Noisy Labels are Treasure: Mean-Teacher-Assisted Confident Learning for Hepatic Vessel Segmentation

Manually segmenting the hepatic vessels from Computer Tomography (CT) is far more expertise-demanding and laborious than other structures due to the low-contrast and complex morphology of vessels, resulting in the extreme lack of high-quality labeled data. Without sufficient high-quality annotations, the usual data-driven learning-based approaches struggle with deficient training. On the other hand, directly introducing additional data with low-quality annotations may confuse the network, leading to undesirable performance degradation. To address this issue, we propose a novel mean-teacher-assisted confident learning framework to robustly exploit the noisy labeled data for the challenging hepatic vessel segmentation task. Specifically, with the adapted confident learning assisted by a third party, i.e., the weight-averaged teacher model, the noisy labels in the additional low-quality dataset can be transformed from "encumbrance" to "treasure" via progressive pixel-wise soft-correction, thus providing productive guidance. Extensive experiments using two public datasets demonstrate the superiority of the proposed framework as well as the effectiveness of each component.

Generalized Organ Segmentation by Imitating One-shot Reasoning using Anatomical Correlation

Learning by imitation is one of the most significant abilities of human beings and plays a vital role in human's computational neural system. In medical image analysis, given several exemplars (anchors), experienced radiologist has the ability to delineate unfamiliar organs by imitating the reasoning process learned from existing types of organs. Inspired by this observation, we propose OrganNet which learns a generalized organ concept from a set of annotated organ classes and then transfer this concept to unseen classes. In this paper, we show that such process can be integrated into the one-shot segmentation task which is a very challenging but meaningful topic. We propose pyramid reasoning modules (PRMs) to model the anatomical correlation between anchor and target volumes. In practice, the proposed module first computes a correlation matrix between target and anchor computerized tomography (CT) volumes. Then, this matrix is used to transform the feature representations of both anchor volume and its segmentation mask. Finally, OrganNet learns to fuse the representations from various inputs and predicts segmentation results for target volume. Extensive experiments show that OrganNet can effectively resist the wide variations in organ morphology and produce state-of-the-art results in one-shot segmentation task. Moreover, even when compared with fully-supervised segmentation models, OrganNet is still able to produce satisfying segmentation results.

Stabilized Medical Image Attacks

Convolutional Neural Networks (CNNs) have advanced existing medical systems for automatic disease diagnosis. However, a threat to these systems arises that adversarial attacks make CNNs vulnerable. Inaccurate diagnosis results make a negative influence on human healthcare. There is a need to investigate potential adversarial attacks to robustify deep medical diagnosis systems. On the other side, there are several modalities of medical images (e.g., CT, fundus, and endoscopic image) of which each type is significantly different from others. It is more challenging to generate adversarial perturbations for different types of medical images. In this paper, we propose an image-based medical adversarial attack method to consistently produce adversarial perturbations on medical images. The objective function of our method consists of a loss deviation term and a loss stabilization term. The loss deviation term increases the divergence between the CNN prediction of an adversarial example and its ground truth label. Meanwhile, the loss stabilization term ensures similar CNN predictions of this example and its smoothed input. From the perspective of the whole iterations for perturbation generation, the proposed loss stabilization term exhaustively searches the perturbation space to smooth the single spot for local optimum escape. We further analyze the KL-divergence of the proposed loss function and find that the loss stabilization term makes the perturbations updated towards a fixed objective spot while deviating from the ground truth. This stabilization ensures the proposed medical attack effective for different types of medical images while producing perturbations in small variance. Experiments on several medical image analysis benchmarks including the recent COVID-19 dataset show the stability of the proposed method.

MixSearch: Searching for Domain Generalized Medical Image Segmentation Architectures

Considering the scarcity of medical data, most datasets in medical image analysis are an order of magnitude smaller than those of natural images. However, most Network Architecture Search (NAS) approaches in medical images focused on specific datasets and did not take into account the generalization ability of the learned architectures on unseen datasets as well as different domains. In this paper, we address this point by proposing to search for generalizable U-shape architectures on a composited dataset that mixes medical images from multiple segmentation tasks and domains creatively, which is named MixSearch. Specifically, we propose a novel approach to mix multiple small-scale datasets from multiple domains and segmentation tasks to produce a large-scale dataset. Then, a novel weaved encoder-decoder structure is designed to search for a generalized segmentation network in both cell-level and network-level. The network produced by the proposed MixSearch framework achieves state-of-the-art results compared with advanced encoder-decoder networks across various datasets.

Ensembled ResUnet for Anatomical Brain Barriers Segmentation

Accuracy segmentation of brain structures could be helpful for glioma and radiotherapy planning. However, due to the visual and anatomical differences between different modalities, the accurate segmentation of brain structures becomes challenging. To address this problem, we first construct a residual block based U-shape network with a deep encoder and shallow decoder, which can trade off the framework performance and efficiency. Then, we introduce the Tversky loss to address the issue of the class imbalance between different foreground and the background classes. Finally, a model ensemble strategy is utilized to remove outliers and further boost performance.

A Hierarchical Feature Constraint to Camouflage Medical Adversarial Attacks

Deep neural networks (DNNs) for medical images are extremely vulnerable to adversarial examples (AEs), which poses security concerns on clinical decision making. Luckily, medical AEs are also easy to detect in hierarchical feature space per our study herein. To better understand this phenomenon, we thoroughly investigate the intrinsic characteristic of medical AEs in feature space, providing both empirical evidence and theoretical explanations for the question: why are medical adversarial attacks easy to detect? We first perform a stress test to reveal the vulnerability of deep representations of medical images, in contrast to natural images. We then theoretically prove that typical adversarial attacks to binary disease diagnosis network manipulate the prediction by continuously optimizing the vulnerable representations in a fixed direction, resulting in outlier features that make medical AEs easy to detect. However, this vulnerability can also be exploited to hide the AEs in the feature space. We propose a novel hierarchical feature constraint (HFC) as an add-on to existing adversarial attacks, which encourages the hiding of the adversarial representation within the normal feature distribution. We evaluate the proposed method on two public medical image datasets, namely {Fundoscopy} and {Chest X-Ray}. Experimental results demonstrate the superiority of our adversarial attack method as it bypasses an array of state-of-the-art adversarial detectors more easily than competing attack methods, supporting that the great vulnerability of medical features allows an attacker more room to manipulate the adversarial representations.

Transport based Graph Kernels

Graph kernel is a powerful tool measuring the similarity between graphs. Most of the existing graph kernels focused on node labels or attributes and ignored graph hierarchical structure information. In order to effectively utilize graph hierarchical structure information, we propose pyramid graph kernel based on optimal transport (OT). Each graph is embedded into hierarchical structures of the pyramid. Then, the OT distance is utilized to measure the similarity between graphs in hierarchical structures. We also utilize the OT distance to measure the similarity between subgraphs and propose subgraph kernel based on OT. The positive semidefinite (p.s.d) of graph kernels based on optimal transport distance is not necessarily possible. We further propose regularized graph kernel based on OT where we add the kernel regularization to the original optimal transport distance to obtain p.s.d kernel matrix. We evaluate the proposed graph kernels on several benchmark classification tasks and compare their performance with the existing state-of-the-art graph kernels. In most cases, our proposed graph kernel algorithms outperform the competing methods.

Ordinal Pattern Kernel for Brain Connectivity Network Classification

Brain connectivity networks, which characterize the functional or structural interaction of brain regions, has been widely used for brain disease classification. Kernel-based method, such as graph kernel (i.e., kernel defined on graphs), has been proposed for measuring the similarity of brain networks, and yields the promising classification performance. However, most of graph kernels are built on unweighted graph (i.e., network) with edge present or not, and neglecting the valuable weight information of edges in brain connectivity network, with edge weights conveying the strengths of temporal correlation or fiber connection between brain regions. Accordingly, in this paper, we present an ordinal pattern kernel for brain connectivity network classification. Different with existing graph kernels that measures the topological similarity of unweighted graphs, the proposed ordinal pattern kernels calculate the similarity of weighted networks by comparing ordinal patterns from weighted networks. To evaluate the effectiveness of the proposed ordinal kernel, we further develop a depth-first-based ordinal pattern kernel, and perform extensive experiments in a real dataset of brain disease from ADNI database. The results demonstrate that our proposed ordinal pattern kernel can achieve better classification performance compared with state-of-the-art graph kernels.

MI^2GAN: Generative Adversarial Network for Medical Image Domain Adaptation using Mutual Information Constraint

Domain shift between medical images from multicentres is still an open question for the community, which degrades the generalization performance of deep learning models. Generative adversarial network (GAN), which synthesize plausible images, is one of the potential solutions to address the problem. However, the existing GAN-based approaches are prone to fail at preserving image-objects in image-to-image (I2I) translation, which reduces their practicality on domain adaptation tasks. In this paper, we propose a novel GAN (namely MI$^2$GAN) to maintain image-contents during cross-domain I2I translation. Particularly, we disentangle the content features from domain information for both the source and translated images, and then maximize the mutual information between the disentangled content features to preserve the image-objects. The proposed MI$^2$GAN is evaluated on two tasks---polyp segmentation using colonoscopic images and the segmentation of optic disc and cup in fundus images. The experimental results demonstrate that the proposed MI$^2$GAN can not only generate elegant translated images, but also significantly improve the generalization performance of widely used deep learning networks (e.g., U-Net).

TR-GAN: Topology Ranking GAN with Triplet Loss for Retinal Artery/Vein Classification

Retinal artery/vein (A/V) classification lays the foundation for the quantitative analysis of retinal vessels, which is associated with potential risks of various cardiovascular and cerebral diseases. The topological connection relationship, which has been proved effective in improving the A/V classification performance for the conventional graph based method, has not been exploited by the deep learning based method. In this paper, we propose a Topology Ranking Generative Adversarial Network (TR-GAN) to improve the topology connectivity of the segmented arteries and veins, and further to boost the A/V classification performance. A topology ranking discriminator based on ordinal regression is proposed to rank the topological connectivity level of the ground-truth, the generated A/V mask and the intentionally shuffled mask. The ranking loss is further back-propagated to the generator to generate better connected A/V masks. In addition, a topology preserving module with triplet loss is also proposed to extract the high-level topological features and further to narrow the feature distance between the predicted A/V mask and the ground-truth. The proposed framework effectively increases the topological connectivity of the predicted A/V masks and achieves state-of-the-art A/V classification performance on the publicly available AV-DRIVE dataset.