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Masked Autoencoders (MAEs) have been shown to be effective in pre-training Vision Transformers (ViTs) for natural and medical image analysis problems. By reconstructing missing pixel/voxel information in visible patches, a ViT encoder can…

Deep neural networks are powerful tools for biomedical image segmentation. These models are often trained with heavy supervision, relying on pairs of images and corresponding voxel-level labels. However, obtaining segmentations of…

Reliably modeling normality and differentiating abnormal appearances from normal cases is a very appealing approach for detecting pathologies in medical images. A plethora of such unsupervised anomaly detection approaches has been made in…

Self-supervised learning has attracted increasing attention as it learns data-driven representation from data without annotations. Vision transformer-based autoencoder (ViT-AE) by He et al. (2021) is a recent self-supervised learning…

Brain tumor segmentation is a challenging problem in medical image analysis. The endpoint is to generate the salient masks that accurately identify brain tumor regions in an fMRI screening. In this paper, we propose a novel attention gate…

The Masked Autoencoder (MAE) has recently demonstrated effectiveness in pre-training Vision Transformers (ViT) for analyzing natural images. By reconstructing complete images from partially masked inputs, the ViT encoder gathers contextual…

Transformer-based methods have demonstrated impressive results in medical image restoration, attributed to the multi-head self-attention (MSA) mechanism in the spatial dimension. However, the majority of existing Transformers conduct…

We propose a novel machine learning strategy for studying neuroanatomical shape variation. Our model works with volumetric binary segmentation images, and requires no pre-processing such as the extraction of surface points or a mesh. The…

Learning meaningful and interpretable representations from high-dimensional volumetric magnetic resonance (MR) images is essential for advancing personalized medicine. While Vision Transformers (ViTs) have shown promise in handling image…

Subjective cognitive decline (SCD) is a preclinical stage of Alzheimer's disease (AD) which occurs even before mild cognitive impairment (MCI). Progressive SCD will convert to MCI with the potential of further evolving to AD. Therefore,…

Deep unsupervised representation learning has recently led to new approaches in the field of Unsupervised Anomaly Detection (UAD) in brain MRI. The main principle behind these works is to learn a model of normal anatomy by learning to…

Integrating domain knowledge into deep learning has emerged as a promising direction for improving model interpretability, generalization, and data efficiency. In this work, we present a novel knowledge-guided ViT-based Masked Autoencoder…

The quality of patient care associated with diagnostic radiology is proportionate to a physician workload. Segmentation is a fundamental limiting precursor to both diagnostic and therapeutic procedures. Advances in machine learning (ML) aim…

Autoencoding, which aims to reconstruct the input images through a bottleneck latent representation, is one of the classic feature representation learning strategies. It has been shown effective as an auxiliary task for semi-supervised…

The application of machine learning algorithms to the diagnosis and analysis of Alzheimer's disease (AD) from multimodal neuroimaging data is a current research hotspot. It remains a formidable challenge to learn brain region information…

The heterogeneity of neurological conditions, ranging from structural anomalies to functional impairments, presents a significant challenge in medical imaging analysis tasks. Moreover, the limited availability of well-annotated datasets…

Recently, self-supervised learning (SSL) methods have been used in pre-training the segmentation models for 2D and 3D medical images. Most of these methods are based on reconstruction, contrastive learning and consistency regularization.…

As Vision Transformers (ViTs) are increasingly adopted in sensitive vision applications, there is a growing demand for improved interpretability. This has led to efforts to forward-align these models with carefully annotated abstract,…

Medical image segmentation is a key task in the imaging workflow, influencing many image-based decisions. Traditional, fully-supervised segmentation models rely on large amounts of labeled training data, typically obtained through manual…

Anomaly detection without priors of the anomalies is challenging. In the field of unsupervised anomaly detection, traditional auto-encoder (AE) tends to fail based on the assumption that by training only on normal images, the model will not…