Generative AI for Medical Imaging: extending the MONAI Framework

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

DeepEdit: Deep Editable Learning for Interactive Segmentation of 3D Medical Images

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

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.

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, and allows researchers to bring their data science workflows implemented in any training libraries (PyTorch, TensorFlow, XGBoost, or even NumPy) and apply them in real-world FL settings. This paper introduces the key design principles of FLARE 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.

MONAI Label: A framework for AI-assisted Interactive Labeling of 3D Medical Images

The lack of annotated datasets is a major challenge in training new task-specific supervised AI algorithms as manual annotation is expensive and time-consuming. To address this problem, we present MONAI Label, a free and open-source platform that facilitates the development of AI-based applications that aim at reducing the time required to annotate 3D medical image datasets. Through MONAI Label researchers can develop 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 (3DSlicer) 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 labeling apps by making them available to other researchers and clinicians alike. Lastly, MONAI Label provides sample labeling apps, namely DeepEdit and DeepGrow, demonstrating dramatically reduced annotation times.

STPLS3D: A Large-Scale Synthetic and Real Aerial Photogrammetry 3D Point Cloud Dataset

Although various 3D datasets with different functions and scales have been proposed recently, it remains challenging for individuals to complete the whole pipeline of large-scale data collection, sanitization, and annotation. Moreover, the created datasets usually suffer from extremely imbalanced class distribution or partial low-quality data samples. Motivated by this, we explore the procedurally synthetic 3D data generation paradigm to equip individuals with the full capability of creating large-scale annotated photogrammetry point clouds. Specifically, we introduce a synthetic aerial photogrammetry point clouds generation pipeline that takes full advantage of open geospatial data sources and off-the-shelf commercial packages. Unlike generating synthetic data in virtual games, where the simulated data usually have limited gaming environments created by artists, the proposed pipeline simulates the reconstruction process of the real environment by following the same UAV flight pattern on different synthetic terrain shapes and building densities, which ensure similar quality, noise pattern, and diversity with real data. In addition, the precise semantic and instance annotations can be generated fully automatically, avoiding the expensive and time-consuming manual annotation. Based on the proposed pipeline, we present a richly-annotated synthetic 3D aerial photogrammetry point cloud dataset, termed STPLS3D, with more than 16 $km^2$ of landscapes and up to 18 fine-grained semantic categories. For verification purposes, we also provide a parallel dataset collected from four areas in the real environment. Extensive experiments conducted on our datasets demonstrate the effectiveness and quality of the proposed synthetic dataset.

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 real FL use-cases and provide a new baseline attack that works for more realistic scenarios where the clients' training involves updating the Batch Normalization (BN) statistics. 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.

Ground material classification and for UAV-based photogrammetric 3D data A 2D-3D Hybrid Approach

In recent years, photogrammetry has been widely used in many areas to create photorealistic 3D virtual data representing the physical environment. The innovation of small unmanned aerial vehicles (sUAVs) has provided additional high-resolution imaging capabilities with low cost for mapping a relatively large area of interest. These cutting-edge technologies have caught the US Army and Navy's attention for the purpose of rapid 3D battlefield reconstruction, virtual training, and simulations. Our previous works have demonstrated the importance of information extraction from the derived photogrammetric data to create semantic-rich virtual environments (Chen et al., 2019). For example, an increase of simulation realism and fidelity was achieved by segmenting and replacing photogrammetric trees with game-ready tree models. In this work, we further investigated the semantic information extraction problem and focused on the ground material segmentation and object detection tasks. The main innovation of this work was that we leveraged both the original 2D images and the derived 3D photogrammetric data to overcome the challenges faced when using each individual data source. For ground material segmentation, we utilized an existing convolutional neural network architecture (i.e., 3DMV) which was originally designed for segmenting RGB-D sensed indoor data. We improved its performance for outdoor photogrammetric data by introducing a depth pooling layer in the architecture to take into consideration the distance between the source images and the reconstructed terrain model. To test the performance of our improved 3DMV, a ground truth ground material database was created using data from the One World Terrain (OWT) data repository. Finally, a workflow for importing the segmented ground materials into a virtual simulation scene was introduced, and visual results are reported in this paper.

Utilizing Satellite Imagery Datasets and Machine Learning Data Models to Evaluate Infrastructure Change in Undeveloped Regions

In the globalized economic world, it has become important to understand the purpose behind infrastructural and construction initiatives occurring within developing regions of the earth. This is critical when the financing for such projects must be coming from external sources, as is occurring throughout major portions of the African continent. When it comes to imagery analysis to research these regions, ground and aerial coverage is either non-existent or not commonly acquired. However, imagery from a large number of commercial, private, and government satellites have produced enormous datasets with global coverage, compiling geospatial resources that can be mined and processed using machine learning algorithms and neural networks. The downside is that a majority of these geospatial data resources are in a state of technical stasis, as it is difficult to quickly parse and determine a plan for request and processing when acquiring satellite image data. A goal of this research is to allow automated monitoring for largescale infrastructure projects, such as railways, to determine reliable metrics that define and predict the direction construction initiatives could take, allowing for a directed monitoring via narrowed and targeted satellite imagery requests. By utilizing photogrammetric techniques on available satellite data to create 3D Meshes and Digital Surface Models (DSM) we hope to effectively predict transport routes. In understanding the potential directions that largescale transport infrastructure will take through predictive modeling, it becomes much easier to track, understand, and monitor progress, especially in areas with limited imagery coverage.

Semantic Segmentation and Data Fusion of Microsoft Bing 3D Cities and Small UAV-based Photogrammetric Data

With state-of-the-art sensing and photogrammetric techniques, Microsoft Bing Maps team has created over 125 highly detailed 3D cities from 11 different countries that cover hundreds of thousands of square kilometer areas. The 3D city models were created using the photogrammetric technique with high-resolution images that were captured from aircraft-mounted cameras. Such a large 3D city database has caught the attention of the US Army for creating virtual simulation environments to support military operations. However, the 3D city models do not have semantic information such as buildings, vegetation, and ground and cannot allow sophisticated user-level and system-level interaction. At I/ITSEC 2019, the authors presented a fully automated data segmentation and object information extraction framework for creating simulation terrain using UAV-based photogrammetric data. This paper discusses the next steps in extending our designed data segmentation framework for segmenting 3D city data. In this study, the authors first investigated the strengths and limitations of the existing framework when applied to the Bing data. The main differences between UAV-based and aircraft-based photogrammetric data are highlighted. The data quality issues in the aircraft-based photogrammetric data, which can negatively affect the segmentation performance, are identified. Based on the findings, a workflow was designed specifically for segmenting Bing data while considering its characteristics. In addition, since the ultimate goal is to combine the use of both small unmanned aerial vehicle (UAV) collected data and the Bing data in a virtual simulation environment, data from these two sources needed to be aligned and registered together. To this end, the authors also proposed a data registration workflow that utilized the traditional iterative closest point (ICP) with the extracted semantic information.