arXiv subjects

Daguang Xu

Publications and source records attributed to Daguang Xu.

At least 73 records · Page 4Linked to original sources

arXiv2023

NVIDIA FLARE: Federated Learning from Simulation to Real-World

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.

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arXiv2023

Communication-Efficient Vertical Federated Learning with Limited Overlapping Samples

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}.

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arXiv2023

Fair Federated Medical Image Segmentation via Client Contribution Estimation

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.

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arXiv2023

Closing the Generalization Gap of Cross-silo Federated Medical Image Segmentation

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.

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arXiv2023

Do Gradient Inversion Attacks Make Federated Learning Unsafe?

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.

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arXiv2022

The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}.

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arXiv2022

MONAI: An open-source framework for deep learning in healthcare

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.

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arXiv2022

Split-U-Net: Preventing Data Leakage in Split Learning for Collaborative Multi-Modal Brain Tumor Segmentation

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.

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arXiv2022

Automated head and neck tumor segmentation from 3D PET/CT

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.

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arXiv2022

Automated ischemic stroke lesion segmentation from 3D MRI

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).

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arXiv2022

Automated segmentation of intracranial hemorrhages from 3D CT

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.

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arXiv2022

Warm Start Active Learning with Proxy Labels \& Selection via Semi-Supervised Fine-Tuning

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.

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arXiv2022

Auto-FedRL: Federated Hyperparameter Optimization for Multi-institutional Medical Image Segmentation

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.

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arXiv2022

Fetal Brain Tissue Annotation and Segmentation Challenge Results

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.

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arXiv2022

UNetFormer: A Unified Vision Transformer Model and Pre-Training Framework for 3D Medical Image Segmentation

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

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arXiv2022

VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images

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.

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arXiv2022

Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis

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

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arXiv2022

GradViT: Gradient Inversion of Vision Transformers

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/.

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