Brain Imaging Foundation Models, Are We There Yet? A Systematic Review of Foundation Models for Brain Imaging and Biomedical Research

Foundation models (FMs), large neural networks pretrained on extensive and diverse datasets, have revolutionized artificial intelligence and shown significant promise in medical imaging by enabling robust performance with limited labeled data. Although numerous surveys have reviewed the application of FM in healthcare care, brain imaging remains underrepresented, despite its critical role in the diagnosis and treatment of neurological diseases using modalities such as MRI, CT, and PET. Existing reviews either marginalize brain imaging or lack depth on the unique challenges and requirements of FM in this domain, such as multimodal data integration, support for diverse clinical tasks, and handling of heterogeneous, fragmented datasets. To address this gap, we present the first comprehensive and curated review of FMs for brain imaging. We systematically analyze 161 brain imaging datasets and 86 FM architectures, providing information on key design choices, training paradigms, and optimizations driving recent advances. Our review highlights the leading models for various brain imaging tasks, summarizes their innovations, and critically examines current limitations and blind spots in the literature. We conclude by outlining future research directions to advance FM applications in brain imaging, with the aim of fostering progress in both clinical and research settings.

Predicting Hypoxia in Brain Tumors from Multiparametric MRI

This research paper presents a novel approach to the prediction of hypoxia in brain tumors, using multi-parametric Magnetic Resonance Imaging (MRI). Hypoxia, a condition characterized by low oxygen levels, is a common feature of malignant brain tumors associated with poor prognosis. Fluoromisonidazole Positron Emission Tomography (FMISO PET) is a well-established method for detecting hypoxia in vivo, but it is expensive and not widely available. Our study proposes the use of MRI, a more accessible and cost-effective imaging modality, to predict FMISO PET signals. We investigate deep learning models (DL) trained on the ACRIN 6684 dataset, a resource that contains paired MRI and FMISO PET images from patients with brain tumors. Our trained models effectively learn the complex relationships between the MRI features and the corresponding FMISO PET signals, thereby enabling the prediction of hypoxia from MRI scans alone. The results show a strong correlation between the predicted and actual FMISO PET signals, with an overall PSNR score above 29.6 and a SSIM score greater than 0.94, confirming MRI as a promising option for hypoxia prediction in brain tumors. This approach could significantly improve the accessibility of hypoxia detection in clinical settings, with the potential for more timely and targeted treatments.

Federated Learning Enables Big Data for Rare Cancer Boundary Detection

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.