Brainomaly: Unsupervised Neurologic Disease Detection Utilizing Unannotated T1-weighted Brain MR Images.

Harnessing the power of deep neural networks in the medical imaging domain is challenging due to the difficulties in acquiring large annotated datasets, especially for rare diseases, which involve high costs, time, and effort for annotation. Unsupervised disease detection methods, such as anomaly detection, can significantly reduce human effort in these scenarios. While anomaly detection typically focuses on learning from images of healthy subjects only, real-world situations often present unannotated datasets with a mixture of healthy and diseased subjects. Recent studies have demonstrated that utilizing such unannotated images can improve unsupervised disease and anomaly detection. However, these methods do not utilize knowledge specific to registered neuroimages, resulting in a subpar performance in neurologic disease detection. To address this limitation, we propose Brainomaly, a GAN-based image-to-image translation method specifically designed for neurologic disease detection. Brainomaly not only offers tailored image-to-image translation suitable for neuroimages but also leverages unannotated mixed images to achieve superior neurologic disease detection. Additionally, we address the issue of model selection for inference without annotated samples by proposing a pseudo-AUC metric, further enhancing Brainomaly's detection performance. Extensive experiments and ablation studies demonstrate that Brainomaly outperforms existing state-of-the-art unsupervised disease and anomaly detection methods by significant margins in Alzheimer's disease detection using a publicly available dataset and headache detection using an institutional dataset. The code is available from https://github.com/mahfuzmohammad/Brainomaly.

Ordinal Classification with Distance Regularization for Robust Brain Age Prediction.

Age is one of the major known risk factors for Alzheimer's Disease (AD). Detecting AD early is crucial for effective treatment and preventing irreversible brain damage. Brain age, a measure derived from brain imaging reflecting structural changes due to aging, may have the potential to identify AD onset, assess disease risk, and plan targeted interventions. Deep learning-based regression techniques to predict brain age from magnetic resonance imaging (MRI) scans have shown great accuracy recently. However, these methods are subject to an inherent regression to the mean effect, which causes a systematic bias resulting in an overestimation of brain age in young subjects and underestimation in old subjects. This weakens the reliability of predicted brain age as a valid biomarker for downstream clinical applications. Here, we reformulate the brain age prediction task from regression to classification to address the issue of systematic bias. Recognizing the importance of preserving ordinal information from ages to understand aging trajectory and monitor aging longitudinally, we propose a novel ORdinal Distance Encoded Regularization (ORDER) loss that incorporates the order of age labels, enhancing the model's ability to capture age-related patterns. Extensive experiments and ablation studies demonstrate that this framework reduces systematic bias, outperforms state-of-art methods by statistically significant margins, and can better capture subtle differences between clinical groups in an independent AD dataset. Our implementation is publicly available at https://github.com/jaygshah/Robust-Brain-Age-Prediction.

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, gray matter, white matter, ventricles, cerebellum, brainstem, deep gray 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.

HealthyGAN: Learning from Unannotated Medical Images to Detect Anomalies Associated with Human Disease.

Automated anomaly detection from medical images, such as MRIs and X-rays, can significantly reduce human effort in disease diagnosis. Owing to the complexity of modeling anomalies and the high cost of manual annotation by domain experts (e.g., radiologists), a typical technique in the current medical imaging literature has focused on deriving diagnostic models from healthy subjects only, assuming the model will detect the images from patients as outliers. However, in many real-world scenarios, unannotated datasets with a mix of both healthy and diseased individuals are abundant. Therefore, this paper poses the research question of how to improve unsupervised anomaly detection by utilizing (1) an unannotated set of mixed images, in addition to (2) the set of healthy images as being used in the literature. To answer the question, we propose HealthyGAN, a novel one-directional image-to-image translation method, which learns to translate the images from the mixed dataset to only healthy images. Being one-directional, HealthyGAN relaxes the requirement of cycle-consistency of existing unpaired image-to-image translation methods, which is unattainable with mixed unannotated data. Once the translation is learned, we generate a difference map for any given image by subtracting its translated output. Regions of significant responses in the difference map correspond to potential anomalies (if any). Our HealthyGAN outperforms the conventional state-of-the-art methods by significant margins on two publicly available datasets: COVID-19 and NIH ChestX-ray14, and one institutional dataset collected from Mayo Clinic. The implementation is publicly available at https://github.com/mahfuzmohammad/HealthyGAN.

UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation.

The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects-an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus.

Learning Fixed Points in Generative Adversarial Networks: From Image-to-Image Translation to Disease Detection and Localization.

Generative adversarial networks (GANs) have ushered in a revolution in image-to-image translation. The development and proliferation of GANs raises an interesting question: can we train a GAN to remove an object, if present, from an image while otherwise preserving the image? Specifically, can a GAN "virtually heal" anyone by turning his medical image, with an unknown health status (diseased or healthy), into a healthy one, so that diseased regions could be revealed by subtracting those two images? Such a task requires a GAN to identify a minimal subset of target pixels for domain translation, an ability that we call fixed-point translation, which no GAN is equipped with yet. Therefore, we propose a new GAN, called Fixed-Point GAN, trained by (1) supervising same-domain translation through a conditional identity loss, and (2) regularizing cross-domain translation through revised adversarial, domain classification, and cycle consistency loss. Based on fixed-point translation, we further derive a novel framework for disease detection and localization using only image-level annotation. Qualitative and quantitative evaluations demonstrate that the proposed method outperforms the state of the art in multi-domain image-to-image translation and that it surpasses predominant weakly-supervised localization methods in both disease detection and localization. Implementation is available at https://github.com/jlianglab/Fixed-Point-GAN.

Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis.

Transfer learning from natural image to medical image has established as one of the most practical paradigms in deep learning for medical image analysis. However, to fit this paradigm, 3D imaging tasks in the most prominent imaging modalities (e.g., CT and MRI) have to be reformulated and solved in 2D, losing rich 3D anatomical information and inevitably compromising the performance. To overcome this limitation, we have built a set of models, called Generic Autodidactic Models, nicknamed Models Genesis, because they are created ex nihilo (with no manual labeling), self-taught (learned by self-supervision), and generic (served as source models for generating application-specific target models). Our extensive experiments demonstrate that our Models Genesis significantly outperform learning from scratch in all five target 3D applications covering both segmentation and classification. More importantly, learning a model from scratch simply in 3D may not necessarily yield performance better than transfer learning from ImageNet in 2D, but our Models Genesis consistently top any 2D approaches including fine-tuning the models pre-trained from ImageNet as well as fine-tuning the 2D versions of our Models Genesis, confirming the importance of 3D anatomical information and significance of our Models Genesis for 3D medical imaging. This performance is attributed to our unified self-supervised learning framework, built on a simple yet powerful observation: the sophisticated yet recurrent anatomy in medical images can serve as strong supervision signals for deep models to learn common anatomical representation automatically via self-supervision. As open science, all pre-trained Models Genesis are available at https://github.com/MrGiovanni/ModelsGenesis.

UNet++: A Nested U-Net Architecture for Medical Image Segmentation.

In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.