Shichuan Zhang

Ran Gu, Guotai Wang, Jiangshan Lu et al.

Generalization to previously unseen images with potential domain shifts and different styles is essential for clinically applicable medical image segmentation, and the ability to disentangle domain-specific and domain-invariant features is key for achieving Domain Generalization (DG). However, existing DG methods can hardly achieve effective disentanglement to get high generalizability. To deal with this problem, we propose an efficient Contrastive Domain Disentanglement and Style Augmentation (CDDSA) framework for generalizable medical image segmentation. First, a disentangle network is proposed to decompose an image into a domain-invariant anatomical representation and a domain-specific style code, where the former is sent to a segmentation model that is not affected by the domain shift, and the disentangle network is regularized by a decoder that combines the anatomical and style codes to reconstruct the input image. Second, to achieve better disentanglement, a contrastive loss is proposed to encourage the style codes from the same domain and different domains to be compact and divergent, respectively. Thirdly, to further improve generalizability, we propose a style augmentation method based on the disentanglement representation to synthesize images in various unseen styles with shared anatomical structures. Our method was validated on a public multi-site fundus image dataset for optic cup and disc segmentation and an in-house multi-site Nasopharyngeal Carcinoma Magnetic Resonance Image (NPC-MRI) dataset for nasopharynx Gross Tumor Volume (GTVnx) segmentation. Experimental results showed that the proposed CDDSA achieved remarkable generalizability across different domains, and it outperformed several state-of-the-art methods in domain-generalizable segmentation.

Litingyu Wang, Yijie Qu, Xiangde Luo et al.

Assessing the presence of potentially malignant lymph nodes aids in estimating cancer progression, and identifying surrounding benign lymph nodes can assist in determining potential metastatic pathways for cancer. For quantitative analysis, automatic segmentation of lymph nodes is crucial. However, due to the labor-intensive and time-consuming manual annotation process required for a large number of lymph nodes, it is more practical to annotate only a subset of the lymph node instances to reduce annotation costs. In this study, we propose a pre-trained Dual-Branch network with Dynamically Mixed Pseudo label (DBDMP) to learn from partial instance annotations for lymph nodes segmentation. To obtain reliable pseudo labels for lymph nodes that are not annotated, we employ a dual-decoder network to generate different outputs that are then dynamically mixed. We integrate the original weak partial annotations with the mixed pseudo labels to supervise the network. To further leverage the extensive amount of unannotated voxels, we apply a self-supervised pre-training strategy to enhance the model's feature extraction capability. Experiments on the mediastinal Lymph Node Quantification (LNQ) dataset demonstrate that our method, compared to directly learning from partial instance annotations, significantly improves the Dice Similarity Coefficient (DSC) from 11.04% to 54.10% and reduces the Average Symmetric Surface Distance (ASSD) from 20.83 $mm$ to 8.72 $mm$. The code is available at https://github.com/WltyBY/LNQ2023_training_code.git

Zhongyi Shui, Sunyi Zheng, Chenglu Zhu et al.

Point-based cell detection (PCD), which pursues high-performance cell sensing under low-cost data annotation, has garnered increased attention in computational pathology community. Unlike mainstream PCD methods that rely on intermediate density map representations, the Point-to-Point network (P2PNet) has recently emerged as an end-to-end solution for PCD, demonstrating impressive cell detection accuracy and efficiency. Nevertheless, P2PNet is limited to decoding from a single-level feature map due to the scale-agnostic property of point proposals, which is insufficient to leverage multi-scale information. Moreover, the spatial distribution of pre-set point proposals is biased from that of cells, leading to inaccurate cell localization. To lift these limitations, we present DPA-P2PNet in this work. The proposed method directly extracts multi-scale features for decoding according to the coordinates of point proposals on hierarchical feature maps. On this basis, we further devise deformable point proposals to mitigate the positional bias between proposals and potential cells to promote cell localization. Inspired by practical pathological diagnosis that usually combines high-level tissue structure and low-level cell morphology for accurate cell classification, we propose a multi-field-of-view (mFoV) variant of DPA-P2PNet to accommodate additional large FoV images with tissue information as model input. Finally, we execute the first self-supervised pre-training on immunohistochemistry histopathology image data and evaluate the suitability of four representative self-supervised methods on the PCD task. Experimental results on three benchmarks and a large-scale and real-world interval dataset demonstrate the superiority of our proposed models over the state-of-the-art counterparts. Codes and pre-trained weights will be available.

Pingyi Chen, Chenglu Zhu, Zhongyi Shui et al.

The success of supervised deep learning models in medical image segmentation relies on detailed annotations. However, labor-intensive manual labeling is costly and inefficient, especially in dense object segmentation. To this end, we propose a self-supervised learning based approach with a Prior Self-activation Module (PSM) that generates self-activation maps from the input images to avoid labeling costs and further produce pseudo masks for the downstream task. To be specific, we firstly train a neural network using self-supervised learning and utilize the gradient information in the shallow layers of the network to generate self-activation maps. Afterwards, a semantic-guided generator is then introduced as a pipeline to transform visual representations from PSM to pixel-level semantic pseudo masks for downstream tasks. Furthermore, a two-stage training module, consisting of a nuclei detection network and a nuclei segmentation network, is adopted to achieve the final segmentation. Experimental results show the effectiveness on two public pathological datasets. Compared with other fully-supervised and weakly-supervised methods, our method can achieve competitive performance without any manual annotations.

Zhongyi Shui, Yizhi Zhao, Sunyi Zheng et al.

Cell recognition is a fundamental task in digital histopathology image analysis. Point-based cell recognition (PCR) methods normally require a vast number of annotations, which is extremely costly, time-consuming and labor-intensive. Semi-supervised learning (SSL) can provide a shortcut to make full use of cell information in gigapixel whole slide images without exhaustive labeling. However, research into semi-supervised point-based cell recognition (SSPCR) remains largely overlooked. Previous SSPCR works are all built on density map-based PCR models, which suffer from unsatisfactory accuracy, slow inference speed and high sensitivity to hyper-parameters. To address these issues, end-to-end PCR models are proposed recently. In this paper, we develop a SSPCR framework suitable for the end-to-end PCR models for the first time. Overall, we use the current models to generate pseudo labels for unlabeled images, which are in turn utilized to supervise the models training. Besides, we introduce a co-teaching strategy to overcome the confirmation bias problem that generally exists in self-training. A distribution alignment technique is also incorporated to produce high-quality, unbiased pseudo labels for unlabeled data. Experimental results on four histopathology datasets concerning different types of staining styles show the effectiveness and versatility of the proposed framework. Code is available at \textcolor{magenta}{\url{https://github.com/windygooo/SSPCR}

Hao Fu, Guotai Wang, Wenhui Lei et al.

Accurate segmentation of Anatomical brain Barriers to Cancer spread (ABCs) plays an important role for automatic delineation of Clinical Target Volume (CTV) of brain tumors in radiotherapy. Despite that variants of U-Net are state-of-the-art segmentation models, they have limited performance when dealing with ABCs structures with various shapes and sizes, especially thin structures (e.g., the falx cerebri) that span only few slices. To deal with this problem, we propose a High and Multi-Resolution Network (HMRNet) that consists of a multi-scale feature learning branch and a high-resolution branch, which can maintain the high-resolution contextual information and extract more robust representations of anatomical structures with various scales. We further design a Bidirectional Feature Calibration (BFC) block to enable the two branches to generate spatial attention maps for mutual feature calibration. Considering the different sizes and positions of ABCs structures, our network was applied after a rough localization of each structure to obtain fine segmentation results. Experiments on the MICCAI 2020 ABCs challenge dataset showed that: 1) Our proposed two-stage segmentation strategy largely outperformed methods segmenting all the structures in just one stage; 2) The proposed HMRNet with two branches can maintain high-resolution representations and is effective to improve the performance on thin structures; 3) The proposed BFC block outperformed existing attention methods using monodirectional feature calibration. Our method won the second place of ABCs 2020 challenge and has a potential for more accurate and reasonable delineation of CTV of brain tumors.

Meng Han, Xiangde Luo, Wenjun Liao et al.

Multi-organ segmentation in abdominal Computed Tomography (CT) images is of great importance for diagnosis of abdominal lesions and subsequent treatment planning. Though deep learning based methods have attained high performance, they rely heavily on large-scale pixel-level annotations that are time-consuming and labor-intensive to obtain. Due to its low dependency on annotation, weakly supervised segmentation has attracted great attention. However, there is still a large performance gap between current weakly-supervised methods and fully supervised learning, leaving room for exploration. In this work, we propose a novel 3D framework with two consistency constraints for scribble-supervised multiple abdominal organ segmentation from CT. Specifically, we employ a Triple-branch multi-Dilated network (TDNet) with one encoder and three decoders using different dilation rates to capture features from different receptive fields that are complementary to each other to generate high-quality soft pseudo labels. For more stable unsupervised learning, we use voxel-wise uncertainty to rectify the soft pseudo labels and then supervise the outputs of each decoder. To further regularize the network, class relationship information is exploited by encouraging the generated class affinity matrices to be consistent across different decoders under multi-view projection. Experiments on the public WORD dataset show that our method outperforms five existing scribble-supervised methods.

Jingxiong Li, Sunyi Zheng, Zhongyi Shui et al.

Karyotyping is of importance for detecting chromosomal aberrations in human disease. However, chromosomes easily appear curved in microscopic images, which prevents cytogeneticists from analyzing chromosome types. To address this issue, we propose a framework for chromosome straightening, which comprises a preliminary processing algorithm and a generative model called masked conditional variational autoencoders (MC-VAE). The processing method utilizes patch rearrangement to address the difficulty in erasing low degrees of curvature, providing reasonable preliminary results for the MC-VAE. The MC-VAE further straightens the results by leveraging chromosome patches conditioned on their curvatures to learn the mapping between banding patterns and conditions. During model training, we apply a masking strategy with a high masking ratio to train the MC-VAE with eliminated redundancy. This yields a non-trivial reconstruction task, allowing the model to effectively preserve chromosome banding patterns and structure details in the reconstructed results. Extensive experiments on three public datasets with two stain styles show that our framework surpasses the performance of state-of-the-art methods in retaining banding patterns and structure details. Compared to using real-world bent chromosomes, the use of high-quality straightened chromosomes generated by our proposed method can improve the performance of various deep learning models for chromosome classification by a large margin. Such a straightening approach has the potential to be combined with other karyotyping systems to assist cytogeneticists in chromosome analysis.

Zhongyi Shui, Shichuan Zhang, Chenglu Zhu et al.

Reliable quantitative analysis of immunohistochemical staining images requires accurate and robust cell detection and classification. Recent weakly-supervised methods usually estimate probability density maps for cell recognition. However, in dense cell scenarios, their performance can be limited by pre- and post-processing as it is impossible to find a universal parameter setting. In this paper, we introduce an end-to-end framework that applies direct regression and classification for preset anchor points. Specifically, we propose a pyramidal feature aggregation strategy to combine low-level features and high-level semantics simultaneously, which provides accurate cell recognition for our purely point-based model. In addition, an optimized cost function is designed to adapt our multi-task learning framework by matching ground truth and predicted points. The experimental results demonstrate the superior accuracy and efficiency of the proposed method, which reveals the high potentiality in assisting pathologist assessments.

Pingyi Chen, Chenglu Zhu, Zhongyi Shui et al.

The success of supervised deep learning models on cell recognition tasks relies on detailed annotations. Many previous works have managed to reduce the dependency on labels. However, considering the large number of cells contained in a patch, costly and inefficient labeling is still inevitable. To this end, we explored label-free methods for cell recognition. Prior self-activation maps (PSM) are proposed to generate pseudo masks as training targets. To be specific, an activation network is trained with self-supervised learning. The gradient information in the shallow layers of the network is aggregated to generate prior self-activation maps. Afterward, a semantic clustering module is then introduced as a pipeline to transform PSMs to pixel-level semantic pseudo masks for downstream tasks. We evaluated our method on two histological datasets: MoNuSeg (cell segmentation) and BCData (multi-class cell detection). Compared with other fully-supervised and weakly-supervised methods, our method can achieve competitive performance without any manual annotations. Our simple but effective framework can also achieve multi-class cell detection which can not be done by existing unsupervised methods. The results show the potential of PSMs that might inspire other research to deal with the hunger for labels in medical area.

Jia Fu, Litingyu Wang, He Li et al.

Accurate delineation of Gross Tumor Volume (GTV), Lymph Node Clinical Target Volume (LN CTV), and Organ-at-Risk (OAR) from Computed Tomography (CT) scans is essential for precise radiotherapy planning in Nasopharyngeal Carcinoma (NPC). Building upon SegRap2023, which focused on OAR and GTV segmentation using single-center paired non-contrast CT (ncCT) and contrast-enhanced CT (ceCT) scans, the SegRap2025 challenge aims to enhance the generalizability and robustness of segmentation models across imaging centers and modalities. SegRap2025 comprises two tasks: Task01 addresses GTV segmentation using paired CT from the SegRap2023 dataset, with an additional external testing set to evaluate cross-center generalization, and Task02 focuses on LN CTV segmentation using multi-center training data and an unseen external testing set, where each case contains paired CT scans or a single modality, emphasizing both cross-center and cross-modality robustness. This paper presents the challenge setup and provides a comprehensive analysis of the solutions submitted by ten participating teams. For GTV segmentation task, the top-performing models achieved average Dice Similarity Coefficient (DSC) of 74.61% and 56.79% on the internal and external testing cohorts, respectively. For LN CTV segmentation task, the highest average DSC values reached 60.24%, 60.50%, and 57.23% on paired CT, ceCT-only, and ncCT-only subsets, respectively. SegRap2025 establishes a large-scale multi-center, multi-modality benchmark for evaluating the generalization and robustness in radiotherapy target segmentation, providing valuable insights toward clinically applicable automated radiotherapy planning systems. The benchmark is available at: https://hilab-git.github.io/SegRap2025_Challenge.

Honglin Li, Yusuan Sun, Chenglu Zhu et al.

Cervical Cancer continues to be the leading gynecological malignancy, posing a persistent threat to women's health on a global scale. Early screening via cytology Whole Slide Image (WSI) diagnosis is critical to prevent this Cancer progression and improve survival rate, but pathologist's single test suffers inevitable false negative due to the immense number of cells that need to be reviewed within a WSI. Though computer-aided automated diagnostic models can serve as strong complement for pathologists, their effectiveness is hampered by the paucity of extensive and detailed annotations, coupled with the limited interpretability and robustness. These factors significantly hinder their practical applicability and reliability in clinical settings. To tackle these challenges, we develop an AI approach, which is a Scalable Technology for Robust and Interpretable Diagnosis built on Extensive data (STRIDE) of cervical cytology. STRIDE addresses the bottleneck of limited annotations by integrating patient-level labels with a small portion of cell-level labels through an end-to-end training strategy, facilitating scalable learning across extensive datasets. To further improve the robustness to real-world domain shifts of cytology slide-making and imaging, STRIDE employs color adversarial samples training that mimic staining and imaging variations. Lastly, to achieve pathologist-level interpretability for the trustworthiness in clinical settings, STRIDE can generate explanatory textual descriptions that simulates pathologists' diagnostic processes by cell image feature and textual description alignment. Conducting extensive experiments and evaluations in 183 medical centers with a dataset of 341,889 WSIs and 0.1 billion cells from cervical cytology patients, STRIDE has demonstrated a remarkable superiority over previous state-of-the-art techniques.

Litingyu Wang, Wenjun Liao, Shichuan Zhang et al.

Head and neck tumors and metastatic lymph nodes are crucial for treatment planning and prognostic analysis. Accurate segmentation and quantitative analysis of these structures require pixel-level annotation, making automated segmentation techniques essential for the diagnosis and treatment of head and neck cancer. In this study, we investigated the effects of multiple strategies on the segmentation of pre-radiotherapy (pre-RT) and mid-radiotherapy (mid-RT) images. For the segmentation of pre-RT images, we utilized: 1) a fully supervised learning approach, and 2) the same approach enhanced with pre-trained weights and the MixUp data augmentation technique. For mid-RT images, we introduced a novel computational-friendly network architecture that features separate encoders for mid-RT images and registered pre-RT images with their labels. The mid-RT encoder branch integrates information from pre-RT images and labels progressively during the forward propagation. We selected the highest-performing model from each fold and used their predictions to create an ensemble average for inference. In the final test, our models achieved a segmentation performance of 82.38% for pre-RT and 72.53% for mid-RT on aggregated Dice Similarity Coefficient (DSC) as HiLab. Our code is available at https://github.com/WltyBY/HNTS-MRG2024_train_code.

Lanfeng Zhong, Xin Liao, Shichuan Zhang et al.

Pathology image classification plays a crucial role in accurate medical diagnosis and treatment planning. Training high-performance models for this task typically requires large-scale annotated datasets, which are both expensive and time-consuming to acquire. Active Learning (AL) offers a solution by iteratively selecting the most informative samples for annotation, thereby reducing the labeling effort. However, most AL methods are designed under the assumption of a closed-set scenario, where all the unannotated images belong to target classes. In real-world clinical environments, the unlabeled pool often contains a substantial amount of Out-Of-Distribution (OOD) data, leading to low efficiency of annotation in traditional AL methods. Furthermore, most existing AL methods start with random selection in the first query round, leading to a significant waste of labeling costs in open-set scenarios. To address these challenges, we propose OpenPath, a novel open-set active learning approach for pathological image classification leveraging a pre-trained Vision-Language Model (VLM). In the first query, we propose task-specific prompts that combine target and relevant non-target class prompts to effectively select In-Distribution (ID) and informative samples from the unlabeled pool. In subsequent queries, Diverse Informative ID Sampling (DIS) that includes Prototype-based ID candidate Selection (PIS) and Entropy-Guided Stochastic Sampling (EGSS) is proposed to ensure both purity and informativeness in a query, avoiding the selection of OOD samples. Experiments on two public pathology image datasets show that OpenPath significantly enhances the model's performance due to its high purity of selected samples, and outperforms several state-of-the-art open-set AL methods. The code is available at \href{https://github.com/HiLab-git/OpenPath}{https://github.com/HiLab-git/OpenPath}..

Zihao Luo, Zijun Gao, Wenjun Liao et al.

Accurate lymph node (LN) segmentation is critical in radiotherapy treatment and prognosis analysis, but is limited by the need for large annotated datasets. While deep learning-based segmentation foundation models show potential in developing high-performing models with fewer samples, their medical adaptation faces LN domain-specific prior deficiencies and inefficient few-shot fine-tuning for complex clinical practices, highlighting the necessity of an LN segmentation foundation model. In this work, we annotated 36,106 visible LNs from 3,346 publicly available head-and-neck CT scans to establish a robust LN segmentation model (nnUNetv2). Building on this, we propose Dynamic Gradient Sparsification Training (DGST), a few-shot fine-tuning approach that preserves foundational knowledge while dynamically updating the most critical parameters of the LN segmentation model with few annotations. We validate it on two publicly available LN segmentation datasets: SegRap2023 and LNQ2023. The results show that DGST outperforms existing few-shot fine-tuning methods, achieving satisfactory performance with limited labeled data. We release the dataset, models and all implementations to facilitate relevant research: https://github.com/Zihaoluoh/LN-Seg-FM.

Lanfeng Zhong, Zongyao Huang, Yang Liu et al.

Classification of pathological images is the basis for automatic cancer diagnosis. Despite that deep learning methods have achieved remarkable performance, they heavily rely on labeled data, demanding extensive human annotation efforts. In this study, we present a novel human annotation-free method by leveraging pre-trained Vision-Language Models (VLMs). Without human annotation, pseudo-labels of the training set are obtained by utilizing the zero-shot inference capabilities of VLM, which may contain a lot of noise due to the domain gap between the pre-training and target datasets. To address this issue, we introduce VLM-CPL, a novel approach that contains two noisy label filtering techniques with a semi-supervised learning strategy. Specifically, we first obtain prompt-based pseudo-labels with uncertainty estimation by zero-shot inference with the VLM using multiple augmented views of an input. Then, by leveraging the feature representation ability of VLM, we obtain feature-based pseudo-labels via sample clustering in the feature space. Prompt-feature consensus is introduced to select reliable samples based on the consensus between the two types of pseudo-labels. We further propose High-confidence Cross Supervision by to learn from samples with reliable pseudo-labels and the remaining unlabeled samples. Additionally, we present an innovative open-set prompting strategy that filters irrelevant patches from whole slides to enhance the quality of selected patches. Experimental results on five public pathological image datasets for patch-level and slide-level classification showed that our method substantially outperformed zero-shot classification by VLMs, and was superior to existing noisy label learning methods. The code is publicly available at https://github.com/HiLab-git/VLM-CPL.

Wenhui Lei, Haochen Mei, Zhengwentai Sun et al.

Nasopharyngeal Carcinoma (NPC) is a leading form of Head-and-Neck (HAN) cancer in the Arctic, China, Southeast Asia, and the Middle East/North Africa. Accurate segmentation of Organs-at-Risk (OAR) from Computed Tomography (CT) images with uncertainty information is critical for effective planning of radiation therapy for NPC treatment. Despite the stateof-the-art performance achieved by Convolutional Neural Networks (CNNs) for automatic segmentation of OARs, existing methods do not provide uncertainty estimation of the segmentation results for treatment planning, and their accuracy is still limited by several factors, including the low contrast of soft tissues in CT, highly imbalanced sizes of OARs and large inter-slice spacing. To address these problems, we propose a novel framework for accurate OAR segmentation with reliable uncertainty estimation. First, we propose a Segmental Linear Function (SLF) to transform the intensity of CT images to make multiple organs more distinguishable than existing methods based on a simple window width/level that often gives a better visibility of one organ while hiding the others. Second, to deal with the large inter-slice spacing, we introduce a novel 2.5D network (named as 3D-SepNet) specially designed for dealing with clinic HAN CT scans with anisotropic spacing. Thirdly, existing hardness-aware loss function often deal with class-level hardness, but our proposed attention to hard voxels (ATH) uses a voxel-level hardness strategy, which is more suitable to dealing with some hard regions despite that its corresponding class may be easy. Our code is now available at https://github.com/HiLab-git/SepNet.

Xiangde Luo, Jia Fu, Yunxin Zhong et al.

Radiation therapy is a primary and effective NasoPharyngeal Carcinoma (NPC) treatment strategy. The precise delineation of Gross Tumor Volumes (GTVs) and Organs-At-Risk (OARs) is crucial in radiation treatment, directly impacting patient prognosis. Previously, the delineation of GTVs and OARs was performed by experienced radiation oncologists. Recently, deep learning has achieved promising results in many medical image segmentation tasks. However, for NPC OARs and GTVs segmentation, few public datasets are available for model development and evaluation. To alleviate this problem, the SegRap2023 challenge was organized in conjunction with MICCAI2023 and presented a large-scale benchmark for OAR and GTV segmentation with 400 Computed Tomography (CT) scans from 200 NPC patients, each with a pair of pre-aligned non-contrast and contrast-enhanced CT scans. The challenge's goal was to segment 45 OARs and 2 GTVs from the paired CT scans. In this paper, we detail the challenge and analyze the solutions of all participants. The average Dice similarity coefficient scores for all submissions ranged from 76.68\% to 86.70\%, and 70.42\% to 73.44\% for OARs and GTVs, respectively. We conclude that the segmentation of large-size OARs is well-addressed, and more efforts are needed for GTVs and small-size or thin-structure OARs. The benchmark will remain publicly available here: https://segrap2023.grand-challenge.org

Shichuan Zhang, Sunyi Zheng, Zhongyi Shui et al.

Multi-modal Learning has attracted widespread attention in medical image analysis. Using multi-modal data, whole slide images (WSIs) and clinical information, can improve the performance of deep learning models in the diagnosis of axillary lymph node metastasis. However, clinical information is not easy to collect in clinical practice due to privacy concerns, limited resources, lack of interoperability, etc. Although patient selection can ensure the training set to have multi-modal data for model development, missing modality of clinical information can appear during test. This normally leads to performance degradation, which limits the use of multi-modal models in the clinic. To alleviate this problem, we propose a bidirectional distillation framework consisting of a multi-modal branch and a single-modal branch. The single-modal branch acquires the complete multi-modal knowledge from the multi-modal branch, while the multi-modal learns the robust features of WSI from the single-modal. We conduct experiments on a public dataset of Lymph Node Metastasis in Early Breast Cancer to validate the method. Our approach not only achieves state-of-the-art performance with an AUC of 0.861 on the test set without missing data, but also yields an AUC of 0.842 when the rate of missing modality is 80\%. This shows the effectiveness of the approach in dealing with multi-modal data and missing modality. Such a model has the potential to improve treatment decision-making for early breast cancer patients who have axillary lymph node metastatic status.

Xiaochuan Ma, Jia Fu, Wenjun Liao et al.

Brain tumor segmentation is important for diagnosis of the tumor, and current deep-learning methods rely on a large set of annotated images for training, with high annotation costs. Unsupervised segmentation is promising to avoid human annotations while the performance is often limited. In this study, we present a novel unsupervised segmentation approach that leverages the capabilities of foundation models, and it consists of three main steps: (1) A vision-language model (i.e., CLIP) is employed to obtain image-level pseudo-labels for training a classification network. Class Activation Mapping (CAM) is then employed to extract Regions of Interest (ROIs), where an adaptive masking-based data augmentation is used to enhance ROI identification.(2) The ROIs are used to generate bounding box and point prompts for the Segment Anything Model (SAM) to obtain segmentation pseudo-labels. (3) A 3D segmentation network is trained with the SAM-derived pseudo-labels, where low-quality pseudo-labels are filtered out in a self-learning process based on the similarity between the SAM's output and the network's prediction. Evaluation on the BraTS2020 dataset demonstrates that our approach obtained an average Dice Similarity Score (DSC) of 85.60%, outperforming five state-of-the-art unsupervised segmentation methods by more than 10 percentage points. Besides, our approach outperforms directly using SAM for zero-shot inference, and its performance is close to fully supervised learning.

Zixia Jia, Junpeng Li, Shichuan Zhang et al.

Traditional supervised learning heavily relies on human-annotated datasets, especially in data-hungry neural approaches. However, various tasks, especially multi-label tasks like document-level relation extraction, pose challenges in fully manual annotation due to the specific domain knowledge and large class sets. Therefore, we address the multi-label positive-unlabelled learning (MLPUL) problem, where only a subset of positive classes is annotated. We propose Mixture Learner for Partially Annotated Classification (MLPAC), an RL-based framework combining the exploration ability of reinforcement learning and the exploitation ability of supervised learning. Experimental results across various tasks, including document-level relation extraction, multi-label image classification, and binary PU learning, demonstrate the generalization and effectiveness of our framework.

Shichuan Zhang, Chenglu Zhu, Honglin Li et al.

Cell classification and counting in immunohistochemical cytoplasm staining images play a pivotal role in cancer diagnosis. Weakly supervised learning is a potential method to deal with labor-intensive labeling. However, the inconstant cell morphology and subtle differences between classes also bring challenges. To this end, we present a novel cell recognition framework based on multi-task learning, which utilizes two additional auxiliary tasks to guide robust representation learning of the main task. To deal with misclassification, the tissue prior learning branch is introduced to capture the spatial representation of tumor cells without additional tissue annotation. Moreover, dynamic masks and consistency learning are adopted to learn the invariance of cell scale and shape. We have evaluated our framework on immunohistochemical cytoplasm staining images, and the results demonstrate that our method outperforms recent cell recognition approaches. Besides, we have also done some ablation studies to show significant improvements after adding the auxiliary branches.

Jiatong Cai, Chenglu Zhu, Can Cui et al.

Ki67 is a significant biomarker in the diagnosis and prognosis of cancer, whose index can be evaluated by quantifying its expression in Ki67 immunohistochemistry (IHC) stained images. However, quantitative analysis on multi-source Ki67 images is yet a challenging task in practice due to cross-domain distribution differences, which result from imaging variation, staining styles, and lesion types. Many recent studies have made some efforts on domain generalization (DG), whereas there are still some noteworthy limitations. Specifically in the case of Ki67 images, learning invariant representation is at the mercy of the insufficient number of domains and the cell categories mismatching in different domains. In this paper, we propose a novel method to improve DG by searching the domain-agnostic subnetwork in a domain merging scenario. Partial model parameters are iteratively pruned according to the domain gap, which is caused by the data converting from a single domain into merged domains during training. In addition, the model is optimized by fine-tuning on merged domains to eliminate the interference of class mismatching among various domains. Furthermore, an appropriate implementation is attained by applying the pruning method to different parts of the framework. Compared with known DG methods, our method yields excellent performance in multiclass nucleus recognition of Ki67 IHC images, especially in the lost category cases. Moreover, our competitive results are also evaluated on the public dataset over the state-of-the-art DG methods.

Haochen Mei, Wenhui Lei, Ran Gu et al.

Radiotherapy is the main treatment modality for nasopharynx cancer. Delineation of Gross Target Volume (GTV) from medical images such as CT and MRI images is a prerequisite for radiotherapy. As manual delineation is time-consuming and laborious, automatic segmentation of GTV has a potential to improve this process. Currently, most of the deep learning-based automatic delineation methods of GTV are mainly performed on medical images like CT images. However, it is challenged by the low contrast between the pathology regions and surrounding soft tissues, small target region, and anisotropic resolution of clinical CT images. To deal with these problems, we propose a 2.5D Convolutional Neural Network (CNN) to handle the difference of inplane and through-plane resolution. Furthermore, we propose a spatial attention module to enable the network to focus on small target, and use channel attention to further improve the segmentation performance. Moreover, we use multi-scale sampling method for training so that the networks can learn features at different scales, which are combined with a multi-model ensemble method to improve the robustness of segmentation results. We also estimate the uncertainty of segmentation results based on our model ensemble, which is of great importance for indicating the reliability of automatic segmentation results for radiotherapy planning.

Xiangde Luo, Wenjun Liao, Jieneng Chen et al.

Gross Target Volume (GTV) segmentation plays an irreplaceable role in radiotherapy planning for Nasopharyngeal Carcinoma (NPC). Despite that Convolutional Neural Networks (CNN) have achieved good performance for this task, they rely on a large set of labeled images for training, which is expensive and time-consuming to acquire. In this paper, we propose a novel framework with Uncertainty Rectified Pyramid Consistency (URPC) regularization for semi-supervised NPC GTV segmentation. Concretely, we extend a backbone segmentation network to produce pyramid predictions at different scales. The pyramid predictions network (PPNet) is supervised by the ground truth of labeled images and a multi-scale consistency loss for unlabeled images, motivated by the fact that prediction at different scales for the same input should be similar and consistent. However, due to the different resolution of these predictions, encouraging them to be consistent at each pixel directly has low robustness and may lose some fine details. To address this problem, we further design a novel uncertainty rectifying module to enable the framework to gradually learn from meaningful and reliable consensual regions at different scales. Experimental results on a dataset with 258 NPC MR images showed that with only 10% or 20% images labeled, our method largely improved the segmentation performance by leveraging the unlabeled images, and it also outperformed five state-of-the-art semi-supervised segmentation methods. Moreover, when only 50% images labeled, URPC achieved an average Dice score of 82.74% that was close to fully supervised learning.