Han Zhou

Yuhao Huang, Xin Yang, Lian Liu et al.

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.

Junxuan Yu, Rusi Chen, Yongsong Zhou et al.

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.

Han Zhou, Dong Ni, Ao Chang et al.

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.

Han Zhou, Aida Ashrafi, Matthew B. Blaschko

Low-bit width neural networks have been extensively explored for deployment on edge devices to reduce computational resources. Existing approaches have focused on gradient-based optimization in a two-stage train-and-compress setting or as a combined optimization where gradients are quantized during training. Such schemes require high-performance hardware during the training phase and usually store an equivalent number of full-precision weights apart from the quantized weights. In this paper, we explore methods of direct combinatorial optimization in the problem of risk minimization with binary weights, which can be made equivalent to a non-monotone submodular maximization under certain conditions. We employ an approximation algorithm for the cases with single and multilayer neural networks. For linear models, it has $\mathcal{O}(nd)$ time complexity where $n$ is the sample size and $d$ is the data dimension. We show that a combination of greedy coordinate descent and this novel approach can attain competitive accuracy on binary classification tasks.

Zhongnuo Yan, Tong Han, Yuhao Huang et al.

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.

Han Zhou, Xingchen Ma, Matthew B Blaschko

Sequential maximization of expected improvement (EI) is one of the most widely used policies in Bayesian optimization because of its simplicity and ability to handle noisy observations. In particular, the improvement function often uses the best posterior mean as the best incumbent in noisy settings. However, the uncertainty associated with the incumbent solution is often neglected in many analytic EI-type methods: a closed-form acquisition function is derived in the noise-free setting, but then applied to the setting with noisy observations. To address this limitation, we propose a modification of EI that corrects its closed-form expression by incorporating the covariance information provided by the Gaussian Process (GP) model. This acquisition function specializes to the classical noise-free result, and we argue should replace that formula in Bayesian optimization software packages, tutorials, and textbooks. This enhanced acquisition provides good generality for noisy and noiseless settings. We show that our method achieves a sublinear convergence rate on the cumulative regret bound under heteroscedastic observation noise. Our empirical results demonstrate that our proposed acquisition function can outperform EI in the presence of noisy observations on benchmark functions for black-box optimization, as well as on parameter search for neural network model compression.

Jun Chen, Jia Wang, Ruibin Li et al.

Optimal transport has found widespread applications in signal processing and machine learning. Among its many equivalent formulations, optimal transport seeks to reconstruct a random variable/vector with a prescribed distribution at the destination while minimizing the expected distortion relative to a given random variable/vector at the source. However, in practice, certain constraints may render the optimal transport plan infeasible. In this work, we consider three types of constraints: rate constraints, dimension constraints, and channel constraints, motivated by perception-aware lossy compression, generative principal component analysis, and deep joint source-channel coding, respectively. Special attenion is given to the setting termed Gaussian Wasserstein optimal transport, where both the source and reconstruction variables are multivariate Gaussian, and the end-to-end distortion is measured by the mean squared error. We derive explicit results for the minimum achievable mean squared error under the three aforementioned constraints when the covariance matrices of the source and reconstruction variables commute.