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Deep learning has achieved impressive results in nuclei segmentation, but the massive requirement for pixel-wise labels remains a significant challenge. To alleviate the annotation burden, existing methods generate pseudo masks for model training using point labels. However, the generated masks are inevitably different from the ground truth, and these dissimilarities are not handled reasonably during the network training, resulting in the subpar performance of the segmentation model. To tackle this issue, we propose a framework named DoNuSeg, enabling \textbf{D}ynamic pseudo label \textbf{O}ptimization in point-supervised \textbf{Nu}clei \textbf{Seg}mentation. Specifically, DoNuSeg takes advantage of class activation maps (CAMs) to adaptively capture regions with semantics similar to annotated points. To leverage semantic diversity in the hierarchical feature levels, we design a dynamic selection module to choose the optimal one among CAMs from different encoder blocks as pseudo masks. Meanwhile, a CAM-guided contrastive module is proposed to further enhance the accuracy of pseudo masks. In addition to exploiting the semantic information provided by CAMs, we consider location priors inherent to point labels, developing a task-decoupled structure for effectively differentiating nuclei. Extensive experiments demonstrate that DoNuSeg outperforms state-of-the-art point-supervised methods. The code is available at https://github.com/shinning0821/MICCAI24-DoNuSeg., Comment: early accepted by MICCAI2024

Survival prediction, utilizing pathological images and genomic profiles, is increasingly important in cancer analysis and prognosis. Despite significant progress, precise survival analysis still faces two main challenges: (1) The massive pixels contained in whole slide images (WSIs) complicate the process of pathological images, making it difficult to generate an effective representation of the tumor microenvironment (TME). (2) Existing multimodal methods often rely on alignment strategies to integrate complementary information, which may lead to information loss due to the inherent heterogeneity between pathology and genes. In this paper, we propose a Multimodal Cross-Task Interaction (MCTI) framework to explore the intrinsic correlations between subtype classification and survival analysis tasks. Specifically, to capture TME-related features in WSIs, we leverage the subtype classification task to mine tumor regions. Simultaneously, multi-head attention mechanisms are applied in genomic feature extraction, adaptively performing genes grouping to obtain task-related genomic embedding. With the joint representation of pathological images and genomic data, we further introduce a Transport-Guided Attention (TGA) module that uses optimal transport theory to model the correlation between subtype classification and survival analysis tasks, effectively transferring potential information. Extensive experiments demonstrate the superiority of our approaches, with MCTI outperforming state-of-the-art frameworks on three public benchmarks. \href{https://github.com/jsh0792/MCTI}{https://github.com/jsh0792/MCTI}.

With the advent of personalized generation models, users can more readily create images resembling existing content, heightening the risk of violating portrait rights and intellectual property (IP). Traditional post-hoc detection and source-tracing methods for AI-generated content (AIGC) employ proactive watermark approaches; however, these are less effective against personalized generation models. Moreover, attribution techniques for AIGC rely on passive detection but often struggle to differentiate AIGC from authentic images, presenting a substantial challenge. Integrating these two processes into a cohesive framework not only meets the practical demands for protection and forensics but also improves the effectiveness of attribution tasks. Inspired by this insight, we propose a unified approach for image copyright source-tracing and attribution, introducing an innovative watermarking-attribution method that blends proactive and passive strategies. We embed copyright watermarks into protected images and train a watermark decoder to retrieve copyright information from the outputs of personalized models, using this watermark as an initial step for confirming if an image is AIGC-generated. To pinpoint specific generation techniques, we utilize powerful visual backbone networks for classification. Additionally, we implement an incremental learning strategy to adeptly attribute new personalized models without losing prior knowledge, thereby enhancing the model's adaptability to novel generation methods. We have conducted experiments using various celebrity portrait series sourced online, and the results affirm the efficacy of our method in source-tracing and attribution tasks, as well as its robustness against knowledge forgetting.

3D Gaussian Splatting (3DGS) has already become the emerging research focus in the fields of 3D scene reconstruction and novel view synthesis. Given that training a 3DGS requires a significant amount of time and computational cost, it is crucial to protect the copyright, integrity, and privacy of such 3D assets. Steganography, as a crucial technique for encrypted transmission and copyright protection, has been extensively studied. However, it still lacks profound exploration targeted at 3DGS. Unlike its predecessor NeRF, 3DGS possesses two distinct features: 1) explicit 3D representation; and 2) real-time rendering speeds. These characteristics result in the 3DGS point cloud files being public and transparent, with each Gaussian point having a clear physical significance. Therefore, ensuring the security and fidelity of the original 3D scene while embedding information into the 3DGS point cloud files is an extremely challenging task. To solve the above-mentioned issue, we first propose a steganography framework for 3DGS, dubbed GS-Hider, which can embed 3D scenes and images into original GS point clouds in an invisible manner and accurately extract the hidden messages. Specifically, we design a coupled secured feature attribute to replace the original 3DGS's spherical harmonics coefficients and then use a scene decoder and a message decoder to disentangle the original RGB scene and the hidden message. Extensive experiments demonstrated that the proposed GS-Hider can effectively conceal multimodal messages without compromising rendering quality and possesses exceptional security, robustness, capacity, and flexibility. Our project is available at: https://xuanyuzhang21.github.io/project/gshider., Comment: 3DGS steganography

Weakly supervised segmentation methods have gained significant attention due to their ability to reduce the reliance on costly pixel-level annotations during model training. However, the current weakly supervised nuclei segmentation approaches typically follow a two-stage pseudo-label generation and network training process. The performance of the nuclei segmentation heavily relies on the quality of the generated pseudo-labels, thereby limiting its effectiveness. This paper introduces a novel domain-adaptive weakly supervised nuclei segmentation framework using cross-task interaction strategies to overcome the challenge of pseudo-label generation. Specifically, we utilize weakly annotated data to train an auxiliary detection task, which assists the domain adaptation of the segmentation network. To enhance the efficiency of domain adaptation, we design a consistent feature constraint module integrating prior knowledge from the source domain. Furthermore, we develop pseudo-label optimization and interactive training methods to improve the domain transfer capability. To validate the effectiveness of our proposed method, we conduct extensive comparative and ablation experiments on six datasets. The results demonstrate the superiority of our approach over existing weakly supervised approaches. Remarkably, our method achieves comparable or even better performance than fully supervised methods. Our code will be released in https://github.com/zhangye-zoe/DAWN., Comment: 13 pages, 11 figures, 8 tables

Multiple instance learning (MIL) is a robust paradigm for whole-slide pathological image (WSI) analysis, processing gigapixel-resolution images with slide-level labels. As pioneering efforts, attention-based MIL (ABMIL) and its variants are increasingly becoming popular due to the characteristics of simultaneously handling clinical diagnosis and tumor localization. However, the attention mechanism exhibits limitations in discriminating between instances, which often misclassifies tissues and potentially impairs MIL performance. This paper proposes an Attribute-Driven MIL (AttriMIL) framework to address these issues. Concretely, we dissect the calculation process of ABMIL and present an attribute scoring mechanism that measures the contribution of each instance to bag prediction effectively, quantifying instance attributes. Based on attribute quantification, we develop a spatial attribute constraint and an attribute ranking constraint to model instance correlations within and across slides, respectively. These constraints encourage the network to capture the spatial correlation and semantic similarity of instances, improving the ability of AttriMIL to distinguish tissue types and identify challenging instances. Additionally, AttriMIL employs a histopathology adaptive backbone that maximizes the pre-trained model's feature extraction capability for collecting pathological features. Extensive experiments on three public benchmarks demonstrate that our AttriMIL outperforms existing state-of-the-art frameworks across multiple evaluation metrics. The implementation code is available at https://github.com/MedCAI/AttriMIL., Comment: 10 pages, 8 figures

Positron emission tomography (PET) combined with computed tomography (CT) imaging is routinely used in cancer diagnosis and prognosis by providing complementary information. Automatically segmenting tumors in PET/CT images can significantly improve examination efficiency. Traditional multi-modal segmentation solutions mainly rely on concatenation operations for modality fusion, which fail to effectively model the non-linear dependencies between PET and CT modalities. Recent studies have investigated various approaches to optimize the fusion of modality-specific features for enhancing joint representations. However, modality-specific encoders used in these methods operate independently, inadequately leveraging the synergistic relationships inherent in PET and CT modalities, for example, the complementarity between semantics and structure. To address these issues, we propose a Hierarchical Adaptive Interaction and Weighting Network termed H2ASeg to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we design a Modality-Cooperative Spatial Attention (MCSA) module that performs intra- and inter-modal interactions globally and locally. Additionally, a Target-Aware Modality Weighting (TAMW) module is developed to highlight tumor-related features within multi-modal features, thereby refining tumor segmentation. By embedding these modules across different layers, H2ASeg can hierarchically model cross-modal correlations, enabling a nuanced understanding of both semantic and structural tumor features. Extensive experiments demonstrate the superiority of H2ASeg, outperforming state-of-the-art methods on AutoPet-II and Hecktor2022 benchmarks. The code is released at https://github.com/JinPLu/H2ASeg., Comment: 10 pages,4 figures

Recently, pathological diagnosis, the gold standard for cancer diagnosis, has achieved superior performance by combining the Transformer with the multiple instance learning (MIL) framework using whole slide images (WSIs). However, the giga-pixel nature of WSIs poses a great challenge for the quadratic-complexity self-attention mechanism in Transformer to be applied in MIL. Existing studies usually use linear attention to improve computing efficiency but inevitably bring performance bottlenecks. To tackle this challenge, we propose a MamMIL framework for WSI classification by cooperating the selective structured state space model (i.e., Mamba) with MIL for the first time, enabling the modeling of instance dependencies while maintaining linear complexity. Specifically, to solve the problem that Mamba can only conduct unidirectional one-dimensional (1D) sequence modeling, we innovatively introduce a bidirectional state space model and a 2D context-aware block to enable MamMIL to learn the bidirectional instance dependencies with 2D spatial relationships. Experiments on two datasets show that MamMIL can achieve advanced classification performance with smaller memory footprints than the state-of-the-art MIL frameworks based on the Transformer. The code will be open-sourced if accepted., Comment: 11 pages, 2 figures

Semi-supervised segmentation methods have demonstrated promising results in natural scenarios, providing a solution to reduce dependency on manual annotation. However, these methods face significant challenges when directly applied to pathological images due to the subtle color differences between nuclei and tissues, as well as the significant morphological variations among nuclei. Consequently, the generated pseudo-labels often contain much noise, especially at the nuclei boundaries. To address the above problem, this paper proposes a boundary-aware contrastive learning network to denoise the boundary noise in a semi-supervised nuclei segmentation task. The model has two key designs: a low-resolution denoising (LRD) module and a cross-RoI contrastive learning (CRC) module. The LRD improves the smoothness of the nuclei boundary by pseudo-labels denoising, and the CRC enhances the discrimination between foreground and background by boundary feature contrastive learning. We conduct extensive experiments to demonstrate the superiority of our proposed method over existing semi-supervised instance segmentation methods., Comment: 12 pages, 3 figures, 6 tables

Nuclei instance segmentation in histopathological images is of great importance for biological analysis and cancer diagnosis but remains challenging for two reasons. (1) Similar visual presentation of intranuclear and extranuclear regions of chromophobe nuclei often causes under-segmentation, and (2) current methods lack the exploration of nuclei structure, resulting in fragmented instance predictions. To address these problems, this paper proposes a structure encoding and interaction network, termed SEINE, which develops the structure modeling scheme of nuclei and exploits the structure similarity between nuclei to improve the integrality of each segmented instance. Concretely, SEINE introduces a contour-based structure encoding (SE) that considers the correlation between nuclei structure and semantics, realizing a reasonable representation of the nuclei structure. Based on the encoding, we propose a structure-guided attention (SGA) module that takes the clear nuclei as prototypes to enhance the structure learning for the fuzzy nuclei. To strengthen the structural learning ability, a semantic feature fusion (SFF) is presented to boost the semantic consistency of semantic and structure branches. Furthermore, a position enhancement (PE) method is applied to suppress incorrect nuclei boundary predictions. Extensive experiments demonstrate the superiority of our approaches, and SEINE achieves state-of-the-art (SOTA) performance on four datasets. The code is available at https://github.com/zhangye-zoe/SEINE., Comment: 10 pages, 12 figures, 6 tables, submitted to TMI

On conformally compact manifolds we study Yang-Mills equations, their boundary conditions, formal asymptotics, and Dirichlet-to-Neumann maps. We find that smooth solutions with "magnetic" Dirichlet boundary data are obstructed by a conformally invariant, higher order boundary current. We study the asymptotics of the interior Yang-Mills energy functional and show that the obstructing current is the variation of the conformally invariant coefficient of the first log term in this expansion which is a higher derivative conformally invariant analog of the Yang-Mills energy. The invariant energy is the anomaly for the renormalized interior Yang-Mills functional and its variation gives higher conformal Yang-Mills equations. Global solutions to the magnetic boundary problem determine higher order "electric" Neumann data. This yields the Dirichlet-to-Neumann map. We also construct conformally invariant, higher transverse derivative boundary operators. Acting on interior connections, they give obstructions to solving the Yang-Mills boundary problem, determine the asymptotics of formal solutions, and yield conformally invariant tensors capturing the (non-local) electric Neumann data. We also characterize a renormalized Yang-Mills action functional that encodes global features analogously to the renormalized volume for Poincar\'e-Einstein structures., Comment: 71 pages LaTeX, improved presentation

Biomarker detection is an indispensable part in the diagnosis and treatment of low-grade glioma (LGG). However, current LGG biomarker detection methods rely on expensive and complex molecular genetic testing, for which professionals are required to analyze the results, and intra-rater variability is often reported. To overcome these challenges, we propose an interpretable deep learning pipeline, a Multi-Biomarker Histomorphology Discoverer (Multi-Beholder) model based on the multiple instance learning (MIL) framework, to predict the status of five biomarkers in LGG using only hematoxylin and eosin-stained whole slide images and slide-level biomarker status labels. Specifically, by incorporating the one-class classification into the MIL framework, accurate instance pseudo-labeling is realized for instance-level supervision, which greatly complements the slide-level labels and improves the biomarker prediction performance. Multi-Beholder demonstrates superior prediction performance and generalizability for five LGG biomarkers (AUROC=0.6469-0.9735) in two cohorts (n=607) with diverse races and scanning protocols. Moreover, the excellent interpretability of Multi-Beholder allows for discovering the quantitative and qualitative correlations between biomarker status and histomorphology characteristics. Our pipeline not only provides a novel approach for biomarker prediction, enhancing the applicability of molecular treatments for LGG patients but also facilitates the discovery of new mechanisms in molecular functionality and LGG progression., Comment: 47 pages, 6 figures

Recognition of mitotic figures in histologic tumor specimens is highly relevant to patient outcome assessment. This task is challenging for algorithms and human experts alike, with deterioration of algorithmic performance under shifts in image representations. Considerable covariate shifts occur when assessment is performed on different tumor types, images are acquired using different digitization devices, or specimens are produced in different laboratories. This observation motivated the inception of the 2022 challenge on MItosis Domain Generalization (MIDOG 2022). The challenge provided annotated histologic tumor images from six different domains and evaluated the algorithmic approaches for mitotic figure detection provided by nine challenge participants on ten independent domains. Ground truth for mitotic figure detection was established in two ways: a three-expert consensus and an independent, immunohistochemistry-assisted set of labels. This work represents an overview of the challenge tasks, the algorithmic strategies employed by the participants, and potential factors contributing to their success. With an $F_1$ score of 0.764 for the top-performing team, we summarize that domain generalization across various tumor domains is possible with today's deep learning-based recognition pipelines. However, we also found that domain characteristics not present in the training set (feline as new species, spindle cell shape as new morphology and a new scanner) led to small but significant decreases in performance. When assessed against the immunohistochemistry-assisted reference standard, all methods resulted in reduced recall scores, but with only minor changes in the order of participants in the ranking.

Fluorodeoxyglucose (FDG) positron emission tomography (PET) combined with computed tomography (CT) is considered the primary solution for detecting some cancers, such as lung cancer and melanoma. Automatic segmentation of tumors in PET/CT images can help reduce doctors' workload, thereby improving diagnostic quality. However, precise tumor segmentation is challenging due to the small size of many tumors and the similarity of high-uptake normal areas to the tumor regions. To address these issues, this paper proposes a localization-to-segmentation framework (L2SNet) for precise tumor segmentation. L2SNet first localizes the possible lesions in the lesion localization phase and then uses the location cues to shape the segmentation results in the lesion segmentation phase. To further improve the segmentation performance of L2SNet, we design an adaptive threshold scheme that takes the segmentation results of the two phases into consideration. The experiments with the MICCAI 2023 Automated Lesion Segmentation in Whole-Body FDG-PET/CT challenge dataset show that our method achieved a competitive result and was ranked in the top 7 methods on the preliminary test set. Our work is available at: https://github.com/MedCAI/L2SNet., Comment: 7 pages,3 figures

Compressed sensing (CS) is a promising tool for reducing sampling costs. Current deep neural network (NN)-based CS methods face the challenges of collecting labeled measurement-ground truth (GT) data and generalizing to real applications. This paper proposes a novel $\mathbf{S}$elf-supervised s$\mathbf{C}$alable deep CS method, comprising a deep $\mathbf{L}$earning scheme called $\mathbf{SCL}$ and a family of $\mathbf{Net}$works named $\mathbf{SCNet}$, which does not require GT and can handle arbitrary sampling ratios and matrices once trained on a partial measurement set. Our SCL contains a dual-domain loss and a four-stage recovery strategy. The former encourages a cross-consistency on two measurement parts and a sampling-reconstruction cycle-consistency regarding arbitrary ratios and matrices to maximize data/information utilization. The latter can progressively leverage common signal prior in external measurements and internal characteristics of test samples and learned NNs to improve accuracy. SCNet combines both the explicit guidance from optimization algorithms with implicit regularization from advanced NN blocks to learn a collaborative signal representation. Our theoretical analyses and experiments on simulated and real captured data, covering 1-/2-/3-D natural and scientific signals, demonstrate the effectiveness, superior performance, flexibility, and generalization ability of our method over existing self-supervised methods and its significant potential in competing against state-of-the-art supervised methods. Code is available at https://github.com/Guaishou74851/SCNet., Comment: Accepted by Internaltional Journal of Computer Vision

Survival prediction based on whole slide images (WSIs) is a challenging task for patient-level multiple instance learning (MIL). Due to the vast amount of data for a patient (one or multiple gigapixels WSIs) and the irregularly shaped property of WSI, it is difficult to fully explore spatial, contextual, and hierarchical interaction in the patient-level bag. Many studies adopt random sampling pre-processing strategy and WSI-level aggregation models, which inevitably lose critical prognostic information in the patient-level bag. In this work, we propose a hierarchical vision Transformer framework named HVTSurv, which can encode the local-level relative spatial information, strengthen WSI-level context-aware communication, and establish patient-level hierarchical interaction. Firstly, we design a feature pre-processing strategy, including feature rearrangement and random window masking. Then, we devise three layers to progressively obtain patient-level representation, including a local-level interaction layer adopting Manhattan distance, a WSI-level interaction layer employing spatial shuffle, and a patient-level interaction layer using attention pooling. Moreover, the design of hierarchical network helps the model become more computationally efficient. Finally, we validate HVTSurv with 3,104 patients and 3,752 WSIs across 6 cancer types from The Cancer Genome Atlas (TCGA). The average C-Index is 2.50-11.30% higher than all the prior weakly supervised methods over 6 TCGA datasets. Ablation study and attention visualization further verify the superiority of the proposed HVTSurv. Implementation is available at: https://github.com/szc19990412/HVTSurv., Comment: accepted by AAAI 2023

For invasive breast cancer, immunohistochemical (IHC) techniques are often used to detect the expression level of human epidermal growth factor receptor-2 (HER2) in breast tissue to formulate a precise treatment plan. From the perspective of saving manpower, material and time costs, directly generating IHC-stained images from Hematoxylin and Eosin (H&E) stained images is a valuable research direction. Therefore, we held the breast cancer immunohistochemical image generation challenge, aiming to explore novel ideas of deep learning technology in pathological image generation and promote research in this field. The challenge provided registered H&E and IHC-stained image pairs, and participants were required to use these images to train a model that can directly generate IHC-stained images from corresponding H&E-stained images. We selected and reviewed the five highest-ranking methods based on their PSNR and SSIM metrics, while also providing overviews of the corresponding pipelines and implementations. In this paper, we further analyze the current limitations in the field of breast cancer immunohistochemical image generation and forecast the future development of this field. We hope that the released dataset and the challenge will inspire more scholars to jointly study higher-quality IHC-stained image generation., Comment: 12 pages, 12 figures, 2tables

Hyperspectral imaging plays a pivotal role in a wide range of applications, like remote sensing, medicine, and cytology. By acquiring 3D hyperspectral images (HSIs) via 2D sensors, the coded aperture snapshot spectral imaging (CASSI) has achieved great success due to its hardware-friendly implementation and fast imaging speed. However, for some less spectrally sparse scenes, single snapshot and unreasonable coded aperture design tend to make HSI recovery more ill-posed and yield poor spatial and spectral fidelity. In this paper, we propose a novel Progressive Content-Aware CASSI framework, dubbed PCA-CASSI, which captures HSIs with multiple optimized content-aware coded apertures and fuses all the snapshots for reconstruction progressively. Simultaneously, by mapping the Range-Null space Decomposition (RND) into a deep network with several phases, an RND-HRNet is proposed for HSI recovery. Each recovery phase can fully exploit the hidden physical information in the coded apertures via explicit $\mathcal{R}$$-$$\mathcal{N}$ decomposition and explore the spatial-spectral correlation by dual transformer blocks. Our method is validated to surpass other state-of-the-art methods on both multiple- and single-shot HSI imaging tasks by large margins., Comment: a novel hyperspectral snapshot compressive imaging and restoration framework

Multiple Instance Learning (MIL), a powerful strategy for weakly supervised learning, is able to perform various prediction tasks on gigapixel Whole Slide Images (WSIs). However, the tens of thousands of patches in WSIs usually incur a vast computational burden for image augmentation, limiting the MIL model's improvement in performance. Currently, the feature augmentation-based MIL framework is a promising solution, while existing methods such as Mixup often produce unrealistic features. To explore a more efficient and practical augmentation method, we introduce the Diffusion Model (DM) into MIL for the first time and propose a feature augmentation framework called AugDiff. Specifically, we employ the generation diversity of DM to improve the quality of feature augmentation and the step-by-step generation property to control the retention of semantic information. We conduct extensive experiments over three distinct cancer datasets, two different feature extractors, and three prevalent MIL algorithms to evaluate the performance of AugDiff. Ablation study and visualization further verify the effectiveness. Moreover, we highlight AugDiff's higher-quality augmented feature over image augmentation and its superiority over self-supervised learning. The generalization over external datasets indicates its broader applications.

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

Recently, Transformer architecture has been introduced into image restoration to replace convolution neural network (CNN) with surprising results. Considering the high computational complexity of Transformer with global attention, some methods use the local square window to limit the scope of self-attention. However, these methods lack direct interaction among different windows, which limits the establishment of long-range dependencies. To address the above issue, we propose a new image restoration model, Cross Aggregation Transformer (CAT). The core of our CAT is the Rectangle-Window Self-Attention (Rwin-SA), which utilizes horizontal and vertical rectangle window attention in different heads parallelly to expand the attention area and aggregate the features cross different windows. We also introduce the Axial-Shift operation for different window interactions. Furthermore, we propose the Locality Complementary Module to complement the self-attention mechanism, which incorporates the inductive bias of CNN (e.g., translation invariance and locality) into Transformer, enabling global-local coupling. Extensive experiments demonstrate that our CAT outperforms recent state-of-the-art methods on several image restoration applications. The code and models are available at https://github.com/zhengchen1999/CAT., Comment: Accepted to NeurIPS 2022. Code is available at https://github.com/zhengchen1999/CAT

Recently, Transformer-based image restoration networks have achieved promising improvements over convolutional neural networks due to parameter-independent global interactions. To lower computational cost, existing works generally limit self-attention computation within non-overlapping windows. However, each group of tokens are always from a dense area of the image. This is considered as a dense attention strategy since the interactions of tokens are restrained in dense regions. Obviously, this strategy could result in restricted receptive fields. To address this issue, we propose Attention Retractable Transformer (ART) for image restoration, which presents both dense and sparse attention modules in the network. The sparse attention module allows tokens from sparse areas to interact and thus provides a wider receptive field. Furthermore, the alternating application of dense and sparse attention modules greatly enhances representation ability of Transformer while providing retractable attention on the input image.We conduct extensive experiments on image super-resolution, denoising, and JPEG compression artifact reduction tasks. Experimental results validate that our proposed ART outperforms state-of-the-art methods on various benchmark datasets both quantitatively and visually. We also provide code and models at https://github.com/gladzhang/ART., Comment: Accepted to ICLR 2023. Code and models are available at https://github.com/gladzhang/ART

Neural networks have been rapidly expanding in recent years, with novel strategies and applications. However, challenges such as interpretability, explainability, robustness, safety, trust, and sensibility remain unsolved in neural network technologies, despite the fact that they will unavoidably be addressed for critical applications. Attempts have been made to overcome the challenges in neural network computing by representing and embedding domain knowledge in terms of symbolic representations. Thus, the neuro-symbolic learning (NeSyL) notion emerged, which incorporates aspects of symbolic representation and bringing common sense into neural networks (NeSyL). In domains where interpretability, reasoning, and explainability are crucial, such as video and image captioning, question-answering and reasoning, health informatics, and genomics, NeSyL has shown promising outcomes. This review presents a comprehensive survey on the state-of-the-art NeSyL approaches, their principles, advances in machine and deep learning algorithms, applications such as opthalmology, and most importantly, future perspectives of this emerging field., Comment: 24 pages, 16 figures

With the development of computational pathology, deep learning methods for Gleason grading through whole slide images (WSIs) have excellent prospects. Since the size of WSIs is extremely large, the image label usually contains only slide-level label or limited pixel-level labels. The current mainstream approach adopts multi-instance learning to predict Gleason grades. However, some methods only considering the slide-level label ignore the limited pixel-level labels containing rich local information. Furthermore, the method of additionally considering the pixel-level labels ignores the inaccuracy of pixel-level labels. To address these problems, we propose a mixed supervision Transformer based on the multiple instance learning framework. The model utilizes both slide-level label and instance-level labels to achieve more accurate Gleason grading at the slide level. The impact of inaccurate instance-level labels is further reduced by introducing an efficient random masking strategy in the mixed supervision training process. We achieve the state-of-the-art performance on the SICAPv2 dataset, and the visual analysis shows the accurate prediction results of instance level. The source code is available at https://github.com/bianhao123/Mixed_supervision., Comment: Accepted by MICCAI 2022

Acute leukemia is a type of blood cancer with a high mortality rate. Current therapeutic methods include bone marrow transplantation, supportive therapy, and chemotherapy. Although a satisfactory remission of the disease can be achieved, the risk of recurrence is still high. Therefore, novel treatments are demanding. Chimeric antigen receptor-T (CAR-T) therapy has emerged as a promising approach to treat and cure acute leukemia. To harness the therapeutic potential of CAR-T cell therapy for blood diseases, reliable cell morphological identification is crucial. Nevertheless, the identification of CAR-T cells is a big challenge posed by their phenotypic similarity with other blood cells. To address this substantial clinical challenge, herein we first construct a CAR-T dataset with 500 original microscopy images after staining. Following that, we create a novel integrated model called RCMNet (ResNet18 with CBAM and MHSA) that combines the convolutional neural network (CNN) and Transformer. The model shows 99.63% top-1 accuracy on the public dataset. Compared with previous reports, our model obtains satisfactory results for image classification. Although testing on the CAR-T cells dataset, a decent performance is observed, which is attributed to the limited size of the dataset. Transfer learning is adapted for RCMNet and a maximum of 83.36% accuracy has been achieved, which is higher than other SOTA models. The study evaluates the effectiveness of RCMNet on a big public dataset and translates it to a clinical dataset for diagnostic applications.

Deep learning techniques have shown great potential in medical image processing, particularly through accurate and reliable image segmentation on magnetic resonance imaging (MRI) scans or computed tomography (CT) scans, which allow the localization and diagnosis of lesions. However, training these segmentation models requires a large number of manually annotated pixel-level labels, which are time-consuming and labor-intensive, in contrast to image-level labels that are easier to obtain. It is imperative to resolve this problem through weakly-supervised semantic segmentation models using image-level labels as supervision since it can significantly reduce human annotation efforts. Most of the advanced solutions exploit class activation mapping (CAM). However, the original CAMs rarely capture the precise boundaries of lesions. In this study, we propose the strategy of multi-scale inference to refine CAMs by reducing the detail loss in single-scale reasoning. For segmentation, we develop a novel model named Mixed-UNet, which has two parallel branches in the decoding phase. The results can be obtained after fusing the extracted features from two branches. We evaluate the designed Mixed-UNet against several prevalent deep learning-based segmentation approaches on our dataset collected from the local hospital and public datasets. The validation results demonstrate that our model surpasses available methods under the same supervision level in the segmentation of various lesions from brain imaging., Comment: 12 pages, 7 figures

Compressed Sensing MRI (CS-MRI) aims at reconstructing de-aliased images from sub-Nyquist sampling k-space data to accelerate MR Imaging, thus presenting two basic issues, i.e., where to sample and how to reconstruct. To deal with both problems simultaneously, we propose a novel end-to-end Probabilistic Under-sampling and Explicable Reconstruction neTwork, dubbed PUERT, to jointly optimize the sampling pattern and the reconstruction network. Instead of learning a deterministic mask, the proposed sampling subnet explores an optimal probabilistic sub-sampling pattern, which describes independent Bernoulli random variables at each possible sampling point, thus retaining robustness and stochastics for a more reliable CS reconstruction. A dynamic gradient estimation strategy is further introduced to gradually approximate the binarization function in backward propagation, which efficiently preserves the gradient information and further improves the reconstruction quality. Moreover, in our reconstruction subnet, we adopt a model-based network design scheme with high efficiency and interpretability, which is shown to assist in further exploitation for the sampling subnet. Extensive experiments on two widely used MRI datasets demonstrate that our proposed PUERT not only achieves state-of-the-art results in terms of both quantitative metrics and visual quality but also yields a sub-sampling pattern and a reconstruction model that are both customized to training data.

Lung cancer is the leading cause of cancer death worldwide, and adenocarcinoma (LUAD) is the most common subtype. Exploiting the potential value of the histopathology images can promote precision medicine in oncology. Tissue segmentation is the basic upstream task of histopathology image analysis. Existing deep learning models have achieved superior segmentation performance but require sufficient pixel-level annotations, which is time-consuming and expensive. To enrich the label resources of LUAD and to alleviate the annotation efforts, we organize this challenge WSSS4LUAD to call for the outstanding weakly-supervised semantic segmentation (WSSS) techniques for histopathology images of LUAD. Participants have to design the algorithm to segment tumor epithelial, tumor-associated stroma and normal tissue with only patch-level labels. This challenge includes 10,091 patch-level annotations (the training set) and over 130 million labeled pixels (the validation and test sets), from 87 WSIs (67 from GDPH, 20 from TCGA). All the labels were generated by a pathologist-in-the-loop pipeline with the help of AI models and checked by the label review board. Among 532 registrations, 28 teams submitted the results in the test phase with over 1,000 submissions. Finally, the first place team achieved mIoU of 0.8413 (tumor: 0.8389, stroma: 0.7931, normal: 0.8919). According to the technical reports of the top-tier teams, CAM is still the most popular approach in WSSS. Cutmix data augmentation has been widely adopted to generate more reliable samples. With the success of this challenge, we believe that WSSS approaches with patch-level annotations can be a complement to the traditional pixel annotations while reducing the annotation efforts. The entire dataset has been released to encourage more researches on computational pathology in LUAD and more novel WSSS techniques.

Lensless imaging is a popular research field for the advantages of small size, wide field-of-view and low aberration in recent years. However, some traditional lensless imaging methods suffer from slow convergence, mechanical errors and conjugate solution interference, which limit its further application and development. In this work, we proposed a lensless imaging method based on spatial light modulator (SLM) with unknown modulation curve. In our imaging system, we use SLM to modulate the wavefront of object, and introduce the ptychographic scanning algorithm that is able to recover the complex amplitude information even the SLM modulation curve is inaccurate or unknown. In addition, we also design a split-beam interference experiment to calibrate the modulation curve of SLM, and using the calibrated modulation function as the initial value of the expended ptychography iterative engine (ePIE) algorithm can improve the convergence speed. We further analyze the effect of modulation function, algorithm parameters and the characteristics of the coherent light source on the quality of reconstructed image. The simulated and real experiments show that the proposed method is superior to traditional mechanical scanning methods in terms of recovering speed and accuracy, with the recovering resolution up to 14 um.

Hyperspectral imaging is an essential imaging modality for a wide range of applications, especially in remote sensing, agriculture, and medicine. Inspired by existing hyperspectral cameras that are either slow, expensive, or bulky, reconstructing hyperspectral images (HSIs) from a low-budget snapshot measurement has drawn wide attention. By mapping a truncated numerical optimization algorithm into a network with a fixed number of phases, recent deep unfolding networks (DUNs) for spectral snapshot compressive sensing (SCI) have achieved remarkable success. However, DUNs are far from reaching the scope of industrial applications limited by the lack of cross-phase feature interaction and adaptive parameter adjustment. In this paper, we propose a novel Hyperspectral Explicable Reconstruction and Optimal Sampling deep Network for SCI, dubbed HerosNet, which includes several phases under the ISTA-unfolding framework. Each phase can flexibly simulate the sensing matrix and contextually adjust the step size in the gradient descent step, and hierarchically fuse and interact the hidden states of previous phases to effectively recover current HSI frames in the proximal mapping step. Simultaneously, a hardware-friendly optimal binary mask is learned end-to-end to further improve the reconstruction performance. Finally, our HerosNet is validated to outperform the state-of-the-art methods on both simulation and real datasets by large margins. The source code is available at https://github.com/jianzhangcs/HerosNet., Comment: CVPR2022

Confocal microscopy is the standard approach for obtaining volumetric images of a sample with high axial and lateral resolution, especially when dealing with scattering samples. Unfortunately, a confocal microscope is quite expensive compared to traditional microscopes. In addition, the point scanning in a confocal leads to slow imaging speed and photobleaching due to the high dose of laser energy. In this paper, we demonstrate how the advances in machine learning can be exploited to "teach" a traditional wide-field microscope, one that's available in every lab, into producing 3D volumetric images like a confocal. The key idea is to obtain multiple images with different focus settings using a wide-field microscope and use a 3D Generative Adversarial Network (GAN) based neural network to learn the mapping between the blurry low-contrast image stack obtained using wide-field and the sharp, high-contrast images obtained using a confocal. After training the network with widefield-confocal image pairs, the network can reliably and accurately reconstruct 3D volumetric images that rival confocal in terms of its lateral resolution, z-sectioning and image contrast. Our experimental results demonstrate generalization ability to handle unseen data, stability in the reconstruction results, high spatial resolution even when imaging thick ($\sim40$ microns) highly-scattering samples. We believe that such learning-based-microscopes have the potential to bring confocal quality imaging to every lab that has a wide-field microscope.

Multiple instance learning (MIL) is a powerful tool to solve the weakly supervised classification in whole slide image (WSI) based pathology diagnosis. However, the current MIL methods are usually based on independent and identical distribution hypothesis, thus neglect the correlation among different instances. To address this problem, we proposed a new framework, called correlated MIL, and provided a proof for convergence. Based on this framework, we devised a Transformer based MIL (TransMIL), which explored both morphological and spatial information. The proposed TransMIL can effectively deal with unbalanced/balanced and binary/multiple classification with great visualization and interpretability. We conducted various experiments for three different computational pathology problems and achieved better performance and faster convergence compared with state-of-the-art methods. The test AUC for the binary tumor classification can be up to 93.09% over CAMELYON16 dataset. And the AUC over the cancer subtypes classification can be up to 96.03% and 98.82% over TCGA-NSCLC dataset and TCGA-RCC dataset, respectively. Implementation is available at: https://github.com/szc19990412/TransMIL.

In this paper, we investigate a cache updating system with a server containing $N$ files, $K$ relays and $M$ users. The server keeps the freshest versions of the files which are updated with fixed rates. Each relay can download the fresh files from the server in a certain period of time. Each user can get the fresh files from any relay as long as the relay has stored the fresh versions of the requested files. Due to the limited storage capacity and updating capacity of each relay, different cache designs will lead to different average freshness of all updating files at users. In order to keep the average freshness as large as possible in the cache updating system, we formulate an average freshness-optimal cache updating problem (AFOCUP) to obtain an optimal cache scheme. However, because of the nonlinearity of the AFOCUP, it is difficult to seek out the optimal cache scheme. As a result, an linear approximate model is suggested by distributing the total update rates completely in accordance with the number of files in the relay in advance. Then we utilize the greedy algorithm to search the optimal cache scheme that is satisfied with the limited storage capacity of each relay. Finally, some numerical examples are provided to illustrate the performance of the approximate solution.

The depth images denoising are increasingly becoming the hot research topic nowadays because they reflect the three-dimensional (3D) scene and can be applied in various fields of computer vision. But the depth images obtained from depth camera usually contain stains such as noise, which greatly impairs the performance of depth related applications. In this paper, considering that group-based image restoration methods are more effective in gathering the similarity among patches, a group based nuclear norm and learning graph (GNNLG) model was proposed. For each patch, we find and group the most similar patches within a searching window. The intrinsic low-rank property of the grouped patches is exploited in our model. In addition, we studied the manifold learning method and devised an effective optimized learning strategy to obtain the graph Laplacian matrix, which reflects the topological structure of image, to further impose the smoothing priors to the denoised depth image. To achieve fast speed and high convergence, the alternating direction method of multipliers (ADMM) is proposed to solve our GNNLG. The experimental results show that the proposed method is superior to other current state-of-the-art denoising methods in both subjective and objective criterion.

Recent works have demonstrated that deep learning (DL) based compressed sensing (CS) implementation can accelerate Magnetic Resonance (MR) Imaging by reconstructing MR images from sub-sampled k-space data. However, network architectures adopted in previous methods are all designed by handcraft. Neural Architecture Search (NAS) algorithms can automatically build neural network architectures which have outperformed human designed ones in several vision tasks. Inspired by this, here we proposed a novel and efficient network for the MR image reconstruction problem via NAS instead of manual attempts. Particularly, a specific cell structure, which was integrated into the model-driven MR reconstruction pipeline, was automatically searched from a flexible pre-defined operation search space in a differentiable manner. Experimental results show that our searched network can produce better reconstruction results compared to previous state-of-the-art methods in terms of PSNR and SSIM with 4-6 times fewer computation resources. Extensive experiments were conducted to analyze how hyper-parameters affect reconstruction performance and the searched structures. The generalizability of the searched architecture was also evaluated on different organ MR datasets. Our proposed method can reach a better trade-off between computation cost and reconstruction performance for MR reconstruction problem with good generalizability and offer insights to design neural networks for other medical image applications. The evaluation code will be available at https://github.com/yjump/NAS-for-CSMRI., Comment: Published on Computerized Medical Imaging and Graphics

Recent advancements in whole slide imaging (WSI) have moved pathology closer to digital practice. Existing systems require precise mechanical control and the cost is prohibitive for most individual pathologists. Here we report a low-cost and high-throughput WSI system termed OpenWSI. The reported system is built using off-the-shelf components including a programmable LED array, a photographic lens, and a low-cost computer numerical control (CNC) router. Different from conventional WSI platforms, our system performs real-time single-frame autofocusing using color-multiplexed illumination. For axial positioning control, we perform coarse adjustment using the CNC router and precise adjustment using the ultrasonic motor ring in the photographic lens. By using a 20X objective lens, we show that the OpenWSI system has a resolution of ~0.7 microns. It can acquire whole slide images of a 225-mm^2 region in ~2 mins, with throughput comparable to existing high-end platforms. The reported system offers a turnkey solution to transform the high-end WSI platforms into one that can be made broadly available and utilizable without loss of capacity.

Fourier ptychography (FP) is a newly developed computational imaging approach that achieves both high resolution and wide field of view by stitching a series of low-resolution images captured under angle-varied illumination. So far, many supervised data-driven models have been applied to solve inverse imaging problems. These models need massive amounts of data to train, and are limited by the dataset characteristics. In FP problems, generic datasets are always scarce, and the optical aberration varies greatly under different acquisition conditions. To address these dilemmas, we model the forward physical imaging process as an interpretable physics-guided neural network (PgNN), where the reconstructed image in the complex domain is considered as the learnable parameters of the neural network. Since the optimal parameters of the PgNN can be derived by minimizing the difference between the model-generated images and real captured angle-varied images corresponding to the same scene, the proposed PgNN can get rid of the problem of massive training data as in traditional supervised methods. Applying the alternate updating mechanism and the total variation regularization, PgNN can flexibly reconstruct images with improved performance. In addition, the Zernike mode is incorporated to compensate for optical aberrations to enhance the robustness of FP reconstructions. As a demonstration, we show our method can reconstruct images with smooth performance and detailed information in both simulated and experimental datasets. In particular, when validated in an extension of a high-defocus, high-exposure tissue section dataset, PgNN outperforms traditional FP methods with fewer artifacts and distinguishable structures.