Jinsong Ouyang

Xiaofeng Liu, Qianru Zhang, Thibault Marin et al.

The synergistic interpretation of anatomical information from computed tomography (CT) and metabolic information from positron emission tomography (PET) is important to oncologic imaging. However, existing deep learning methods for PET/CT remain largely task-specific, are often trained on single-center cohorts, or adopt dual-branch fusion schemes that delay cross-modal interaction and underutilize early spatial correspondence between PET and CT. To address these limitations, we present an open-source, multi-center, whole-body FDG PET/CT foundation model utilizing 4,997 harmonized scans from four public datasets. Our framework employs hierarchical UNet-shaped backbones with early channel-wise concatenation, enabling anatomical and metabolic features to interact from the first embedding layer onward. We further introduce a masked autoencoding objective based on zero-mean imputation, combined with a weighted global reconstruction loss. This design avoids non-physical intensity discontinuities at masked-region boundaries that arise from learnable mask tokens. On downstream AutoPET lesion segmentation, the proposed models demonstrate strong label efficiency: with only 10\% of the labeled training data, they achieve performance comparable to models trained from scratch on the full dataset. Under extreme 5-shot linear probing, joint PET/CT pretraining also achieves higher Dice scores than separated-modality pretraining. This multi-center foundation model demonstrates label efficiency and cross-modality representation learning for PET/CT tumor segmentation. It provides a robust, open-source basis for advancing automated oncologic imaging, significantly reducing the need for large-scale manual annotations in clinical practice.

Xiaofeng Liu, Jonghye Woo, Chao Ma et al.

Delineating lesions and anatomical structure is important for image-guided interventions. Point-supervised medical image segmentation (PSS) has great potential to alleviate costly expert delineation labeling. However, due to the lack of precise size and boundary guidance, the effectiveness of PSS often falls short of expectations. Although recent vision foundational models, such as the medical segment anything model (MedSAM), have made significant advancements in bounding-box-prompted segmentation, it is not straightforward to utilize point annotation, and is prone to semantic ambiguity. In this preliminary study, we introduce an iterative framework to facilitate semantic-aware point-supervised MedSAM. Specifically, the semantic box-prompt generator (SBPG) module has the capacity to convert the point input into potential pseudo bounding box suggestions, which are explicitly refined by the prototype-based semantic similarity. This is then succeeded by a prompt-guided spatial refinement (PGSR) module that harnesses the exceptional generalizability of MedSAM to infer the segmentation mask, which also updates the box proposal seed in SBPG. Performance can be progressively improved with adequate iterations. We conducted an evaluation on BraTS2018 for the segmentation of whole brain tumors and demonstrated its superior performance compared to traditional PSS methods and on par with box-supervised methods.

Xiaofeng Liu, Thibault Marin, Tiss Amal et al.

Background: In medical imaging, images are usually treated as deterministic, while their uncertainties are largely underexplored. Purpose: This work aims at using deep learning to efficiently estimate posterior distributions of imaging parameters, which in turn can be used to derive the most probable parameters as well as their uncertainties. Methods: Our deep learning-based approaches are based on a variational Bayesian inference framework, which is implemented using two different deep neural networks based on conditional variational auto-encoder (CVAE), CVAE-dual-encoder and CVAE-dual-decoder. The conventional CVAE framework, i.e., CVAE-vanilla, can be regarded as a simplified case of these two neural networks. We applied these approaches to a simulation study of dynamic brain PET imaging using a reference region-based kinetic model. Results: In the simulation study, we estimated posterior distributions of PET kinetic parameters given a measurement of time-activity curve. Our proposed CVAE-dual-encoder and CVAE-dual-decoder yield results that are in good agreement with the asymptotically unbiased posterior distributions sampled by Markov Chain Monte Carlo (MCMC). The CVAE-vanilla can also be used for estimating posterior distributions, although it has an inferior performance to both CVAE-dual-encoder and CVAE-dual-decoder. Conclusions: We have evaluated the performance of our deep learning approaches for estimating posterior distributions in dynamic brain PET. Our deep learning approaches yield posterior distributions, which are in good agreement with unbiased distributions estimated by MCMC. All these neural networks have different characteristics and can be chosen by the user for specific applications. The proposed methods are general and can be adapted to other problems.

Xiaofeng Liu, Thibault Marin, Tiss Amal et al.

This work aims efficiently estimating the posterior distribution of kinetic parameters for dynamic positron emission tomography (PET) imaging given a measurement of time of activity curve. Considering the inherent information loss from parametric imaging to measurement space with the forward kinetic model, the inverse mapping is ambiguous. The conventional (but expensive) solution can be the Markov Chain Monte Carlo (MCMC) sampling, which is known to produce unbiased asymptotical estimation. We propose a deep-learning-based framework for efficient posterior estimation. Specifically, we counteract the information loss in the forward process by introducing latent variables. Then, we use a conditional variational autoencoder (CVAE) and optimize its evidence lower bound. The well-trained decoder is able to infer the posterior with a given measurement and the sampled latent variables following a simple multivariate Gaussian distribution. We validate our CVAE-based method using unbiased MCMC as the reference for low-dimensional data (a single brain region) with the simplified reference tissue model.

Xiaofeng Liu, Menghua Xia, Yanis Chemli et al.

In this work, we propose an unsupervised domain adaptation (UDA) framework for 3D volumetric lesion detection that adapts a detector trained on labeled FDG PET/CT to unlabeled PSMA PET/CT. Beyond covariate shift, cross tracer adaptation also exhibits label shift in both lesion size composition and the number of lesions per subject. We introduce self-training with two mechanisms that explicitly model and compensate for this label shift. First, we adaptively adjust the detection anchor shapes by re-estimating target domain box scales from selected pseudo labels and updating anchors with an exponential moving average. This increases positive anchor coverage for small PSMA lesions and stabilizes box regression. Second, instead of a fixed confidence threshold for pseudo-label selection, we allocate size bin-wise quotas according to the estimated target domain histogram over lesion volumes. The self-training alternates between supervised learning with prior-guided pseudo labeling on PSMA and supervised learning on labeled FDG. On AutoPET 2024, adapting from 501 labeled FDG studies to 369 $^{18}$F-PSMA studies, the proposed method improves both AP and FROC over the source-only baseline and conventional self-training without label-shift mitigation, indicating that modeling target lesion prevalence and size composition is an effective path to robust cross-tracer detection.

Xiaoqi Zhao, Peiqian Cao, Chenyang Yu et al.

Power batteries are essential components in electric vehicles, where internal structural defects can pose serious safety risks. We conduct a comprehensive study on a new task, power battery detection (PBD), which aims to localize the dense endpoints of cathode and anode plates from industrial X-ray images for quality inspection. Manual inspection is inefficient and error-prone, while traditional vision algorithms struggle with densely packed plates, low contrast, scale variation, and imaging artifacts. To address this issue and drive more attention into this meaningful task, we present PBD5K, the first large-scale benchmark for this task, consisting of 5,000 X-ray images from nine battery types with fine-grained annotations and eight types of real-world visual interference. To support scalable and consistent labeling, we develop an intelligent annotation pipeline that combines image filtering, model-assisted pre-labeling, cross-verification, and layered quality evaluation. We formulate PBD as a point-level segmentation problem and propose MDCNeXt, a model designed to extract and integrate multi-dimensional structure clues including point, line, and count information from the plate itself. To improve discrimination between plates and suppress visual interference, MDCNeXt incorporates two state space modules. The first is a prompt-filtered module that learns contrastive relationships guided by task-specific prompts. The second is a density-aware reordering module that refines segmentation in regions with high plate density. In addition, we propose a distance-adaptive mask generation strategy to provide robust supervision under varying spatial distributions of anode and cathode positions. The source code and datasets will be publicly available at \href{https://github.com/Xiaoqi-Zhao-DLUT/X-ray-PBD}{PBD5K}.

Xiaoqi Zhao, Youwei Pang, Shijie Chang et al.

As large-scale foundation models trained on billions of image--mask pairs covering a vast diversity of scenes, objects, and contexts, SAM and its upgraded version, SAM~2, have significantly influenced multiple fields within computer vision. Leveraging such unprecedented data diversity, they exhibit strong open-world segmentation capabilities, with SAM~2 further enhancing these capabilities to support high-quality video segmentation. While SAMs (SAM and SAM~2) have demonstrated excellent performance in segmenting context-independent concepts like people, cars, and roads, they overlook more challenging context-dependent (CD) concepts, such as visual saliency, camouflage, industrial defects, and medical lesions. CD concepts rely heavily on global and local contextual information, making them susceptible to shifts in different contexts, which requires strong discriminative capabilities from the model. The lack of comprehensive evaluation of SAMs limits understanding of their performance boundaries, which may hinder the design of future models. In this paper, we conduct a thorough evaluation of SAMs on 11 CD concepts across 2D and 3D images and videos in various visual modalities within natural, medical, and industrial scenes. We develop a unified evaluation framework for SAM and SAM~2 that supports manual, automatic, and intermediate self-prompting, aided by our specific prompt generation and interaction strategies. We further explore the potential of SAM~2 for in-context learning and introduce prompt robustness testing to simulate real-world imperfect prompts. Finally, we analyze the benefits and limitations of SAMs in understanding CD concepts and discuss their future development in segmentation tasks.

Jihoon Cho, Xiaofeng Liu, Fangxu Xing et al.

Multimodal Magnetic Resonance (MR) Imaging plays a crucial role in disease diagnosis due to its ability to provide complementary information by analyzing a relationship between multimodal images on the same subject. Acquiring all MR modalities, however, can be expensive, and, during a scanning session, certain MR images may be missed depending on the study protocol. The typical solution would be to synthesize the missing modalities from the acquired images such as using generative adversarial networks (GANs). Yet, GANs constructed with convolutional neural networks (CNNs) are likely to suffer from a lack of global relationships and mechanisms to condition the desired modality. To address this, in this work, we propose a transformer-based modality infuser designed to synthesize multimodal brain MR images. In our method, we extract modality-agnostic features from the encoder and then transform them into modality-specific features using the modality infuser. Furthermore, the modality infuser captures long-range relationships among all brain structures, leading to the generation of more realistic images. We carried out experiments on the BraTS 2018 dataset, translating between four MR modalities, and our experimental results demonstrate the superiority of our proposed method in terms of synthesis quality. In addition, we conducted experiments on a brain tumor segmentation task and different conditioning methods.

Xiaofeng Liu, Yongsong Huang, Thibault Marin et al.

The to-be-denoised positron emission tomography (PET) volumes are inherent with diverse count levels, which imposes challenges for a unified model to tackle varied cases. In this work, we resort to the recently flourished prompt learning to achieve generalizable PET denoising with different count levels. Specifically, we propose dual prompts to guide the PET denoising in a divide-and-conquer manner, i.e., an explicitly count-level prompt to provide the specific prior information and an implicitly general denoising prompt to encode the essential PET denoising knowledge. Then, a novel prompt fusion module is developed to unify the heterogeneous prompts, followed by a prompt-feature interaction module to inject prompts into the features. The prompts are able to dynamically guide the noise-conditioned denoising process. Therefore, we are able to efficiently train a unified denoising model for various count levels, and deploy it to different cases with personalized prompts. We evaluated on 1940 low-count PET 3D volumes with uniformly randomly selected 13-22\% fractions of events from 97 $^{18}$F-MK6240 tau PET studies. It shows our dual prompting can largely improve the performance with informed count-level and outperform the count-conditional model.

Jia Wei, Xiaoqi Zhao, Jonghye Woo et al.

Single domain generalization (SDG) has recently attracted growing attention in medical image segmentation. One promising strategy for SDG is to leverage consistent semantic shape priors across different imaging protocols, scanner vendors, and clinical sites. However, existing dictionary learning methods that encode shape priors often suffer from limited representational power with a small set of offline computed shape elements, or overfitting when the dictionary size grows. Moreover, they are not readily compatible with large foundation models such as the Segment Anything Model (SAM). In this paper, we propose a novel Mixture-of-Shape-Experts (MoSE) framework that seamlessly integrates the idea of mixture-of-experts (MoE) training into dictionary learning to efficiently capture diverse and robust shape priors. Our method conceptualizes each dictionary atom as a shape expert, which specializes in encoding distinct semantic shape information. A gating network dynamically fuses these shape experts into a robust shape map, with sparse activation guided by SAM encoding to prevent overfitting. We further provide this shape map as a prompt to SAM, utilizing the powerful generalization capability of SAM through bidirectional integration. All modules, including the shape dictionary, are trained in an end-to-end manner. Extensive experiments on multiple public datasets demonstrate its effectiveness.

Xiaofeng Liu, Bo Hu, Linghao Jin et al.

In this work, we propose a domain generalization (DG) approach to learn on several labeled source domains and transfer knowledge to a target domain that is inaccessible in training. Considering the inherent conditional and label shifts, we would expect the alignment of $p(x|y)$ and $p(y)$. However, the widely used domain invariant feature learning (IFL) methods relies on aligning the marginal concept shift w.r.t. $p(x)$, which rests on an unrealistic assumption that $p(y)$ is invariant across domains. We thereby propose a novel variational Bayesian inference framework to enforce the conditional distribution alignment w.r.t. $p(x|y)$ via the prior distribution matching in a latent space, which also takes the marginal label shift w.r.t. $p(y)$ into consideration with the posterior alignment. Extensive experiments on various benchmarks demonstrate that our framework is robust to the label shift and the cross-domain accuracy is significantly improved, thereby achieving superior performance over the conventional IFL counterparts.