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Lossy compression has become an important technique to reduce data size in many domains. This type of compression is especially valuable for large-scale scientific data, whose size ranges up to several petabytes. Although Autoencoder-based…
Supervised Deep-Learning (DL)-based reconstruction algorithms have shown state-of-the-art results for highly-undersampled dynamic Magnetic Resonance Imaging (MRI) reconstruction. However, the requirement of excessive high-quality…
Deep neural networks have achieved strong performance in image classification tasks due to their ability to learn complex patterns from high-dimensional data. However, their large computational and memory requirements often limit deployment…
Recently Implicit Neural Representations (INRs) gained attention as a novel and effective representation for various data types. Thus far, prior work mostly focused on optimizing their reconstruction performance. This work investigates INRs…
Recently deep learning-based methods have been applied in image compression and achieved many promising results. In this paper, we propose an improved hybrid layered image compression framework by combining deep learning and the traditional…
In the field of medical image compression, Implicit Neural Representation (INR) networks have shown remarkable versatility due to their flexible compression ratios, yet they are constrained by a one-to-one fitting approach that results in…
Functional Magnetic Resonance Imaging (fMRI) data is a widely used kind of four-dimensional biomedical data, which requires effective compression. However, fMRI compressing poses unique challenges due to its intricate temporal dynamics, low…
This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron…
Cryo-electron microscopy (cryo-EM), the subject of the 2017 Nobel Prize in Chemistry, is a technology for determining the 3-D structure of macromolecules from many noisy 2-D projections of instances of these macromolecules, whose…
Cellular Electron Cryotomography (CryoET) offers the ability to look inside cells and observe macromolecules frozen in action. A primary challenge for this technique is identifying and extracting the molecular components within the crowded…
There has been much interest in deploying deep learning algorithms on low-powered devices, including smartphones, drones, and medical sensors. However, full-scale deep neural networks are often too resource-intensive in terms of energy and…
We present a geometry-aware method for heterogeneous single-particle cryogenic electron microscopy (cryo-EM) reconstruction that predicts atomic backbone conformations. To incorporate protein-structure priors, we represent the backbone as a…
Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
Differentiating signals from the background in micrographs is a critical initial step for cryogenic electron microscopy (cryo-EM), yet it remains laborious due to low signal-to-noise ratio (SNR), the presence of contaminants and densely…
Critical aspects of computational imaging systems, such as experimental design and image priors, can be optimized through deep networks formed by the unrolled iterations of classical model-based reconstructions (termed physics-based…
Cryogenic electron microscopy (cryo-EM) has transformed structural biology by allowing to reconstruct 3D biomolecular structures up to near-atomic resolution. However, the 3D reconstruction process remains challenging, as the 3D structures…
Many imaging modalities involve reconstruction of unknown objects from collections of noisy projections related by random rotations. In one of these modalities, cryogenic electron microscopy (cryo-EM), the extremely low signal-to-noise…
Recent breakthroughs in high-resolution imaging of biomolecules in solution with cryo-electron microscopy (cryo-EM) have unlocked new doors for the reconstruction of molecular volumes, thereby promising further advances in biology,…
Protein function is inherently linked to its localization within the cell, and fluorescent microscopy data is an indispensable resource for learning representations of proteins. Despite major developments in molecular representation…