Huai Chen

Nicholas Heller, Fabian Isensee, Dasha Trofimova et al.

This paper presents the challenge report for the 2021 Kidney and Kidney Tumor Segmentation Challenge (KiTS21) held in conjunction with the 2021 international conference on Medical Image Computing and Computer Assisted Interventions (MICCAI). KiTS21 is a sequel to its first edition in 2019, and it features a variety of innovations in how the challenge was designed, in addition to a larger dataset. A novel annotation method was used to collect three separate annotations for each region of interest, and these annotations were performed in a fully transparent setting using a web-based annotation tool. Further, the KiTS21 test set was collected from an outside institution, challenging participants to develop methods that generalize well to new populations. Nonetheless, the top-performing teams achieved a significant improvement over the state of the art set in 2019, and this performance is shown to inch ever closer to human-level performance. An in-depth meta-analysis is presented describing which methods were used and how they faired on the leaderboard, as well as the characteristics of which cases generally saw good performance, and which did not. Overall KiTS21 facilitated a significant advancement in the state of the art in kidney tumor segmentation, and provides useful insights that are applicable to the field of semantic segmentation as a whole.

Huai Chen, Xiuying Wang, Lisheng Wang

Delineating 3D blood vessels is essential for clinical diagnosis and treatment, however, is challenging due to complex structure variations and varied imaging conditions. Supervised deep learning has demonstrated its superior capacity in automatic 3D vessel segmentation. However, the reliance on expensive 3D manual annotations and limited capacity for annotation reuse hinder the clinical applications of supervised models. To avoid the repetitive and laborious annotating and make full use of existing vascular annotations, this paper proposes a novel 3D shape-guided local discrimination model for 3D vascular segmentation under limited guidance from public 2D vessel annotations. The primary hypothesis is that 3D vessels are composed of semantically similar voxels and exhibit tree-shaped morphology. Accordingly, the 3D region discrimination loss is firstly proposed to learn the discriminative representation measuring voxel-wise similarities and cluster semantically consistent voxels to form the candidate 3D vascular segmentation in unlabeled images; secondly, based on the similarity of the tree-shaped morphology between 2D and 3D vessels, the Crop-and-Overlap strategy is presented to generate reference masks from 2D structure-agnostic vessel annotations, which are fit for varied vascular structures, and the adversarial loss is introduced to guide the tree-shaped morphology of 3D vessels; thirdly, the temporal consistency loss is proposed to foster the training stability and keep the model updated smoothly. To further enhance the model's robustness and reliability, the orientation-invariant CNN module and Reliability-Refinement algorithm are presented. Experimental results from the public 3D cerebrovascular and 3D arterial tree datasets demonstrate that our model achieves comparable effectiveness against nine supervised models.

Huai Chen, Renzhen Wang, Xiuying Wang et al.

Contrastive learning, which aims to capture general representation from unlabeled images to initialize the medical analysis models, has been proven effective in alleviating the high demand for expensive annotations. Current methods mainly focus on instance-wise comparisons to learn the global discriminative features, however, pretermitting the local details to distinguish tiny anatomical structures, lesions, and tissues. To address this challenge, in this paper, we propose a general unsupervised representation learning framework, named local discrimination (LD), to learn local discriminative features for medical images by closely embedding semantically similar pixels and identifying regions of similar structures across different images. Specifically, this model is equipped with an embedding module for pixel-wise embedding and a clustering module for generating segmentation. And these two modules are unified through optimizing our novel region discrimination loss function in a mutually beneficial mechanism, which enables our model to reflect structure information as well as measure pixel-wise and region-wise similarity. Furthermore, based on LD, we propose a center-sensitive one-shot landmark localization algorithm and a shape-guided cross-modality segmentation model to foster the generalizability of our model. When transferred to downstream tasks, the learned representation by our method shows a better generalization, outperforming representation from 18 state-of-the-art (SOTA) methods and winning 9 out of all 12 downstream tasks. Especially for the challenging lesion segmentation tasks, the proposed method achieves significantly better performances. The source codes are publicly available at https://github.com/HuaiChen-1994/LDLearning.

Huai Chen, Jieyu Li, Renzhen Wang et al.

Local discriminative representation is needed in many medical image analysis tasks such as identifying sub-types of lesion or segmenting detailed components of anatomical structures. However, the commonly applied supervised representation learning methods require a large amount of annotated data, and unsupervised discriminative representation learning distinguishes different images by learning a global feature, both of which are not suitable for localized medical image analysis tasks. In order to avoid the limitations of these two methods, we introduce local discrimination into unsupervised representation learning in this work. The model contains two branches: one is an embedding branch which learns an embedding function to disperse dissimilar pixels over a low-dimensional hypersphere; and the other is a clustering branch which learns a clustering function to classify similar pixels into the same cluster. These two branches are trained simultaneously in a mutually beneficial pattern, and the learnt local discriminative representations are able to well measure the similarity of local image regions. These representations can be transferred to enhance various downstream tasks. Meanwhile, they can also be applied to cluster anatomical structures from unlabeled medical images under the guidance of topological priors from simulation or other structures with similar topological characteristics. The effectiveness and usefulness of the proposed method are demonstrated by enhancing various downstream tasks and clustering anatomical structures in retinal images and chest X-ray images.

Guoqing Bao, Huai Chen, Tongliang Liu et al.

There is an urgent need for automated methods to assist accurate and effective assessment of COVID-19. Radiology and nucleic acid test (NAT) are complementary COVID-19 diagnosis methods. In this paper, we present an end-to-end multitask learning (MTL) framework (COVID-MTL) that is capable of automated and simultaneous detection (against both radiology and NAT) and severity assessment of COVID-19. COVID-MTL learns different COVID-19 tasks in parallel through our novel random-weighted loss function, which assigns learning weights under Dirichlet distribution to prevent task dominance; our new 3D real-time augmentation algorithm (Shift3D) introduces space variances for 3D CNN components by shifting low-level feature representations of volumetric inputs in three dimensions; thereby, the MTL framework is able to accelerate convergence and improve joint learning performance compared to single-task models. By only using chest CT scans, COVID-MTL was trained on 930 CT scans and tested on separate 399 cases. COVID-MTL achieved AUCs of 0.939 and 0.846, and accuracies of 90.23% and 79.20% for detection of COVID-19 against radiology and NAT, respectively, which outperformed the state-of-the-art models. Meanwhile, COVID-MTL yielded AUC of 0.800 $\pm$ 0.020 and 0.813 $\pm$ 0.021 (with transfer learning) for classifying control/suspected, mild/regular, and severe/critically-ill cases. To decipher the recognition mechanism, we also identified high-throughput lung features that were significantly related (P < 0.001) to the positivity and severity of COVID-19.

Huai Chen, Yuxiao Qi, Yong Yin et al.

Segmentation of nasopharyngeal carcinoma (NPC) from Magnetic Resonance Images (MRI) is a crucial prerequisite for NPC radiotherapy. However, manually segmenting of NPC is time-consuming and labor-intensive. Additionally, single-modality MRI generally cannot provide enough information for its accurate delineation. Therefore, a multi-modality MRI fusion network (MMFNet) based on three modalities of MRI (T1, T2 and contrast-enhanced T1) is proposed to complete accurate segmentation of NPC. The backbone of MMFNet is designed as a multi-encoder-based network, consisting of several encoders to capture modality-specific features and one single decoder to fuse them and obtain high-level features for NPC segmentation. A fusion block is presented to effectively fuse features from multi-modality MRI. It firstly recalibrates low-level features captured from modality-specific encoders to highlight both informative features and regions of interest, then fuses weighted features by a residual fusion block to keep balance between fused ones and high-level features from decoder. Moreover, a training strategy named self-transfer, which utilizes pre-trained modality-specific encoders to initialize multi-encoder-based network, is proposed to make full mining of information from different modalities of MRI. The proposed method based on multi-modality MRI can effectively segment NPC and its advantages are validated by extensive experiments.