Daguang Xu

Andres Diaz-Pinto, Sachidanand Alle, Vishwesh Nath et al. · microsoft-research

The lack of annotated datasets is a major bottleneck for training new task-specific supervised machine learning models, considering that manual annotation is extremely expensive and time-consuming. To address this problem, we present MONAI Label, a free and open-source framework that facilitates the development of applications based on artificial intelligence (AI) models that aim at reducing the time required to annotate radiology datasets. Through MONAI Label, researchers can develop AI annotation applications focusing on their domain of expertise. It allows researchers to readily deploy their apps as services, which can be made available to clinicians via their preferred user interface. Currently, MONAI Label readily supports locally installed (3D Slicer) and web-based (OHIF) frontends and offers two active learning strategies to facilitate and speed up the training of segmentation algorithms. MONAI Label allows researchers to make incremental improvements to their AI-based annotation application by making them available to other researchers and clinicians alike. Additionally, MONAI Label provides sample AI-based interactive and non-interactive labeling applications, that can be used directly off the shelf, as plug-and-play to any given dataset. Significant reduced annotation times using the interactive model can be observed on two public datasets.

Holger R. Roth, Yan Cheng, Yuhong Wen et al.

Federated learning (FL) enables building robust and generalizable AI models by leveraging diverse datasets from multiple collaborators without centralizing the data. We created NVIDIA FLARE as an open-source software development kit (SDK) to make it easier for data scientists to use FL in their research and real-world applications. The SDK includes solutions for state-of-the-art FL algorithms and federated machine learning approaches, which facilitate building workflows for distributed learning across enterprises and enable platform developers to create a secure, privacy-preserving offering for multiparty collaboration utilizing homomorphic encryption or differential privacy. The SDK is a lightweight, flexible, and scalable Python package. It allows researchers to apply their data science workflows in any training libraries (PyTorch, TensorFlow, XGBoost, or even NumPy) in real-world FL settings. This paper introduces the key design principles of NVFlare and illustrates some use cases (e.g., COVID analysis) with customizable FL workflows that implement different privacy-preserving algorithms. Code is available at https://github.com/NVIDIA/NVFlare.

Chulin Xie, De-An Huang, Wenda Chu et al.

Personalized Federated Learning (pFL) has emerged as a promising solution to tackle data heterogeneity across clients in FL. However, existing pFL methods either (1) introduce high communication and computation costs or (2) overfit to local data, which can be limited in scope, and are vulnerable to evolved test samples with natural shifts. In this paper, we propose PerAda, a parameter-efficient pFL framework that reduces communication and computational costs and exhibits superior generalization performance, especially under test-time distribution shifts. PerAda reduces the costs by leveraging the power of pretrained models and only updates and communicates a small number of additional parameters from adapters. PerAda has good generalization since it regularizes each client's personalized adapter with a global adapter, while the global adapter uses knowledge distillation to aggregate generalized information from all clients. Theoretically, we provide generalization bounds to explain why PerAda improves generalization, and we prove its convergence to stationary points under non-convex settings. Empirically, PerAda demonstrates competitive personalized performance (+4.85% on CheXpert) and enables better out-of-distribution generalization (+5.23% on CIFAR-10-C) on different datasets across natural and medical domains compared with baselines, while only updating 12.6% of parameters per model based on the adapter. Our code is available at https://github.com/NVlabs/PerAda.

M. Jorge Cardoso, Wenqi Li, Richard Brown et al.

Artificial Intelligence (AI) is having a tremendous impact across most areas of science. Applications of AI in healthcare have the potential to improve our ability to detect, diagnose, prognose, and intervene on human disease. For AI models to be used clinically, they need to be made safe, reproducible and robust, and the underlying software framework must be aware of the particularities (e.g. geometry, physiology, physics) of medical data being processed. This work introduces MONAI, a freely available, community-supported, and consortium-led PyTorch-based framework for deep learning in healthcare. MONAI extends PyTorch to support medical data, with a particular focus on imaging, and provide purpose-specific AI model architectures, transformations and utilities that streamline the development and deployment of medical AI models. MONAI follows best practices for software-development, providing an easy-to-use, robust, well-documented, and well-tested software framework. MONAI preserves the simple, additive, and compositional approach of its underlying PyTorch libraries. MONAI is being used by and receiving contributions from research, clinical and industrial teams from around the world, who are pursuing applications spanning nearly every aspect of healthcare.

Ali Hatamizadeh, Ziyue Xu, Dong Yang et al.

Vision Transformers (ViT)s have recently become popular due to their outstanding modeling capabilities, in particular for capturing long-range information, and scalability to dataset and model sizes which has led to state-of-the-art performance in various computer vision and medical image analysis tasks. In this work, we introduce a unified framework consisting of two architectures, dubbed UNetFormer, with a 3D Swin Transformer-based encoder and Convolutional Neural Network (CNN) and transformer-based decoders. In the proposed model, the encoder is linked to the decoder via skip connections at five different resolutions with deep supervision. The design of proposed architecture allows for meeting a wide range of trade-off requirements between accuracy and computational cost. In addition, we present a methodology for self-supervised pre-training of the encoder backbone via learning to predict randomly masked volumetric tokens using contextual information of visible tokens. We pre-train our framework on a cohort of $5050$ CT images, gathered from publicly available CT datasets, and present a systematic investigation of various components such as masking ratio and patch size that affect the representation learning capability and performance of downstream tasks. We validate the effectiveness of our pre-training approach by fine-tuning and testing our model on liver and liver tumor segmentation task using the Medical Segmentation Decathlon (MSD) dataset and achieve state-of-the-art performance in terms of various segmentation metrics. To demonstrate its generalizability, we train and test the model on BraTS 21 dataset for brain tumor segmentation using MRI images and outperform other methods in terms of Dice score. Code: https://github.com/Project-MONAI/research-contributions

Chun-Yin Huang, Ruinan Jin, Can Zhao et al.

While Federated Learning (FL) is gaining popularity for training machine learning models in a decentralized fashion, numerous challenges persist, such as asynchronization, computational expenses, data heterogeneity, and gradient and membership privacy attacks. Lately, dataset distillation has emerged as a promising solution for addressing the aforementioned challenges by generating a compact synthetic dataset that preserves a model's training efficacy. However, we discover that using distilled local datasets can amplify the heterogeneity issue in FL. To address this, we propose Federated Learning on Virtual Heterogeneous Data with Local-Global Dataset Distillation (FedLGD), where we seamlessly integrate dataset distillation algorithms into FL pipeline and train FL using a smaller synthetic dataset (referred as virtual data). Specifically, to harmonize the domain shifts, we propose iterative distribution matching to inpaint global information to local virtual data and use federated gradient matching to distill global virtual data that serve as anchor points to rectify heterogeneous local training, without compromising data privacy. We experiment on both benchmark and real-world datasets that contain heterogeneous data from different sources, and further scale up to an FL scenario that contains a large number of clients with heterogeneous and class-imbalanced data. Our method outperforms state-of-the-art heterogeneous FL algorithms under various settings. Our code is available at https://github.com/ubc-tea/FedLGD.

Yufan He, Pengfei Guo, Yucheng Tang et al.

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.

Pengfei Guo, Can Zhao, Dong Yang et al.

Medical imaging analysis faces challenges such as data scarcity, high annotation costs, and privacy concerns. This paper introduces the Medical AI for Synthetic Imaging (MAISI), an innovative approach using the diffusion model to generate synthetic 3D computed tomography (CT) images to address those challenges. MAISI leverages the foundation volume compression network and the latent diffusion model to produce high-resolution CT images (up to a landmark volume dimension of 512 x 512 x 768 ) with flexible volume dimensions and voxel spacing. By incorporating ControlNet, MAISI can process organ segmentation, including 127 anatomical structures, as additional conditions and enables the generation of accurately annotated synthetic images that can be used for various downstream tasks. Our experiment results show that MAISI's capabilities in generating realistic, anatomically accurate images for diverse regions and conditions reveal its promising potential to mitigate challenges using synthetic data.

Pengfei Guo, Dong Yang, Ali Hatamizadeh et al.

Federated learning (FL) is a distributed machine learning technique that enables collaborative model training while avoiding explicit data sharing. The inherent privacy-preserving property of FL algorithms makes them especially attractive to the medical field. However, in case of heterogeneous client data distributions, standard FL methods are unstable and require intensive hyperparameter tuning to achieve optimal performance. Conventional hyperparameter optimization algorithms are impractical in real-world FL applications as they involve numerous training trials, which are often not affordable with limited compute budgets. In this work, we propose an efficient reinforcement learning (RL)-based federated hyperparameter optimization algorithm, termed Auto-FedRL, in which an online RL agent can dynamically adjust hyperparameters of each client based on the current training progress. Extensive experiments are conducted to investigate different search strategies and RL agents. The effectiveness of the proposed method is validated on a heterogeneous data split of the CIFAR-10 dataset as well as two real-world medical image segmentation datasets for COVID-19 lesion segmentation in chest CT and pancreas segmentation in abdominal CT.

Kelly Payette, Hongwei Li, Priscille de Dumast et al.

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.

Ali Hatamizadeh, Hongxu Yin, Holger Roth et al.

In this work we demonstrate the vulnerability of vision transformers (ViTs) to gradient-based inversion attacks. During this attack, the original data batch is reconstructed given model weights and the corresponding gradients. We introduce a method, named GradViT, that optimizes random noise into naturally looking images via an iterative process. The optimization objective consists of (i) a loss on matching the gradients, (ii) image prior in the form of distance to batch-normalization statistics of a pretrained CNN model, and (iii) a total variation regularization on patches to guide correct recovery locations. We propose a unique loss scheduling function to overcome local minima during optimization. We evaluate GadViT on ImageNet1K and MS-Celeb-1M datasets, and observe unprecedentedly high fidelity and closeness to the original (hidden) data. During the analysis we find that vision transformers are significantly more vulnerable than previously studied CNNs due to the presence of the attention mechanism. Our method demonstrates new state-of-the-art results for gradient inversion in both qualitative and quantitative metrics. Project page at https://gradvit.github.io/.

Meirui Jiang, Holger R Roth, Wenqi Li et al.

How to ensure fairness is an important topic in federated learning (FL). Recent studies have investigated how to reward clients based on their contribution (collaboration fairness), and how to achieve uniformity of performance across clients (performance fairness). Despite achieving progress on either one, we argue that it is critical to consider them together, in order to engage and motivate more diverse clients joining FL to derive a high-quality global model. In this work, we propose a novel method to optimize both types of fairness simultaneously. Specifically, we propose to estimate client contribution in gradient and data space. In gradient space, we monitor the gradient direction differences of each client with respect to others. And in data space, we measure the prediction error on client data using an auxiliary model. Based on this contribution estimation, we propose a FL method, federated training via contribution estimation (FedCE), i.e., using estimation as global model aggregation weights. We have theoretically analyzed our method and empirically evaluated it on two real-world medical datasets. The effectiveness of our approach has been validated with significant performance improvements, better collaboration fairness, better performance fairness, and comprehensive analytical studies.

An Xu, Wenqi Li, Pengfei Guo et al.

Cross-silo federated learning (FL) has attracted much attention in medical imaging analysis with deep learning in recent years as it can resolve the critical issues of insufficient data, data privacy, and training efficiency. However, there can be a generalization gap between the model trained from FL and the one from centralized training. This important issue comes from the non-iid data distribution of the local data in the participating clients and is well-known as client drift. In this work, we propose a novel training framework FedSM to avoid the client drift issue and successfully close the generalization gap compared with the centralized training for medical image segmentation tasks for the first time. We also propose a novel personalized FL objective formulation and a new method SoftPull to solve it in our proposed framework FedSM. We conduct rigorous theoretical analysis to guarantee its convergence for optimizing the non-convex smooth objective function. Real-world medical image segmentation experiments using deep FL validate the motivations and effectiveness of our proposed method.

Jeya Maria Jose Valanarasu, Yucheng Tang, Dong Yang et al.

Harnessing the power of pre-training on large-scale datasets like ImageNet forms a fundamental building block for the progress of representation learning-driven solutions in computer vision. Medical images are inherently different from natural images as they are acquired in the form of many modalities (CT, MR, PET, Ultrasound etc.) and contain granulated information like tissue, lesion, organs etc. These characteristics of medical images require special attention towards learning features representative of local context. In this work, we focus on designing an effective pre-training framework for 3D radiology images. First, we propose a new masking strategy called local masking where the masking is performed across channel embeddings instead of tokens to improve the learning of local feature representations. We combine this with classical low-level perturbations like adding noise and downsampling to further enable low-level representation learning. To this end, we introduce Disruptive Autoencoders, a pre-training framework that attempts to reconstruct the original image from disruptions created by a combination of local masking and low-level perturbations. Additionally, we also devise a cross-modal contrastive loss (CMCL) to accommodate the pre-training of multiple modalities in a single framework. We curate a large-scale dataset to enable pre-training of 3D medical radiology images (MRI and CT). The proposed pre-training framework is tested across multiple downstream tasks and achieves state-of-the-art performance. Notably, our proposed method tops the public test leaderboard of BTCV multi-organ segmentation challenge.

Vishwesh Nath, Dong Yang, Holger R. Roth et al.

Which volume to annotate next is a challenging problem in building medical imaging datasets for deep learning. One of the promising methods to approach this question is active learning (AL). However, AL has been a hard nut to crack in terms of which AL algorithm and acquisition functions are most useful for which datasets. Also, the problem is exacerbated with which volumes to label first when there is zero labeled data to start with. This is known as the cold start problem in AL. We propose two novel strategies for AL specifically for 3D image segmentation. First, we tackle the cold start problem by proposing a proxy task and then utilizing uncertainty generated from the proxy task to rank the unlabeled data to be annotated. Second, we craft a two-stage learning framework for each active iteration where the unlabeled data is also used in the second stage as a semi-supervised fine-tuning strategy. We show the promise of our approach on two well-known large public datasets from medical segmentation decathlon. The results indicate that the initial selection of data and semi-supervised framework both showed significant improvement for several AL strategies.

Jingwei Sun, Ziyue Xu, Dong Yang et al.

Federated learning is a popular collaborative learning approach that enables clients to train a global model without sharing their local data. Vertical federated learning (VFL) deals with scenarios in which the data on clients have different feature spaces but share some overlapping samples. Existing VFL approaches suffer from high communication costs and cannot deal efficiently with limited overlapping samples commonly seen in the real world. We propose a practical vertical federated learning (VFL) framework called \textbf{one-shot VFL} that can solve the communication bottleneck and the problem of limited overlapping samples simultaneously based on semi-supervised learning. We also propose \textbf{few-shot VFL} to improve the accuracy further with just one more communication round between the server and the clients. In our proposed framework, the clients only need to communicate with the server once or only a few times. We evaluate the proposed VFL framework on both image and tabular datasets. Our methods can improve the accuracy by more than 46.5\% and reduce the communication cost by more than 330$\times$ compared with state-of-the-art VFL methods when evaluated on CIFAR-10. Our code will be made publicly available at \url{https://nvidia.github.io/NVFlare/research/one-shot-vfl}.

Jingwei Sun, Ziyue Xu, Hongxu Yin et al.

Pre-trained language models (PLM) have revolutionized the NLP landscape, achieving stellar performances across diverse tasks. These models, while benefiting from vast training data, often require fine-tuning on specific data to cater to distinct downstream tasks. However, this data adaptation process has inherent security and privacy concerns, primarily when leveraging user-generated, device-residing data. Federated learning (FL) provides a solution, allowing collaborative model fine-tuning without centralized data collection. However, applying FL to finetune PLMs is hampered by challenges, including restricted model parameter access, high computational requirements, and communication overheads. This paper introduces Federated Black-box Prompt Tuning (FedBPT), a framework designed to address these challenges. FedBPT does not require the clients to access the model parameters. By focusing on training optimal prompts and utilizing gradient-free optimization methods, FedBPT reduces the number of exchanged variables, boosts communication efficiency, and minimizes computational and storage costs. Experiments highlight the framework's ability to drastically cut communication and memory costs while maintaining competitive performance. Ultimately, FedBPT presents a promising solution for efficient, privacy-preserving fine-tuning of PLM in the age of large language models.

Andriy Myronenko, Dong Yang, Yufan He et al.

Kidney and Kidney Tumor Segmentation Challenge (KiTS) 2023 offers a platform for researchers to compare their solutions to segmentation from 3D CT. In this work, we describe our submission to the challenge using automated segmentation of Auto3DSeg available in MONAI. Our solution achieves the average dice of 0.835 and surface dice of 0.723, which ranks first and wins the KiTS 2023 challenge.

Andriy Myronenko, Md Mahfuzur Rahman Siddiquee, Dong Yang et al.

Head and neck tumor segmentation challenge (HECKTOR) 2022 offers a platform for researchers to compare their solutions to segmentation of tumors and lymph nodes from 3D CT and PET images. In this work, we describe our solution to HECKTOR 2022 segmentation task. We re-sample all images to a common resolution, crop around head and neck region, and train SegResNet semantic segmentation network from MONAI. We use 5-fold cross validation to select best model checkpoints. The final submission is an ensemble of 15 models from 3 runs. Our solution (team name NVAUTO) achieves the 1st place on the HECKTOR22 challenge leaderboard with an aggregated dice score of 0.78802.

Holger R. Roth, Ali Hatamizadeh, Ziyue Xu et al.

Split learning (SL) has been proposed to train deep learning models in a decentralized manner. For decentralized healthcare applications with vertical data partitioning, SL can be beneficial as it allows institutes with complementary features or images for a shared set of patients to jointly develop more robust and generalizable models. In this work, we propose "Split-U-Net" and successfully apply SL for collaborative biomedical image segmentation. Nonetheless, SL requires the exchanging of intermediate activation maps and gradients to allow training models across different feature spaces, which might leak data and raise privacy concerns. Therefore, we also quantify the amount of data leakage in common SL scenarios for biomedical image segmentation and provide ways to counteract such leakage by applying appropriate defense strategies.

Md Mahfuzur Rahman Siddique, Dong Yang, Yufan He et al.

Ischemic Stroke Lesion Segmentation challenge (ISLES 2022) offers a platform for researchers to compare their solutions to 3D segmentation of ischemic stroke regions from 3D MRIs. In this work, we describe our solution to ISLES 2022 segmentation task. We re-sample all images to a common resolution, use two input MRI modalities (DWI and ADC) and train SegResNet semantic segmentation network from MONAI. The final submission is an ensemble of 15 models (from 3 runs of 5-fold cross validation). Our solution (team name NVAUTO) achieves the top place in terms of Dice metric (0.824), and overall rank 2 (based on the combined metric ranking).

Yucheng Tang, Yufan He, Vishwesh Nath et al.

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.

Junqi Liu, Xinze Zhou, Wenxuan Li et al.

Photon-counting CT (PCCT) provides superior image quality with higher spatial resolution and lower noise compared to conventional energy-integrating CT (EICT), but its limited clinical availability restricts large-scale research and clinical deployment. To bridge this gap, we propose SUMI, a simulated degradation-to-enhancement method that learns to reverse realistic acquisition artifacts in low-quality EICT by leveraging high-quality PCCT as reference. Our central insight is to explicitly model realistic acquisition degradations, transforming PCCT into clinically plausible lower-quality counterparts and learning to invert this process. The simulated degradations were validated for clinical realism by board-certified radiologists, enabling faithful supervision without requiring paired acquisitions at scale. As outcomes of this technical contribution, we: (1) train a latent diffusion model on 1,046 PCCTs, using an autoencoder first pre-trained on both these PCCTs and 405,379 EICTs from 145 hospitals to extract general CT latent features that we release for reuse in other generative medical imaging tasks; (2) construct a large-scale dataset of over 17,316 publicly available EICTs enhanced to PCCT-like quality, with radiologist-validated voxel-wise annotations of airway trees, arteries, veins, lungs, and lobes; and (3) demonstrate substantial improvements: across external data, SUMI outperforms state-of-the-art image translation methods by 15% in SSIM and 20% in PSNR, improves radiologist-rated clinical utility in reader studies, and enhances downstream top-ranking lesion detection performance, increasing sensitivity by up to 15% and F1 score by up to 10%. Our results suggest that emerging imaging advances can be systematically distilled into routine EICT using limited high-quality scans as reference.

Andriy Myronenko, Dong Yang, Yufan He et al.

Aorta provides the main blood supply of the body. Screening of aorta with imaging helps for early aortic disease detection and monitoring. In this work, we describe our solution to the Segmentation of the Aorta (SEG.A.231) from 3D CT challenge. We use automated segmentation method Auto3DSeg available in MONAI. Our solution achieves an average Dice score of 0.920 and 95th percentile of the Hausdorff Distance (HD95) of 6.013, which ranks first and wins the SEG.A. 2023 challenge.

Md Mahfuzur Rahman Siddiquee, Dong Yang, Yufan He et al.

Intracranial hemorrhage segmentation challenge (INSTANCE 2022) offers a platform for researchers to compare their solutions to segmentation of hemorrhage stroke regions from 3D CTs. In this work, we describe our solution to INSTANCE 2022. We use a 2D segmentation network, SegResNet from MONAI, operating slice-wise without resampling. The final submission is an ensemble of 18 models. Our solution (team name NVAUTO) achieves the top place in terms of Dice metric (0.721), and overall rank 2. It is implemented with Auto3DSeg.

Yufan He, Pengfei Guo, Mengya Xu et al.

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 SurgWorld, 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 SurgeWorld 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.

Zhijian Liu, Ligeng Zhu, Baifeng Shi et al.

Visual language models (VLMs) have made significant advances in accuracy in recent years. However, their efficiency has received much less attention. This paper introduces NVILA, a family of open VLMs designed to optimize both efficiency and accuracy. Building on top of VILA, we improve its model architecture by first scaling up the spatial and temporal resolutions, and then compressing visual tokens. This "scale-then-compress" approach enables NVILA to efficiently process high-resolution images and long videos. We also conduct a systematic investigation to enhance the efficiency of NVILA throughout its entire lifecycle, from training and fine-tuning to deployment. NVILA matches or surpasses the accuracy of many leading open and proprietary VLMs across a wide range of image and video benchmarks. At the same time, it reduces training costs by 4.5X, fine-tuning memory usage by 3.4X, pre-filling latency by 1.6-2.2X, and decoding latency by 1.2-2.8X. We will soon make our code and models available to facilitate reproducibility.

Puyang Wang, Pengfei Guo, Keyi Chai et al.

Clinical MRI encompasses diverse imaging protocols--spanning anatomical targets (cardiac, brain, knee), contrasts (T1, T2, mapping), sampling patterns (Cartesian, radial, spiral, kt-space), and acceleration factors--yet current deep learning reconstructions are typically protocol-specific, hindering generalization and deployment. We introduce Scalable Deep Unrolled Model (SDUM), a universal framework combining a Restormer-based reconstructor, a learned coil sensitivity map estimator (CSME), sampling-aware weighted data consistency (SWDC), universal conditioning (UC) on cascade index and protocol metadata, and progressive cascade expansion training. SDUM exhibits foundation-model-like scaling behavior: reconstruction quality follows PSNR ${\sim}$ log(parameters) with correlation $r{=}0.986$ ($R^2{=}0.973$) up to 18 cascades, demonstrating predictable performance gains with model depth. A single SDUM trained on heterogeneous data achieves state-of-the-art results across all four CMRxRecon2025 challenge tracks--multi-center, multi-disease, 5T, and pediatric--without task-specific fine-tuning, surpassing specialized baselines by up to ${+}1.0$~dB. On CMRxRecon2024, SDUM outperforms the winning method PromptMR+ by ${+}0.55$~dB; on fastMRI brain, it exceeds PC-RNN by ${+}1.8$~dB. Ablations validate each component: SWDC ${+}0.43$~dB over standard DC, per-cascade CSME ${+}0.51$~dB, UC ${+}0.38$~dB. These results establish SDUM as a practical path toward universal, scalable MRI reconstruction.

Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang et al.

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

Junchao Zhu, Ruining Deng, Junlin Guo et al.

Recent advances in multi-modal AI have demonstrated promising potential for generating the currently expensive spatial transcriptomics (ST) data directly from routine histology images, offering a means to reduce the high cost and time-intensive nature of ST data acquisition. However, the increasing resolution of ST, particularly with platforms such as Visium HD achieving 8um or finer, introduces significant computational and modeling challenges. Conventional spot-by-spot sequential regression frameworks become inefficient and unstable at this scale, while the inherent extreme sparsity and low expression levels of high-resolution ST further complicate both prediction and evaluation. To address these limitations, we propose Img2ST-Net, a novel histology-to-ST generation framework for efficient and parallel high-resolution ST prediction. Unlike conventional spot-by-spot inference methods, Img2ST-Net employs a fully convolutional architecture to generate dense, HD gene expression maps in a parallelized manner. By modeling HD ST data as super-pixel representations, the task is reformulated from image-to-omics inference into a super-content image generation problem with hundreds or thousands of output channels. This design not only improves computational efficiency but also better preserves the spatial organization intrinsic to spatial omics data. To enhance robustness under sparse expression patterns, we further introduce SSIM-ST, a structural-similarity-based evaluation metric tailored for high-resolution ST analysis. We present a scalable, biologically coherent framework for high-resolution ST prediction. Img2ST-Net offers a principled solution for efficient and accurate ST inference at scale. Our contributions lay the groundwork for next-generation ST modeling that is robust and resolution-aware. The source code has been made publicly available at https://github.com/hrlblab/Img2ST-Net.

Can Zhao, Pengfei Guo, Dong Yang et al.

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.

Ibrahim Ethem Hamamci, Sezgin Er, Suprosanna Shit et al.

Recent progress in vision-language modeling for 3D medical imaging has been fueled by large-scale computed tomography (CT) corpora with paired free-text reports, stronger architectures, and powerful pretrained models. This has enabled applications such as automated report generation and text-conditioned 3D image synthesis. Yet, current approaches struggle with high-resolution, long-sequence volumes: contrastive pretraining often yields vision encoders that are misaligned with clinical language, and slice-wise tokenization blurs fine anatomy, reducing diagnostic performance on downstream tasks. We introduce BTB3D (Better Tokens for Better 3D), a causal convolutional encoder-decoder that unifies 2D and 3D training and inference while producing compact, frequency-aware volumetric tokens. A three-stage training curriculum enables (i) local reconstruction, (ii) overlapping-window tiling, and (iii) long-context decoder refinement, during which the model learns from short slice excerpts yet generalizes to scans exceeding 300 slices without additional memory overhead. BTB3D sets a new state-of-the-art on two key tasks: it improves BLEU scores and increases clinical F1 by 40% over CT2Rep, CT-CHAT, and Merlin for report generation; and it reduces FID by 75% and halves FVD compared to GenerateCT and MedSyn for text-to-CT synthesis, producing anatomically consistent 512*512*241 volumes. These results confirm that precise three-dimensional tokenization, rather than larger language backbones alone, is essential for scalable vision-language modeling in 3D medical imaging. The codebase is available at: https://github.com/ibrahimethemhamamci/BTB3D

Yufan He, Pengfei Guo, Yucheng Tang et al.

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.

Andres Diaz-Pinto, Pritesh Mehta, Sachidanand Alle et al.

Automatic segmentation of medical images is a key step for diagnostic and interventional tasks. However, achieving this requires large amounts of annotated volumes, which can be tedious and time-consuming task for expert annotators. In this paper, we introduce DeepEdit, a deep learning-based method for volumetric medical image annotation, that allows automatic and semi-automatic segmentation, and click-based refinement. DeepEdit combines the power of two methods: a non-interactive (i.e. automatic segmentation using nnU-Net, UNET or UNETR) and an interactive segmentation method (i.e. DeepGrow), into a single deep learning model. It allows easy integration of uncertainty-based ranking strategies (i.e. aleatoric and epistemic uncertainty computation) and active learning. We propose and implement a method for training DeepEdit by using standard training combined with user interaction simulation. Once trained, DeepEdit allows clinicians to quickly segment their datasets by using the algorithm in auto segmentation mode or by providing clicks via a user interface (i.e. 3D Slicer, OHIF). We show the value of DeepEdit through evaluation on the PROSTATEx dataset for prostate/prostatic lesions and the Multi-Atlas Labeling Beyond the Cranial Vault (BTCV) dataset for abdominal CT segmentation, using state-of-the-art network architectures as baseline for comparison. DeepEdit could reduce the time and effort annotating 3D medical images compared to DeepGrow alone. Source code is available at https://github.com/Project-MONAI/MONAILabel

Ali Hatamizadeh, Hongxu Yin, Pavlo Molchanov et al.

Federated learning (FL) allows the collaborative training of AI models without needing to share raw data. This capability makes it especially interesting for healthcare applications where patient and data privacy is of utmost concern. However, recent works on the inversion of deep neural networks from model gradients raised concerns about the security of FL in preventing the leakage of training data. In this work, we show that these attacks presented in the literature are impractical in FL use-cases where the clients' training involves updating the Batch Normalization (BN) statistics and provide a new baseline attack that works for such scenarios. Furthermore, we present new ways to measure and visualize potential data leakage in FL. Our work is a step towards establishing reproducible methods of measuring data leakage in FL and could help determine the optimal tradeoffs between privacy-preserving techniques, such as differential privacy, and model accuracy based on quantifiable metrics. Code is available at https://nvidia.github.io/NVFlare/research/quantifying-data-leakage.

Wentao Zhu, Can Zhao, Wenqi Li et al.

Deep Learning (DL) models are becoming larger, because the increase in model size might offer significant accuracy gain. To enable the training of large deep networks, data parallelism and model parallelism are two well-known approaches for parallel training. However, data parallelism does not help reduce memory footprint per device. In this work, we introduce Large deep 3D ConvNets with Automated Model Parallelism (LAMP) and investigate the impact of both input's and deep 3D ConvNets' size on segmentation accuracy. Through automated model parallelism, it is feasible to train large deep 3D ConvNets with a large input patch, even the whole image. Extensive experiments demonstrate that, facilitated by the automated model parallelism, the segmentation accuracy can be improved through increasing model size and input context size, and large input yields significant inference speedup compared with sliding window of small patches in the inference. Code is available\footnote{https://monai.io/research/lamp-automated-model-parallelism}.

Anjany Sekuboyina, Malek E. Husseini, Amirhossein Bayat et al.

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse.

Vishwesh Nath, Wenqi Li, Dong Yang et al.

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.

Xinran Li, Yi Shuai, Chen Liu et al.

Tumor synthesis can generate examples that AI often misses or over-detects, improving AI performance by training on these challenging cases. However, existing synthesis methods, which are typically unconditional -- generating images from random variables -- or conditioned only by tumor shapes, lack controllability over specific tumor characteristics such as texture, heterogeneity, boundaries, and pathology type. As a result, the generated tumors may be overly similar or duplicates of existing training data, failing to effectively address AI's weaknesses. We propose a new text-driven tumor synthesis approach, termed TextoMorph, that provides textual control over tumor characteristics. This is particularly beneficial for examples that confuse the AI the most, such as early tumor detection (increasing Sensitivity by +8.5%), tumor segmentation for precise radiotherapy (increasing DSC by +6.3%), and classification between benign and malignant tumors (improving Sensitivity by +8.2%). By incorporating text mined from radiology reports into the synthesis process, we increase the variability and controllability of the synthetic tumors to target AI's failure cases more precisely. Moreover, TextoMorph uses contrastive learning across different texts and CT scans, significantly reducing dependence on scarce image-report pairs (only 141 pairs used in this study) by leveraging a large corpus of 34,035 radiology reports. Finally, we have developed rigorous tests to evaluate synthetic tumors, including Text-Driven Visual Turing Test and Radiomics Pattern Analysis, showing that our synthetic tumors is realistic and diverse in texture, heterogeneity, boundaries, and pathology.

Holger R. Roth, Ziyue Xu, Yuan-Ting Hsieh et al.

In the ever-evolving landscape of artificial intelligence (AI) and large language models (LLMs), handling and leveraging data effectively has become a critical challenge. Most state-of-the-art machine learning algorithms are data-centric. However, as the lifeblood of model performance, necessary data cannot always be centralized due to various factors such as privacy, regulation, geopolitics, copyright issues, and the sheer effort required to move vast datasets. In this paper, we explore how federated learning enabled by NVIDIA FLARE can address these challenges with easy and scalable integration capabilities, enabling parameter-efficient and full supervised fine-tuning of LLMs for natural language processing and biopharmaceutical applications to enhance their accuracy and robustness.

Pengfei Guo, Can Zhao, Dong Yang et al.

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.

Jiawei Mao, Yuhan Wang, Yucheng Tang et al.

This paper presents MedSegFactory, a versatile medical synthesis framework that generates high-quality paired medical images and segmentation masks across modalities and tasks. It aims to serve as an unlimited data repository, supplying image-mask pairs to enhance existing segmentation tools. The core of MedSegFactory is a dual-stream diffusion model, where one stream synthesizes medical images and the other generates corresponding segmentation masks. To ensure precise alignment between image-mask pairs, we introduce Joint Cross-Attention (JCA), enabling a collaborative denoising paradigm by dynamic cross-conditioning between streams. This bidirectional interaction allows both representations to guide each other's generation, enhancing consistency between generated pairs. MedSegFactory unlocks on-demand generation of paired medical images and segmentation masks through user-defined prompts that specify the target labels, imaging modalities, anatomical regions, and pathological conditions, facilitating scalable and high-quality data generation. This new paradigm of medical image synthesis enables seamless integration into diverse medical imaging workflows, enhancing both efficiency and accuracy. Extensive experiments show that MedSegFactory generates data of superior quality and usability, achieving competitive or state-of-the-art performance in 2D and 3D segmentation tasks while addressing data scarcity and regulatory constraints.

Wenxuan Li, Xinze Zhou, Qi Chen et al.

PanTS is a large-scale, multi-institutional dataset curated to advance research in pancreatic CT analysis. It contains 36,390 CT scans from 145 medical centers, with expert-validated, voxel-wise annotations of over 993,000 anatomical structures, covering pancreatic tumors, pancreas head, body, and tail, and 24 surrounding anatomical structures such as vascular/skeletal structures and abdominal/thoracic organs. Each scan includes metadata such as patient age, sex, diagnosis, contrast phase, in-plane spacing, slice thickness, etc. AI models trained on PanTS achieve significantly better performance in pancreatic tumor detection, localization, and segmentation compared to those trained on existing public datasets. Our analysis indicates that these gains are directly attributable to the 16x larger-scale tumor annotations and indirectly supported by the 24 additional surrounding anatomical structures. As the largest and most comprehensive resource of its kind, PanTS offers a new benchmark for developing and evaluating AI models in pancreatic CT analysis.

Jiawei Mao, Yuhan Wang, Lifeng Chen et al.

Recent advances in generative medical models are constrained by modality-specific scenarios that hinder the integration of complementary evidence from imaging, pathology, and clinical notes. This fragmentation limits their evolution into foundation models that can learn and reason across the full spectrum of biomedical data. We propose MeDiM, the first medical discrete diffusion model that learns shared distributions across modalities without modality-specific components. MeDiM unifies multiple generative tasks: translating between images and text, and jointly producing image-report pairs across domains in response to prompts. Built on a discrete diffusion framework, MeDiM bridges vision and language representations through a shared probabilistic space. To enable unified and flexible medical generation, we employ a multimodal large language model (MLLM) as the diffusion backbone, leveraging its prior knowledge and cross-modal reasoning. Two key designs are introduced: (1) removing the causal attention mask for bidirectional context, and (2) injecting continuous timestep embeddings for diffusion awareness. Experiments demonstrate high-fidelity medical generation (FID 16.60 on MIMIC-CXR and FID 24.19 on PathGen) and accurate report generation (METEOR 0.2650 and 0.2580). Jointly generated image-report pairs further enhance downstream performance (plus6.43 percent BLEU-1, plus18.57 percent BLEU-2, plus31.58 percent BLEU-3, plus4.80 percent METEOR), showing that MeDiM supports coherent and clinically grounded multimodal outputs.

Niklas Bubeck, Suprosanna Shit, Chen Chen et al.

Cardiac Magnetic Resonance (CMR) imaging is a critical tool for diagnosing and managing cardiovascular disease, yet its utility is often limited by the sparse acquisition of 2D short-axis slices, resulting in incomplete volumetric information. Accurate 3D reconstruction from these sparse slices is essential for comprehensive cardiac assessment, but existing methods face challenges, including reliance on predefined interpolation schemes (e.g., linear or spherical), computational inefficiency, and dependence on additional semantic inputs such as segmentation labels or motion data. To address these limitations, we propose a novel Cardiac Latent Interpolation Diffusion (CaLID) framework that introduces three key innovations. First, we present a data-driven interpolation scheme based on diffusion models, which can capture complex, non-linear relationships between sparse slices and improves reconstruction accuracy. Second, we design a computationally efficient method that operates in the latent space and speeds up 3D whole-heart upsampling time by a factor of 24, reducing computational overhead compared to previous methods. Third, with only sparse 2D CMR images as input, our method achieves SOTA performance against baseline methods, eliminating the need for auxiliary input such as morphological guidance, thus simplifying workflows. We further extend our method to 2D+T data, enabling the effective modeling of spatiotemporal dynamics and ensuring temporal coherence. Extensive volumetric evaluations and downstream segmentation tasks demonstrate that CaLID achieves superior reconstruction quality and efficiency. By addressing the fundamental limitations of existing approaches, our framework advances the state of the art for spatio and spatiotemporal whole-heart reconstruction, offering a robust and clinically practical solution for cardiovascular imaging.

Ali Hatamizadeh, Vishwesh Nath, Yucheng Tang et al.

Semantic segmentation of brain tumors is a fundamental medical image analysis task involving multiple MRI imaging modalities that can assist clinicians in diagnosing the patient and successively studying the progression of the malignant entity. In recent years, Fully Convolutional Neural Networks (FCNNs) approaches have become the de facto standard for 3D medical image segmentation. The popular "U-shaped" network architecture has achieved state-of-the-art performance benchmarks on different 2D and 3D semantic segmentation tasks and across various imaging modalities. However, due to the limited kernel size of convolution layers in FCNNs, their performance of modeling long-range information is sub-optimal, and this can lead to deficiencies in the segmentation of tumors with variable sizes. On the other hand, transformer models have demonstrated excellent capabilities in capturing such long-range information in multiple domains, including natural language processing and computer vision. Inspired by the success of vision transformers and their variants, we propose a novel segmentation model termed Swin UNEt TRansformers (Swin UNETR). Specifically, the task of 3D brain tumor semantic segmentation is reformulated as a sequence to sequence prediction problem wherein multi-modal input data is projected into a 1D sequence of embedding and used as an input to a hierarchical Swin transformer as the encoder. The swin transformer encoder extracts features at five different resolutions by utilizing shifted windows for computing self-attention and is connected to an FCNN-based decoder at each resolution via skip connections. We have participated in BraTS 2021 segmentation challenge, and our proposed model ranks among the top-performing approaches in the validation phase. Code: https://monai.io/research/swin-unetr

Cheng Peng, Andriy Myronenko, Ali Hatamizadeh et al.

Semantic segmentation of 3D medical images is a challenging task due to the high variability of the shape and pattern of objects (such as organs or tumors). Given the recent success of deep learning in medical image segmentation, Neural Architecture Search (NAS) has been introduced to find high-performance 3D segmentation network architectures. However, because of the massive computational requirements of 3D data and the discrete optimization nature of architecture search, previous NAS methods require a long search time or necessary continuous relaxation, and commonly lead to sub-optimal network architectures. While one-shot NAS can potentially address these disadvantages, its application in the segmentation domain has not been well studied in the expansive multi-scale multi-path search space. To enable one-shot NAS for medical image segmentation, our method, named HyperSegNAS, introduces a HyperNet to assist super-net training by incorporating architecture topology information. Such a HyperNet can be removed once the super-net is trained and introduces no overhead during architecture search. We show that HyperSegNAS yields better performing and more intuitive architectures compared to the previous state-of-the-art (SOTA) segmentation networks; furthermore, it can quickly and accurately find good architecture candidates under different computing constraints. Our method is evaluated on public datasets from the Medical Segmentation Decathlon (MSD) challenge, and achieves SOTA performances.

Yucheng Tang, Dong Yang, Wenqi Li et al.

Vision Transformers (ViT)s have shown great performance in self-supervised learning of global and local representations that can be transferred to downstream applications. Inspired by these results, we introduce a novel self-supervised learning framework with tailored proxy tasks for medical image analysis. Specifically, we propose: (i) a new 3D transformer-based model, dubbed Swin UNEt TRansformers (Swin UNETR), with a hierarchical encoder for self-supervised pre-training; (ii) tailored proxy tasks for learning the underlying pattern of human anatomy. We demonstrate successful pre-training of the proposed model on 5,050 publicly available computed tomography (CT) images from various body organs. The effectiveness of our approach is validated by fine-tuning the pre-trained models on the Beyond the Cranial Vault (BTCV) Segmentation Challenge with 13 abdominal organs and segmentation tasks from the Medical Segmentation Decathlon (MSD) dataset. Our model is currently the state-of-the-art (i.e. ranked 1st) on the public test leaderboards of both MSD and BTCV datasets. Code: https://monai.io/research/swin-unetr

Dong Yang, Andriy Myronenko, Xiaosong Wang et al.

Lesion segmentation in medical imaging has been an important topic in clinical research. Researchers have proposed various detection and segmentation algorithms to address this task. Recently, deep learning-based approaches have significantly improved the performance over conventional methods. However, most state-of-the-art deep learning methods require the manual design of multiple network components and training strategies. In this paper, we propose a new automated machine learning algorithm, T-AutoML, which not only searches for the best neural architecture, but also finds the best combination of hyper-parameters and data augmentation strategies simultaneously. The proposed method utilizes the modern transformer model, which is introduced to adapt to the dynamic length of the search space embedding and can significantly improve the ability of the search. We validate T-AutoML on several large-scale public lesion segmentation data-sets and achieve state-of-the-art performance.

Andriy Myronenko, Ziyue Xu, Dong Yang et al.

Multiple instance learning (MIL) is a key algorithm for classification of whole slide images (WSI). Histology WSIs can have billions of pixels, which create enormous computational and annotation challenges. Typically, such images are divided into a set of patches (a bag of instances), where only bag-level class labels are provided. Deep learning based MIL methods calculate instance features using convolutional neural network (CNN). Our proposed approach is also deep learning based, with the following two contributions: Firstly, we propose to explicitly account for dependencies between instances during training by embedding self-attention Transformer blocks to capture dependencies between instances. For example, a tumor grade may depend on the presence of several particular patterns at different locations in WSI, which requires to account for dependencies between patches. Secondly, we propose an instance-wise loss function based on instance pseudo-labels. We compare the proposed algorithm to multiple baseline methods, evaluate it on the PANDA challenge dataset, the largest publicly available WSI dataset with over 11K images, and demonstrate state-of-the-art results.