Weakly supervised semantic segmentation (WSSS) reduces annotation burden by using only image-level labels for histopathology image segmentation. Current WSSS methods face the challenge of bridging the information gap between weak labels and dense prediction tasks, which often results in insufficient class activation maps (CAMs) and increased false positives. Most approaches address this by mining additional object-related information. Following this direction, we propose IPAU, a framework that integrates Prototype, Affinity, and Uncertainty to enhance WSSS. In our IPAU, Prototype-based Information Enhancement (PIE) that uses class-wise prototypes to enrich CAM generation. Affinity-based Self-Refinement (ASR) that refines CAMs into pseudo-masks using affinity correlations without extra training. And Uncertainty-Aware PseudoSupervision (UAPS) that mitigates noise by focusing learning on reliable regions. Experiments on two public histopathology WSSS datasets demonstrate that our IPAU achieves state-of-theart performance.

In the field of gland segmentation in histopathology, deep-learning methods have made significant progress. However, most existing methods not only require a large amount of high-quality annotated data but also tend to confuse the internal of the gland with the background. To address this challenge, we propose a new semi-supervised method named DCCL-Seg for gland segmentation, which follows the teacher-student framework. Our approach can be divided into follows steps. First, we design a contrastive learning module to improve the ability of the student model's feature extractor to distinguish between gland and background features. Then, we introduce a Signed Distance Field (SDF) prediction task and employ dual-consistency strategy (across tasks and models) to better reinforce the learning of gland internal. Next, we proposed a pseudo label filtering and reweighting mechanism, which filters and reweights the pseudo labels generated by the teacher model based on confidence. However, even after reweighting, the pseudo labels may still be influenced by unreliable pixels. Finally, we further designed an assistant predictor to learn the reweighted pseudo labels, which do not interfere with the student model's predictor and ensure the reliability of the student model's predictions. Experimental results on the publicly available GlaS and CRAG datasets demonstrate that our method outperforms other semi-supervised medical image segmentation methods.

Ultrasonography plays an essential role in breast cancer diagnosis. Current deep learning based studies train the models on either images or videos in a centralized learning manner, lacking consideration of joint benefits between two different modality models or the privacy issue of data centralization. In this study, we propose the first decentralized learning solution for joint learning with breast ultrasound video and image, called FedBCD. To enable the model to learn from images and videos simultaneously and seamlessly in client-level local training, we propose a Joint Ultrasound Video and Image Learning (JUVIL) model to bridge the dimension gap between video and image data by incorporating temporal and spatial adapters. The parameter-efficient design of JUVIL with trainable adapters and frozen backbone further reduces the computational cost and communication burden of federated learning, finally improving the overall efficiency. Moreover, considering conventional model-wise aggregation may lead to unstable federated training due to different modalities, data capacities in different clients, and different functionalities across layers. We further propose a Fisher information matrix (FIM) guided Layer-wise Aggregation method named FILA. By measuring layer-wise sensitivity with FIM, FILA assigns higher contributions to the clients with lower sensitivity, improving personalized performance during federated training. Extensive experiments on three image clients and one video client demonstrate the benefits of joint learning architecture, especially for the ones with small-scale data. FedBCD significantly outperforms nine federated learning methods on both video-based and image-based diagnoses, demonstrating the superiority and potential for clinical practice. Code is released at https://github.com/tianpeng-deng/FedBCD.

Semantic segmentation for histopathology images is one of the fundamental tasks in computational pathology. Due to the high cost of pixel-level annotation acquisition, the weakly supervised semantic segmentation (WSSS) attempts to achieve information-intensive segmentation task for histopathology images to reduce the labeling effort of pathologists by leveraging image-level labels. However, traditional WSSS requires a large-scale training set with image-level labels, which still imposes considerable labeling costs on pathologists. To this end, this work proposes a Small-Scale Weakly Supervised Semantic Segmentation (SS-WSSS) approach to achieve the comparable performance only with small-scale weakly-labeled data to further reduce pathologist’s labeling effort. Since histopathology images can easily generate massive unlabeled data, our SS-WSSS aims to learn with the unlabeled data to bridge the information gap. First, we propose a Single-to-Multi Prototype Similarity (S2M-PS) method to generate reliable pseudo-labels for unlabeled data by measuring the similarity between single-label prototypes and multi-label feature maps. Then, we introduce a Cross-Task CoTraining (CT2) method for pseudo-supervision of models with pseudo-labels self-refinement to avoid overfitting to noisy labels. We conduct the experiment on two public datasets to demonstrate the effectiveness of our SS-WSSS. In the experiment, our method achieves comparable performance with SOTA methods only using 30% labeled data.

Histopathological tissue classification is a fundamental task in computational pathology. Deep learning (DL)-based models have achieved superior performance but centralized training suffers from the privacy leakage problem. Federated learning (FL) can safeguard privacy by keeping training samples locally, while existing FL-based frameworks require a large number of well-annotated training samples and numerous rounds of communication which hinder their viability in real-world clinical scenarios. In this article, we propose a lightweight and universal FL framework, named federated deep-broad learning (FedDBL), to achieve superior classification performance with limited training samples and only one-round communication. By simply integrating a pretrained DL feature extractor, a fast and lightweight broad learning inference system with a classical federated aggregation approach, FedDBL can dramatically reduce data dependency and improve communication efficiency. Five-fold cross-validation demonstrates that FedDBL greatly outperforms the competitors with only one-round communication and limited training samples, while it even achieves comparable performance with the ones under multiple-round communications. Furthermore, due to the lightweight design and one-round communication, FedDBL reduces the communication burden from 4.6 GB to only 138.4 KB per client using the ResNet-50 backbone at 50-round training. Extensive experiments also show the scalability of FedDBL on model generalization to the unseen dataset, various client numbers, model personalization and other image modalities. Since no data or deep model sharing across different clients, the privacy issue is well-solved and the model security is guaranteed with no model inversion attack risk. Code is available at https://github.com/tianpeng-deng/FedDBL.

Magnetic resonance imaging (MRI)-based deep neural networks (DNN) have been widely developed to perform prostate cancer (PCa) classification. However, in real-world clinical situations, prostate MRIs can be easily impacted by rectal artifacts, which have been found to lead to incorrect PCa classification. Existing DNN-based methods typically do not consider the interference of rectal artifacts on PCa classification, and do not design specific strategy to address this problem. In this study, we proposed a novel Targeted adversarial training with Proprietary Adversarial Samples (TPAS) strategy to defend the PCa classification model against the influence of rectal artifacts. Specifically, based on clinical prior knowledge, we generated proprietary adversarial samples with rectal artifact-pattern adversarial noise, which can severely mislead PCa classification models optimized by the ordinary training strategy. We then jointly exploited the generated proprietary adversarial samples and original samples to train the models. To demonstrate the effectiveness of our strategy, we conducted analytical experiments on multiple PCa classification models. Compared with ordinary training strategy, TPAS can effectively improve the single- and multi-parametric PCa classification at patient, slice and lesion level, and bring substantial gains to recent advanced models. In conclusion, TPAS strategy can be identified as a valuable way to mitigate the influence of rectal artifacts on deep learning models for PCa classification.

Brain tumor segmentation (BTS) in magnetic resonance image (MRI) is crucial for brain tumor diagnosis, cancer management and research purposes. With the great success of the ten-year BraTS challenges as well as the advances of CNN and Transformer algorithms, a lot of outstanding BTS models have been proposed to tackle the difficulties of BTS in different technical aspects. However, existing studies hardly consider how to fuse the multi-modality images in a reasonable manner. In this paper, we leverage the clinical knowledge of how radiologists diagnose brain tumors from multiple MRI modalities and propose a clinical knowledge-driven brain tumor segmentation model, called CKD-TransBTS. Instead of directly concatenating all the modalities, we re-organize the input modalities by separating them into two groups according to the imaging principle of MRI. A dual-branch hybrid encoder with the proposed modality-correlated cross-attention block (MCCA) is designed to extract the multi-modality image features. The proposed model inherits the strengths from both Transformer and CNN with the local feature representation ability for precise lesion boundaries and long-range feature extraction for 3D volumetric images. To bridge the gap between Transformer and CNN features, we propose a Trans&CNN Feature Calibration block (TCFC) in the decoder. We compare the proposed model with six CNN-based models and six transformer-based models on the BraTS 2021 challenge dataset. Extensive experiments demonstrate that the proposed model achieves state-of-the-art brain tumor segmentation performance compared with all the competitors.

Ultrasonography is an important routine examination for breast cancer diagnosis, due to its non-invasive, radiation-free and low-cost properties. However, the diagnostic accuracy of breast cancer is still limited due to its inherent limitations. Then, a precise diagnose using breast ultrasound (BUS) image would be significant useful. Many learning-based computer-aided diagnostic methods have been proposed to achieve breast cancer diagnosis/lesion classification. However, most of them require a pre-define region of interest (ROI) and then classify the lesion inside the ROI. Conventional classification backbones, such as VGG16 and ResNet50, can achieve promising classification results with no ROI requirement. But these models lack interpretability, thus restricting their use in clinical practice. In this study, we propose a novel ROI-free model for breast cancer diagnosis in ultrasound images with interpretable feature representations. We leverage the anatomical prior knowledge that malignant and benign tumors have different spatial relationships between different tissue layers, and propose a HoVer-Transformer to formulate this prior knowledge. The proposed HoVer-Trans block extracts the inter- and intra-layer spatial information horizontally and vertically. We conduct and release an open dataset GDPH&SYSUCC for breast cancer diagnosis in BUS. The proposed model is evaluated in three datasets by comparing with four CNN-based models and three vision transformer models via five-fold cross validation. It achieves state-of-the-art classification performance (GDPH&SYSUCC AUC: 0.924, ACC: 0.893, Spec: 0.836, Sens: 0.926) with the best model interpretability. In the meanwhile, our proposed model outperforms two senior sonographers on the breast cancer diagnosis when only one BUS image is given (GDPH&SYSUCC-AUC ours: 0.924 vs. reader1: 0.825 vs. reader2: 0.820).

Tissue-level semantic segmentation is a vital step in computational pathology. Fully-supervised models have already achieved outstanding performance with dense pixel-level annotations. However, drawing such labels on the giga-pixel whole slide images is extremely expensive and time-consuming. In this paper, we use only patch-level classification labels to achieve tissue semantic segmentation on histopathology images, finally reducing the annotation efforts. We propose a two-step model including a classification and a segmentation phases. In the classification phase, we propose a CAM-based model to generate pseudo masks by patch-level labels. In the segmentation phase, we achieve tissue semantic segmentation by our propose Multi-Layer Pseudo-Supervision. Several technical novelties have been proposed to reduce the information gap between pixel-level and patch-level annotations. As a part of this paper, we introduce a new weakly-supervised semantic segmentation (WSSS) dataset for lung adenocarcinoma (LUAD-HistoSeg). We conduct several experiments to evaluate our proposed model on two datasets. Our proposed model outperforms five state-of-the-art WSSS approaches. Note that we can achieve comparable quantitative and qualitative results with the fully-supervised model, with only around a 2% gap for MIoU and FwIoU. By comparing with manual labeling on a randomly sampled 100 patches dataset, patch-level labeling can greatly reduce the annotation time from hours to minutes. The source code and the released datasets are available at: https://github.com/ChuHan89/WSSS-Tissue.

Histopathological tissue classification is a simpler way to achieve semantic segmentation for the whole slide images, which can alleviate the requirement of pixel-level dense annotations. Existing works mostly leverage the popular CNN classification backbones in computer vision to achieve histopathological tissue classification. In this paper, we propose a super lightweight plug-and-play module, named Pyramidal Deep-Broad Learning (PDBL), for any well-trained classification backbone to improve the classification performance without a re-training burden. For each patch, we construct a multi-resolution image pyramid to obtain the pyramidal contextual information. For each level in the pyramid, we extract the multi-scale deep-broad features by our proposed Deep-Broad block (DB-block). We equip PDBL in three popular classification backbones, ShuffLeNetV2, EfficientNetb0, and ResNet50 to evaluate the effectiveness and efficiency of our proposed module on two datasets (Kather Multiclass Dataset and the LC25000 Dataset). Experimental results demonstrate the proposed PDBL can steadily improve the tissue-level classification performance for any CNN backbones, especially for the lightweight models when given a small among of training samples (less than 10%). It greatly saves the computational resources and annotation efforts. The source code is available at: https://github.com/linjiatai/PDBL.