Zhiwen Yang

Yang Zhou, Zhiwen Yang, Hui Zhang et al.

Potential radioactive hazards in full-dose positron emission tomography (PET) imaging remain a concern, whereas the quality of low-dose images is never desirable for clinical use. So it is of great interest to translate low-dose PET images into full-dose. Previous studies based on deep learning methods usually directly extract hierarchical features for reconstruction. We notice that the importance of each feature is different and they should be weighted dissimilarly so that tiny information can be captured by the neural network. Furthermore, the synthesis on some regions of interest is important in some applications. Here we propose a novel segmentation guided style-based generative adversarial network (SGSGAN) for PET synthesis. (1) We put forward a style-based generator employing style modulation, which specifically controls the hierarchical features in the translation process, to generate images with more realistic textures. (2) We adopt a task-driven strategy that couples a segmentation task with a generative adversarial network (GAN) framework to improve the translation performance. Extensive experiments show the superiority of our overall framework in PET synthesis, especially on those regions of interest.

Zhiwen Yang, Jiayin Li, Hui Zhang et al.

Transformers have revolutionized medical image restoration, but the quadratic complexity still poses limitations for their application to high-resolution medical images. The recent advent of the Receptance Weighted Key Value (RWKV) model in the natural language processing field has attracted much attention due to its ability to process long sequences efficiently. To leverage its advanced design, we propose Restore-RWKV, the first RWKV-based model for medical image restoration. Since the original RWKV model is designed for 1D sequences, we make two necessary modifications for modeling spatial relations in 2D medical images. First, we present a recurrent WKV (Re-WKV) attention mechanism that captures global dependencies with linear computational complexity. Re-WKV incorporates bidirectional attention as basic for a global receptive field and recurrent attention to effectively model 2D dependencies from various scan directions. Second, we develop an omnidirectional token shift (Omni-Shift) layer that enhances local dependencies by shifting tokens from all directions and across a wide context range. These adaptations make the proposed Restore-RWKV an efficient and effective model for medical image restoration. Even a lightweight variant of Restore-RWKV, with only 1.16 million parameters, achieves comparable or even superior results compared to existing state-of-the-art (SOTA) methods. Extensive experiments demonstrate that the resulting Restore-RWKV achieves SOTA performance across a range of medical image restoration tasks, including PET image synthesis, CT image denoising, MRI image super-resolution, and all-in-one medical image restoration. Code is available at: https://github.com/Yaziwel/Restore-RWKV.

Zhiwen Yang, Yang Zhou, Hui Zhang et al.

Multi-center positron emission tomography (PET) image synthesis aims at recovering low-dose PET images from multiple different centers. The generalizability of existing methods can still be suboptimal for a multi-center study due to domain shifts, which result from non-identical data distribution among centers with different imaging systems/protocols. While some approaches address domain shifts by training specialized models for each center, they are parameter inefficient and do not well exploit the shared knowledge across centers. To address this, we develop a generalist model that shares architecture and parameters across centers to utilize the shared knowledge. However, the generalist model can suffer from the center interference issue, \textit{i.e.} the gradient directions of different centers can be inconsistent or even opposite owing to the non-identical data distribution. To mitigate such interference, we introduce a novel dynamic routing strategy with cross-layer connections that routes data from different centers to different experts. Experiments show that our generalist model with dynamic routing (DRMC) exhibits excellent generalizability across centers. Code and data are available at: https://github.com/Yaziwel/Multi-Center-PET-Image-Synthesis.

Zhiwen Yang, Haowei Chen, Ziniu Qian et al.

Transformer-based methods have demonstrated impressive results in medical image restoration, attributed to the multi-head self-attention (MSA) mechanism in the spatial dimension. However, the majority of existing Transformers conduct attention within fixed and coarsely partitioned regions (\text{e.g.} the entire image or fixed patches), resulting in interference from irrelevant regions and fragmentation of continuous image content. To overcome these challenges, we introduce a novel Region Attention Transformer (RAT) that utilizes a region-based multi-head self-attention mechanism (R-MSA). The R-MSA dynamically partitions the input image into non-overlapping semantic regions using the robust Segment Anything Model (SAM) and then performs self-attention within these regions. This region partitioning is more flexible and interpretable, ensuring that only pixels from similar semantic regions complement each other, thereby eliminating interference from irrelevant regions. Moreover, we introduce a focal region loss to guide our model to adaptively focus on recovering high-difficulty regions. Extensive experiments demonstrate the effectiveness of RAT in various medical image restoration tasks, including PET image synthesis, CT image denoising, and pathological image super-resolution. Code is available at \href{https://github.com/Yaziwel/Region-Attention-Transformer-for-Medical-Image-Restoration.git}{https://github.com/RAT}.

Zhiwen Yang, Jiaju Zhang, Yang Yi et al.

Medical image restoration (MedIR) aims to recover high-quality medical images from their low-quality counterparts. Recent advancements in MedIR have focused on All-in-One models capable of simultaneously addressing multiple different MedIR tasks. However, due to significant differences in both modality and degradation types, using a shared model for these diverse tasks requires careful consideration of two critical inter-task relationships: task interference, which occurs when conflicting gradient update directions arise across tasks on the same parameter, and task imbalance, which refers to uneven optimization caused by varying learning difficulties inherent to each task. To address these challenges, we propose a task-adaptive Transformer (TAT), a novel framework that dynamically adapts to different tasks through two key innovations. First, a task-adaptive weight generation strategy is introduced to mitigate task interference by generating task-specific weight parameters for each task, thereby eliminating potential gradient conflicts on shared weight parameters. Second, a task-adaptive loss balancing strategy is introduced to dynamically adjust loss weights based on task-specific learning difficulties, preventing task domination or undertraining. Extensive experiments demonstrate that our proposed TAT achieves state-of-the-art performance in three MedIR tasks--PET synthesis, CT denoising, and MRI super-resolution--both in task-specific and All-in-One settings. Code is available at https://github.com/Yaziwel/TAT.

Zhiwen Yang, Jinglin Xu, Yuxin Pen

Few-shot fine-grained visual categorization (FS-FGVC) focuses on identifying various subcategories within a common superclass given just one or few support examples. Most existing methods aim to boost classification accuracy by enriching the extracted features with discriminative part-level details. However, they often overlook the fact that the set of support samples acts as a confounding variable, which hampers the FS-FGVC performance by introducing biased data distribution and misguiding the extraction of discriminative features. To address this issue, we propose a new causal FS-FGVC (CausalFSFG) approach inspired by causal inference for addressing biased data distributions through causal intervention. Specifically, based on the structural causal model (SCM), we argue that FS-FGVC infers the subcategories (i.e., effect) from the inputs (i.e., cause), whereas both the few-shot condition disturbance and the inherent fine-grained nature (i.e., large intra-class variance and small inter-class variance) lead to unobservable variables that bring spurious correlations, compromising the final classification performance. To further eliminate the spurious correlations, our CausalFSFG approach incorporates two key components: (1) Interventional multi-scale encoder (IMSE) conducts sample-level interventions, (2) Interventional masked feature reconstruction (IMFR) conducts feature-level interventions, which together reveal real causalities from inputs to subcategories. Extensive experiments and thorough analyses on the widely-used public datasets, including CUB-200-2011, Stanford Dogs, and Stanford Cars, demonstrate that our CausalFSFG achieves new state-of-the-art performance. The code is available at https://github.com/PKU-ICST-MIPL/CausalFSFG_TMM.

Zhiwen Yang, Yuxin Peng

Camera-based 3D semantic scene completion (SSC) offers a cost-effective solution for assessing the geometric occupancy and semantic labels of each voxel in the surrounding 3D scene with image inputs, providing a voxel-level scene perception foundation for the perception-prediction-planning autonomous driving systems. Although significant progress has been made in existing methods, their optimization rely solely on the supervision from voxel labels and face the challenge of voxel sparsity as a large portion of voxels in autonomous driving scenarios are empty, which limits both optimization efficiency and model performance. To address this issue, we propose a \textit{Multi-Resolution Alignment (MRA)} approach to mitigate voxel sparsity in camera-based 3D semantic scene completion, which exploits the scene and instance level alignment across multi-resolution 3D features as auxiliary supervision. Specifically, we first propose the Multi-resolution View Transformer module, which projects 2D image features into multi-resolution 3D features and aligns them at the scene level through fusing discriminative seed features. Furthermore, we design the Cubic Semantic Anisotropy module to identify the instance-level semantic significance of each voxel, accounting for the semantic differences of a specific voxel against its neighboring voxels within a cubic area. Finally, we devise a Critical Distribution Alignment module, which selects critical voxels as instance-level anchors with the guidance of cubic semantic anisotropy, and applies a circulated loss for auxiliary supervision on the critical feature distribution consistency across different resolutions. The code is available at https://github.com/PKU-ICST-MIPL/MRA_TIP.

Zhiwen Yang, Jiehua Zhang, Liang Li et al.

Image-guided depth completion aims at generating a dense depth map from sparse LiDAR data and RGB image. Recent methods have shown promising performance by reformulating it as a classification problem with two sub-tasks: depth discretization and probability prediction. They divide the depth range into several discrete depth values as depth categories, serving as priors for scene depth distributions. However, previous depth discretization methods are easy to be impacted by depth distribution variations across different scenes, resulting in suboptimal scene depth distribution priors. To address the above problem, we propose a progressive depth decoupling and modulating network, which incrementally decouples the depth range into bins and adaptively generates multi-scale dense depth maps in multiple stages. Specifically, we first design a Bins Initializing Module (BIM) to construct the seed bins by exploring the depth distribution information within a sparse depth map, adapting variations of depth distribution. Then, we devise an incremental depth decoupling branch to progressively refine the depth distribution information from global to local. Meanwhile, an adaptive depth modulating branch is developed to progressively improve the probability representation from coarse-grained to fine-grained. And the bi-directional information interactions are proposed to strengthen the information interaction between those two branches (sub-tasks) for promoting information complementation in each branch. Further, we introduce a multi-scale supervision mechanism to learn the depth distribution information in latent features and enhance the adaptation capability across different scenes. Experimental results on public datasets demonstrate that our method outperforms the state-of-the-art methods. The code will be open-sourced at [this https URL](https://github.com/Cisse-away/PDDM).

Yeqi He, Liang Li, Zhiwen Yang et al.

Diffusion models have demonstrated remarkable performance in image generation, particularly within the domain of style transfer. Prevailing style transfer approaches typically leverage pre-trained diffusion models' robust feature extraction capabilities alongside external modular control pathways to explicitly impose style guidance signals. However, these methods often fail to capture complex style reference or retain the identity of user-provided content images, thus falling into the trap of style-content balance. Thus, we propose a training-free style transfer approach via $\textbf{h}$eterogeneous $\textbf{a}$ttention $\textbf{m}$odulation ($\textbf{HAM}$) to protect identity information during image/text-guided style reference transfer, thereby addressing the style-content trade-off challenge. Specifically, we first introduces style noise initialization to initialize latent noise for diffusion. Then, during the diffusion process, it innovatively employs HAM for different attention mechanisms, including Global Attention Regulation (GAR) and Local Attention Transplantation (LAT), which better preserving the details of the content image while capturing complex style references. Our approach is validated through a series of qualitative and quantitative experiments, achieving state-of-the-art performance on multiple quantitative metrics.

Zhiwen Yang, Yuxin Peng

Camera-based 3D Semantic Scene Completion (SSC) is a critical task in autonomous driving systems, assessing voxel-level geometry and semantics for holistic scene perception. While existing voxel-based and plane-based SSC methods have achieved considerable progress, they struggle to capture physical regularities for realistic geometric details. On the other hand, neural reconstruction methods like NeRF and 3DGS demonstrate superior physical awareness, but suffer from high computational cost and slow convergence when handling large-scale, complex autonomous driving scenes, leading to inferior semantic accuracy. To address these issues, we propose the Semantic-PHysical Engaged REpresentation (SPHERE) for camera-based SSC, which integrates voxel and Gaussian representations for joint exploitation of semantic and physical information. First, the Semantic-guided Gaussian Initialization (SGI) module leverages dual-branch 3D scene representations to locate focal voxels as anchors to guide efficient Gaussian initialization. Then, the Physical-aware Harmonics Enhancement (PHE) module incorporates semantic spherical harmonics to model physical-aware contextual details and promote semantic-geometry consistency through focal distribution alignment, generating SSC results with realistic details. Extensive experiments and analyses on the popular SemanticKITTI and SSCBench-KITTI-360 benchmarks validate the effectiveness of SPHERE. The code is available at https://github.com/PKU-ICST-MIPL/SPHERE_ACMMM2025.

Huihan Wang, Zhiwen Yang, Hui Zhang et al.

Synthesizing high-quality dynamic medical videos remains a significant challenge due to the need for modeling both spatial consistency and temporal dynamics. Existing Transformer-based approaches face critical limitations, including insufficient channel interactions, high computational complexity from self-attention, and coarse denoising guidance from timestep embeddings when handling varying noise levels. In this work, we propose FEAT, a full-dimensional efficient attention Transformer, which addresses these issues through three key innovations: (1) a unified paradigm with sequential spatial-temporal-channel attention mechanisms to capture global dependencies across all dimensions, (2) a linear-complexity design for attention mechanisms in each dimension, utilizing weighted key-value attention and global channel attention, and (3) a residual value guidance module that provides fine-grained pixel-level guidance to adapt to different noise levels. We evaluate FEAT on standard benchmarks and downstream tasks, demonstrating that FEAT-S, with only 23\% of the parameters of the state-of-the-art model Endora, achieves comparable or even superior performance. Furthermore, FEAT-L surpasses all comparison methods across multiple datasets, showcasing both superior effectiveness and scalability. Code is available at https://github.com/Yaziwel/FEAT.

Zhiwen Yang, Pan Liu, Yifan Li et al.

Tandem mass spectrometry provides a high-throughput framework for identifying and quantifying proteins in complex biological samples. In computational proteomics, predicting peptide MS/MS spectra is a critical task, enabling downstream applications such as large-scale peptide identification and quantification. While deep learning architectures have substantially improved prediction accuracy, three evaluation challenges obscure the true progress of the field. First, inconsistent data preprocessing and incompatible model output spaces hinder fair model comparison. Second, flawed data splitting strategies can permit hidden sequence leakage and inflate reported performance. Third, existing evaluations typically lack comprehensive cross-species benchmarking and systematic assessment of model robustness to influential experimental conditions. To address these challenges, we propose PepSpecBench, a unified benchmark for peptide MS/MS spectrum prediction. PepSpecBench standardizes data preprocessing across complementary public datasets, enforces a strict backbone-disjoint splitting strategy to eliminate sequence leakage, and evaluates diverse architectures within a shared fragment-ion representation space. It further introduces a comprehensive multi-species evaluation suite and physically grounded metadata perturbation probes to assess model robustness and instrument awareness. We uncover previously unrecognized performance discrepancies and robustness limitations across six representative models, providing actionable insights for future model design, evaluation and practical deployment.

Zhiwen Yang, Yuxin Peng

Camera-based 3D semantic scene completion (SSC) plays a crucial role in autonomous driving, enabling voxelized 3D scene understanding for effective scene perception and decision-making. Existing SSC methods have shown efficacy in improving 3D scene representations, but suffer from the inherent input-output dimension gap and annotation-reality density gap, where the 2D planner view from input images with sparse annotated labels leads to inferior prediction of real-world dense occupancy with a 3D stereoscopic view. In light of this, we propose the corresponding High-Dimension High-Density Semantic Scene Completion (HD$^2$-SSC) framework with expanded pixel semantics and refined voxel occupancies. To bridge the dimension gap, a High-dimension Semantic Decoupling module is designed to expand 2D image features along a pseudo third dimension, decoupling coarse pixel semantics from occlusions, and then identify focal regions with fine semantics to enrich image features. To mitigate the density gap, a High-density Occupancy Refinement module is devised with a "detect-and-refine" architecture to leverage contextual geometric and semantic structures for enhanced semantic density with the completion of missing voxels and correction of erroneous ones. Extensive experiments and analyses on the SemanticKITTI and SSCBench-KITTI-360 datasets validate the effectiveness of our HD$^2$-SSC framework.

Haowei Chen, Zhiwen Yang, Haotian Hou et al.

All-in-one medical image restoration (MedIR) aims to address multiple MedIR tasks using a unified model, concurrently recovering various high-quality (HQ) medical images (e.g., MRI, CT, and PET) from low-quality (LQ) counterparts. However, all-in-one MedIR presents significant challenges due to the heterogeneity across different tasks. Each task involves distinct degradations, leading to diverse information losses in LQ images. Existing methods struggle to handle these diverse information losses associated with different tasks. To address these challenges, we propose a latent diffusion-enhanced vector-quantized codebook prior and develop \textbf{DiffCode}, a novel framework leveraging this prior for all-in-one MedIR. Specifically, to compensate for diverse information losses associated with different tasks, DiffCode constructs a task-adaptive codebook bank to integrate task-specific HQ prior features across tasks, capturing a comprehensive prior. Furthermore, to enhance prior retrieval from the codebook bank, DiffCode introduces a latent diffusion strategy that utilizes the diffusion model's powerful mapping capabilities to iteratively refine the latent feature distribution, estimating more accurate HQ prior features during restoration. With the help of the task-adaptive codebook bank and latent diffusion strategy, DiffCode achieves superior performance in both quantitative metrics and visual quality across three MedIR tasks: MRI super-resolution, CT denoising, and PET synthesis.

Lin Wang, Lie Ju, Xin Wang et al.

It is difficult to accurately label ambiguous and complex shaped targets manually by binary masks. The weakness of binary mask under-expression is highlighted in medical image segmentation, where blurring is prevalent. In the case of multiple annotations, reaching a consensus for clinicians by binary masks is more challenging. Moreover, these uncertain areas are related to the lesions' structure and may contain anatomical information beneficial to diagnosis. However, current studies on uncertainty mainly focus on the uncertainty in model training and data labels. None of them investigate the influence of the ambiguous nature of the lesion itself.Inspired by image matting, this paper introduces alpha matte as a soft mask to represent uncertain areas in medical scenes and accordingly puts forward a new uncertainty quantification method to fill the gap of uncertainty research for lesion structure. In this work, we introduce a new architecture to generate binary masks and alpha mattes in a multitasking framework, which outperforms all state-of-the-art matting algorithms compared. The proposed uncertainty map is able to highlight the ambiguous regions and a novel multitasking loss weighting strategy we presented can improve performance further and demonstrate their concrete benefits. To fully-evaluate the effectiveness of our proposed method, we first labelled three medical datasets with alpha matte to address the shortage of available matting datasets in medical scenes and prove the alpha matte to be a more efficient labeling method than a binary mask from both qualitative and quantitative aspects.