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Generative self-supervised learning demonstrates outstanding representation learning capabilities in both Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs). However, there are currently no generative pre-training methods related to selective state space models (Mamba) that can handle long-range dependencies effectively. To address this challenge, we introduce a generative self-supervised learning method for Mamba (MambaMIM) based on Selective Structure State Space Sequence Token-interpolation (S6T), a general-purpose pre-training method for arbitrary Mamba architectures. Our method, MambaMIM, incorporates a bottom-up 3D hybrid masking strategy in the encoder to maintain masking consistency across different architectures. Additionally, S6T is employed to learn causal relationships between the masked sequence in the state space. MambaMIM can be used on any single or hybrid Mamba architectures to enhance the Mamba long-range representation capability. Extensive downstream experiments reveal the feasibility and advancement of using Mamba for pre-training medical image tasks. The code is available at: https://github.com/FengheTan9/MambaMIM, Comment: 10 pages, 7 figures

The generative self-supervised learning strategy exhibits remarkable learning representational capabilities. However, there is limited attention to end-to-end pre-training methods based on a hybrid architecture of CNN and Transformer, which can learn strong local and global representations simultaneously. To address this issue, we propose a generative pre-training strategy called Hybrid Sparse masKing (HySparK) based on masked image modeling and apply it to large-scale pre-training on medical images. First, we perform a bottom-up 3D hybrid masking strategy on the encoder to keep consistency masking. Then we utilize sparse convolution for the top CNNs and encode unmasked patches for the bottom vision Transformers. Second, we employ a simple hierarchical decoder with skip-connections to achieve dense multi-scale feature reconstruction. Third, we implement our pre-training method on a collection of multiple large-scale 3D medical imaging datasets. Extensive experiments indicate that our proposed pre-training strategy demonstrates robust transfer-ability in supervised downstream tasks and sheds light on HySparK's promising prospects. The code is available at https://github.com/FengheTan9/HySparK, Comment: Early accept at MICCAI 2024

The advent of foundation models (FMs) in healthcare offers unprecedented opportunities to enhance medical diagnostics through automated classification and segmentation tasks. However, these models also raise significant concerns about their fairness, especially when applied to diverse and underrepresented populations in healthcare applications. Currently, there is a lack of comprehensive benchmarks, standardized pipelines, and easily adaptable libraries to evaluate and understand the fairness performance of FMs in medical imaging, leading to considerable challenges in formulating and implementing solutions that ensure equitable outcomes across diverse patient populations. To fill this gap, we introduce FairMedFM, a fairness benchmark for FM research in medical imaging.FairMedFM integrates with 17 popular medical imaging datasets, encompassing different modalities, dimensionalities, and sensitive attributes. It explores 20 widely used FMs, with various usages such as zero-shot learning, linear probing, parameter-efficient fine-tuning, and prompting in various downstream tasks -- classification and segmentation. Our exhaustive analysis evaluates the fairness performance over different evaluation metrics from multiple perspectives, revealing the existence of bias, varied utility-fairness trade-offs on different FMs, consistent disparities on the same datasets regardless FMs, and limited effectiveness of existing unfairness mitigation methods. Checkout FairMedFM's project page and open-sourced codebase, which supports extendible functionalities and applications as well as inclusive for studies on FMs in medical imaging over the long term., Comment: 29 pages, 17 figures

Emerging unsupervised reconstruction techniques based on implicit neural representation (INR), such as NeRP, CoIL, and SCOPE, have shown unique capabilities in CT linear inverse imaging. In this work, we propose a novel unsupervised density neural representation (Diner) to tackle the challenging problem of CT metal artifacts when scanned objects contain metals. The drastic variation of linear attenuation coefficients (LACs) of metals over X-ray spectra leads to a nonlinear beam hardening effect (BHE) in CT measurements. Recovering CT images from metal-affected measurements therefore poses a complicated nonlinear inverse problem. Existing metal artifact reduction (MAR) techniques mostly formulate the MAR as an image inpainting task, which ignores the energy-induced BHE and produces suboptimal performance. Instead, our Diner introduces an energy-dependent polychromatic CT forward model to the INR framework, addressing the nonlinear nature of the MAR problem. Specifically, we decompose the energy-dependent LACs into energy-independent densities and energy-dependent mass attenuation coefficients (MACs) by fully considering the physical model of X-ray absorption. Using the densities as pivot variables and the MACs as known prior knowledge, the LACs can be accurately reconstructed from the raw measurements. Technically, we represent the unknown density map as an implicit function of coordinates. Combined with a novel differentiable forward model simulating the physical acquisition from the densities to the measurements, our Diner optimizes a multi-layer perception network to approximate the implicit function by minimizing predicted errors between the estimated and real measurements. Experimental results on simulated and real datasets confirm the superiority of our unsupervised Diner against popular supervised techniques in MAR performance and robustness., Comment: 13 pages

Limited-angle and sparse-view computed tomography (LACT and SVCT) are crucial for expanding the scope of X-ray CT applications. However, they face challenges due to incomplete data acquisition, resulting in diverse artifacts in the reconstructed CT images. Emerging implicit neural representation (INR) techniques, such as NeRF, NeAT, and NeRP, have shown promise in under-determined CT imaging reconstruction tasks. However, the unsupervised nature of INR architecture imposes limited constraints on the solution space, particularly for the highly ill-posed reconstruction task posed by LACT and ultra-SVCT. In this study, we introduce the Diffusion Prior Driven Neural Representation (DPER), an advanced unsupervised framework designed to address the exceptionally ill-posed CT reconstruction inverse problems. DPER adopts the Half Quadratic Splitting (HQS) algorithm to decompose the inverse problem into data fidelity and distribution prior sub-problems. The two sub-problems are respectively addressed by INR reconstruction scheme and pre-trained score-based diffusion model. This combination first injects the implicit image local consistency prior from INR. Additionally, it effectively augments the feasibility of the solution space for the inverse problem through the generative diffusion model, resulting in increased stability and precision in the solutions. We conduct comprehensive experiments to evaluate the performance of DPER on LACT and ultra-SVCT reconstruction with two public datasets (AAPM and LIDC), an in-house clinical COVID-19 dataset and a public raw projection dataset created by Mayo Clinic. The results show that our method outperforms the state-of-the-art reconstruction methods on in-domain datasets, while achieving significant performance improvements on out-of-domain (OOD) datasets., Comment: 16 pages, 11 figures

Image-to-image translation is a vital component in medical imaging processing, with many uses in a wide range of imaging modalities and clinical scenarios. Previous methods include Generative Adversarial Networks (GANs) and Diffusion Models (DMs), which offer realism but suffer from instability and lack uncertainty estimation. Even though both GAN and DM methods have individually exhibited their capability in medical image translation tasks, the potential of combining a GAN and DM to further improve translation performance and to enable uncertainty estimation remains largely unexplored. In this work, we address these challenges by proposing a Cascade Multi-path Shortcut Diffusion Model (CMDM) for high-quality medical image translation and uncertainty estimation. To reduce the required number of iterations and ensure robust performance, our method first obtains a conditional GAN-generated prior image that will be used for the efficient reverse translation with a DM in the subsequent step. Additionally, a multi-path shortcut diffusion strategy is employed to refine translation results and estimate uncertainty. A cascaded pipeline further enhances translation quality, incorporating residual averaging between cascades. We collected three different medical image datasets with two sub-tasks for each dataset to test the generalizability of our approach. Our experimental results found that CMDM can produce high-quality translations comparable to state-of-the-art methods while providing reasonable uncertainty estimations that correlate well with the translation error., Comment: Accepted at Medical Image Analysis Journal

With the recent advancements in single-image-based human mesh recovery, there is a growing interest in enhancing its performance in certain extreme scenarios, such as occlusion, while maintaining overall model accuracy. Although obtaining accurately annotated 3D human poses under occlusion is challenging, there is still a wealth of rich and precise 2D pose annotations that can be leveraged. However, existing works mostly focus on directly leveraging 2D pose coordinates to estimate 3D pose and mesh. In this paper, we present PostoMETRO($\textbf{Pos}$e $\textbf{to}$ken enhanced $\textbf{ME}$sh $\textbf{TR}$ansf$\textbf{O}$rmer), which integrates occlusion-resilient 2D pose representation into transformers in a token-wise manner. Utilizing a specialized pose tokenizer, we efficiently condense 2D pose data to a compact sequence of pose tokens and feed them to the transformer together with the image tokens. This process not only ensures a rich depiction of texture from the image but also fosters a robust integration of pose and image information. Subsequently, these combined tokens are queried by vertex and joint tokens to decode 3D coordinates of mesh vertices and human joints. Facilitated by the robust pose token representation and the effective combination, we are able to produce more precise 3D coordinates, even under extreme scenarios like occlusion. Experiments on both standard and occlusion-specific benchmarks demonstrate the effectiveness of PostoMETRO. Qualitative results further illustrate the clarity of how 2D pose can help 3D reconstruction. Code will be made available.

Weakly supervised surgical instrument segmentation with only instrument presence labels has been rarely explored in surgical domain. To mitigate the highly under-constrained challenges, we extend a two-stage weakly supervised segmentation paradigm with temporal attributes from two perspectives. From a temporal equivariance perspective, we propose a prototype-based temporal equivariance regulation loss to enhance pixel-wise consistency between adjacent features. From a semantic continuity perspective, we propose a class-aware temporal semantic continuity loss to constrain the semantic consistency between a global view of target frame and local non-discriminative regions of adjacent reference frame. To the best of our knowledge, WeakSurg is the first instrument-presence-only weakly supervised segmentation architecture to take temporal information into account for surgical scenarios. Extensive experiments are validated on Cholec80, an open benchmark for phase and instrument recognition. We annotate instance-wise instrument labels with fixed time-steps which are double checked by a clinician with 3-years experience. Our results show that WeakSurg compares favorably with state-of-the-art methods not only on semantic segmentation metrics but also on instance segmentation metrics.

Fully-supervised airway segmentation has accomplished significant triumphs over the years in aiding pre-operative diagnosis and intra-operative navigation. However, full voxel-level annotation constitutes a labor-intensive and time-consuming task, often plagued by issues such as missing branches, branch annotation discontinuity, or erroneous edge delineation. label-efficient solutions for airway extraction are rarely explored yet primarily demanding in medical practice. To this end, we introduce a novel skeleton-level annotation (SkA) tailored to the airway, which simplifies the annotation workflow while enhancing annotation consistency and accuracy, preserving the complete topology. Furthermore, we propose a skeleton-supervised learning framework to achieve accurate airway segmentation. Firstly, a dual-stream buffer inference is introduced to realize initial label propagation from SkA, avoiding the collapse of direct learning from SkA. Then, we construct a geometry-aware dual-path propagation framework (GDP) to further promote complementary propagation learning, composed of hard geometry-aware propagation learning and soft geometry-aware propagation guidance. Experiments reveal that our proposed framework outperforms the competing methods with SKA, which amounts to only 1.96% airways, and achieves comparable performance with the baseline model that is fully supervised with 100% airways, demonstrating its significant potential in achieving label-efficient segmentation for other tubular structures, such as vessels.

Multi-contrast (MC) Magnetic Resonance Imaging (MRI) reconstruction aims to incorporate a reference image of auxiliary modality to guide the reconstruction process of the target modality. Known MC reconstruction methods perform well with a fully sampled reference image, but usually exhibit inferior performance, compared to single-contrast (SC) methods, when the reference image is missing or of low quality. To address this issue, we propose DuDoUniNeXt, a unified dual-domain MRI reconstruction network that can accommodate to scenarios involving absent, low-quality, and high-quality reference images. DuDoUniNeXt adopts a hybrid backbone that combines CNN and ViT, enabling specific adjustment of image domain and k-space reconstruction. Specifically, an adaptive coarse-to-fine feature fusion module (AdaC2F) is devised to dynamically process the information from reference images of varying qualities. Besides, a partially shared shallow feature extractor (PaSS) is proposed, which uses shared and distinct parameters to handle consistent and discrepancy information among contrasts. Experimental results demonstrate that the proposed model surpasses state-of-the-art SC and MC models significantly. Ablation studies show the effectiveness of the proposed hybrid backbone, AdaC2F, PaSS, and the dual-domain unified learning scheme., Comment: 11 pages, 4 figures, 2 tables

Ensuring fairness in deep-learning-based segmentors is crucial for health equity. Much effort has been dedicated to mitigating unfairness in the training datasets or procedures. However, with the increasing prevalence of foundation models in medical image analysis, it is hard to train fair models from scratch while preserving utility. In this paper, we propose a novel method, Adversarial Privacy-aware Perturbations on Latent Embedding (APPLE), that can improve the fairness of deployed segmentors by introducing a small latent feature perturber without updating the weights of the original model. By adding perturbation to the latent vector, APPLE decorates the latent vector of segmentors such that no fairness-related features can be passed to the decoder of the segmentors while preserving the architecture and parameters of the segmentor. Experiments on two segmentation datasets and five segmentors (three U-Net-like and two SAM-like) illustrate the effectiveness of our proposed method compared to several unfairness mitigation methods.

With the proposal of the Segment Anything Model (SAM), fine-tuning SAM for medical image segmentation (MIS) has become popular. However, due to the large size of the SAM model and the significant domain gap between natural and medical images, fine-tuning-based strategies are costly with potential risk of instability, feature damage and catastrophic forgetting. Furthermore, some methods of transferring SAM to a domain-specific MIS through fine-tuning strategies disable the model's prompting capability, severely limiting its utilization scenarios. In this paper, we propose an Auto-Prompting Module (APM), which provides SAM-based foundation model with Euclidean adaptive prompts in the target domain. Our experiments demonstrate that such adaptive prompts significantly improve SAM's non-fine-tuned performance in MIS. In addition, we propose a novel non-invasive method called Incremental Pattern Shifting (IPS) to adapt SAM to specific medical domains. Experimental results show that the IPS enables SAM to achieve state-of-the-art or competitive performance in MIS without the need for fine-tuning. By coupling these two methods, we propose ProMISe, an end-to-end non-fine-tuned framework for Promptable Medical Image Segmentation. Our experiments demonstrate that both using our methods individually or in combination achieves satisfactory performance in low-cost pattern shifting, with all of SAM's parameters frozen.

The advancement of Zero-Shot Learning in the medical domain has been driven forward by using pre-trained models on large-scale image-text pairs, focusing on image-text alignment. However, existing methods primarily rely on cosine similarity for alignment, which may not fully capture the complex relationship between medical images and reports. To address this gap, we introduce a novel approach called Cross-Attention Alignment for Radiology Zero-Shot Classification (CARZero). Our approach innovatively leverages cross-attention mechanisms to process image and report features, creating a Similarity Representation that more accurately reflects the intricate relationships in medical semantics. This representation is then linearly projected to form an image-text similarity matrix for cross-modality alignment. Additionally, recognizing the pivotal role of prompt selection in zero-shot learning, CARZero incorporates a Large Language Model-based prompt alignment strategy. This strategy standardizes diverse diagnostic expressions into a unified format for both training and inference phases, overcoming the challenges of manual prompt design. Our approach is simple yet effective, demonstrating state-of-the-art performance in zero-shot classification on five official chest radiograph diagnostic test sets, including remarkable results on datasets with long-tail distributions of rare diseases. This achievement is attributed to our new image-text alignment strategy, which effectively addresses the complex relationship between medical images and reports. Code and models are available at https://github.com/laihaoran/CARZero.

Implicit visual knowledge in a large latent diffusion model (LLDM) pre-trained on natural images is rich and hypothetically universal to natural and medical images. To test this hypothesis from a practical perspective, we propose a novel framework for undersampled MRI Reconstruction by Prompting a large latent Diffusion model (MRPD). While the existing methods trained on MRI datasets are typically of limited generalizability toward diverse data acquisition scenarios, MRPD supports unsupervised and universally adaptive MRI reconstruction. For unsupervised reconstruction, MRSampler guides LLDM with a random-phase-modulated hard-to-soft control. With any single- or multiple-source MRI dataset, MRPD's performance is boosted universally by a lightweight MRAdapter that only finetunes the LLDM's autoencoder. Experiments on FastMRI and IXI show that MRPD is the only model that supports both MRI database-free and database-available scenarios and attains the best generalizability towards out-of-domain (OOD) samplings, contrasts, and organs among compared unsupervised, supervised, and MRI diffusion methods. To our knowledge, MRPD is the first method that empirically shows the universal prowess of an LLDM pre-trained on vast natural images for MRI. Our official implementation is at https://github.com/Z7Gao/MRPD., Comment: 10 pages, 5 figures, 7 tables, 1 pseudocode

When deploying a trained machine learning model in the real world, it is inevitable to receive inputs from out-of-distribution (OOD) sources. For instance, in continual learning settings, it is common to encounter OOD samples due to the non-stationarity of a domain. More generally, when we have access to a set of test inputs, the existing rich line of OOD detection solutions, especially the recent promise of distance-based methods, falls short in effectively utilizing the distribution information from training samples and test inputs. In this paper, we argue that empirical probability distributions that incorporate geometric information from both training samples and test inputs can be highly beneficial for OOD detection in the presence of test inputs available. To address this, we propose to model OOD detection as a discrete optimal transport problem. Within the framework of optimal transport, we propose a novel score function known as the \emph{conditional distribution entropy} to quantify the uncertainty of a test input being an OOD sample. Our proposal inherits the merits of certain distance-based methods while eliminating the reliance on distribution assumptions, a-prior knowledge, and specific training mechanisms. Extensive experiments conducted on benchmark datasets demonstrate that our method outperforms its competitors in OOD detection.

Sparse-view CT is a promising strategy for reducing the radiation dose of traditional CT scans, but reconstructing high-quality images from incomplete and noisy data is challenging. Recently, 3D Gaussian has been applied to model complex natural scenes, demonstrating fast convergence and better rendering of novel views compared to implicit neural representations (INRs). Taking inspiration from the successful application of 3D Gaussians in natural scene modeling and novel view synthesis, we investigate their potential for sparse-view CT reconstruction. We leverage prior information from the filtered-backprojection reconstructed image to initialize the Gaussians; and update their parameters via comparing difference in the projection space. Performance is further enhanced by adaptive density control. Compared to INRs, 3D Gaussians benefit more from prior information to explicitly bypass learning in void spaces and allocate the capacity efficiently, accelerating convergence. 3D Gaussians also efficiently learn high-frequency details. Trained in a self-supervised manner, 3D Gaussians avoid the need for large-scale paired data. Our experiments on the AAPM-Mayo dataset demonstrate that 3D Gaussians can provide superior performance compared to INR-based methods. This work is in progress, and the code will be publicly available.

Despite significant advancements in medical vision-language pre-training, existing methods have largely overlooked the inherent entity-specific context within radiology reports and the complex cross-modality contextual relationships between text and images. To close this gap, we propose a novel Entity-centered Context-aware Medical Vision-language Pre-training (ECAMP) framework, which is designed to enable a more entity-centered and context-sensitive interpretation of medical data. Utilizing the recent powerful large language model, we distill entity-centered context from medical reports, which enables ECAMP to gain more effective supervision from the text modality. By further pre-training our model with carefully designed entity-aware, context-enhanced masked language modeling and context-guided super-resolution tasks, ECAMP significantly refines the interplay between text and image modalities, leading to an enhanced ability to extract entity-centered contextual features. Besides, our proposed multi-scale context fusion design also improves the semantic integration of both coarse and fine-level image representations, prompting better performance for multi-scale downstream applications. Combining these components leads to significant performance leaps over current state-of-the-art methods and establishes a new standard for cross-modality learning in medical imaging, whose effectiveness is demonstrated by our extensive experiments on various tasks including classification, segmentation, and detection across several public datasets. Code and models are available at https://github.com/ToniChopp/ECAMP.

With the rapid expansion of machine learning and deep learning (DL), researchers are increasingly employing learning-based algorithms to alleviate diagnostic challenges across diverse medical tasks and applications. While advancements in diagnostic precision are notable, some researchers have identified a concerning trend: their models exhibit biased performance across subgroups characterized by different sensitive attributes. This bias not only infringes upon the rights of patients but also has the potential to lead to life-altering consequences. In this paper, we inspect a series of DL segmentation models using two ultrasound datasets, aiming to assess the presence of model unfairness in these specific tasks. Our findings reveal that even state-of-the-art DL algorithms demonstrate unfair behavior in ultrasound segmentation tasks. These results serve as a crucial warning, underscoring the necessity for careful model evaluation before their deployment in real-world scenarios. Such assessments are imperative to ensure ethical considerations and mitigate the risk of adverse impacts on patient outcomes., Comment: Submitted to ISBI 2024

Due to the scarcity and specific imaging characteristics in medical images, light-weighting Vision Transformers (ViTs) for efficient medical image segmentation is a significant challenge, and current studies have not yet paid attention to this issue. This work revisits the relationship between CNNs and Transformers in lightweight universal networks for medical image segmentation, aiming to integrate the advantages of both worlds at the infrastructure design level. In order to leverage the inductive bias inherent in CNNs, we abstract a Transformer-like lightweight CNNs block (ConvUtr) as the patch embeddings of ViTs, feeding Transformer with denoised, non-redundant and highly condensed semantic information. Moreover, an adaptive Local-Global-Local (LGL) block is introduced to facilitate efficient local-to-global information flow exchange, maximizing Transformer's global context information extraction capabilities. Finally, we build an efficient medical image segmentation model (MobileUtr) based on CNN and Transformer. Extensive experiments on five public medical image datasets with three different modalities demonstrate the superiority of MobileUtr over the state-of-the-art methods, while boasting lighter weights and lower computational cost. Code is available at https://github.com/FengheTan9/MobileUtr., Comment: 13 pages

In this paper, we present a high-performance deep neural network for weak target image segmentation, including medical image segmentation and infrared image segmentation. To this end, this work analyzes the existing dynamic convolutions and proposes dynamic parameter convolution (DPConv). Furthermore, it reevaluates the relationship between reconstruction tasks and segmentation tasks from the perspective of DPConv, leading to the proposal of a dual-network model called the Siamese Reconstruction-Segmentation Network (SRSNet). The proposed model is not only a universal network but also enhances the segmentation performance without altering its structure, leveraging the reconstruction task. Additionally, as the amount of training data for the reconstruction network increases, the performance of the segmentation network also improves synchronously. On seven datasets including five medical datasets and two infrared image datasets, our SRSNet consistently achieves the best segmentation results. The code is released at https://github.com/fidshu/SRSNet., Comment: 14 pages

Deep learning based methods for medical images can be easily compromised by adversarial examples (AEs), posing a great security flaw in clinical decision-making. It has been discovered that conventional adversarial attacks like PGD which optimize the classification logits, are easy to distinguish in the feature space, resulting in accurate reactive defenses. To better understand this phenomenon and reassess the reliability of the reactive defenses for medical AEs, we thoroughly investigate the characteristic of conventional medical AEs. Specifically, we first theoretically prove that conventional adversarial attacks change the outputs by continuously optimizing vulnerable features in a fixed direction, thereby leading to outlier representations in the feature space. Then, a stress test is conducted to reveal the vulnerability of medical images, by comparing with natural images. Interestingly, this vulnerability is a double-edged sword, which can be exploited to hide AEs. We then propose a simple-yet-effective hierarchical feature constraint (HFC), a novel add-on to conventional white-box attacks, which assists to hide the adversarial feature in the target feature distribution. The proposed method is evaluated on three medical datasets, both 2D and 3D, with different modalities. The experimental results demonstrate the superiority of HFC, \emph{i.e.,} it bypasses an array of state-of-the-art adversarial medical AE detectors more efficiently than competing adaptive attacks, which reveals the deficiencies of medical reactive defense and allows to develop more robust defenses in future., Comment: Our code is available at \url{https://github.com/qsyao/Hierarchical_Feature_Constraint}. arXiv admin note: text overlap with arXiv:2012.09501

Recent text-to-image diffusion models have reached an unprecedented level in generating high-quality images. However, their exclusive reliance on textual prompts often falls short in precise control of image compositions. In this paper, we propose LoCo, a training-free approach for layout-to-image Synthesis that excels in producing high-quality images aligned with both textual prompts and layout instructions. Specifically, we introduce a Localized Attention Constraint (LAC), leveraging semantic affinity between pixels in self-attention maps to create precise representations of desired objects and effectively ensure the accurate placement of objects in designated regions. We further propose a Padding Token Constraint (PTC) to leverage the semantic information embedded in previously neglected padding tokens, improving the consistency between object appearance and layout instructions. LoCo seamlessly integrates into existing text-to-image and layout-to-image models, enhancing their performance in spatial control and addressing semantic failures observed in prior methods. Extensive experiments showcase the superiority of our approach, surpassing existing state-of-the-art training-free layout-to-image methods both qualitatively and quantitatively across multiple benchmarks., Comment: Demo: https://huggingface.co/spaces/Pusheen/LoCo; Project page: https://momopusheen.github.io/LoCo/

The Segment Anything Model (SAM) has achieved a notable success in two-dimensional image segmentation in natural images. However, the substantial gap between medical and natural images hinders its direct application to medical image segmentation tasks. Particularly in 3D medical images, SAM struggles to learn contextual relationships between slices, limiting its practical applicability. Moreover, applying 2D SAM to 3D images requires prompting the entire volume, which is time- and label-consuming. To address these problems, we propose Slide-SAM, which treats a stack of three adjacent slices as a prediction window. It firstly takes three slices from a 3D volume and point- or bounding box prompts on the central slice as inputs to predict segmentation masks for all three slices. Subsequently, the masks of the top and bottom slices are then used to generate new prompts for adjacent slices. Finally, step-wise prediction can be achieved by sliding the prediction window forward or backward through the entire volume. Our model is trained on multiple public and private medical datasets and demonstrates its effectiveness through extensive 3D segmetnation experiments, with the help of minimal prompts. Code is available at \url{https://github.com/Curli-quan/Slide-SAM}.

Despite major advances in artificial intelligence (AI) for medicine and healthcare, the deployment and adoption of AI technologies remain limited in real-world clinical practice. In recent years, concerns have been raised about the technical, clinical, ethical and legal risks associated with medical AI. To increase real world adoption, it is essential that medical AI tools are trusted and accepted by patients, clinicians, health organisations and authorities. This work describes the FUTURE-AI guideline as the first international consensus framework for guiding the development and deployment of trustworthy AI tools in healthcare. The FUTURE-AI consortium was founded in 2021 and currently comprises 118 inter-disciplinary experts from 51 countries representing all continents, including AI scientists, clinicians, ethicists, and social scientists. Over a two-year period, the consortium defined guiding principles and best practices for trustworthy AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. The FUTURE-AI framework was established based on 6 guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 28 best practices were defined, addressing technical, clinical, legal and socio-ethical dimensions. The recommendations cover the entire lifecycle of medical AI, from design, development and validation to regulation, deployment, and monitoring. FUTURE-AI is a risk-informed, assumption-free guideline which provides a structured approach for constructing medical AI tools that will be trusted, deployed and adopted in real-world practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of medical AI.

The U-shaped architecture has emerged as a crucial paradigm in the design of medical image segmentation networks. However, due to the inherent local limitations of convolution, a fully convolutional segmentation network with U-shaped architecture struggles to effectively extract global context information, which is vital for the precise localization of lesions. While hybrid architectures combining CNNs and Transformers can address these issues, their application in real medical scenarios is limited due to the computational resource constraints imposed by the environment and edge devices. In addition, the convolutional inductive bias in lightweight networks adeptly fits the scarce medical data, which is lacking in the Transformer based network. In order to extract global context information while taking advantage of the inductive bias, we propose CMUNeXt, an efficient fully convolutional lightweight medical image segmentation network, which enables fast and accurate auxiliary diagnosis in real scene scenarios. CMUNeXt leverages large kernel and inverted bottleneck design to thoroughly mix distant spatial and location information, efficiently extracting global context information. We also introduce the Skip-Fusion block, designed to enable smooth skip-connections and ensure ample feature fusion. Experimental results on multiple medical image datasets demonstrate that CMUNeXt outperforms existing heavyweight and lightweight medical image segmentation networks in terms of segmentation performance, while offering a faster inference speed, lighter weights, and a reduced computational cost. The code is available at https://github.com/FengheTan9/CMUNeXt., Comment: 8 pages, 3 figures

Limited by expensive pixel-level labels, polyp segmentation models are plagued by data shortage and suffer from impaired generalization. In contrast, polyp bounding box annotations are much cheaper and more accessible. Thus, to reduce labeling cost, we propose to learn a weakly supervised polyp segmentation model (i.e., WeakPolyp) completely based on bounding box annotations. However, coarse bounding boxes contain too much noise. To avoid interference, we introduce the mask-to-box (M2B) transformation. By supervising the outer box mask of the prediction instead of the prediction itself, M2B greatly mitigates the mismatch between the coarse label and the precise prediction. But, M2B only provides sparse supervision, leading to non-unique predictions. Therefore, we further propose a scale consistency (SC) loss for dense supervision. By explicitly aligning predictions across the same image at different scales, the SC loss largely reduces the variation of predictions. Note that our WeakPolyp is a plug-and-play model, which can be easily ported to other appealing backbones. Besides, the proposed modules are only used during training, bringing no computation cost to inference. Extensive experiments demonstrate the effectiveness of our proposed WeakPolyp, which surprisingly achieves a comparable performance with a fully supervised model, requiring no mask annotations at all., Comment: accepted by MICCAI 2023, codes are available at https://github.com/weijun88/WeakPolyp

Emerging neural reconstruction techniques based on tomography (e.g., NeRF, NeAT, and NeRP) have started showing unique capabilities in medical imaging. In this work, we present a novel Polychromatic neural representation (Polyner) to tackle the challenging problem of CT imaging when metallic implants exist within the human body. CT metal artifacts arise from the drastic variation of metal's attenuation coefficients at various energy levels of the X-ray spectrum, leading to a nonlinear metal effect in CT measurements. Recovering CT images from metal-affected measurements hence poses a complicated nonlinear inverse problem where empirical models adopted in previous metal artifact reduction (MAR) approaches lead to signal loss and strongly aliased reconstructions. Polyner instead models the MAR problem from a nonlinear inverse problem perspective. Specifically, we first derive a polychromatic forward model to accurately simulate the nonlinear CT acquisition process. Then, we incorporate our forward model into the implicit neural representation to accomplish reconstruction. Lastly, we adopt a regularizer to preserve the physical properties of the CT images across different energy levels while effectively constraining the solution space. Our Polyner is an unsupervised method and does not require any external training data. Experimenting with multiple datasets shows that our Polyner achieves comparable or better performance than supervised methods on in-domain datasets while demonstrating significant performance improvements on out-of-domain datasets. To the best of our knowledge, our Polyner is the first unsupervised MAR method that outperforms its supervised counterparts. The code for this work is available at: https://github.com/iwuqing/Polyner., Comment: Accepted by NeurIPS 2023

One-shot medical landmark detection gains much attention and achieves great success for its label-efficient training process. However, existing one-shot learning methods are highly specialized in a single domain and suffer domain preference heavily in the situation of multi-domain unlabeled data. Moreover, one-shot learning is not robust that it faces performance drop when annotating a sub-optimal image. To tackle these issues, we resort to developing a domain-adaptive one-shot landmark detection framework for handling multi-domain medical images, named Universal One-shot Detection (UOD). UOD consists of two stages and two corresponding universal models which are designed as combinations of domain-specific modules and domain-shared modules. In the first stage, a domain-adaptive convolution model is self-supervised learned to generate pseudo landmark labels. In the second stage, we design a domain-adaptive transformer to eliminate domain preference and build the global context for multi-domain data. Even though only one annotated sample from each domain is available for training, the domain-shared modules help UOD aggregate all one-shot samples to detect more robust and accurate landmarks. We investigated both qualitatively and quantitatively the proposed UOD on three widely-used public X-ray datasets in different anatomical domains (i.e., head, hand, chest) and obtained state-of-the-art performances in each domain. The code is available at https://github.com/heqin-zhu/UOD_universal_oneshot_detection., Comment: Eealy accepted by MICCAI 2023. 11pages, 4 figures, 2 tables. arXiv admin note: text overlap with arXiv:2203.06433

The augmentation parameters matter to few-shot semantic segmentation since they directly affect the training outcome by feeding the networks with varying perturbated samples. However, searching optimal augmentation parameters for few-shot segmentation models without annotations is a challenge that current methods fail to address. In this paper, we first propose a framework to determine the ``optimal'' parameters without human annotations by solving a distribution-matching problem between the intra-instance and intra-class similarity distribution, with the intra-instance similarity describing the similarity between the original sample of a particular anatomy and its augmented ones and the intra-class similarity representing the similarity between the selected sample and the others in the same class. Extensive experiments demonstrate the superiority of our optimized augmentation in boosting few-shot segmentation models. We greatly improve the top competing method by 1.27\% and 1.11\% on Abd-MRI and Abd-CT datasets, respectively, and even achieve a significant improvement for SSL-ALP on the left kidney by 3.39\% on the Abd-CT dataset.

Domain shift and label scarcity heavily limit deep learning applications to various medical image analysis tasks. Unsupervised domain adaptation (UDA) techniques have recently achieved promising cross-modality medical image segmentation by transferring knowledge from a label-rich source domain to an unlabeled target domain. However, it is also difficult to collect annotations from the source domain in many clinical applications, rendering most prior works suboptimal with the label-scarce source domain, particularly for few-shot scenarios, where only a few source labels are accessible. To achieve efficient few-shot cross-modality segmentation, we propose a novel transformation-consistent meta-hallucination framework, meta-hallucinator, with the goal of learning to diversify data distributions and generate useful examples for enhancing cross-modality performance. In our framework, hallucination and segmentation models are jointly trained with the gradient-based meta-learning strategy to synthesize examples that lead to good segmentation performance on the target domain. To further facilitate data hallucination and cross-domain knowledge transfer, we develop a self-ensembling model with a hallucination-consistent property. Our meta-hallucinator can seamlessly collaborate with the meta-segmenter for learning to hallucinate with mutual benefits from a combined view of meta-learning and self-ensembling learning. Extensive studies on MM-WHS 2017 dataset for cross-modality cardiac segmentation demonstrate that our method performs favorably against various approaches by a lot in the few-shot UDA scenario., Comment: Accepted by MICCAI 2022 (top 13% paper; early accept)

The pelvis, the lower part of the trunk, supports and balances the trunk. Landmark detection from a pelvic X-ray (PXR) facilitates downstream analysis and computer-assisted diagnosis and treatment of pelvic diseases. Although PXRs have the advantages of low radiation and reduced cost compared to computed tomography (CT) images, their 2D pelvis-tissue superposition of 3D structures confuses clinical decision-making. In this paper, we propose a PELvis Extraction (PELE) module that utilizes 3D prior anatomical knowledge in CT to guide and well isolate the pelvis from PXRs, thereby eliminating the influence of soft tissue. We conduct an extensive evaluation based on two public datasets and one private dataset, totaling 850 PXRs. The experimental results show that the proposed PELE module significantly improves the accuracy of PXRs landmark detection and achieves state-of-the-art performances in several benchmark metrics, thus better serving downstream tasks., Comment: will revise it and resubmit it again later

Multi-modal medical images provide complementary soft-tissue characteristics that aid in the screening and diagnosis of diseases. However, limited scanning time, image corruption and various imaging protocols often result in incomplete multi-modal images, thus limiting the usage of multi-modal data for clinical purposes. To address this issue, in this paper, we propose a novel unified multi-modal image synthesis method for missing modality imputation. Our method overall takes a generative adversarial architecture, which aims to synthesize missing modalities from any combination of available ones with a single model. To this end, we specifically design a Commonality- and Discrepancy-Sensitive Encoder for the generator to exploit both modality-invariant and specific information contained in input modalities. The incorporation of both types of information facilitates the generation of images with consistent anatomy and realistic details of the desired distribution. Besides, we propose a Dynamic Feature Unification Module to integrate information from a varying number of available modalities, which enables the network to be robust to random missing modalities. The module performs both hard integration and soft integration, ensuring the effectiveness of feature combination while avoiding information loss. Verified on two public multi-modal magnetic resonance datasets, the proposed method is effective in handling various synthesis tasks and shows superior performance compared to previous methods., Comment: IEEE TMI accepted final version

Low-count PET is an efficient way to reduce radiation exposure and acquisition time, but the reconstructed images often suffer from low signal-to-noise ratio (SNR), thus affecting diagnosis and other downstream tasks. Recent advances in deep learning have shown great potential in improving low-count PET image quality, but acquiring a large, centralized, and diverse dataset from multiple institutions for training a robust model is difficult due to privacy and security concerns of patient data. Moreover, low-count PET data at different institutions may have different data distribution, thus requiring personalized models. While previous federated learning (FL) algorithms enable multi-institution collaborative training without the need of aggregating local data, addressing the large domain shift in the application of multi-institutional low-count PET denoising remains a challenge and is still highly under-explored. In this work, we propose FedFTN, a personalized federated learning strategy that addresses these challenges. FedFTN uses a local deep feature transformation network (FTN) to modulate the feature outputs of a globally shared denoising network, enabling personalized low-count PET denoising for each institution. During the federated learning process, only the denoising network's weights are communicated and aggregated, while the FTN remains at the local institutions for feature transformation. We evaluated our method using a large-scale dataset of multi-institutional low-count PET imaging data from three medical centers located across three continents, and showed that FedFTN provides high-quality low-count PET images, outperforming previous baseline FL reconstruction methods across all low-count levels at all three institutions., Comment: 13 pages, 6 figures, Accepted at Medical Image Analysis Journal (MedIA)

Deep neural networks have been widely studied for predicting a medical condition, such as total knee replacement (TKR). It has shown that data of different modalities, such as imaging data, clinical variables and demographic information, provide complementary information and thus can improve the prediction accuracy together. However, the data sources of various modalities may not always be of high quality, and each modality may have only partial information of medical condition. Thus, predictions from different modalities can be opposite, and the final prediction may fail in the presence of such a conflict. Therefore, it is important to consider the reliability of each source data and the prediction output when making a final decision. In this paper, we propose an evidence-aware multi-modal data fusion framework based on the Dempster-Shafer theory (DST). The backbone models contain an image branch, a non-image branch and a fusion branch. For each branch, there is an evidence network that takes the extracted features as input and outputs an evidence score, which is designed to represent the reliability of the output from the current branch. The output probabilities along with the evidence scores from multiple branches are combined with the Dempster's combination rule to make a final prediction. Experimental results on the public OA initiative (OAI) dataset for the TKR prediction task show the superiority of the proposed fusion strategy on various backbone models.

Undersampled MRI reconstruction is crucial for accelerating clinical scanning. Dual-domain reconstruction network is performant among SoTA deep learning methods. In this paper, we rethink dual-domain model design from the perspective of the receptive field, which is needed for image recovery and K-space interpolation problems. Further, we introduce domain-specific modules for dual-domain reconstruction, namely k-space global initialization and image-domain parallel local detail enhancement. We evaluate our modules by translating a SoTA method DuDoRNet under different conventions of MRI reconstruction including image-domain, dual-domain, and reference-guided reconstruction on the public IXI dataset. Our model DuDoRNet+ achieves significant improvements over competing deep learning methods., Comment: 2024 IEEE International Symposium on Biomedical Imaging (ISBI)

Airway segmentation, especially bronchioles segmentation, is an important but challenging task because distal bronchus are sparsely distributed and of a fine scale. Existing neural networks usually exploit sparse topology to learn the connectivity of bronchioles and inefficient shallow features to capture such high-frequency information, leading to the breakage or missed detection of individual thin branches. To address these problems, we contribute a new bronchial segmentation method based on Group Deep Dense Supervision (GDDS) that emphasizes fine-scale bronchioles segmentation in a simple-but-effective manner. First, Deep Dense Supervision (DDS) is proposed by constructing local dense topology skillfully and implementing dense topological learning on a specific shallow feature layer. GDDS further empowers the shallow features with better perception ability to detect bronchioles, even the ones that are not easily discernible to the naked eye. Extensive experiments on the BAS benchmark dataset have shown that our method promotes the network to have a high sensitivity in capturing fine-scale branches and outperforms state-of-the-art methods by a large margin (+12.8 % in BD and +8.8 % in TD) while only introducing a small number of extra parameters., Comment: Submitted to MICCAI2023

Radiologists possess diverse training and clinical experiences, leading to variations in the segmentation annotations of lung nodules and resulting in segmentation uncertainty.Conventional methods typically select a single annotation as the learning target or attempt to learn a latent space comprising multiple annotations. However, these approaches fail to leverage the valuable information inherent in the consensus and disagreements among the multiple annotations. In this paper, we propose an Uncertainty-Aware Attention Mechanism (UAAM) that utilizes consensus and disagreements among multiple annotations to facilitate better segmentation. To this end, we introduce the Multi-Confidence Mask (MCM), which combines a Low-Confidence (LC) Mask and a High-Confidence (HC) Mask.The LC mask indicates regions with low segmentation confidence, where radiologists may have different segmentation choices. Following UAAM, we further design an Uncertainty-Guide Multi-Confidence Segmentation Network (UGMCS-Net), which contains three modules: a Feature Extracting Module that captures a general feature of a lung nodule, an Uncertainty-Aware Module that produces three features for the the annotations' union, intersection, and annotation set, and an Intersection-Union Constraining Module that uses distances between the three features to balance the predictions of final segmentation and MCM. To comprehensively demonstrate the performance of our method, we propose a Complex Nodule Validation on LIDC-IDRI, which tests UGMCS-Net's segmentation performance on lung nodules that are difficult to segment using common methods. Experimental results demonstrate that our method can significantly improve the segmentation performance on nodules that are difficult to segment using conventional methods., Comment: 10 pages, 10 figures. We have reported a preliminary version of this work in MICCAI 2022

Deep learning is becoming increasingly ubiquitous in medical research and applications while involving sensitive information and even critical diagnosis decisions. Researchers observe a significant performance disparity among subgroups with different demographic attributes, which is called model unfairness, and put lots of effort into carefully designing elegant architectures to address unfairness, which poses heavy training burden, brings poor generalization, and reveals the trade-off between model performance and fairness. To tackle these issues, we propose FairAdaBN by making batch normalization adaptive to sensitive attribute. This simple but effective design can be adopted to several classification backbones that are originally unaware of fairness. Additionally, we derive a novel loss function that restrains statistical parity between subgroups on mini-batches, encouraging the model to converge with considerable fairness. In order to evaluate the trade-off between model performance and fairness, we propose a new metric, named Fairness-Accuracy Trade-off Efficiency (FATE), to compute normalized fairness improvement over accuracy drop. Experiments on two dermatological datasets show that our proposed method outperforms other methods on fairness criteria and FATE., Comment: Accepted by MICCAI 2023

Targeted diagnosis and treatment plans for patients with coronary artery disease vary according to atherosclerotic plaque component. Coronary CT angiography (CCTA) is widely used for artery imaging and determining the stenosis degree. However, the limited spatial resolution and susceptibility to artifacts fail CCTA in obtaining lumen morphological characteristics and plaque composition. It can be settled by invasive optical coherence tomography (OCT) without much trouble for physicians, but bringing higher costs and potential risks to patients. Therefore, it is clinically critical to introduce annotations of plaque tissue and lumen characteristics from OCT to paired CCTA scans, denoted as \textbf{the O2CTA problem} in this paper. We propose a method to handle the O2CTA problem. CCTA scans are first reconstructed into multi-planar reformatted (MPR) images, which agree with OCT images in term of semantic contents. The artery segment in OCT, which is manually labelled, is then spatially aligned with the entire artery in MPR images via the proposed alignment strategy. Finally, a classification model involving a 3D CNN and a Transformer, is learned to extract local features and capture dependence along arteries. Experiments on 55 paired OCT and CCTA we curate demonstrate that it is feasible to classify the CCTA based on the OCT labels, with an accuracy of 86.2%, while the manual readings of OCT and CCTA vary significantly, with a Kappa coefficient of 0.113. We will make our source codes, models, data, and results publicly available to benefit the research community., Comment: Accepted for oral presentation in MICCAI-BTSD 2023 workshop

Self-supervised learning is well known for its remarkable performance in representation learning and various downstream computer vision tasks. Recently, Positive-pair-Only Contrastive Learning (POCL) has achieved reliable performance without the need to construct positive-negative training sets. It reduces memory requirements by lessening the dependency on the batch size. The POCL method typically uses a single loss function to extract the distortion invariant representation (DIR) which describes the proximity of positive-pair representations affected by different distortions. This loss function implicitly enables the model to filter out or ignore the distortion variant representation (DVR) affected by different distortions. However, existing POCL methods do not explicitly enforce the disentanglement and exploitation of the actually valuable DVR. In addition, these POCL methods have been observed to be sensitive to augmentation strategies. To address these limitations, we propose a novel POCL framework named Distortion-Disentangled Contrastive Learning (DDCL) and a Distortion-Disentangled Loss (DDL). Our approach is the first to explicitly disentangle and exploit the DVR inside the model and feature stream to improve the overall representation utilization efficiency, robustness and representation ability. Experiments carried out demonstrate the superiority of our framework to Barlow Twins and Simsiam in terms of convergence, representation quality, and robustness on several benchmark datasets., Comment: Oral in WACV2024

Self-paced curriculum learning (SCL) has demonstrated its great potential in computer vision, natural language processing, etc. During training, it implements easy-to-hard sampling based on online estimation of data difficulty. Most SCL methods commonly adopt a loss-based strategy of estimating data difficulty and deweighting the `hard' samples in the early training stage. While achieving success in a variety of applications, SCL stills confront two challenges in a medical image analysis task, such as universal lesion detection, featuring insufficient and highly class-imbalanced data: (i) the loss-based difficulty measurer is inaccurate; ii) the hard samples are under-utilized from a deweighting mechanism. To overcome these challenges, in this paper we propose a novel mixed-order self-paced curriculum learning (Mo-SCL) method. We integrate both uncertainty and loss to better estimate difficulty online and mix both hard and easy samples in the same mini-batch to appropriately alleviate the problem of under-utilization of hard samples. We provide a theoretical investigation of our method in the context of stochastic gradient descent optimization and extensive experiments based on the DeepLesion benchmark dataset for universal lesion detection (ULD). When applied to two state-of-the-art ULD methods, the proposed mixed-order SCL method can provide a free boost to lesion detection accuracy without extra special network designs., Comment: 11 pages, 3 figures

Objective and Impact Statement: Accurate organ segmentation is critical for many clinical applications at different clinical sites, which may have their specific application requirements that concern different organs. Introduction: However, learning high-quality, site-specific organ segmentation models is challenging as it often needs on-site curation of a large number of annotated images. Security concerns further complicate the matter. Methods: The paper aims to tackle these challenges via a two-phase aggregation-then-adaptation approach. The first phase of federated aggregation learns a single multi-organ segmentation model by leveraging the strength of 'bigger data', which are formed by (i) aggregating together datasets from multiple sites that with different organ labels to provide partial supervision, and (ii) conducting partially supervised learning without data breach. The second phase of site adaptation is to transfer the federated multi-organ segmentation model to site-specific organ segmentation models, one model per site, in order to further improve the performance of each site's organ segmentation task. Furthermore, improved marginal loss and exclusion loss functions are used to avoid 'knowledge conflict' problem in a partially supervision mechanism. Results and Conclusion: Extensive experiments on five organ segmentation datasets demonstrate the effectiveness of our multi-site approach, significantly outperforming the site-per-se learned models and achieving the performance comparable to the centrally learned models.

For medical image segmentation, contrastive learning is the dominant practice to improve the quality of visual representations by contrasting semantically similar and dissimilar pairs of samples. This is enabled by the observation that without accessing ground truth labels, negative examples with truly dissimilar anatomical features, if sampled, can significantly improve the performance. In reality, however, these samples may come from similar anatomical regions and the models may struggle to distinguish the minority tail-class samples, making the tail classes more prone to misclassification, both of which typically lead to model collapse. In this paper, we propose ARCO, a semi-supervised contrastive learning (CL) framework with stratified group theory for medical image segmentation. In particular, we first propose building ARCO through the concept of variance-reduced estimation and show that certain variance-reduction techniques are particularly beneficial in pixel/voxel-level segmentation tasks with extremely limited labels. Furthermore, we theoretically prove these sampling techniques are universal in variance reduction. Finally, we experimentally validate our approaches on eight benchmarks, i.e., five 2D/3D medical and three semantic segmentation datasets, with different label settings, and our methods consistently outperform state-of-the-art semi-supervised methods. Additionally, we augment the CL frameworks with these sampling techniques and demonstrate significant gains over previous methods. We believe our work is an important step towards semi-supervised medical image segmentation by quantifying the limitation of current self-supervision objectives for accomplishing such challenging safety-critical tasks., Comment: Accepted by Advances in Neural Information Processing Systems (NeurIPS 2023)

Autonomous robotic surgery has advanced significantly based on analysis of visual and temporal cues in surgical workflow, but relational cues from domain knowledge remain under investigation. Complex relations in surgical annotations can be divided into intra- and inter-relations, both valuable to autonomous systems to comprehend surgical workflows. Intra- and inter-relations describe the relevance of various categories within a particular annotation type and the relevance of different annotation types, respectively. This paper aims to systematically investigate the importance of relational cues in surgery. First, we contribute the RLLS12M dataset, a large-scale collection of robotic left lateral sectionectomy (RLLS), by curating 50 videos of 50 patients operated by 5 surgeons and annotating a hierarchical workflow, which consists of 3 inter- and 6 intra-relations, 6 steps, 15 tasks, and 38 activities represented as the triplet of 11 instruments, 8 actions, and 16 objects, totaling 2,113,510 video frames and 12,681,060 annotation entities. Correspondingly, we propose a multi-relation purification hybrid network (MURPHY), which aptly incorporates novel relation modules to augment the feature representation by purifying relational features using the intra- and inter-relations embodied in annotations. The intra-relation module leverages a R-GCN to implant visual features in different graph relations, which are aggregated using a targeted relation purification with affinity information measuring label consistency and feature similarity. The inter-relation module is motivated by attention mechanisms to regularize the influence of relational features based on the hierarchy of annotation types from the domain knowledge. Extensive experimental results on the curated RLLS dataset confirm the effectiveness of our approach, demonstrating that relations matter in surgical workflow analysis.

Accurate polyp segmentation is of great importance for colorectal cancer diagnosis and treatment. However, due to the high cost of producing accurate mask annotations, existing polyp segmentation methods suffer from severe data shortage and impaired model generalization. Reversely, coarse polyp bounding box annotations are more accessible. Thus, in this paper, we propose a boosted BoxPolyp model to make full use of both accurate mask and extra coarse box annotations. In practice, box annotations are applied to alleviate the over-fitting issue of previous polyp segmentation models, which generate fine-grained polyp area through the iterative boosted segmentation model. To achieve this goal, a fusion filter sampling (FFS) module is firstly proposed to generate pixel-wise pseudo labels from box annotations with less noise, leading to significant performance improvements. Besides, considering the appearance consistency of the same polyp, an image consistency (IC) loss is designed. Such IC loss explicitly narrows the distance between features extracted by two different networks, which improves the robustness of the model. Note that our BoxPolyp is a plug-and-play model, which can be merged into any appealing backbone. Quantitative and qualitative experimental results on five challenging benchmarks confirm that our proposed model outperforms previous state-of-the-art methods by a large margin., Comment: Accepted by MICCAI2022, Codes Available

While deep learning methods hitherto have achieved considerable success in medical image segmentation, they are still hampered by two limitations: (i) reliance on large-scale well-labeled datasets, which are difficult to curate due to the expert-driven and time-consuming nature of pixel-level annotations in clinical practices, and (ii) failure to generalize from one domain to another, especially when the target domain is a different modality with severe domain shifts. Recent unsupervised domain adaptation~(UDA) techniques leverage abundant labeled source data together with unlabeled target data to reduce the domain gap, but these methods degrade significantly with limited source annotations. In this study, we address this underexplored UDA problem, investigating a challenging but valuable realistic scenario, where the source domain not only exhibits domain shift~w.r.t. the target domain but also suffers from label scarcity. In this regard, we propose a novel and generic framework called ``Label-Efficient Unsupervised Domain Adaptation"~(LE-UDA). In LE-UDA, we construct self-ensembling consistency for knowledge transfer between both domains, as well as a self-ensembling adversarial learning module to achieve better feature alignment for UDA. To assess the effectiveness of our method, we conduct extensive experiments on two different tasks for cross-modality segmentation between MRI and CT images. Experimental results demonstrate that the proposed LE-UDA can efficiently leverage limited source labels to improve cross-domain segmentation performance, outperforming state-of-the-art UDA approaches in the literature. Code is available at: https://github.com/jacobzhaoziyuan/LE-UDA., Comment: Accepted by IEEE Transactions on Medical Imaging, 2022

Contrastive learning (CL) is a form of self-supervised learning and has been widely used for various tasks. Different from widely studied instance-level contrastive learning, pixel-wise contrastive learning mainly helps with pixel-wise tasks such as medical landmark detection. The counterpart to an instance in instance-level CL is a pixel, along with its neighboring context, in pixel-wise CL. Aiming to build better feature representation, there is a vast literature about designing instance augmentation strategies for instance-level CL; but there is little similar work on pixel augmentation for pixel-wise CL with a pixel granularity. In this paper, we attempt to bridge this gap. We first classify a pixel into three categories, namely low-, medium-, and high-informative, based on the information quantity the pixel contains. Inspired by the ``InfoMin" principle, we then design separate augmentation strategies for each category in terms of augmentation intensity and sampling ratio. Extensive experiments validate that our information-guided pixel augmentation strategy succeeds in encoding more discriminative representations and surpassing other competitive approaches in unsupervised local feature matching. Furthermore, our pretrained model improves the performance of both one-shot and fully supervised models. To the best of our knowledge, we are the first to propose a pixel augmentation method with a pixel granularity for enhancing unsupervised pixel-wise contrastive learning.

Fast screening and diagnosis are critical in COVID-19 patient treatment. In addition to the gold standard RT-PCR, radiological imaging like X-ray and CT also works as an important means in patient screening and follow-up. However, due to the excessive number of patients, writing reports becomes a heavy burden for radiologists. To reduce the workload of radiologists, we propose DeltaNet to generate medical reports automatically. Different from typical image captioning approaches that generate reports with an encoder and a decoder, DeltaNet applies a conditional generation process. In particular, given a medical image, DeltaNet employs three steps to generate a report: 1) first retrieving related medical reports, i.e., the historical reports from the same or similar patients; 2) then comparing retrieved images and current image to find the differences; 3) finally generating a new report to accommodate identified differences based on the conditional report. We evaluate DeltaNet on a COVID-19 dataset, where DeltaNet outperforms state-of-the-art approaches. Besides COVID-19, the proposed DeltaNet can be applied to other diseases as well. We validate its generalization capabilities on the public IU-Xray and MIMIC-CXR datasets for chest-related diseases. Code is available at \url{https://github.com/LX-doctorAI1/DeltaNet}.

Artificial Intelligence (AI) is having a tremendous impact across most areas of science. Applications of AI in healthcare have the potential to improve our ability to detect, diagnose, prognose, and intervene on human disease. For AI models to be used clinically, they need to be made safe, reproducible and robust, and the underlying software framework must be aware of the particularities (e.g. geometry, physiology, physics) of medical data being processed. This work introduces MONAI, a freely available, community-supported, and consortium-led PyTorch-based framework for deep learning in healthcare. MONAI extends PyTorch to support medical data, with a particular focus on imaging, and provide purpose-specific AI model architectures, transformations and utilities that streamline the development and deployment of medical AI models. MONAI follows best practices for software-development, providing an easy-to-use, robust, well-documented, and well-tested software framework. MONAI preserves the simple, additive, and compositional approach of its underlying PyTorch libraries. MONAI is being used by and receiving contributions from research, clinical and industrial teams from around the world, who are pursuing applications spanning nearly every aspect of healthcare., Comment: www.monai.io

Computed tomography (CT) is a widely-used imaging technology that assists clinical decision-making with high-quality human body representations. To reduce the radiation dose posed by CT, sparse-view and limited-angle CT are developed with preserved image quality. However, these methods are still stuck with a fixed or uniform sampling strategy, which inhibits the possibility of acquiring a better image with an even reduced dose. In this paper, we explore this possibility via learning an active sampling policy that optimizes the sampling positions for patient-specific, high-quality reconstruction. To this end, we design an \textit{intelligent agent} for active recommendation of sampling positions based on on-the-fly reconstruction with obtained sinograms in a progressive fashion. With such a design, we achieve better performances on the NIH-AAPM dataset over popular uniform sampling, especially when the number of views is small. Finally, such a design also enables RoI-aware reconstruction with improved reconstruction quality within regions of interest (RoI's) that are clinically important. Experiments on the VerSe dataset demonstrate this ability of our sampling policy, which is difficult to achieve based on uniform sampling.