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.
The detection of critical heat flux (CHF) is crucial in heat boiling applications as failure to do so can cause rapid temperature ramp leading to device failures. Many machine learning models exist ...to detect CHF, but their performance reduces significantly when tested on data from different domains. To deal with datasets from new domains a model needs to be trained from scratch. Moreover, the dataset needs to be annotated by a domain expert. To address this issue, we propose a new framework to support the generalizability and adaptability of trained CHF detection models in an unsupervised manner. This approach uses an unsupervised Image-to-Image (UI2I) translation model to transform images in the target dataset to look like they were obtained from the same domain the model previously trained on. Unlike other frameworks dealing with domain shift, our framework does not require retraining or fine-tuning of the trained classification model nor does it require synthesized datasets in the training process of either the classification model or the UI2I model. The framework was tested on three boiling datasets from different domains, and we show that the CHF detection model trained on one dataset was able to generalize to the other two previously unseen datasets with high accuracy. Overall, the framework enables CHF detection models to adapt to data generated from different domains without requiring additional annotation effort or retraining of the model.
•Unsupervised Framework to generalize critical heat flux detection models.•Pretrained models can classify unlabeled datasets never seen before by the model.•Framework uses FP-GAN to adapt the new data to the model’s domain.•Framework is agonistic to the translation and classification models used.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
There is a growing interest in the application of machine learning (ML) in Alzheimer's disease (AD) research. However, neuropsychiatric symptoms (NPS), frequent in subjects with AD, mild cognitive ...impairment (MCI), and other related dementias have not been analyzed sufficiently using ML methods. To portray the landscape and potential of ML research in AD and NPS studies, we present a comprehensive literature review of existing ML approaches and commonly studied AD biomarkers. We conducted PubMed searches with keywords related to NPS, AD biomarkers, machine learning, and cognition. We included a total of 38 articles in this review after excluding some irrelevant studies from the search results and including 6 articles based on a snowball search from the bibliography of the relevant studies. We found a limited number of studies focused on NPS with or without AD biomarkers. In contrast, multiple statistical machine learning and deep learning methods have been used to build predictive diagnostic models using commonly known AD biomarkers. These mainly included multiple imaging biomarkers, cognitive scores, and various omics biomarkers. Deep learning approaches that combine these biomarkers or multi-modality datasets typically outperform single-modality datasets. We conclude ML may be leveraged to untangle the complex relationships of NPS and AD biomarkers with cognition. This may potentially help to predict the progression of MCI or dementia and develop more targeted early intervention approaches based on NPS.
The ability to classify images is dependent on having access to large labeled datasets and testing on data from the same domain of which the model was trained on. Classification becomes more ...challenging when dealing with new data from a different domain, where gathering and especially labeling a larger image dataset for retraining a classification model requires a labor-intensive human effort. Cross-domain classification frameworks were developed to handle this data domain shift problem by utilizing unsupervised image-to-image translation models to translate an input image from the unlabeled domain to the labeled domain. The problem with these unsupervised models lies in their unsupervised nature. For lack of annotations, it is not possible to use the traditional supervised metrics to evaluate these translation models to pick the best-saved checkpoint model. This paper introduces a new method called Domain-knowledge Inspired Pseudo Supervision (DIPS) which utilizes Gaussian Mixture Models and domain knowledge to generate pseudo annotations to enable the use of traditional supervised metrics. This method was designed specifically to support cross-domain classification applications contrary to other typically used metrics such as the Fréchet Inception Distance (FID) which were designed to evaluate the model in terms of the quality of the generated image from a human-eye perspective. DIPS outperforms state-of-the-art GAN evaluation metrics when selecting the optimal saved checkpoint. Furthermore, DIPS showcases its robustness and interpretability by demonstrating a strong correlation with truly supervised metrics, highlighting its superiority over existing state-of-the-art alternatives The boiling crisis problem has been approached as a case study. The code and data to replicate the results can be found on the official GitHub-repository11https://github.com/Hindawi91/DIPS..
•DIPS utilizes domain knowledge and a GMM model to provide pseudo supervision.•DIPS introduces a metric for evaluating UI2I models in cross-domain classification.•DIPS outperforms SOTA unsupervised metrics such as the FID, KID, IS and MMD.•DIPS correlates highly with true supervision, making it robust and explainable.•DIPS real-world applicability is demonstrated through the boiling crisis problem.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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.
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.
Abstract
Data-driven machine-learning methods on neuroimaging (e.g. MRI) are of great interest for the investigation and classification of neurological diseases. However, traditional machine learning ...requires domain knowledge to delineate the brain regions first, followed by feature extraction from the regions. Compared with this semi-automated approach, recently developed deep learning methods have advantages since they do not require such prior knowledge; instead, deep learning methods can automatically find features that differentiate MRIs from different cohorts. In the present study, we developed a deep learning-based classification pipeline distinguishing brain MRIs of individuals with one of three types of headaches migraine (n = 95), acute post-traumatic headache (n = 48) and persistent post-traumatic headache (n = 49) from those of healthy controls (n = 532) and identified the brain regions that most contributed to each classification task. Our pipeline included: (i) data preprocessing; (ii) binary classification of healthy controls versus headache type using a 3D ResNet-18; and (iii) biomarker extraction from the trained 3D ResNet-18. During the classification at the second step of our pipeline, we resolved two common issues in deep learning methods, limited training data and imbalanced samples from different categories, by incorporating a large public data set and resampling among the headache cohorts. Our method achieved the following classification accuracies when tested on independent test sets: (i) migraine versus healthy controls—75% accuracy, 66.7% sensitivity and 83.3% specificity; (2) acute post-traumatic headache versus healthy controls—75% accuracy, 66.7% sensitivity and 83.3% specificity; and (3) persistent post-traumatic headache versus healthy controls—91.7% accuracy, 100% sensitivity and 83.3% specificity. The most significant biomarkers identified by the classifier for migraine were caudate, caudal anterior cingulate, superior frontal, thalamus and ventral diencephalon. For acute post-traumatic headache, lateral occipital, cuneus, lingual, pericalcarine and superior parietal regions were identified as most significant biomarkers. Finally, for persistent post-traumatic headache, the most significant biomarkers were cerebellum, middle temporal, inferior temporal, inferior parietal and superior parietal. In conclusion, our study shows that the deep learning methods can automatically detect aberrations in the brain regions associated with different headache types. It does not require any human knowledge as input which significantly reduces human effort. It uncovers the great potential of deep learning methods for classification and automatic extraction of brain imaging–based biomarkers for these headache types.
Rahman Siddiquee et al. report a deep learning-based classification method that automatically discovered imaging biomarkers specifically associated with migraine (for example, caudate, caudal anterior cingulate and superior frontal), acute post-traumatic headache (for example, lateral occipital, cuneus and lingual) and persistent post-traumatic headache (for example, cerebellum, middle temporal and inferior temporal).
Graphical Abstract
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Video Abstract
10.1093/brain/fcac311_video1
Video Abstract
fcac311media1
6317920989112
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.
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