arXiv subjects

Jiancheng Yang

Publications and source records attributed to Jiancheng Yang.

At least 19 recordsLinked to original sources

arXiv2026

What Makes a Good Medical Image Tokenizer? Rethinking Reconstruction and Generation in Medical Image Tokenization

Latent diffusion models now dominate medical image generation, and every such pipeline rests on a \emph{tokenizer} that compresses images into the latent codes for image generation to operate on. Thereby, the tokenizer choice bounds every downstream task from reconstruction fidelity and generation quality to the representations available for downstream analysis. Yet, medical imaging pipelines routinely utilize tokenizers from natural imaging on the hypothesis that their behavior carries over. However, this is an assumption never tested in the medical imaging regime, where datasets are orders of magnitude smaller and images exhibit far lower inter-sample variance. We present a systematic evaluation of medical image tokenizers evaluating thirty configurations across ten model families on twelve datasets at three compression factors, spanning reconstruction, generation, latent geometry, downstream classification, and memorization. We find that (1) performance on image reconstruction and generation strongly correlate, unlike prior reports on natural images; (2) modern tokenizers use nearly all of their codebook entries, but still leave most of the latent space unused; (3) training-set memorization is mild and is further suppressed by stronger latent space compression; and (4) discrete quantization can largely preserve downstream classification, with lookup-free schemes being the main exception.

cs.CV↗

arXiv2026

Are LLMs Ready to Assist Physicians? PhysAssistBench for Interactive Doctor-Patient-EHR Assistance

The most plausible near-term role of medical LLMs is to assist rather than replace physicians, yet current evaluations often test isolated capabilities: clinical knowledge, EHR system interaction, or patient communication. Physician assistance instead requires coordinating these capabilities within the same interaction, where physicians issue underspecified requests, patients describe symptoms ambiguously, and EHR systems demand precise tool use. We introduce PhysAssistBench, a benchmark for interactive doctor-patient-EHR assistance. Built from real MIMIC-IV cases, PhysAssistBench uses a scalable pipeline to construct agentic patients: interactive, record-grounded agents that turn static EHR records into multi-turn clinical scenarios while preserving clinical factuality. PhysAssistBench provides a curated bilingual evaluation set of 1,296 manually reviewed and physician-validated turns. Experiments with leading LLMs show that current models remain unreliable in this setting, which exposes a key bottleneck for clinical LLMs: reliable assistance requires coordination across knowledge, communication, and systems, not isolated gains in any of them.

cs.CL↗

arXiv2026

End-to-End 4D Heart Mesh Recovery Across Full-Stack and Sparse Cardiac MRI

Reconstructing cardiac motion from CMR sequences is critical for diagnosis, prognosis, and intervention. Existing methods rely on complete CMR stacks to infer full heart motion, limiting their applicability during intervention when only sparse observations are available. We present TetHeart, the first end-to-end framework for unified 4D heart mesh recovery from both offline full-stack and intra-procedural sparse-slice observations. Our method leverages deformable tetrahedra to capture shape and motion in a coherent space shared across cardiac structures. Before a procedure, it initializes detailed, patient-specific heart meshes from high-quality full stacks, which can then be updated using whatever slices can be obtained in real-time, down to a single one during the procedure. TetHeart incorporates several key innovations: (i) an attentive slice-adaptive 2D-3D feature assembly mechanism that integrates information from arbitrary numbers of slices at any position; (ii) a distillation strategy to ensure accurate reconstruction under extreme sparsity; and (iii) a weakly supervised motion learning scheme requiring annotations only at keyframes, such as the end-diastolic and end-systolic phases. Trained and validated on three large public datasets and evaluated zero-shot on additional private interventional and public datasets without retraining, TetHeart achieves state-of-the-art accuracy and strong generalization in both pre- and intra-procedural settings. Code and dataset is available at https://github.com/Scalsol/TetHeart.

cs.CV↗

arXiv2026

Learning Topology-Aware Implicit Field for Unified Pulmonary Tree Modeling with Incomplete Topological Supervision

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, explicit graph reasoning, or generic point cloud completion priors, leading to limited efficiency, weak structural awareness, 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. We further validate TopoField on real incomplete outputs from an external segmentation model, demonstrating its applicability to realistic segmentation pipelines. 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.

cs.CV↗

arXiv2026

DDX-TRACE: A Benchmark for Medical Diagnostic Trajectories in VLMs

Medical diagnosis is not a single prediction from a fully specified vignette. It is a sequential workup: clinicians decide what evidence to obtain, revise a differential diagnosis, and stop when the diagnosis is sufficiently supported. Most medical AI benchmarks instead reveal the relevant context upfront and score only the final answer, making unsupported correct guesses, premature closure, inefficient workups, and poor uncertainty updating invisible. We introduce DDX-TRACE, a physician-adjudicated benchmark for multimodal neuroradiology that evaluates diagnostic trajectories under hidden evidence over 211 challenging cases. Each case begins with limited clinical history; models request imaging studies in free form, receive matched image bundles when available, update a probabilistic differential diagnosis after each turn, and stop with a localized final diagnosis. Evaluating state-of-the-art VLMs, we find that final diagnosis scores can substantially misrepresent workup quality: models may guess plausible diagnoses without essential evidence, request useful studies but misinterpret raw images, or acquire evidence inefficiently while updating uncertainty poorly. Controlled evidence variants isolate bottlenecks in planning, visual evidence extraction, and downstream differential reasoning. DDX-TRACE shifts medical AI evaluation from final answers to evidence-supported diagnostic trajectories.

cs.CV↗

arXiv2026

GenMed: A Pairwise Generative Reformulation of Medical Diagnostic Tasks

Data-driven medical AI is traditionally formulated as a discriminative mapping from input $X$ to output $Y$ via a learned function $f$, which does not generalize well across heterogeneous data and modalities encountered in real-world clinical settings. In this work, we propose a fundamentally different, generative paradigm. We model the joint distribution $P(X,Y)$ using diffusion models and reframe inference as a test-time output optimization problem. By guiding the generative process to match observed inputs, our framework enables flexible, gradient-based conditioning at inference time without architectural changes or retraining, effectively supporting arbitrary and previously unseen combinations of observations. Extensive experiments demonstrate strong performance across standard and cross-modality medical image segmentation, few-shot segmentation with only 2 or 4 training samples, degraded-input segmentation, shape completion from sparse and partial observations, and zero-shot application to demonstrate generality. To support these evaluations, we curated and released a large-scale text-shape dataset derived from MedShapeNet. Our results highlight the versatility of generative joint modeling as a foundation for reusable, task-agnostic medical AI systems.

cs.CV↗

arXiv2026

PlaneCycle: Training-Free 2D-to-3D Lifting of Foundation Models Without Adapters

Large-scale 2D foundation models exhibit strong transferable representations, yet extending them to 3D volumetric data typically requires retraining, adapters, or architectural redesign. We introduce PlaneCycle, a training-free, adapter-free operator for architecture-agnostic 2D-to-3D lifting of foundation models. PlaneCycle reuses the original pretrained 2D backbone by cyclically distributing spatial aggregation across orthogonal HW, DW, and DH planes throughout network depth, enabling progressive 3D fusion while preserving pretrained inductive biases. The method introduces no additional parameters and is applicable to arbitrary 2D networks. Using pretrained DINOv3 models, we evaluate PlaneCycle on six 3D classification and three 3D segmentation benchmarks. Without any training, the lifted models exhibit intrinsic 3D fusion capability and, under linear probing, outperform slice-wise 2D baselines and strong 3D counterparts, approaching the performance of fully trained models. With full fine-tuning, PlaneCycle matches standard 3D architectures, highlighting its potential as a seamless and practical 2D-to-3D lifting operator. These results demonstrate that 3D capability can be unlocked from pretrained 2D foundation models without structural modification or retraining. Code is available at https://github.com/HINTLab/PlaneCycle.

cs.CV↗

arXiv2026

Refining 3D Medical Segmentation with Verbal Instruction

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.

cs.CV↗

arXiv2026

EyeWorld: A Generative World Model of Ocular State and Dynamics

Ophthalmic decision-making depends on subtle lesion-scale cues interpreted across multimodal imaging and over time, yet most medical foundation models remain static and degrade under modality and acquisition shifts. Here we introduce EyeWorld, a generative world model that conceptualizes the eye as a partially observed dynamical system grounded in clinical imaging. EyeWorld learns an observation-stable latent ocular state shared across modalities, unifying fine-grained parsing, structure-preserving cross-modality translation and quality-robust enhancement within a single framework. Longitudinal supervision further enables time-conditioned state transitions, supporting forecasting of clinically meaningful progression while preserving stable anatomy. By moving from static representation learning to explicit dynamical modeling, EyeWorld provides a unified approach to robust multimodal interpretation and prognosis-oriented simulation in medicine.

cs.CV↗

arXiv2026

EyeAgent: An Agentic AI System for Multimodal Clinical Decision Support in Ophthalmology

Artificial intelligence has shown promise in medical imaging, yet most existing systems lack flexibility, interpretability, and adaptability - challenges especially pronounced in ophthalmology, where diverse imaging modalities are essential. We present EyeAgent, the first agentic AI framework for comprehensive and interpretable clinical decision support in ophthalmology. Using a large language model (DeepSeek-V3) as its central reasoning engine, EyeAgent interprets user queries and dynamically orchestrates 53 validated ophthalmic tools across 23 imaging modalities for diverse tasks including classification, segmentation, detection, image/report generation, and quantitative analysis. Stepwise ablation analysis demonstrated a progressive improvement in diagnostic accuracy, rising from a baseline of 69.71% (using only 5 general tools) to 80.79% when the full suite of 53 specialized tools was integrated. In an expert rating study on 200 real-world clinical cases, EyeAgent achieved 93.7% tool selection accuracy and received expert ratings of more than 88% across accuracy, completeness, safety, reasoning, and interpretability. In human-AI collaboration, EyeAgent matched or exceeded the performance of senior ophthalmologists and, when used as an assistant, improved overall diagnostic accuracy by 18.51% and report quality scores by 19%, with the greatest benefit observed among junior ophthalmologists. These findings establish EyeAgent as a scalable and trustworthy AI framework for ophthalmology and provide a blueprint for modular, multimodal, and clinically aligned next-generation AI systems.

cs.HC↗

arXiv2026

Learning to Read Where to Look: Disease-Aware Vision-Language Pretraining for 3D CT

Recent 3D CT vision-language models align volumes with reports via contrastive pretraining, but typically rely on limited public data and provide only coarse global supervision. We train a 3D CT vision-language model on 98k report-volume pairs (50k patients) collected at a single hospital, combined with public datasets, using SigLIP-style contrastive pretraining together with prompt-based disease supervision in the shared vision-text embedding space. On CT-RATE, our model achieves state-of-the-art text-to-image retrieval (R@10 31.5 vs. 22.2) and competitive disease classification (AUC 83.8 vs. 83.8), with consistent results on Rad-ChestCT (AUC 77.0 vs. 77.3). We further observe that radiologists routinely reference specific images within their reports (e.g., ``series X, image Y''), linking textual descriptions to precise axial locations. We automatically mine 262k such snippet-slice pairs and introduce the task of intra-scan snippet localization -- predicting the axial depth referred to by a text snippet -- reducing mean absolute error to 36.3 mm at 12 mm feature resolution, compared with 67.0 mm for the best baseline. Adding this localization objective leaves retrieval and classification broadly unchanged within confidence bounds, yielding a single unified model for retrieval, classification, and intra-scan grounding.

cs.CV↗

arXiv2026

Bonnet: Ultra-fast whole-body bone segmentation from CT scans

This work proposes Bonnet, an ultra-fast sparse-volume pipeline for whole-body bone segmentation from CT scans. Accurate bone segmentation is important for surgical planning and anatomical analysis, but existing 3D voxel-based models such as nnU-Net and STU-Net require heavy computation and often take several minutes per scan, which limits time-critical use. The proposed Bonnet addresses this by integrating a series of novel framework components including HU-based bone thresholding, patch-wise inference with a sparse spconv-based U-Net, and multi-window fusion into a full-volume prediction. Trained on TotalSegmentator and evaluated without additional tuning on RibSeg, CT-Pelvic1K, and CT-Spine1K, Bonnet achieves high Dice across ribs, pelvis, and spine while running in only 2.69 seconds per scan on an RTX A6000. Compared to strong voxel baselines, Bonnet attains a similar accuracy but reduces inference time by roughly 25x on the same hardware and tiling setup. The toolkit and pre-trained models will be released at https://github.com/HINTLab/Bonnet.

eess.IV↗

arXiv2025

Template-Guided Reconstruction of Pulmonary Segments with Neural Implicit Functions

High-quality 3D reconstruction of pulmonary segments plays a crucial role in segmentectomy and surgical planning for the treatment of 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 comprehensively assess the quality of the reconstruction. Furthermore, to address the lack of publicly available shape datasets for benchmarking reconstruction algorithms, we developed a shape dataset named Lung3D, which includes the 3D models of 800 labeled pulmonary segments and their 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/HINTLab/ImPulSe.

cs.GR↗

arXiv2025

AortaDiff: A Unified Multitask Diffusion Framework For Contrast-Free AAA Imaging

While contrast-enhanced CT (CECT) is standard for assessing abdominal aortic aneurysms (AAA), the required iodinated contrast agents pose significant risks, including nephrotoxicity, patient allergies, and environmental harm. To reduce contrast agent use, recent deep learning methods have focused on generating synthetic CECT from non-contrast CT (NCCT) scans. However, most adopt a multi-stage pipeline that first generates images and then performs segmentation, which leads to error accumulation and fails to leverage shared semantic and anatomical structures. To address this, we propose a unified deep learning framework that generates synthetic CECT images from NCCT scans while simultaneously segmenting the aortic lumen and thrombus. Our approach integrates conditional diffusion models (CDM) with multi-task learning, enabling end-to-end joint optimization of image synthesis and anatomical segmentation. Unlike previous multitask diffusion models, our approach requires no initial predictions (e.g., a coarse segmentation mask), shares both encoder and decoder parameters across tasks, and employs a semi-supervised training strategy to learn from scans with missing segmentation labels, a common constraint in real-world clinical data. We evaluated our method on a cohort of 264 patients, where it consistently outperformed state-of-the-art single-task and multi-stage models. For image synthesis, our model achieved a PSNR of 25.61 dB, compared to 23.80 dB from a single-task CDM. For anatomical segmentation, it improved the lumen Dice score to 0.89 from 0.87 and the challenging thrombus Dice score to 0.53 from 0.48 (nnU-Net). These segmentation enhancements led to more accurate clinical measurements, reducing the lumen diameter MAE to 4.19 mm from 5.78 mm and the thrombus area error to 33.85% from 41.45% when compared to nnU-Net. Code is available at https://github.com/yuxuanou623/AortaDiff.git.

cs.CV↗

arXiv2025

PrIntMesh: Precise Intersection Surfaces for 3D Organ Mesh Reconstruction

Human organs are composed of interconnected substructures whose geometry and spatial relationships constrain one another. Yet, most deep-learning approaches treat these parts independently, producing anatomically implausible reconstructions. We introduce PrIntMesh, a template-based, topology-preserving framework that reconstructs organs as unified systems. Starting from a connected template, PrIntMesh jointly deforms all substructures to match patient-specific anatomy, while explicitly preserving internal boundaries and enforcing smooth, artifact-free surfaces. We demonstrate its effectiveness on the heart, hippocampus, and lungs, achieving high geometric accuracy, correct topology, and robust performance even with limited or noisy training data. Compared to voxel- and surface-based methods, PrIntMesh better reconstructs shared interfaces, maintains structural consistency, and provides a data-efficient solution suitable for clinical use.

cs.CV↗

arXiv2025

Frenet-Serret Frame-based Decomposition for Part Segmentation of 3D Curvilinear Structures

Accurately segmenting 3D curvilinear structures in medical imaging remains challenging due to their complex geometry and the scarcity of diverse, large-scale datasets for algorithm development and evaluation. In this paper, we use dendritic spine segmentation as a case study and address these challenges by introducing a novel Frenet--Serret Frame-based Decomposition, which decomposes 3D curvilinear structures into a globally $ C^2 $ continuous curve that captures the overall shape, and a cylindrical primitive that encodes local geometric properties. This approach leverages Frenet--Serret Frames and arc length parameterization to preserve essential geometric features while reducing representational complexity, facilitating data-efficient learning, improved segmentation accuracy, and generalization on 3D curvilinear structures. To rigorously evaluate our method, we introduce two datasets: CurviSeg, a synthetic dataset for 3D curvilinear structure segmentation that validates our method's key properties, and DenSpineEM, a benchmark for dendritic spine segmentation, which comprises 4,476 manually annotated spines from 70 dendrites across three public electron microscopy datasets, covering multiple brain regions and species. Our experiments on DenSpineEM demonstrate exceptional cross-region and cross-species generalization: models trained on the mouse somatosensory cortex subset achieve 91.9\% Dice, maintaining strong performance in zero-shot segmentation on both mouse visual cortex (94.1\% Dice) and human frontal lobe (81.8\% Dice) subsets. Moreover, we test the generalizability of our method on the IntrA dataset, where it achieves 77.08\% Dice (5.29\% higher than prior arts) on intracranial aneurysm segmentation. These findings demonstrate the potential of our approach for accurately analyzing complex curvilinear structures across diverse medical imaging fields.

cs.CV↗

arXiv2025

Simulation studies on compensation for incoherent magnet error driven half-integer and 3rd-order resonances with space charge in HIAF-BRing

Magnet error driven resonances under space-charge-induced resonance crossing represents a significant limitation on beam intensity in low-injection-energy high-intensity synchrotrons. Unstable particle motion arises from the combined effects of space-charge-induced tune spread and magnetic field imperfections, which limits the intensity. This paper introduces a space-charge-Twiss modification to the Resonance Driving Terms (RDTs). The new RDTs are named modified RDTs. Modified RDTs aim to describe the nonlinear behavior under incoherent error driven resonances induced by the combined effect of space charge and magnetic field imperfections. The feasibility of the compensation scheme with modified RDTs is demonstrated through coasting-beam simulations under space-charge-induced half-integer and 3rd-order resonances, using the lattice of the High Intensity Heavy-Ion Accelerator Facility Booster Ring (HIAF-BRing). The simulations demonstrate that the compensation through minimizing modified RDTs significantly suppresses the emittance growth and the unstable particle motion. Besides, the effect of compensation scheme with modified RDTs against periodical resonance crossing is evaluated in bunched-beam simulations.

physics.acc-ph↗

arXiv2025

Numerical simulations of electron acceleration driven by heavy ion beams in plasma with alternating density gradients

Plasma-Based Acceleration (PBA) has been demonstrated using laser, electron, and proton drivers. However, significant challenges remain in achieving high efficiency, stable acceleration, and scalable energy gain. Heavy ion beam drivers, with their high kinetic energy, offer the potential for greater energy transfer to the witness beam. Unfortunately, limited by the relatively low velocity of heavy ion, the dephasing length is really short leading to a low energy gain of the witness beam. Conventional method that increase plasma density linearly is ineffective in this context because the mismatch between the RMS beam radius and plasma wavelength will make the wakefield degrade or even disappear. In this paper, we propose a method that periodically switches the witness beam between different accelerating phase, allowing it to shift between adjacent accelerating cavities. Therefore, the plasma density does not only strictly increase, but also decrease. This will help maintain the structure of wakefield and increase the energy gain of the witness beam.

physics.acc-ph↗