep model. With the shared feature extraction backbone, our model is able to facilitate knowledge sharing between the two components while preserving a low computational complexity. To encourage high-quality knowledge interaction, we propose a novel alternative self-dual teaching (ASDT) mechanism. Unlike the conventional distillation strategy, the knowledge of the two teacher branches in our model is alternatively distilled to the student branch by a Pulse Width Modulation (PWM), which generates PW wave-like selection signal to guide the knowledge distillation process. In this way, the student branch can help prevent the model from falling into local minimum solutions caused by the imperfect knowledge provided of either teacher branch. Comprehensive experiments on the PASCAL VOC 2012 and COCO-Stuff 10K demonstrate the effectiveness of the proposed alternative self-dual teaching mechanism as well as the new state-of-the-art performance of our approach.

MVCNet: Multiview Contrastive Network for Unsupervised Representation Learning for 3D CT Lesions

\emph{Objective and Impact Statement}. With the renaissance of deep learning, automatic diagnostic systems for computed tomography (CT) have achieved many successful applications. However, they are mostly attributed to careful expert annotations, which are often scarce in practice. This drives our interest to the unsupervised representation learning. \emph{Introduction}. Recent studies have shown that self-supervised learning is an effective approach for learning representations, but most of them rely on the empirical design of transformations and pretext tasks. \emph{Methods}. To avoid the subjectivity associated with these methods, we propose the MVCNet, a novel unsupervised three dimensional (3D) representation learning method working in a transformation-free manner. We view each 3D lesion from different orientations to collect multiple two dimensional (2D) views. Then, an embedding function is learned by minimizing a contrastive loss so that the 2D views of the same 3D lesion are aggregated, and the 2D views of different lesions are separated. We evaluate the representations by training a simple classification head upon the embedding layer. \emph{Results}. Experimental results show that MVCNet achieves state-of-the-art accuracies on the LIDC-IDRI (89.55\%), LNDb (77.69\%) and TianChi (79.96\%) datasets for \emph{unsupervised representation learning}. When fine-tuned on 10\% of the labeled data, the accuracies are comparable to the supervised learning model (89.46\% vs. 85.03\%, 73.85\% vs. 73.44\%, 83.56\% vs. 83.34\% on the three datasets, respectively). \emph{Conclusion}. Results indicate the superiority of MVCNet in \emph{learning representations with limited annotations}.

Trash to Treasure: Harvesting OOD Data with Cross-Modal Matching for Open-Set Semi-Supervised Learning

Open-set semi-supervised learning (open-set SSL) investigates a challenging but practical scenario where out-of-distribution (OOD) samples are contained in the unlabeled data. While the mainstream technique seeks to completely filter out the OOD samples for semi-supervised learning (SSL), we propose a novel training mechanism that could effectively exploit the presence of OOD data for enhanced feature learning while avoiding its adverse impact on the SSL. We achieve this goal by first introducing a warm-up training that leverages all the unlabeled data, including both the in-distribution (ID) and OOD samples. Specifically, we perform a pretext task that enforces our feature extractor to obtain a high-level semantic understanding of the training images, leading to more discriminative features that can benefit the downstream tasks. Since the OOD samples are inevitably detrimental to SSL, we propose a novel cross-modal matching strategy to detect OOD samples. Instead of directly applying binary classification, we train the network to predict whether the data sample is matched to an assigned one-hot class label. The appeal of the proposed cross-modal matching over binary classification is the ability to generate a compatible feature space that aligns with the core classification task. Extensive experiments show that our approach substantially lifts the performance on open-set SSL and outperforms the state-of-the-art by a large margin.

GREN: Graph-Regularized Embedding Network for Weakly-Supervised Disease Localization in X-ray images

Locating diseases in chest X-ray images with few careful annotations saves large human effort. Recent works approached this task with innovative weakly-supervised algorithms such as multi-instance learning (MIL) and class activation maps (CAM), however, these methods often yield inaccurate or incomplete regions. One of the reasons is the neglection of the pathological implications hidden in the relationship across anatomical regions within each image and the relationship across images. In this paper, we argue that the cross-region and cross-image relationship, as contextual and compensating information, is vital to obtain more consistent and integral regions. To model the relationship, we propose the Graph Regularized Embedding Network (GREN), which leverages the intra-image and inter-image information to locate diseases on chest X-ray images. GREN uses a pre-trained U-Net to segment the lung lobes, and then models the intra-image relationship between the lung lobes using an intra-image graph to compare different regions. Meanwhile, the relationship between in-batch images is modeled by an inter-image graph to compare multiple images. This process mimics the training and decision-making process of a radiologist: comparing multiple regions and images for diagnosis. In order for the deep embedding layers of the neural network to retain structural information (important in the localization task), we use the Hash coding and Hamming distance to compute the graphs, which are used as regularizers to facilitate training. By means of this, our approach achieves the state-of-the-art result on NIH chest X-ray dataset for weakly-supervised disease localization. Our codes are accessible online.