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Alzheimer's disease (AD), the predominant form of dementia, is a growing global challenge, emphasizing the urgent need for accurate and early diagnosis. Current clinical diagnoses rely on radiologist expert interpretation, which is prone to…

Fully Convolutional Neural Networks (FCNNs) with contracting and expanding paths have shown prominence for the majority of medical image segmentation applications since the past decade. In FCNNs, the encoder plays an integral role by…

Image reconstruction from undersampled k-space data has been playing an important role for fast MRI. Recently, deep learning has demonstrated tremendous success in various fields and also shown potential to significantly speed up MR…

The astounding performance of transformers in natural language processing (NLP) has motivated researchers to explore their applications in computer vision tasks. DEtection TRansformer (DETR) introduces transformers to object detection tasks…

Deep Neural Networks (DNN) have been widely used to carry out segmentation tasks in both electron and light microscopy. Most DNNs developed for this purpose are based on some variation of the encoder-decoder type U-Net architecture, in…

This dissertation is devoted to provide advanced nonconvex nonsmooth variational models of (Magnetic Resonance Image) MRI reconstruction, efficient learnable image reconstruction algorithms and parameter training algorithms that improve the…

Ultra-thin multimode optical fiber imaging promises next-generation medical endoscopes reaching high image resolution for deep tissues. However, current technology suffers from severe optical distortion, as the fiber's calibration is…

3D reconstruction is a longstanding ill-posed problem, which has been explored for decades by the computer vision, computer graphics, and machine learning communities. Since 2015, image-based 3D reconstruction using convolutional neural…

Reconstructing magnetic resonance (MR) images from undersampled data is a challenging problem due to various artifacts introduced by the under-sampling operation. Recent deep learning-based methods for MR image reconstruction usually…

The study of neurodegenerative diseases relies on the reconstruction and analysis of the brain cortex from magnetic resonance imaging (MRI). Traditional frameworks for this task like FreeSurfer demand lengthy runtimes, while its accelerated…

Deep neural networks have been applied to improve the image quality of fluorescence microscopy imaging. Previous methods are based on convolutional neural networks (CNNs) which generally require more time-consuming training of separate…

Recent successes in deep learning have started to impact neuroscience. Of particular significance are claims that current segmentation algorithms achieve "super-human" accuracy in an area known as connectomics. However, as we will show,…

Advances in optical and electrophysiological recording technologies have made it possible to record the dynamics of thousands of neurons, opening up new possibilities for interpreting and controlling large neural populations in behaving…

We describe a class of systems theory based neural networks called "Network Of Recurrent neural networks" (NOR), which introduces a new structure level to RNN related models. In NOR, RNNs are viewed as the high-level neurons and are used to…

Deep learning models have become popular in the analysis of tabular data, as they address the limitations of decision trees and enable valuable applications like semi-supervised learning, online learning, and transfer learning. However,…

Deep-neural-network-based image reconstruction has demonstrated promising performance in medical imaging for under-sampled and low-dose scenarios. However, it requires large amount of memory and extensive time for the training. It is…

Recurrent Neural Networks (RNNs) are a class of machine learning algorithms used for applications with time-series and sequential data. Recently, there has been a strong interest in executing RNNs on embedded devices. However, difficulties…

We present a novel convolutional neural network architecture for photometric stereo (Woodham, 1980), a problem of recovering 3D object surface normals from multiple images observed under varying illuminations. Despite its long history in…

Over the long history of machine learning, which dates back several decades, recurrent neural networks (RNNs) have been used mainly for sequential data and time series and generally with 1D information. Even in some rare studies on 2D…

In this work, we present the Deep Newton Reconstruction Network (DNR-Net), a hybrid data-driven reconstruction technique for emission tomography inspired by Newton's method, a well-known iterative optimization algorithm. The DNR-Net employs…