Kangxian Xie

Jianning Li, Zongwei Zhou, Jiancheng Yang et al.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Kangxian Xie, Jiancheng Yang, Donglai Wei et al.

Pulmonary diseases rank prominently among the principal causes of death worldwide. Curing them will require, among other things, a better understanding of the complex 3D tree-shaped structures within the pulmonary system, such as airways, arteries, and veins. Traditional approaches using high-resolution image stacks and standard CNNs on dense voxel grids face challenges in computational efficiency, limited resolution, local context, and inadequate preservation of shape topology. Our method addresses these issues by shifting from dense voxel to sparse point representation, offering better memory efficiency and global context utilization. However, the inherent sparsity in point representation can lead to a loss of crucial connectivity in tree-shaped structures. To mitigate this, we introduce graph learning on skeletonized structures, incorporating differentiable feature fusion for improved topology and long-distance context capture. Furthermore, we employ an implicit function for efficient conversion of sparse representations into dense reconstructions end-to-end. The proposed method not only delivers state-of-the-art performance in labeling accuracy, both overall and at key locations, but also enables efficient inference and the generation of closed surface shapes. Addressing data scarcity in this field, we have also curated a comprehensive dataset to validate our approach. Data and code are available at \url{https://github.com/M3DV/pulmonary-tree-labeling}.

Kangxian Xie, Jiancheng Yang, Nandor Pinter et al.

Accurate 3D anatomical segmentation is essential for clinical diagnosis and surgical planning. However, automated models frequently generate suboptimal shape predictions due to factors such as limited and imbalanced training data, inadequate labeling quality, and distribution shifts between training and deployment settings. A natural solution is to iteratively refine the predicted shape based on the radiologists' verbal instructions. However, this is hindered by the scarcity of paired data that explicitly links erroneous shapes to corresponding corrective instructions. As an initial step toward addressing this limitation, we introduce CoWTalk, a benchmark comprising 3D arterial anatomies with controllable synthesized anatomical errors and their corresponding repairing instructions. Building on this benchmark, we further propose an iterative refinement model that represents 3D shapes as vector sets and interacts with textual instructions to progressively update the target shape. Experimental results demonstrate that our method achieves significant improvements over corrupted inputs and competitive baselines, highlighting the feasibility of language-driven clinician-in-the-loop refinement for 3D medical shapes modeling.

Kangxian Xie, Siyu Huang, Sebastian Andres Cajas Ordonez et al.

Deep-learning models have been successful in biomedical image segmentation. To generalize for real-world deployment, test-time augmentation (TTA) methods are often used to transform the test image into different versions that are hopefully closer to the training domain. Unfortunately, due to the vast diversity of instance scale and image styles, many augmented test images produce undesirable results, thus lowering the overall performance. This work proposes a new TTA framework, S$^3$-TTA, which selects the suitable image scale and style for each test image based on a transformation consistency metric. In addition, S$^3$-TTA constructs an end-to-end augmentation-segmentation joint-training pipeline to ensure a task-oriented augmentation. On public benchmarks for cell and lung segmentation, S$^3$-TTA demonstrates improvements over the prior art by 3.4% and 1.3%, respectively, by simply augmenting the input data in testing phase.

Ziqiao Weng, Jiancheng Yang, Kangxian Xie et al.

Pulmonary trees extracted from CT images frequently exhibit topological incompleteness, such as missing or disconnected branches, which substantially degrades downstream anatomical analysis and limits the applicability of existing pulmonary tree modeling pipelines. Current approaches typically rely on dense volumetric processing or explicit graph reasoning, leading to limited efficiency and reduced robustness under realistic structural corruption. We propose TopoField, a topology-aware implicit modeling framework that treats topology repair as a first-class modeling problem and enables unified multi-task inference for pulmonary tree analysis. TopoField represents pulmonary anatomy using sparse surface and skeleton point clouds and learns a continuous implicit field that supports topology repair without relying on complete or explicit disconnection annotations, by training on synthetically introduced structural disruptions over \textit{already} incomplete trees. Building upon the repaired implicit representation, anatomical labeling and lung segment reconstruction are jointly inferred through task-specific implicit functions within a single forward pass.Extensive experiments on the Lung3D+ dataset demonstrate that TopoField consistently improves topological completeness and achieves accurate anatomical labeling and lung segment reconstruction under challenging incomplete scenarios. Owing to its implicit formulation, TopoField attains high computational efficiency, completing all tasks in just over one second per case, highlighting its practicality for large-scale and time-sensitive clinical applications. Code and data will be available at https://github.com/HINTLab/TopoField.

Kangxian Xie, Yufei Zhu, Kaiming Kuang et al.

High-quality 3D reconstruction of pulmonary segments plays a crucial role in segmentectomy and surgical treatment planning for lung cancer. Due to the resolution requirement of the target reconstruction, conventional deep learning-based methods often suffer from computational resource constraints or limited granularity. Conversely, implicit modeling is favored due to its computational efficiency and continuous representation at any resolution. We propose a neural implicit function-based method to learn a 3D surface to achieve anatomy-aware, precise pulmonary segment reconstruction, represented as a shape by deforming a learnable template. Additionally, we introduce two clinically relevant evaluation metrics to assess the reconstruction comprehensively. Further, due to the absence of publicly available shape datasets to benchmark reconstruction algorithms, we developed a shape dataset named Lung3D, including the 3D models of 800 labeled pulmonary segments and the corresponding airways, arteries, veins, and intersegmental veins. We demonstrate that the proposed approach outperforms existing methods, providing a new perspective for pulmonary segment reconstruction. Code and data will be available at https://github.com/M3DV/ImPulSe.

Chao Wu, Kangxian Xie, Mingchen Gao

Equivocal 3D lesion segmentation exhibits high inter-observer variability. Conventional deterministic models ignore this aleatoric uncertainty, producing over-confident masks that obscure clinical risks. Conversely, while generative methods (e.g., standard diffusion) capture sample diversity, recovering complex topology from pure noise frequently leads to severe structural fractures and out-of-distribution anatomical hallucinations. To resolve this fidelity-diversity trade-off, we propose Volumetric Directional Diffusion (VDD). Unlike standard diffusion models that denoise isotropic Gaussian noise, VDD mathematically anchors the generative trajectory to a deterministic consensus prior. By restricting the generative search space to iteratively predict a 3D boundary residual field, VDD accurately explores the fine-grained geometric variations inherent in expert disagreements without risking topological collapse. Extensive validation on three multi-rater datasets (LIDC-IDRI, KiTS21, and ISBI 2015) demonstrates that VDD achieves state-of-the-art uncertainty quantification (significantly improving GED and CI) while remaining highly competitive in segmentation accuracy against deterministic upper bounds. Ultimately, VDD provides clinicians with anatomically coherent uncertainty maps, enabling safer decision-making and mitigating risks in downstream tasks (e.g., radiotherapy planning or surgical margin assessment).

Chao Wu, Zhenyi Wang, Kangxian Xie et al.

Text-to-image (T2I) diffusion models often exhibit gender bias, particularly by generating stereotypical associations between professions and gendered subjects. This paper presents SAE Debias, a lightweight and model-agnostic framework for mitigating such bias in T2I generation. Unlike prior approaches that rely on CLIP-based filtering or prompt engineering, which often require model-specific adjustments and offer limited control, SAE Debias operates directly within the feature space without retraining or architectural modifications. By leveraging a k-sparse autoencoder pre-trained on a gender bias dataset, the method identifies gender-relevant directions within the sparse latent space, capturing professional stereotypes. Specifically, a biased direction per profession is constructed from sparse latents and suppressed during inference to steer generations toward more gender-balanced outputs. Trained only once, the sparse autoencoder provides a reusable debiasing direction, offering effective control and interpretable insight into biased subspaces. Extensive evaluations across multiple T2I models, including Stable Diffusion 1.4, 1.5, 2.1, and SDXL, demonstrate that SAE Debias substantially reduces gender bias while preserving generation quality. To the best of our knowledge, this is the first work to apply sparse autoencoders for identifying and intervening in gender bias within T2I models. These findings contribute toward building socially responsible generative AI, providing an interpretable and model-agnostic tool to support fairness in text-to-image generation.