arXiv subjects

Yufan He

Publications and source records attributed to Yufan He.

At least 19 recordsLinked to original sources

arXiv2026

BaT: Towards Self-Evolving Medical Research Agent with Stage Rubrics

Long-horizon agents are beginning to automate complete workflows that produce code, reports, and research artifacts. Medical imaging workflows are multi-stage and data-sensitive, while expert trajectories remain scarce and difficult to share. Structured benchmarks can localize failures through stage-level rubrics, but standard post-training discards these diagnostics before the next training round. We present Benchmark-as-Teacher (BaT), a recursive self-improvement system for agent post-training. BaT contains two linked components: the asynchronous Stage Bank data pipeline and BiCuRL (Bilevel Curriculum Reinforcement Learning), its self-improving post-training method. Stage Bank synthesizes content-isolated training states outside the policy-update loop. BiCuRL uses a fixed held-out evaluation to select the next stage curriculum, verifies rollouts with task rubrics, updates the policy with GRPO, and returns the candidate checkpoint to evaluation. On AutoMedBench-Lite, BaT-4B and BaT-9B more than double the Overall scores of their Qwen Instruct baselines. BaT-9B Agent reaches 79.6 Overall, exceeding Claude Opus 4.6 with Claude Code at 77.5.

cs.AI↗

arXiv2026

AutoMedBench: Towards Medical AutoResearch with Agentic AI Models

Autonomous agents are increasingly expected to support end-to-end medical-AI research workflows, moving beyond isolated prediction tasks or short-form clinical question answering. However, existing medical agent benchmarks primarily evaluate final outputs, providing limited visibility into agent behavior within the research process. To address this gap, we present AutoMedBench, a workflow-aware benchmark for autonomous medical-AI research across diverse medical imaging and multimodal inference tasks, organizing agent execution into a unified five-stage workflow (S1-S5): Plan, Setup, Validate, Inference, and Submit. It comprises long-horizon tasks with each run averaging 33 agent turns, spanning five research tracks: segmentation, image enhancement, visual question answering (VQA), report generation, and lesion detection. Each task is evaluated under two difficulty tiers, Lite and Standard, which use the same data and metrics but differ in the amount of task-brief scaffolding, and each run is scored using both final task performance and S1-S5 stage scores, enabling stage-level analysis from the initial task brief to the final submitted artifact. Across thousands of recorded runs, stage-level scoring reveals that Validate is the weakest workflow stage on average, whereas Setup is the strongest, suggesting that current agents are better at making pipelines executable than at verifying their reliability. Post-run error analysis further shows that verification and submission failures dominate tagged errors, accounting for 37.7% and 38.1% of fired codes respectively, whereas task-understanding errors are rare at 0.9%, and runs with one fired error code have a 48% lower overall score than runs with no error code on average.

cs.AI↗

arXiv2026

Cosmos 3: Omnimodal World Models for Physical AI

We introduce Cosmos 3, a family of omnimodal world models designed to jointly process and generate language, image, video, audio, and action sequences within a unified mixture-of-transformers architecture. By supporting highly flexible input-output configurations, Cosmos 3 seamlessly unifies critical modalities for Physical AI -- effectively subsuming vision-language models, video generators, world simulators, and world-action models into a single framework. Our evaluation demonstrates that Cosmos 3 establishes a new state-of-the-art across a diverse suite of understanding and generation tasks, demonstrating omnimodal world models as scalable, general-purpose backbones for embodied agents. Our post-trained Cosmos 3 models were ranked as the best open-source Text-to-Image and Image-to-Video models by Artificial Analysis, and the best policy model by RoboArena at the time the technical report was written. To accelerate open research and deployment in Physical AI, we make our code, model checkpoints, curated synthetic datasets, and evaluation benchmark available under the Linux Foundation's OpenMDW-1.1 License at https://github.com/nvidia/cosmos and https://huggingface.co/collections/nvidia/cosmos3. The project website is available at https://research.nvidia.com/labs/cosmos-lab/cosmos3.

cs.CV↗

arXiv2026

Surg$\Sigma$: A Spectrum of Large-Scale Multimodal Data and Foundation Models for Surgical Intelligence

Surgical intelligence has the potential to improve the safety and consistency of surgical care, yet most existing surgical AI frameworks remain task-specific and struggle to generalize across procedures and institutions. Although multimodal foundation models, particularly multimodal large language models, have demonstrated strong cross-task capabilities across various medical domains, their advancement in surgery remains constrained by the lack of large-scale, systematically curated multimodal data. To address this challenge, we introduce Surg$\Sigma$, a spectrum of large-scale multimodal data and foundation models for surgical intelligence. At the core of this framework lies Surg$\Sigma$-DB, a large-scale multimodal data foundation designed to support diverse surgical tasks. Surg$\Sigma$-DB consolidates heterogeneous surgical data sources (including open-source datasets, curated in-house clinical collections and web-source data) into a unified schema, aiming to improve label consistency and data standardization across heterogeneous datasets. Surg$\Sigma$-DB spans 6 clinical specialties and diverse surgical types, providing rich image- and video-level annotations across 18 practical surgical tasks covering understanding, reasoning, planning, and generation, at an unprecedented scale (over 5.98M conversations). Beyond conventional multimodal conversations, Surg$\Sigma$-DB incorporates hierarchical reasoning annotations, providing richer semantic cues to support deeper contextual understanding in complex surgical scenarios. We further provide empirical evidence through recently developed surgical foundation models built upon Surg$\Sigma$-DB, illustrating the practical benefits of large-scale multimodal annotations, unified semantic design, and structured reasoning annotations for improving cross-task generalization and interpretability.

cs.AI↗

arXiv2026

SAW: Toward a Surgical Action World Model via Controllable and Scalable Video Generation

A surgical world model capable of generating realistic surgical action videos with precise control over tool-tissue interactions can address fundamental challenges in surgical AI and simulation -- from data scarcity and rare event synthesis to bridging the sim-to-real gap for surgical automation. However, current video generation methods, the very core of such surgical world models, require expensive annotations or complex structured intermediates as conditioning signals at inference, limiting their scalability. Other approaches exhibit limited temporal consistency across complex laparoscopic scenes and do not possess sufficient realism. We propose Surgical Action World (SAW) -- a step toward surgical action world modeling through video diffusion conditioned on four lightweight signals: language prompts encoding tool-action context, a reference surgical scene, tissue affordance mask, and 2D tool-tip trajectories. We design a conditional video diffusion approach that reformulates video-to-video diffusion into trajectory-conditioned surgical action synthesis. The backbone diffusion model is fine-tuned on a custom-curated dataset of 12,044 laparoscopic clips with lightweight spatiotemporal conditioning signals, leveraging a depth consistency loss to enforce geometric plausibility without requiring depth at inference. SAW achieves state-of-the-art temporal consistency (CD-FVD: 199.19 vs. 546.82) and strong visual quality on held-out test data. Furthermore, we demonstrate its downstream utility for (a) surgical AI, where augmenting rare actions with SAW-generated videos improves action recognition (clipping F1-score: 20.93% to 43.14%; cutting: 0.00% to 8.33%) on real test data, and (b) surgical simulation, where rendering tool-tissue interaction videos from simulator-derived trajectory points toward a visually faithful simulation engine.

cs.CV↗

arXiv2026

Humanoid Robots as First Assistants in Endoscopic Surgery

Humanoid robots have become a focal point of technological ambition, with claims of surgical capability within years in mainstream discourse. These projections are aspirational yet lack empirical grounding. To date, no humanoid has assisted a surgeon through an actual procedure, let alone performed one. The work described here breaks this new ground. Here we report a proof of concept in which a teleoperated Unitree G1 provided endoscopic visualization while an attending otolaryngologist performed a cadaveric sphenoidectomy. The procedure was completed successfully, with stable visualization maintained throughout. Teleoperation allowed assessment of whether the humanoid form factor could meet the physical demands of surgical assistance in terms of sustenance and precision; the cognitive demands were satisfied -- for now -- by the operator. Post-procedure analysis identified engineering targets for clinical translation, alongside near-term opportunities such as autonomous diagnostic scoping. This work establishes form-factor feasibility for humanoid surgical assistance while identifying challenges for continued development.

cs.RO↗

arXiv2025

Cosmos-H-Surgical: Learning Surgical Robot Policies from Videos via World Modeling

Data scarcity remains a fundamental barrier to achieving fully autonomous surgical robots. While large scale vision language action (VLA) models have shown impressive generalization in household and industrial manipulation by leveraging paired video action data from diverse domains, surgical robotics suffers from the paucity of datasets that include both visual observations and accurate robot kinematics. In contrast, vast corpora of surgical videos exist, but they lack corresponding action labels, preventing direct application of imitation learning or VLA training. In this work, we aim to alleviate this problem by learning policy models from Cosmos-H-Surgical, a world model designed for surgical physical AI. We curated the Surgical Action Text Alignment (SATA) dataset with detailed action description specifically for surgical robots. Then we built Cosmos-H-Surgical based on the most advanced physical AI world model and SATA. It's able to generate diverse, generalizable and realistic surgery videos. We are also the first to use an inverse dynamics model to infer pseudokinematics from synthetic surgical videos, producing synthetic paired video action data. We demonstrate that a surgical VLA policy trained with these augmented data significantly outperforms models trained only on real demonstrations on a real surgical robot platform. Our approach offers a scalable path toward autonomous surgical skill acquisition by leveraging the abundance of unlabeled surgical video and generative world modeling, thus opening the door to generalizable and data efficient surgical robot policies.

cs.RO↗

arXiv2025

Analysis of SINR Coverage in LEO Satellite Networks through Spatial Network Calculus

We introduce a new analytical framework, developed based on the spatial network calculus, for performance assessment of Low Earth Orbit (LEO) satellite networks. Specifically, we model the satellites' spatial positions as a strong ball-regulated point process on the sphere. Under this model, proximal points in space exhibit a locally repulsive property, reflecting the fact that intersatellite links are protected by a safety distance and would not be arbitrarily close. Subsequently, we derive analytical lower bounds on the conditional coverage probabilities under Nakagami-$m$ and Rayleigh fading, respectively. These expressions have a low computational complexity, enabling efficient numerical evaluations. We validate the effectiveness of our theoretical model by contrasting the coverage probability obtained from our analysis with that estimated from a Starlink constellation. The results show that our analysis provides a tight lower bound on the actual value and, surprisingly, matches the empirical simulations almost perfectly with a 1 dB shift. This demonstrates our framework as an appropriate theoretical model for LEO satellite networks.

cs.IT↗

arXiv2025

Auto3DSeg for Brain Tumor Segmentation from 3D MRI in BraTS 2023 Challenge

In this work, we describe our solution to the BraTS 2023 cluster of challenges using Auto3DSeg from MONAI. We participated in all 5 segmentation challenges, and achieved the 1st place results in three of them: Brain Metastasis, Brain Meningioma, BraTS-Africa challenges, and the 2nd place results in the remaining two: Adult and Pediatic Glioma challenges.

cs.CV↗

arXiv2025

Reasoning Visual Language Model for Chest X-Ray Analysis

Vision-language models (VLMs) have shown strong promise for medical image analysis, but most remain opaque, offering predictions without the transparent, stepwise reasoning clinicians rely on. We present a framework that brings chain-of-thought (CoT) reasoning to chest X-ray interpretation. Inspired by reasoning-first training paradigms, our approach is designed to learn how experts reason, not just what they conclude, by aligning intermediate steps with observable image evidence and radiology workflow. Beyond accuracy, the explicit reasoning traces support clinical auditability: they reveal why a conclusion was reached, which alternatives were considered, and where uncertainty remains, enabling quality assurance, error analysis, and safer human-AI collaboration. Our model couples high-fidelity visual encoding with a two-stage training recipe: a reasoning-style supervised fine-tuning (SFT) followed by reinforcement learning (RL) that uses verifiable rewards over a list of X-ray abnormalities. The model outputs reasoning that mirrors radiologists systematic thought process, uncertainty, and differential diagnosis. In out-of-distribution evaluation, the approach achieves competitive multi-label classification while improving interpretability. In a reader study with expert radiologists, full reasoning traces increased confidence, supported error auditing, and reduced time to finalize reports. We release code and the model NV-Reason-CXR-3B to support community progress toward trustworthy, explainable AI in chest radiography and other medical imaging tasks where reasoning quality is as critical as prediction quality.

cs.CV↗

arXiv2025

Towards the Automatic Segmentation, Modeling and Meshing of the Aortic Vessel Tree from Multicenter Acquisitions: An Overview of the SEG.A. 2023 Segmentation of the Aorta Challenge

The automated analysis of the aortic vessel tree (AVT) from computed tomography angiography (CTA) holds immense clinical potential, but its development has been impeded by a lack of shared, high-quality data. We launched the SEG.A. challenge to catalyze progress in this field by introducing a large, publicly available, multi-institutional dataset for AVT segmentation. The challenge benchmarked automated algorithms on a hidden test set, with subsequent optional tasks in surface meshing for computational simulations. Our findings reveal a clear convergence on deep learning methodologies, with 3D U-Net architectures dominating the top submissions. A key result was that an ensemble of the highest-ranking algorithms significantly outperformed individual models, highlighting the benefits of model fusion. Performance was strongly linked to algorithmic design, particularly the use of customized post-processing steps, and the characteristics of the training data. This initiative not only establishes a new performance benchmark but also provides a lasting resource to drive future innovation toward robust, clinically translatable tools.

cs.CV↗

arXiv2025

MAISI-v2: Accelerated 3D High-Resolution Medical Image Synthesis with Rectified Flow and Region-specific Contrastive Loss

Medical image synthesis is an important topic for both clinical and research applications. Recently, diffusion models have become a leading approach in this area. Despite their strengths, many existing methods struggle with (1) limited generalizability that only work for specific body regions or voxel spacings, (2) slow inference, which is a common issue for diffusion models, and (3) weak alignment with input conditions, which is a critical issue for medical imaging. MAISI, a previously proposed framework, addresses generalizability issues but still suffers from slow inference and limited condition consistency. In this work, we present MAISI-v2, the first accelerated 3D medical image synthesis framework that integrates rectified flow to enable fast and high quality generation. To further enhance condition fidelity, we introduce a novel region-specific contrastive loss to enhance the sensitivity to region of interest. Our experiments show that MAISI-v2 can achieve SOTA image quality with $33 \times$ acceleration for latent diffusion model. We also conducted a downstream segmentation experiment to show that the synthetic images can be used for data augmentation. We release our code, training details, model weights, and a GUI demo to facilitate reproducibility and promote further development within the community.

cs.CV↗

arXiv2025

Text2CT: Towards 3D CT Volume Generation from Free-text Descriptions Using Diffusion Model

Generating 3D CT volumes from descriptive free-text inputs presents a transformative opportunity in diagnostics and research. In this paper, we introduce Text2CT, a novel approach for synthesizing 3D CT volumes from textual descriptions using the diffusion model. Unlike previous methods that rely on fixed-format text input, Text2CT employs a novel prompt formulation that enables generation from diverse, free-text descriptions. The proposed framework encodes medical text into latent representations and decodes them into high-resolution 3D CT scans, effectively bridging the gap between semantic text inputs and detailed volumetric representations in a unified 3D framework. Our method demonstrates superior performance in preserving anatomical fidelity and capturing intricate structures as described in the input text. Extensive evaluations show that our approach achieves state-of-the-art results, offering promising potential applications in diagnostics, and data augmentation.

eess.IV↗

arXiv2024

Unsupervised learning of spatially varying regularization for diffeomorphic image registration

Spatially varying regularization accommodates the deformation variations that may be necessary for different anatomical regions during deformable image registration. Historically, optimization-based registration models have harnessed spatially varying regularization to address anatomical subtleties. However, most modern deep learning-based models tend to gravitate towards spatially invariant regularization, wherein a homogenous regularization strength is applied across the entire image, potentially disregarding localized variations. In this paper, we propose a hierarchical probabilistic model that integrates a prior distribution on the deformation regularization strength, enabling the end-to-end learning of a spatially varying deformation regularizer directly from the data. The proposed method is straightforward to implement and easily integrates with various registration network architectures. Additionally, automatic tuning of hyperparameters is achieved through Bayesian optimization, allowing efficient identification of optimal hyperparameters for any given registration task. Comprehensive evaluations on publicly available datasets demonstrate that the proposed method significantly improves registration performance and enhances the interpretability of deep learning-based registration, all while maintaining smooth deformations.

cs.CV↗

arXiv2024

VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging

Foundation models for interactive segmentation in 2D natural images and videos have sparked significant interest in building 3D foundation models for medical imaging. However, the domain gaps and clinical use cases for 3D medical imaging require a dedicated model that diverges from existing 2D solutions. Specifically, such foundation models should support a full workflow that can actually reduce human effort. Treating 3D medical images as sequences of 2D slices and reusing interactive 2D foundation models seems straightforward, but 2D annotation is too time-consuming for 3D tasks. Moreover, for large cohort analysis, it's the highly accurate automatic segmentation models that reduce the most human effort. However, these models lack support for interactive corrections and lack zero-shot ability for novel structures, which is a key feature of "foundation". While reusing pre-trained 2D backbones in 3D enhances zero-shot potential, their performance on complex 3D structures still lags behind leading 3D models. To address these issues, we present VISTA3D, Versatile Imaging SegmenTation and Annotation model, that targets to solve all these challenges and requirements with one unified foundation model. VISTA3D is built on top of the well-established 3D segmentation pipeline, and it is the first model to achieve state-of-the-art performance in both 3D automatic (supporting 127 classes) and 3D interactive segmentation, even when compared with top 3D expert models on large and diverse benchmarks. Additionally, VISTA3D's 3D interactive design allows efficient human correction, and a novel 3D supervoxel method that distills 2D pretrained backbones grants VISTA3D top 3D zero-shot performance. We believe the model, recipe, and insights represent a promising step towards a clinically useful 3D foundation model. Code and weights are publicly available at https://github.com/Project-MONAI/VISTA.

cs.CV↗

arXiv2024

VILA-M3: Enhancing Vision-Language Models with Medical Expert Knowledge

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data$-$features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

cs.CV↗

arXiv2024

A Short Review and Evaluation of SAM2's Performance in 3D CT Image Segmentation

Since the release of Segment Anything 2 (SAM2), the medical imaging community has been actively evaluating its performance for 3D medical image segmentation. However, different studies have employed varying evaluation pipelines, resulting in conflicting outcomes that obscure a clear understanding of SAM2's capabilities and potential applications. We shortly review existing benchmarks and point out that the SAM2 paper clearly outlines a zero-shot evaluation pipeline, which simulates user clicks iteratively for up to eight iterations. We reproduced this interactive annotation simulation on 3D CT datasets and provided the results and code~\url{https://github.com/Project-MONAI/VISTA}. Our findings reveal that directly applying SAM2 on 3D medical imaging in a zero-shot manner is far from satisfactory. It is prone to generating false positives when foreground objects disappear, and annotating more slices cannot fully offset this tendency. For smaller single-connected objects like kidney and aorta, SAM2 performs reasonably well but for most organs it is still far behind state-of-the-art 3D annotation methods. More research and innovation are needed for 3D medical imaging community to use SAM2 correctly.

cs.CV↗

arXiv2024

HoloHisto: End-to-end Gigapixel WSI Segmentation with 4K Resolution Sequential Tokenization

In digital pathology, the traditional method for deep learning-based image segmentation typically involves a two-stage process: initially segmenting high-resolution whole slide images (WSI) into smaller patches (e.g., 256x256, 512x512, 1024x1024) and subsequently reconstructing them to their original scale. This method often struggles to capture the complex details and vast scope of WSIs. In this paper, we propose the holistic histopathology (HoloHisto) segmentation method to achieve end-to-end segmentation on gigapixel WSIs, whose maximum resolution is above 80,000$\times$70,000 pixels. HoloHisto fundamentally shifts the paradigm of WSI segmentation to an end-to-end learning fashion with 1) a large (4K) resolution base patch for elevated visual information inclusion and efficient processing, and 2) a novel sequential tokenization mechanism to properly model the contextual relationships and efficiently model the rich information from the 4K input. To our best knowledge, HoloHisto presents the first holistic approach for gigapixel resolution WSI segmentation, supporting direct I/O of complete WSI and their corresponding gigapixel masks. Under the HoloHisto platform, we unveil a random 4K sampler that transcends ultra-high resolution, delivering 31 and 10 times more pixels than standard 2D and 3D patches, respectively, for advancing computational capabilities. To facilitate efficient 4K resolution dense prediction, we leverage sequential tokenization, utilizing a pre-trained image tokenizer to group image features into a discrete token grid. To assess the performance, our team curated a new kidney pathology image segmentation (KPIs) dataset with WSI-level glomeruli segmentation from whole mouse kidneys. From the results, HoloHisto-4K delivers remarkable performance gains over previous state-of-the-art models.

eess.IV↗