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Dimensionality reduction represents a crucial step in extracting meaningful insights from Molecular Dynamics (MD) simulations. Conventional approaches, including linear methods such as principal component analysis as well as various…
Cryo-electron tomography (cryo-ET) provides direct 3D visualization of macromolecules inside the cell, enabling analysis of their in situ morphology. This morphology can be regarded as an SE(3)-invariant, denoised volumetric representation…
We systematically study various network Expectation-Maximization (EM) algorithms for the Gaussian mixture model within the framework of decentralized federated learning. Our theoretical investigation reveals that directly extending the…
The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…
Advances on cryo-electron imaging technologies have led to a rapidly increasing number of density maps. Alignment and comparison of density maps play a crucial role in interpreting structural information, such as conformational…
Although freeform devices with complex internal structures promise drastic increases in performance, the discreteness of the set of available materials presents challenges for gradient-based optimization necessary for the efficient…
This paper studies the problem of estimating physical properties (system identification) through visual observations. To facilitate geometry-aware guidance in physical property estimation, we introduce a novel hybrid framework that…
Background: Single-particle cryo-electron microscopy (cryo-EM) has become a popular tool for structural determination of biological macromolecular complexes. High-resolution cryo-EM reconstruction often requires hundreds of thousands of…
In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our…
Developing world models that understand complex physical interactions is essential for advancing robotic planning and simulation.However, existing methods often struggle to accurately model the environment under conditions of data scarcity…
In this work we introduce an Autoencoder for molecular conformations. Our proposed model converts the discrete spatial arrangements of atoms in a given molecular graph (conformation) into and from a continuous fixed-sized latent…
Recovering physical properties of objects in motion is a core task across scientific and industrial applications. When the relative motion between the object and the sensing apparatus provides sufficient angular coverage, Computerized…
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…
This paper develops a Bayesian graphical model for fusing disparate types of count data. The motivating application is the study of bacterial communities from diverse high dimensional features, in this case transcripts, collected from…
Cryogenic electron microscopy (Cryo-EM) has become an essential tool for capturing high-resolution biological structures. Despite its advantage in visualizations, the large storage size of Cryo-EM data file poses significant challenges for…
In cryo-electron microscopy (cryo-EM), a microscope generates a top view of a sample of randomly-oriented copies of a molecule. The problem of single particle reconstruction (SPR) from cryo-EM is to use the resulting set of noisy 2D…
Transmission electron microscopy (TEM) is a potent technique for the determination of three-dimensional atomic scale structure of samples in structural biology and materials science. In structural biology, three-dimensional structures of…
We revisit the topic of common lines between projection images in single particle cryo-electron microscopy (cryo-EM). We derive a novel low-rank constraint on a certain $2n \times n$ matrix storing properly-scaled basis vectors for the…
A common task in cryo-electron microscopy (cryo-EM) data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps that exploits common…
Cryo-EM is a vital technique for determining 3D structure of biological molecules such as proteins and viruses. The cryo-EM reconstruction problem is challenging due to the high noise levels, the missing poses of particles, and the…