The Brain Tumor Segmentation (BraTS) Challenge 2023: Local Synthesis of Healthy Brain Tissue via Inpainting

A myriad of algorithms for the automatic analysis of brain MR images is available to support clinicians in their decision-making. For brain tumor patients, the image acquisition time series typically starts with a scan that is already pathological. This poses problems, as many algorithms are designed to analyze healthy brains and provide no guarantees for images featuring lesions. Examples include but are not limited to algorithms for brain anatomy parcellation, tissue segmentation, and brain extraction. To solve this dilemma, we introduce the BraTS 2023 inpainting challenge. Here, the participants' task is to explore inpainting techniques to synthesize healthy brain scans from lesioned ones. The following manuscript contains the task formulation, dataset, and submission procedure. Later it will be updated to summarize the findings of the challenge. The challenge is organized as part of the BraTS 2023 challenge hosted at the MICCAI 2023 conference in Vancouver, Canada.

BenchMD: A Benchmark for Modality-Agnostic Learning on Medical Images and Sensors

Medical data poses a daunting challenge for AI algorithms: it exists in many different modalities, experiences frequent distribution shifts, and suffers from a scarcity of examples and labels. Recent advances, including transformers and self-supervised learning, promise a more universal approach that can be applied flexibly across these diverse conditions. To measure and drive progress in this direction, we present BenchMD: a benchmark that tests how modality-agnostic methods, including architectures and training techniques (e.g. self-supervised learning, ImageNet pretraining), perform on a diverse array of clinically-relevant medical tasks. BenchMD combines 19 publicly available datasets for 7 medical modalities, including 1D sensor data, 2D images, and 3D volumetric scans. Our benchmark reflects real-world data constraints by evaluating methods across a range of dataset sizes, including challenging few-shot settings that incentivize the use of pretraining. Finally, we evaluate performance on out-of-distribution data collected at different hospitals than the training data, representing naturally-occurring distribution shifts that frequently degrade the performance of medical AI models. Our baseline results demonstrate that no modality-agnostic technique achieves strong performance across all modalities, leaving ample room for improvement on the benchmark. Code is released at https://github.com/rajpurkarlab/BenchMD .

Federated Learning on Heterogenous Data using Chest CT

Large data have accelerated advances in AI. While it is well known that population differences from genetics, sex, race, diet, and various environmental factors contribute significantly to disease, AI studies in medicine have largely focused on locoregional patient cohorts with less diverse data sources. Such limitation stems from barriers to large-scale data share in medicine and ethical concerns over data privacy. Federated learning (FL) is one potential pathway for AI development that enables learning across hospitals without data share. In this study, we show the results of various FL strategies on one of the largest and most diverse COVID-19 chest CT datasets: 21 participating hospitals across five continents that comprise >10,000 patients with >1 million images. We present three techniques: Fed Averaging (FedAvg), Incremental Institutional Learning (IIL), and Cyclical Incremental Institutional Learning (CIIL). We also propose an FL strategy that leverages synthetically generated data to overcome class imbalances and data size disparities across centers. We show that FL can achieve comparable performance to Centralized Data Sharing (CDS) while maintaining high performance across sites with small, underrepresented data. We investigate the strengths and weaknesses for all technical approaches on this heterogeneous dataset including the robustness to non-Independent and identically distributed (non-IID) diversity of data. We also describe the sources of data heterogeneity such as age, sex, and site locations in the context of FL and show how even among the correctly labeled populations, disparities can arise due to these biases.

NanoBatch DPSGD: Exploring Differentially Private learning on ImageNet with low batch sizes on the IPU

Differentially private SGD (DPSGD) has recently shown promise in deep learning. However, compared to non-private SGD, the DPSGD algorithm places computational overheads that can undo the benefit of batching in GPUs. Microbatching is a standard method to alleviate this and is fully supported in the TensorFlow Privacy library (TFDP). However, this technique, while improving training times also reduces the quality of the gradients and degrades the classification accuracy. Recent works that for example use the JAX framework show promise in also alleviating this but still show degradation in throughput from non-private to private SGD on CNNs, and have not yet shown ImageNet implementations. In our work, we argue that low batch sizes using group normalization on ResNet-50 can yield high accuracy and privacy on Graphcore IPUs. This enables DPSGD training of ResNet-50 on ImageNet in just 6 hours (100 epochs) on an IPU-POD16 system.

The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification

The BraTS 2021 challenge celebrates its 10th anniversary and is jointly organized by the Radiological Society of North America (RSNA), the American Society of Neuroradiology (ASNR), and the Medical Image Computing and Computer Assisted Interventions (MICCAI) society. Since its inception, BraTS has been focusing on being a common benchmarking venue for brain glioma segmentation algorithms, with well-curated multi-institutional multi-parametric magnetic resonance imaging (mpMRI) data. Gliomas are the most common primary malignancies of the central nervous system, with varying degrees of aggressiveness and prognosis. The RSNA-ASNR-MICCAI BraTS 2021 challenge targets the evaluation of computational algorithms assessing the same tumor compartmentalization, as well as the underlying tumor's molecular characterization, in pre-operative baseline mpMRI data from 2,000 patients. Specifically, the two tasks that BraTS 2021 focuses on are: a) the segmentation of the histologically distinct brain tumor sub-regions, and b) the classification of the tumor's O[6]-methylguanine-DNA methyltransferase (MGMT) promoter methylation status. The performance evaluation of all participating algorithms in BraTS 2021 will be conducted through the Sage Bionetworks Synapse platform (Task 1) and Kaggle (Task 2), concluding in distributing to the top ranked participants monetary awards of $60,000 collectively.

A Real-World Demonstration of Machine Learning Generalizability: Intracranial Hemorrhage Detection on Head CT

Machine learning (ML) holds great promise in transforming healthcare. While published studies have shown the utility of ML models in interpreting medical imaging examinations, these are often evaluated under laboratory settings. The importance of real world evaluation is best illustrated by case studies that have documented successes and failures in the translation of these models into clinical environments. A key prerequisite for the clinical adoption of these technologies is demonstrating generalizable ML model performance under real world circumstances. The purpose of this study was to demonstrate that ML model generalizability is achievable in medical imaging with the detection of intracranial hemorrhage (ICH) on non-contrast computed tomography (CT) scans serving as the use case. An ML model was trained using 21,784 scans from the RSNA Intracranial Hemorrhage CT dataset while generalizability was evaluated using an external validation dataset obtained from our busy trauma and neurosurgical center. This real world external validation dataset consisted of every unenhanced head CT scan (n = 5,965) performed in our emergency department in 2019 without exclusion. The model demonstrated an AUC of 98.4%, sensitivity of 98.8%, and specificity of 98.0%, on the test dataset. On external validation, the model demonstrated an AUC of 95.4%, sensitivity of 91.3%, and specificity of 94.1%. Evaluating the ML model using a real world external validation dataset that is temporally and geographically distinct from the training dataset indicates that ML generalizability is achievable in medical imaging applications.

Deep Sequential Learning for Cervical Spine Fracture Detection on Computed Tomography Imaging

Fractures of the cervical spine are a medical emergency and may lead to permanent paralysis and even death. Accurate diagnosis in patients with suspected fractures by computed tomography (CT) is critical to patient management. In this paper, we propose a deep convolutional neural network (DCNN) with a bidirectional long-short term memory (BLSTM) layer for the automated detection of cervical spine fractures in CT axial images. We used an annotated dataset of 3,666 CT scans (729 positive and 2,937 negative cases) to train and validate the model. The validation results show a classification accuracy of 70.92% and 79.18% on the balanced (104 positive and 104 negative cases) and imbalanced (104 positive and 419 negative cases) test datasets, respectively.

Cylindrical Transform: 3D Semantic Segmentation of Kidneys With Limited Annotated Images

In this paper, we propose a novel technique for sampling sequential images using a cylindrical transform in a cylindrical coordinate system for kidney semantic segmentation in abdominal computed tomography (CT). The images generated from a cylindrical transform augment a limited annotated set of images in three dimensions. This approach enables us to train contemporary classification deep convolutional neural networks (DCNNs) instead of fully convolutional networks (FCNs) for semantic segmentation. Typical semantic segmentation models segment a sequential set of images (e.g. CT or video) by segmenting each image independently. However, the proposed method not only considers the spatial dependency in the x-y plane, but also the spatial sequential dependency along the z-axis. The results show that classification DCNNs, trained on cylindrical transformed images, can achieve a higher segmentation performance value than FCNs using a limited number of annotated images.

Recent Advances in Recurrent Neural Networks

Recurrent neural networks (RNNs) are capable of learning features and long term dependencies from sequential and time-series data. The RNNs have a stack of non-linear units where at least one connection between units forms a directed cycle. A well-trained RNN can model any dynamical system; however, training RNNs is mostly plagued by issues in learning long-term dependencies. In this paper, we present a survey on RNNs and several new advances for newcomers and professionals in the field. The fundamentals and recent advances are explained and the research challenges are introduced.