Linmin Pei

Sarthak Pati, Ujjwal Baid, Brandon Edwards et al.

Although machine learning (ML) has shown promise in numerous domains, there are concerns about generalizability to out-of-sample data. This is currently addressed by centrally sharing ample, and importantly diverse, data from multiple sites. However, such centralization is challenging to scale (or even not feasible) due to various limitations. Federated ML (FL) provides an alternative to train accurate and generalizable ML models, by only sharing numerical model updates. Here we present findings from the largest FL study to-date, involving data from 71 healthcare institutions across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, utilizing the largest dataset of such patients ever used in the literature (25,256 MRI scans from 6,314 patients). We demonstrate a 33% improvement over a publicly trained model to delineate the surgically targetable tumor, and 23% improvement over the tumor's entire extent. We anticipate our study to: 1) enable more studies in healthcare informed by large and diverse data, ensuring meaningful results for rare diseases and underrepresented populations, 2) facilitate further quantitative analyses for glioblastoma via performance optimization of our consensus model for eventual public release, and 3) demonstrate the effectiveness of FL at such scale and task complexity as a paradigm shift for multi-site collaborations, alleviating the need for data sharing.

Gowtham Krishnan Murugesan, Diana McCrumb, Rahul Soni et al.

AI in Medical Imaging project aims to enhance the National Cancer Institute's (NCI) Image Data Commons (IDC) by developing nnU-Net models and providing AI-assisted segmentations for cancer radiology images. We created high-quality, AI-annotated imaging datasets for 11 IDC collections. These datasets include images from various modalities, such as computed tomography (CT) and magnetic resonance imaging (MRI), covering the lungs, breast, brain, kidneys, prostate, and liver. The nnU-Net models were trained using open-source datasets. A portion of the AI-generated annotations was reviewed and corrected by radiologists. Both the AI and radiologist annotations were encoded in compliance with the the Digital Imaging and Communications in Medicine (DICOM) standard, ensuring seamless integration into the IDC collections. All models, images, and annotations are publicly accessible, facilitating further research and development in cancer imaging. This work supports the advancement of imaging tools and algorithms by providing comprehensive and accurate annotated datasets.

Linmin Pei, Granger Sutton, Michael Rutherford et al.

The de-identification (deID) of protected health information (PHI) and personally identifiable information (PII) is a fundamental requirement for sharing medical images, particularly through public repositories, to ensure compliance with patient privacy laws. In addition, preservation of non-PHI metadata to inform and enable downstream development of imaging artificial intelligence (AI) is an important consideration in biomedical research. The goal of MIDI-B was to provide a standardized platform for benchmarking of DICOM image deID tools based on a set of rules conformant to the HIPAA Safe Harbor regulation, the DICOM Attribute Confidentiality Profiles, and best practices in preservation of research-critical metadata, as defined by The Cancer Imaging Archive (TCIA). The challenge employed a large, diverse, multi-center, and multi-modality set of real de-identified radiology images with synthetic PHI/PII inserted. The MIDI-B Challenge consisted of three phases: training, validation, and test. Eighty individuals registered for the challenge. In the training phase, we encouraged participants to tune their algorithms using their in-house or public data. The validation and test phases utilized the DICOM images containing synthetic identifiers (of 216 and 322 subjects, respectively). Ten teams successfully completed the test phase of the challenge. To measure success of a rule-based approach to image deID, scores were computed as the percentage of correct actions from the total number of required actions. The scores ranged from 97.91% to 99.93%. Participants employed a variety of open-source and proprietary tools with customized configurations, large language models, and optical character recognition (OCR). In this paper we provide a comprehensive report on the MIDI-B Challenge's design, implementation, results, and lessons learned.

Michael W. Rutherford, Tracy Nolan, Linmin Pei et al.

Medical imaging research increasingly depends on large-scale data sharing to promote reproducibility and train Artificial Intelligence (AI) models. Ensuring patient privacy remains a significant challenge for open-access data sharing. Digital Imaging and Communications in Medicine (DICOM), the global standard data format for medical imaging, encodes both essential clinical metadata and extensive protected health information (PHI) and personally identifiable information (PII). Effective de-identification must remove identifiers, preserve scientific utility, and maintain DICOM validity. Tools exist to perform de-identification, but few assess its effectiveness, and most rely on subjective reviews, limiting reproducibility and regulatory confidence. To address this gap, we developed an openly accessible DICOM dataset infused with synthetic PHI/PII and an evaluation framework for benchmarking image de-identification workflows. The Medical Image de-identification (MIDI) dataset was built using publicly available de-identified data from The Cancer Imaging Archive (TCIA). It includes 538 subjects (216 for validation, 322 for testing), 605 studies, 708 series, and 53,581 DICOM image instances. These span multiple vendors, imaging modalities, and cancer types. Synthetic PHI and PII were embedded into structured data elements, plain text data elements, and pixel data to simulate real-world identity leaks encountered by TCIA curation teams. Accompanying evaluation tools include a Python script, answer keys (known truth), and mapping files that enable automated comparison of curated data against expected transformations. The framework is aligned with the HIPAA Privacy Rule "Safe Harbor" method, DICOM PS3.15 Confidentiality Profiles, and TCIA best practices. It supports objective, standards-driven evaluation of de-identification workflows, promoting safer and more consistent medical image sharing.

Spyridon Bakas, Mauricio Reyes, Andras Jakab et al.

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.