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Deformable image registration remains a fundamental task in clinical practice, yet solving registration problems involving complex deformations remains challenging. Current deep learning-based registration methods employ continuous deformation to model large deformations, which often suffer from accumulated registration errors and interpolation inaccuracies. Moreover, achieving satisfactory results with these frameworks typically requires a large number of cascade stages, demanding substantial computational resources. Therefore, we propose a novel approach, the field refinement framework (FiRework), tailored for unsupervised deformable registration, aiming to address these challenges. In FiRework, we redesign the continuous deformation framework to mitigate the aforementioned errors. Notably, our FiRework requires only one level of recursion during training and supports continuous inference, offering improved efficacy compared to continuous deformation frameworks. We conducted experiments on two brain MRI datasets, enhancing two existing deformable registration networks with FiRework. The experimental results demonstrate the superior performance of our proposed framework in deformable registration. The code is publicly available at https://github.com/ZAX130/FiRework.

Convolutional neural networks have primarily led 3D medical image segmentation but may be limited by small receptive fields. Transformer models excel in capturing global relationships through self-attention but are challenged by high computational costs at high resolutions. Recently, Mamba, a state space model, has emerged as an effective approach for sequential modeling. Inspired by its success, we introduce a novel Mamba-based 3D medical image segmentation model called EM-Net. It not only efficiently captures attentive interaction between regions by integrating and selecting channels, but also effectively utilizes frequency domain to harmonize the learning of features across varying scales, while accelerating training speed. Comprehensive experiments on two challenging multi-organ datasets with other state-of-the-art (SOTA) algorithms show that our method exhibits better segmentation accuracy while requiring nearly half the parameter size of SOTA models and 2x faster training speed., Comment: 10 pages, 3 figures, accepted by MICCAI 2024

In the medical field, the limited availability of large-scale datasets and labor-intensive annotation processes hinder the performance of deep models. Diffusion-based generative augmentation approaches present a promising solution to this issue, having been proven effective in advancing downstream medical recognition tasks. Nevertheless, existing works lack sufficient semantic and sequential steerability for challenging video/3D sequence generation, and neglect quality control of noisy synthesized samples, resulting in unreliable synthetic databases and severely limiting the performance of downstream tasks. In this work, we present Ctrl-GenAug, a novel and general generative augmentation framework that enables highly semantic- and sequential-customized sequence synthesis and suppresses incorrectly synthesized samples, to aid medical sequence classification. Specifically, we first design a multimodal conditions-guided sequence generator for controllably synthesizing diagnosis-promotive samples. A sequential augmentation module is integrated to enhance the temporal/stereoscopic coherence of generated samples. Then, we propose a noisy synthetic data filter to suppress unreliable cases at semantic and sequential levels. Extensive experiments on 3 medical datasets, using 11 networks trained on 3 paradigms, comprehensively analyze the effectiveness and generality of Ctrl-GenAug, particularly in underrepresented high-risk populations and out-domain conditions., Comment: 17 pages, 7 figures, 7 tables

Segmentation of the fetal and maternal structures, particularly intrapartum ultrasound imaging as advocated by the International Society of Ultrasound in Obstetrics and Gynecology (ISUOG) for monitoring labor progression, is a crucial first step for quantitative diagnosis and clinical decision-making. This requires specialized analysis by obstetrics professionals, in a task that i) is highly time- and cost-consuming and ii) often yields inconsistent results. The utility of automatic segmentation algorithms for biometry has been proven, though existing results remain suboptimal. To push forward advancements in this area, the Grand Challenge on Pubic Symphysis-Fetal Head Segmentation (PSFHS) was held alongside the 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023). This challenge aimed to enhance the development of automatic segmentation algorithms at an international scale, providing the largest dataset to date with 5,101 intrapartum ultrasound images collected from two ultrasound machines across three hospitals from two institutions. The scientific community's enthusiastic participation led to the selection of the top 8 out of 179 entries from 193 registrants in the initial phase to proceed to the competition's second stage. These algorithms have elevated the state-of-the-art in automatic PSFHS from intrapartum ultrasound images. A thorough analysis of the results pinpointed ongoing challenges in the field and outlined recommendations for future work. The top solutions and the complete dataset remain publicly available, fostering further advancements in automatic segmentation and biometry for intrapartum ultrasound imaging.

Mitral regurgitation (MR) is a serious heart valve disease. Early and accurate diagnosis of MR via ultrasound video is critical for timely clinical decision-making and surgical intervention. However, manual MR diagnosis heavily relies on the operator's experience, which may cause misdiagnosis and inter-observer variability. Since MR data is limited and has large intra-class variability, we propose an unsupervised out-of-distribution (OOD) detection method to identify MR rather than building a deep classifier. To our knowledge, we are the first to explore OOD in MR ultrasound videos. Our method consists of a feature extractor, a feature reconstruction model, and a residual accumulation amplification algorithm. The feature extractor obtains features from the video clips and feeds them into the feature reconstruction model to restore the original features. The residual accumulation amplification algorithm then iteratively performs noise feature reconstruction, amplifying the reconstructed error of OOD features. This algorithm is straightforward yet efficient and can seamlessly integrate as a plug-and-play component in reconstruction-based OOD detection methods. We validated the proposed method on a large ultrasound dataset containing 893 non-MR and 267 MR videos. Experimental results show that our OOD detection method can effectively identify MR samples., Comment: Accepted by MICCAI MLMI 2024, 11 pages, 3 figures

Echocardiography video is a primary modality for diagnosing heart diseases, but the limited data poses challenges for both clinical teaching and machine learning training. Recently, video generative models have emerged as a promising strategy to alleviate this issue. However, previous methods often relied on holistic conditions during generation, hindering the flexible movement control over specific cardiac structures. In this context, we propose an explainable and controllable method for echocardiography video generation, taking an initial frame and a motion curve as guidance. Our contributions are three-fold. First, we extract motion information from each heart substructure to construct motion curves, enabling the diffusion model to synthesize customized echocardiography videos by modifying these curves. Second, we propose the structure-to-motion alignment module, which can map semantic features onto motion curves across cardiac structures. Third, The position-aware attention mechanism is designed to enhance video consistency utilizing Gaussian masks with structural position information. Extensive experiments on three echocardiography datasets show that our method outperforms others regarding fidelity and consistency. The full code will be released at https://github.com/mlmi-2024-72/ECM., Comment: Accepted by MICCAI MLMI 2024

The Segment Anything Model (SAM) can achieve satisfactory segmentation performance under high-quality box prompts. However, SAM's robustness is compromised by the decline in box quality, limiting its practicality in clinical reality. In this study, we propose a novel Robust Box prompt based SAM (\textbf{RoBox-SAM}) to ensure SAM's segmentation performance under prompts with different qualities. Our contribution is three-fold. First, we propose a prompt refinement module to implicitly perceive the potential targets, and output the offsets to directly transform the low-quality box prompt into a high-quality one. We then provide an online iterative strategy for further prompt refinement. Second, we introduce a prompt enhancement module to automatically generate point prompts to assist the box-promptable segmentation effectively. Last, we build a self-information extractor to encode the prior information from the input image. These features can optimize the image embeddings and attention calculation, thus, the robustness of SAM can be further enhanced. Extensive experiments on the large medical segmentation dataset including 99,299 images, 5 modalities, and 25 organs/targets validated the efficacy of our proposed RoBox-SAM., Comment: Accepted by MICCAI MLMI 2024

In the context of proxy modeling for process systems, traditional data-driven deep learning approaches frequently encounter significant challenges, such as substantial training costs induced by large amounts of data, and limited generalization capabilities. As a promising alternative, physics-aware models incorporate partial physics knowledge to ameliorate these challenges. Although demonstrating efficacy, they fall short in terms of exploration depth and universality. To address these shortcomings, we introduce a physics-aware proxy model (PAPM) that fully incorporates partial prior physics of process systems, which includes multiple input conditions and the general form of conservation relations, resulting in better out-of-sample generalization. Additionally, PAPM contains a holistic temporal-spatial stepping module for flexible adaptation across various process systems. Through systematic comparisons with state-of-the-art pure data-driven and physics-aware models across five two-dimensional benchmarks in nine generalization tasks, PAPM notably achieves an average performance improvement of 6.7%, while requiring fewer FLOPs, and just 1% of the parameters compared to the prior leading method. The code is available at https://github.com/pengwei07/PAPM., Comment: ICML 2024

Fine-grained spatio-temporal learning is crucial for freehand 3D ultrasound reconstruction. Previous works mainly resorted to the coarse-grained spatial features and the separated temporal dependency learning and struggles for fine-grained spatio-temporal learning. Mining spatio-temporal information in fine-grained scales is extremely challenging due to learning difficulties in long-range dependencies. In this context, we propose a novel method to exploit the long-range dependency management capabilities of the state space model (SSM) to address the above challenge. Our contribution is three-fold. First, we propose ReMamba, which mines multi-scale spatio-temporal information by devising a multi-directional SSM. Second, we propose an adaptive fusion strategy that introduces multiple inertial measurement units as auxiliary temporal information to enhance spatio-temporal perception. Last, we design an online alignment strategy that encodes the temporal information as pseudo labels for multi-modal alignment to further improve reconstruction performance. Extensive experimental validations on two large-scale datasets show remarkable improvement from our method over competitors., Comment: Accepted at MICCAI 2024. This is the submitted manuscript and the preprint has not undergone peer review (when applicable) or any post-submission improvements or corrections

Prostate cancer (PCa) poses a significant threat to men's health, with early diagnosis being crucial for improving prognosis and reducing mortality rates. Transrectal ultrasound (TRUS) plays a vital role in the diagnosis and image-guided intervention of PCa.To facilitate physicians with more accurate and efficient computer-assisted diagnosis and interventions, many image processing algorithms in TRUS have been proposed and achieved state-of-the-art performance in several tasks, including prostate gland segmentation, prostate image registration, PCa classification and detection, and interventional needle detection. The rapid development of these algorithms over the past two decades necessitates a comprehensive summary. In consequence, this survey provides a \textcolor{blue}{narrative } analysis of this field, outlining the evolution of image processing methods in the context of TRUS image analysis and meanwhile highlighting their relevant contributions. Furthermore, this survey discusses current challenges and suggests future research directions to possibly advance this field further., Comment: Accepted by Ultrasound in Medicine & Biology

Echocardiography (ECHO) video is widely used for cardiac examination. In clinical, this procedure heavily relies on operator experience, which needs years of training and maybe the assistance of deep learning-based systems for enhanced accuracy and efficiency. However, it is challenging since acquiring sufficient customized data (e.g., abnormal cases) for novice training and deep model development is clinically unrealistic. Hence, controllable ECHO video synthesis is highly desirable. In this paper, we propose a novel diffusion-based framework named HeartBeat towards controllable and high-fidelity ECHO video synthesis. Our highlight is three-fold. First, HeartBeat serves as a unified framework that enables perceiving multimodal conditions simultaneously to guide controllable generation. Second, we factorize the multimodal conditions into local and global ones, with two insertion strategies separately provided fine- and coarse-grained controls in a composable and flexible manner. In this way, users can synthesize ECHO videos that conform to their mental imagery by combining multimodal control signals. Third, we propose to decouple the visual concepts and temporal dynamics learning using a two-stage training scheme for simplifying the model training. One more interesting thing is that HeartBeat can easily generalize to mask-guided cardiac MRI synthesis in a few shots, showcasing its scalability to broader applications. Extensive experiments on two public datasets show the efficacy of the proposed HeartBeat., Comment: Accepted by MICCAI 2024

Ultrasound is widely used in clinical practice due to its affordability, portability, and safety. However, current AI research often overlooks combined disease prediction and tissue segmentation. We propose UniUSNet, a universal framework for ultrasound image classification and segmentation. This model handles various ultrasound types, anatomical positions, and input formats, excelling in both segmentation and classification tasks. Trained on a comprehensive dataset with over 9.7K annotations from 7 distinct anatomical positions, our model matches state-of-the-art performance and surpasses single-dataset and ablated models. Zero-shot and fine-tuning experiments show strong generalization and adaptability with minimal fine-tuning. We plan to expand our dataset and refine the prompting mechanism, with model weights and code available at (https://github.com/Zehui-Lin/UniUSNet)., Comment: Accepted to BIBM 2024

Deformable image registration plays a crucial role in medical imaging, aiding in disease diagnosis and image-guided interventions. Traditional iterative methods are slow, while deep learning (DL) accelerates solutions but faces usability and precision challenges. This study introduces a pyramid network with the enhanced motion decomposition Transformer (ModeTv2) operator, showcasing superior pairwise optimization (PO) akin to traditional methods. We re-implement ModeT operator with CUDA extensions to enhance its computational efficiency. We further propose RegHead module which refines deformation fields, improves the realism of deformation and reduces parameters. By adopting the PO, the proposed network balances accuracy, efficiency, and generalizability. Extensive experiments on two public brain MRI datasets and one abdominal CT dataset demonstrate the network's suitability for PO, providing a DL model with enhanced usability and interpretability. The code is publicly available.

Bandwidth constraints during signal acquisition frequently impede real-time detection applications. Hyperspectral data is a notable example, whose vast volume compromises real-time hyperspectral detection. To tackle this hurdle, we introduce a novel approach leveraging pre-acquisition modulation to reduce the acquisition volume. This modulation process is governed by a deep learning model, utilizing prior information. Central to our approach is LUM-ViT, a Vision Transformer variant. Uniquely, LUM-ViT incorporates a learnable under-sampling mask tailored for pre-acquisition modulation. To further optimize for optical calculations, we propose a kernel-level weight binarization technique and a three-stage fine-tuning strategy. Our evaluations reveal that, by sampling a mere 10% of the original image pixels, LUM-ViT maintains the accuracy loss within 1.8% on the ImageNet classification task. The method sustains near-original accuracy when implemented on real-world optical hardware, demonstrating its practicality. Code will be available at https://github.com/MaxLLF/LUM-ViT., Comment: Accepted to ICLR 2024

Thyroid nodule classification and segmentation in ultrasound images are crucial for computer-aided diagnosis; however, they face limitations owing to insufficient labeled data. In this study, we proposed a multi-view contrastive self-supervised method to improve thyroid nodule classification and segmentation performance with limited manual labels. Our method aligns the transverse and longitudinal views of the same nodule, thereby enabling the model to focus more on the nodule area. We designed an adaptive loss function that eliminates the limitations of the paired data. Additionally, we adopted a two-stage pre-training to exploit the pre-training on ImageNet and thyroid ultrasound images. Extensive experiments were conducted on a large-scale dataset collected from multiple centers. The results showed that the proposed method significantly improves nodule classification and segmentation performance with limited manual labels and outperforms state-of-the-art self-supervised methods. The two-stage pre-training also significantly exceeded ImageNet pre-training., Comment: The article has been accepted by the journal of Computers in Biology and Medicine

Different diseases, such as histological subtypes of breast lesions, have severely varying incidence rates. Even trained with substantial amount of in-distribution (ID) data, models often encounter out-of-distribution (OOD) samples belonging to unseen classes in clinical reality. To address this, we propose a novel framework built upon a long-tailed OOD detection task for breast ultrasound images. It is equipped with a triplet state augmentation (TriAug) which improves ID classification accuracy while maintaining a promising OOD detection performance. Meanwhile, we designed a balanced sphere loss to handle the class imbalanced problem. Experimental results show that the model outperforms state-of-art OOD approaches both in ID classification (F1-score=42.12%) and OOD detection (AUROC=78.06%).

Objective: Ultrasound (US) examination has unique advantages in diagnosing carpal tunnel syndrome (CTS) while identifying the median nerve (MN) and diagnosing CTS depends heavily on the expertise of examiners. To alleviate this problem, we aimed to develop a one-stop automated CTS diagnosis system (OSA-CTSD) and evaluate its effectiveness as a computer-aided diagnostic tool. Methods: We combined real-time MN delineation, accurate biometric measurements, and explainable CTS diagnosis into a unified framework, called OSA-CTSD. We collected a total of 32,301 static images from US videos of 90 normal wrists and 40 CTS wrists for evaluation using a simplified scanning protocol. Results: The proposed model showed better segmentation and measurement performance than competing methods, reporting that HD95 score of 7.21px, ASSD score of 2.64px, Dice score of 85.78%, and IoU score of 76.00%, respectively. In the reader study, it demonstrated comparable performance with the average performance of the experienced in classifying the CTS, while outperformed that of the inexperienced radiologists in terms of classification metrics (e.g., accuracy score of 3.59% higher and F1 score of 5.85% higher). Conclusion: The OSA-CTSD demonstrated promising diagnostic performance with the advantages of real-time, automation, and clinical interpretability. The application of such a tool can not only reduce reliance on the expertise of examiners, but also can help to promote the future standardization of the CTS diagnosis process, benefiting both patients and radiologists., Comment: Accepted by Ultrasound in Medicine & Biology

Breast lesion segmentation from breast ultrasound (BUS) videos could assist in early diagnosis and treatment. Existing video object segmentation (VOS) methods usually require dense annotation, which is often inaccessible for medical datasets. Furthermore, they suffer from accumulative errors and a lack of explicit space-time awareness. In this work, we propose a novel two-shot training paradigm for BUS video segmentation. It not only is able to capture free-range space-time consistency but also utilizes a source-dependent augmentation scheme. This label-efficient learning framework is validated on a challenging in-house BUS video dataset. Results showed that it gained comparable performance to the fully annotated ones given only 1.9% training labels., Comment: 5 pages, 4 figure, 2 tables, accepted by ISBI 2024

Diffusion models have emerged as the de facto paradigm for video generation. However, their reliance on web-scale data of varied quality often yields results that are visually unappealing and misaligned with the textual prompts. To tackle this problem, we propose InstructVideo to instruct text-to-video diffusion models with human feedback by reward fine-tuning. InstructVideo has two key ingredients: 1) To ameliorate the cost of reward fine-tuning induced by generating through the full DDIM sampling chain, we recast reward fine-tuning as editing. By leveraging the diffusion process to corrupt a sampled video, InstructVideo requires only partial inference of the DDIM sampling chain, reducing fine-tuning cost while improving fine-tuning efficiency. 2) To mitigate the absence of a dedicated video reward model for human preferences, we repurpose established image reward models, e.g., HPSv2. To this end, we propose Segmental Video Reward, a mechanism to provide reward signals based on segmental sparse sampling, and Temporally Attenuated Reward, a method that mitigates temporal modeling degradation during fine-tuning. Extensive experiments, both qualitative and quantitative, validate the practicality and efficacy of using image reward models in InstructVideo, significantly enhancing the visual quality of generated videos without compromising generalization capabilities. Code and models will be made publicly available., Comment: Project page: https://instructvideo.github.io/

In medical image segmentation, domain generalization poses a significant challenge due to domain shifts caused by variations in data acquisition devices and other factors. These shifts are particularly pronounced in the most common scenario, which involves only single-source domain data due to privacy concerns. To address this, we draw inspiration from the self-supervised learning paradigm that effectively discourages overfitting to the source domain. We propose the Denoising Y-Net (DeY-Net), a novel approach incorporating an auxiliary denoising decoder into the basic U-Net architecture. The auxiliary decoder aims to perform denoising training, augmenting the domain-invariant representation that facilitates domain generalization. Furthermore, this paradigm provides the potential to utilize unlabeled data. Building upon denoising training, we propose Denoising Test Time Adaptation (DeTTA) that further: (i) adapts the model to the target domain in a sample-wise manner, and (ii) adapts to the noise-corrupted input. Extensive experiments conducted on widely-adopted liver segmentation benchmarks demonstrate significant domain generalization improvements over our baseline and state-of-the-art results compared to other methods. Code is available at https://github.com/WenRuxue/DeTTA., Comment: Accepted to WACV 2024

Fetal pose estimation in 3D ultrasound (US) involves identifying a set of associated fetal anatomical landmarks. Its primary objective is to provide comprehensive information about the fetus through landmark connections, thus benefiting various critical applications, such as biometric measurements, plane localization, and fetal movement monitoring. However, accurately estimating the 3D fetal pose in US volume has several challenges, including poor image quality, limited GPU memory for tackling high dimensional data, symmetrical or ambiguous anatomical structures, and considerable variations in fetal poses. In this study, we propose a novel 3D fetal pose estimation framework (called FetusMapV2) to overcome the above challenges. Our contribution is three-fold. First, we propose a heuristic scheme that explores the complementary network structure-unconstrained and activation-unreserved GPU memory management approaches, which can enlarge the input image resolution for better results under limited GPU memory. Second, we design a novel Pair Loss to mitigate confusion caused by symmetrical and similar anatomical structures. It separates the hidden classification task from the landmark localization task and thus progressively eases model learning. Last, we propose a shape priors-based self-supervised learning by selecting the relatively stable landmarks to refine the pose online. Extensive experiments and diverse applications on a large-scale fetal US dataset including 1000 volumes with 22 landmarks per volume demonstrate that our method outperforms other strong competitors., Comment: 16 pages, 11 figures, accepted by Medical Image Analysis(2023)

Medical image segmentation aims to delineate the anatomical or pathological structures of interest, playing a crucial role in clinical diagnosis. A substantial amount of high-quality annotated data is crucial for constructing high-precision deep segmentation models. However, medical annotation is highly cumbersome and time-consuming, especially for medical videos or 3D volumes, due to the huge labeling space and poor inter-frame consistency. Recently, a fundamental task named Moving Object Segmentation (MOS) has made significant advancements in natural images. Its objective is to delineate moving objects from the background within image sequences, requiring only minimal annotations. In this paper, we propose the first foundation model, named iMOS, for MOS in medical images. Extensive experiments on a large multi-modal medical dataset validate the effectiveness of the proposed iMOS. Specifically, with the annotation of only a small number of images in the sequence, iMOS can achieve satisfactory tracking and segmentation performance of moving objects throughout the entire sequence in bi-directions. We hope that the proposed iMOS can help accelerate the annotation speed of experts, and boost the development of medical foundation models., Comment: 5 pages, 7 figures, 3 tables. This paper has been accepted by ISBI 2024

Ultrasound (US) image segmentation is an active research area that requires real-time and highly accurate analysis in many scenarios. The detect-to-segment (DTS) frameworks have been recently proposed to balance accuracy and efficiency. However, existing approaches may suffer from inadequate contour encoding or fail to effectively leverage the encoded results. In this paper, we introduce a novel Fourier-anchor-based DTS framework called Fourier Feature Pyramid Network (FFPN) to address the aforementioned issues. The contributions of this paper are two fold. First, the FFPN utilizes Fourier Descriptors to adequately encode contours. Specifically, it maps Fourier series with similar amplitudes and frequencies into the same layer of the feature map, thereby effectively utilizing the encoded Fourier information. Second, we propose a Contour Sampling Refinement (CSR) module based on the contour proposals and refined features produced by the FFPN. This module extracts rich features around the predicted contours to further capture detailed information and refine the contours. Extensive experimental results on three large and challenging datasets demonstrate that our method outperforms other DTS methods in terms of accuracy and efficiency. Furthermore, our framework can generalize well to other detection or segmentation tasks., Comment: 10 pages, 5 figures, Accepted by MLMI 2023

Interactive medical image segmentation refers to the accurate segmentation of the target of interest through interaction (e.g., click) between the user and the image. It has been widely studied in recent years as it is less dependent on abundant annotated data and more flexible than fully automated segmentation. However, current studies have not fully explored user-provided prompt information (e.g., points), including the knowledge mined in one interaction, and the relationship between multiple interactions. Thus, in this paper, we introduce a novel framework equipped with prompt enhancement, called PE-MED, for interactive medical image segmentation. First, we introduce a Self-Loop strategy to generate warm initial segmentation results based on the first prompt. It can prevent the highly unfavorable scenarios, such as encountering a blank mask as the initial input after the first interaction. Second, we propose a novel Prompt Attention Learning Module (PALM) to mine useful prompt information in one interaction, enhancing the responsiveness of the network to user clicks. Last, we build a Time Series Information Propagation (TSIP) mechanism to extract the temporal relationships between multiple interactions and increase the model stability. Comparative experiments with other state-of-the-art (SOTA) medical image segmentation algorithms show that our method exhibits better segmentation accuracy and stability., Comment: Accepted by MICCAI MLMI 2023

Relational Language-Image Pre-training (RLIP) aims to align vision representations with relational texts, thereby advancing the capability of relational reasoning in computer vision tasks. However, hindered by the slow convergence of RLIPv1 architecture and the limited availability of existing scene graph data, scaling RLIPv1 is challenging. In this paper, we propose RLIPv2, a fast converging model that enables the scaling of relational pre-training to large-scale pseudo-labelled scene graph data. To enable fast scaling, RLIPv2 introduces Asymmetric Language-Image Fusion (ALIF), a mechanism that facilitates earlier and deeper gated cross-modal fusion with sparsified language encoding layers. ALIF leads to comparable or better performance than RLIPv1 in a fraction of the time for pre-training and fine-tuning. To obtain scene graph data at scale, we extend object detection datasets with free-form relation labels by introducing a captioner (e.g., BLIP) and a designed Relation Tagger. The Relation Tagger assigns BLIP-generated relation texts to region pairs, thus enabling larger-scale relational pre-training. Through extensive experiments conducted on Human-Object Interaction Detection and Scene Graph Generation, RLIPv2 shows state-of-the-art performance on three benchmarks under fully-finetuning, few-shot and zero-shot settings. Notably, the largest RLIPv2 achieves 23.29mAP on HICO-DET without any fine-tuning, yields 32.22mAP with just 1% data and yields 45.09mAP with 100% data. Code and models are publicly available at https://github.com/JacobYuan7/RLIPv2., Comment: Accepted to ICCV 2023. Code and models: https://github.com/JacobYuan7/RLIPv2

Ultrasound (US) imaging is indispensable in clinical practice. To diagnose certain diseases, sonographers must observe corresponding dynamic anatomic structures to gather comprehensive information. However, the limited availability of specific US video cases causes teaching difficulties in identifying corresponding diseases, which potentially impacts the detection rate of such cases. The synthesis of US videos may represent a promising solution to this issue. Nevertheless, it is challenging to accurately animate the intricate motion of dynamic anatomic structures while preserving image fidelity. To address this, we present a novel online feature-decoupling framework called OnUVS for high-fidelity US video synthesis. Our highlights can be summarized by four aspects. First, we introduced anatomic information into keypoint learning through a weakly-supervised training strategy, resulting in improved preservation of anatomical integrity and motion while minimizing the labeling burden. Second, to better preserve the integrity and textural information of US images, we implemented a dual-decoder that decouples the content and textural features in the generator. Third, we adopted a multiple-feature discriminator to extract a comprehensive range of visual cues, thereby enhancing the sharpness and fine details of the generated videos. Fourth, we constrained the motion trajectories of keypoints during online learning to enhance the fluidity of generated videos. Our validation and user studies on in-house echocardiographic and pelvic floor US videos showed that OnUVS synthesizes US videos with high fidelity., Comment: 14 pages, 13 figures and 6 tables

Electroencephalography (EEG) is an objective tool for emotion recognition with promising applications. However, the scarcity of labeled data remains a major challenge in this field, limiting the widespread use of EEG-based emotion recognition. In this paper, a semi-supervised Dual-stream Self-Attentive Adversarial Graph Contrastive learning framework (termed as DS-AGC) is proposed to tackle the challenge of limited labeled data in cross-subject EEG-based emotion recognition. The DS-AGC framework includes two parallel streams for extracting non-structural and structural EEG features. The non-structural stream incorporates a semi-supervised multi-domain adaptation method to alleviate distribution discrepancy among labeled source domain, unlabeled source domain, and unknown target domain. The structural stream develops a graph contrastive learning method to extract effective graph-based feature representation from multiple EEG channels in a semi-supervised manner. Further, a self-attentive fusion module is developed for feature fusion, sample selection, and emotion recognition, which highlights EEG features more relevant to emotions and data samples in the labeled source domain that are closer to the target domain. Extensive experiments conducted on two benchmark databases (SEED and SEED-IV) using a semi-supervised cross-subject leave-one-subject-out cross-validation evaluation scheme show that the proposed model outperforms existing methods under different incomplete label conditions (with an average improvement of 5.83% on SEED and 6.99% on SEED-IV), demonstrating its effectiveness in addressing the label scarcity problem in cross-subject EEG-based emotion recognition., Comment: arXiv admin note: text overlap with arXiv:2304.06496

Early diagnosis of renal cancer can greatly improve the survival rate of patients. Contrast-enhanced ultrasound (CEUS) is a cost-effective and non-invasive imaging technique and has become more and more frequently used for renal tumor diagnosis. However, the classification of benign and malignant renal tumors can still be very challenging due to the highly heterogeneous appearance of cancer and imaging artifacts. Our aim is to detect and classify renal tumors by integrating B-mode and CEUS-mode ultrasound videos. To this end, we propose a novel multi-modal ultrasound video fusion network that can effectively perform multi-modal feature fusion and video classification for renal tumor diagnosis. The attention-based multi-modal fusion module uses cross-attention and self-attention to extract modality-invariant features and modality-specific features in parallel. In addition, we design an object-level temporal aggregation (OTA) module that can automatically filter low-quality features and efficiently integrate temporal information from multiple frames to improve the accuracy of tumor diagnosis. Experimental results on a multicenter dataset show that the proposed framework outperforms the single-modal models and the competing methods. Furthermore, our OTA module achieves higher classification accuracy than the frame-level predictions. Our code is available at \url{https://github.com/JeunyuLi/MUAF}., Comment: MICCAI 2023

Ultrasound (US) imaging is a popular tool in clinical diagnosis, offering safety, repeatability, and real-time capabilities. Freehand 3D US is a technique that provides a deeper understanding of scanned regions without increasing complexity. However, estimating elevation displacement and accumulation error remains challenging, making it difficult to infer the relative position using images alone. The addition of external lightweight sensors has been proposed to enhance reconstruction performance without adding complexity, which has been shown to be beneficial. We propose a novel online self-consistency network (OSCNet) using multiple inertial measurement units (IMUs) to improve reconstruction performance. OSCNet utilizes a modal-level self-supervised strategy to fuse multiple IMU information and reduce differences between reconstruction results obtained from each IMU data. Additionally, a sequence-level self-consistency strategy is proposed to improve the hierarchical consistency of prediction results among the scanning sequence and its sub-sequences. Experiments on large-scale arm and carotid datasets with multiple scanning tactics demonstrate that our OSCNet outperforms previous methods, achieving state-of-the-art reconstruction performance., Comment: Accepted by MICCAI-2023

Deep learning-based deformable registration methods have been widely investigated in diverse medical applications. Learning-based deformable registration relies on weighted objective functions trading off registration accuracy and smoothness of the deformation field. Therefore, they inevitably require tuning the hyperparameter for optimal registration performance. Tuning the hyperparameters is highly computationally expensive and introduces undesired dependencies on domain knowledge. In this study, we construct a registration model based on the gradient surgery mechanism, named GSMorph, to achieve a hyperparameter-free balance on multiple losses. In GSMorph, we reformulate the optimization procedure by projecting the gradient of similarity loss orthogonally to the plane associated with the smoothness constraint, rather than additionally introducing a hyperparameter to balance these two competing terms. Furthermore, our method is model-agnostic and can be merged into any deep registration network without introducing extra parameters or slowing down inference. In this study, We compared our method with state-of-the-art (SOTA) deformable registration approaches over two publicly available cardiac MRI datasets. GSMorph proves superior to five SOTA learning-based registration models and two conventional registration techniques, SyN and Demons, on both registration accuracy and smoothness., Comment: Accepted at MICCAI 2023

The Transformer structures have been widely used in computer vision and have recently made an impact in the area of medical image registration. However, the use of Transformer in most registration networks is straightforward. These networks often merely use the attention mechanism to boost the feature learning as the segmentation networks do, but do not sufficiently design to be adapted for the registration task. In this paper, we propose a novel motion decomposition Transformer (ModeT) to explicitly model multiple motion modalities by fully exploiting the intrinsic capability of the Transformer structure for deformation estimation. The proposed ModeT naturally transforms the multi-head neighborhood attention relationship into the multi-coordinate relationship to model multiple motion modes. Then the competitive weighting module (CWM) fuses multiple deformation sub-fields to generate the resulting deformation field. Extensive experiments on two public brain magnetic resonance imaging (MRI) datasets show that our method outperforms current state-of-the-art registration networks and Transformers, demonstrating the potential of our ModeT for the challenging non-rigid deformation estimation problem. The benchmarks and our code are publicly available at https://github.com/ZAX130/SmileCode., Comment: Early accepted by MICCAI 2023

Deep neural networks have been widely applied in dichotomous medical image segmentation (DMIS) of many anatomical structures in several modalities, achieving promising performance. However, existing networks tend to struggle with task-specific, heavy and complex designs to improve accuracy. They made little instructions to which feature channels would be more beneficial for segmentation, and that may be why the performance and universality of these segmentation models are hindered. In this study, we propose an instructive feature enhancement approach, namely IFE, to adaptively select feature channels with rich texture cues and strong discriminability to enhance raw features based on local curvature or global information entropy criteria. Being plug-and-play and applicable for diverse DMIS tasks, IFE encourages the model to focus on texture-rich features which are especially important for the ambiguous and challenging boundary identification, simultaneously achieving simplicity, universality, and certain interpretability. To evaluate the proposed IFE, we constructed the first large-scale DMIS dataset Cosmos55k, which contains 55,023 images from 7 modalities and 26 anatomical structures. Extensive experiments show that IFE can improve the performance of classic segmentation networks across different anatomies and modalities with only slight modifications. Code is available at https://github.com/yezi-66/IFE, Comment: Accepted by MICCAI 2023

Localization of the narrowest position of the vessel and corresponding vessel and remnant vessel delineation in carotid ultrasound (US) are essential for carotid stenosis grading (CSG) in clinical practice. However, the pipeline is time-consuming and tough due to the ambiguous boundaries of plaque and temporal variation. To automatize this procedure, a large number of manual delineations are usually required, which is not only laborious but also not reliable given the annotation difficulty. In this study, we present the first video classification framework for automatic CSG. Our contribution is three-fold. First, to avoid the requirement of laborious and unreliable annotation, we propose a novel and effective video classification network for weakly-supervised CSG. Second, to ease the model training, we adopt an inflation strategy for the network, where pre-trained 2D convolution weights can be adapted into the 3D counterpart in our network for an effective warm start. Third, to enhance the feature discrimination of the video, we propose a novel attention-guided multi-dimension fusion (AMDF) transformer encoder to model and integrate global dependencies within and across spatial and temporal dimensions, where two lightweight cross-dimensional attention mechanisms are designed. Our approach is extensively validated on a large clinically collected carotid US video dataset, demonstrating state-of-the-art performance compared with strong competitors., Comment: Accepted by MICCAI 2023

Deep classifiers may encounter significant performance degradation when processing unseen testing data from varying centers, vendors, and protocols. Ensuring the robustness of deep models against these domain shifts is crucial for their widespread clinical application. In this study, we propose a novel approach called Fourier Test-time Adaptation (FTTA), which employs a dual-adaptation design to integrate input and model tuning, thereby jointly improving the model robustness. The main idea of FTTA is to build a reliable multi-level consistency measurement of paired inputs for achieving self-correction of prediction. Our contribution is two-fold. First, we encourage consistency in global features and local attention maps between the two transformed images of the same input. Here, the transformation refers to Fourier-based input adaptation, which can transfer one unseen image into source style to reduce the domain gap. Furthermore, we leverage style-interpolated images to enhance the global and local features with learnable parameters, which can smooth the consistency measurement and accelerate convergence. Second, we introduce a regularization technique that utilizes style interpolation consistency in the frequency space to encourage self-consistency in the logit space of the model output. This regularization provides strong self-supervised signals for robustness enhancement. FTTA was extensively validated on three large classification datasets with different modalities and organs. Experimental results show that FTTA is general and outperforms other strong state-of-the-art methods., Comment: Accepted by MICCAI 2023

The Segment Anything Model (SAM) is the first foundation model for general image segmentation. It has achieved impressive results on various natural image segmentation tasks. However, medical image segmentation (MIS) is more challenging because of the complex modalities, fine anatomical structures, uncertain and complex object boundaries, and wide-range object scales. To fully validate SAM's performance on medical data, we collected and sorted 53 open-source datasets and built a large medical segmentation dataset with 18 modalities, 84 objects, 125 object-modality paired targets, 1050K 2D images, and 6033K masks. We comprehensively analyzed different models and strategies on the so-called COSMOS 1050K dataset. Our findings mainly include the following: 1) SAM showed remarkable performance in some specific objects but was unstable, imperfect, or even totally failed in other situations. 2) SAM with the large ViT-H showed better overall performance than that with the small ViT-B. 3) SAM performed better with manual hints, especially box, than the Everything mode. 4) SAM could help human annotation with high labeling quality and less time. 5) SAM was sensitive to the randomness in the center point and tight box prompts, and may suffer from a serious performance drop. 6) SAM performed better than interactive methods with one or a few points, but will be outpaced as the number of points increases. 7) SAM's performance correlated to different factors, including boundary complexity, intensity differences, etc. 8) Finetuning the SAM on specific medical tasks could improve its average DICE performance by 4.39% and 6.68% for ViT-B and ViT-H, respectively. We hope that this comprehensive report can help researchers explore the potential of SAM applications in MIS, and guide how to appropriately use and develop SAM., Comment: Accepted by Medical Image Analysis. 23 pages, 18 figures, 8 tables

Ultrasound is the primary modality to examine fetal growth during pregnancy, while the image quality could be affected by various factors. Quality assessment is essential for controlling the quality of ultrasound images to guarantee both the perceptual and diagnostic values. Existing automated approaches often require heavy structural annotations and the predictions may not necessarily be consistent with the assessment results by human experts. Furthermore, the overall quality of a scan and the correlation between the quality of frames should not be overlooked. In this work, we propose a reinforcement learning framework powered by two hierarchical agents that collaboratively learn to perform both frame-level and video-level quality assessments. It is equipped with a specially-designed reward mechanism that considers temporal dependency among frame quality and only requires sparse binary annotations to train. Experimental results on a challenging fetal brain dataset verify that the proposed framework could perform dual-level quality assessment and its predictions correlate well with the subjective assessment results.

Scribble-supervised medical image segmentation tackles the limitation of sparse masks. Conventional approaches alternate between: labeling pseudo-masks and optimizing network parameters. However, such iterative two-stage paradigm is unwieldy and could be trapped in poor local optima since the networks undesirably regress to the erroneous pseudo-masks. To address these issues, we propose a non-iterative method where a stream of varying (pacing) pseudo-masks teach a network via consistency training, named PacingPseudo. Our motivation lies first in a non-iterative process. Interestingly, it can be achieved gracefully by a siamese architecture, wherein a stream of pseudo-masks naturally assimilate a stream of predicted masks during training. Second, we make the consistency training effective with two necessary designs: (i) entropy regularization to obtain high-confidence pseudo-masks for effective teaching; and (ii) distorted augmentations to create discrepancy between the pseudo-mask and predicted-mask streams for consistency regularization. Third, we devise a new memory bank mechanism that provides an extra source of ensemble features to complement scarce labeled pixels. The efficacy of the proposed PacingPseudo is validated on three public medical image datasets, including the segmentation tasks of abdominal multi-organs, cardiac structures, and myocardium. Extensive experiments demonstrate our PacingPseudo improves the baseline by large margins and consistently outcompetes several previous methods. In some cases, our PacingPseudo achieves comparable performance with its fully-supervised counterparts, showing the feasibility of our method for the challenging scribble-supervised segmentation applications. The code and scribble annotations will be publicly available., Comment: 12 pages, 8 figures

The task of Human-Object Interaction (HOI) detection targets fine-grained visual parsing of humans interacting with their environment, enabling a broad range of applications. Prior work has demonstrated the benefits of effective architecture design and integration of relevant cues for more accurate HOI detection. However, the design of an appropriate pre-training strategy for this task remains underexplored by existing approaches. To address this gap, we propose Relational Language-Image Pre-training (RLIP), a strategy for contrastive pre-training that leverages both entity and relation descriptions. To make effective use of such pre-training, we make three technical contributions: (1) a new Parallel entity detection and Sequential relation inference (ParSe) architecture that enables the use of both entity and relation descriptions during holistically optimized pre-training; (2) a synthetic data generation framework, Label Sequence Extension, that expands the scale of language data available within each minibatch; (3) mechanisms to account for ambiguity, Relation Quality Labels and Relation Pseudo-Labels, to mitigate the influence of ambiguous/noisy samples in the pre-training data. Through extensive experiments, we demonstrate the benefits of these contributions, collectively termed RLIP-ParSe, for improved zero-shot, few-shot and fine-tuning HOI detection performance as well as increased robustness to learning from noisy annotations. Code will be available at https://github.com/JacobYuan7/RLIP., Comment: Accepted to NeurIPS 2022 as a Spotlight paper

Breast cancer is one of the leading causes of cancer deaths in women. As the primary output of breast screening, breast ultrasound (US) video contains exclusive dynamic information for cancer diagnosis. However, training models for video analysis is non-trivial as it requires a voluminous dataset which is also expensive to annotate. Furthermore, the diagnosis of breast lesion faces unique challenges such as inter-class similarity and intra-class variation. In this paper, we propose a pioneering approach that directly utilizes US videos in computer-aided breast cancer diagnosis. It leverages masked video modeling as pretraining to reduce reliance on dataset size and detailed annotations. Moreover, a correlation-aware contrastive loss is developed to facilitate the identifying of the internal and external relationship between benign and malignant lesions. Experimental results show that our proposed approach achieved promising classification performance and can outperform other state-of-the-art methods., Comment: Accepted by MICCAI-REMIA oral 2022

Ultrasound (US) is the primary imaging technique for the diagnosis of thyroid cancer. However, accurate identification of nodule malignancy is a challenging task that can elude less-experienced clinicians. Recently, many computer-aided diagnosis (CAD) systems have been proposed to assist this process. However, most of them do not provide the reasoning of their classification process, which may jeopardize their credibility in practical use. To overcome this, we propose a novel deep learning framework called multi-attribute attention network (MAA-Net) that is designed to mimic the clinical diagnosis process. The proposed model learns to predict nodular attributes and infer their malignancy based on these clinically-relevant features. A multi-attention scheme is adopted to generate customized attention to improve each task and malignancy diagnosis. Furthermore, MAA-Net utilizes nodule delineations as nodules spatial prior guidance for the training rather than cropping the nodules with additional models or human interventions to prevent losing the context information. Validation experiments were performed on a large and challenging dataset containing 4554 patients. Results show that the proposed method outperformed other state-of-the-art methods and provides interpretable predictions that may better suit clinical needs., Comment: 11 pages, 7 figures

Over the past decades, the incidence of thyroid cancer has been increasing globally. Accurate and early diagnosis allows timely treatment and helps to avoid over-diagnosis. Clinically, a nodule is commonly evaluated from both transverse and longitudinal views using thyroid ultrasound. However, the appearance of the thyroid gland and lesions can vary dramatically across individuals. Identifying key diagnostic information from both views requires specialized expertise. Furthermore, finding an optimal way to integrate multi-view information also relies on the experience of clinicians and adds further difficulty to accurate diagnosis. To address these, we propose a personalized diagnostic tool that can customize its decision-making process for different patients. It consists of a multi-view classification module for feature extraction and a personalized weighting allocation network that generates optimal weighting for different views. It is also equipped with a self-supervised view-aware contrastive loss to further improve the model robustness towards different patient groups. Experimental results show that the proposed framework can better utilize multi-view information and outperform the competing methods., Comment: Accepted by MICCAI 2022