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Motivation: Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and…
An electrocardiogram (ECG) is vital for identifying cardiac diseases, offering crucial insights for diagnosing heart conditions and informing potentially life-saving treatments. However, like other types of medical data, ECGs are subject to…
The computational intensity of detector simulation and event reconstruction poses a significant difficulty for data analysis in collider experiments. This challenge inspires the continued development of machine learning techniques to serve…
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…
Accurate single cell detection in brightfield microscopy is crucial for biological research, yet data scarcity and annotation bottlenecks limit the progress of deep learning methods. We investigate the use of unconditional models to…
Cellular Electron Cryo-Tomography (CECT) is a powerful 3D imaging tool for studying the native structure and organization of macromolecules inside single cells. For systematic recognition and recovery of macromolecular structures captured…
We introduce OneDiffusion, a versatile, large-scale diffusion model that seamlessly supports bidirectional image synthesis and understanding across diverse tasks. It enables conditional generation from inputs such as text, depth, pose,…
Three-dimensional electron diffraction (3DED) is a powerful technique providing for crystal structure solutions of sub-micron sized crystals too small for structure determination via X-ray techniques. The entry requirement, however, of a…
The traditional techniques for extracting polycrystalline grain structures from microscopy images, such as transmission electron microscopy (TEM) and scanning electron microscopy (SEM), are labour-intensive, subjective, and time-consuming,…
The growing role of data-driven approaches to scientific discovery has unveiled a large class of models that involve latent transformations with a rigid algebraic constraint. Three-dimensional molecule reconstruction in Cryo-Electron…
Simulation-based inference provides a powerful framework for cryo-electron microscopy, employing neural networks in methods like CryoSBI to infer biomolecular conformations via learned latent representations. This latent space represents a…
High-fidelity electron microscopy simulations required for quantitative crystal structure refinements face a fundamental challenge: while physical interactions are well-described theoretically, real-world experimental effects are…
Constructing atomic models from cryo-electron microscopy (cryo-EM) maps is a crucial yet intricate task in structural biology. While advancements in deep learning, such as convolutional neural networks (CNNs) and graph neural networks…
Particle picking is a crucial first step in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM). Selecting particles from the micrographs is difficult especially for small particles with low contrast. As…
Three-dimensional electron diffraction (3D ED) has emerged as a powerful method for solving the structures of sub-micron-sized particles down to nanoparticles. However, it faces technical challenges when applied to beam-sensitive samples or…
Cardiovascular disease (CVD) is a leading cause of mortality worldwide. Electrocardiograms (ECGs) are the most widely used non-invasive tool for cardiac assessment, yet large, well-annotated ECG corpora are scarce due to cost, privacy, and…
Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here, we developed a refinement protocol based on Gaussian mixture models that integrates particle…
In this paper we study the formal algebraic structure underlying the intrinsic classification algorithm, recently introduced by Hadani, Shkolnisky, Singer and Zhao, for classifying noisy projection images of similar viewing directions in…
In single-particle cryo-electron microscopy (cryo-EM), the efficient determination of orientation parameters for 2D projection images poses a significant challenge yet is crucial for reconstructing 3D structures. This task is complicated by…
Cryo-electron microscopy (cryo-EM) has emerged as a powerful technique for resolving the three-dimensional structures of macromolecules. A key challenge in cryo-EM is characterizing continuous heterogeneity, where molecules adopt a…