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Integrating physics models within machine learning models holds considerable promise toward learning robust models with improved interpretability and abilities to extrapolate. In this work, we focus on the integration of incomplete physics…

Energy-based models (EBMs) have recently been successful in representing complex distributions of small images. However, sampling from them requires expensive Markov chain Monte Carlo (MCMC) iterations that mix slowly in high dimensional…

Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships…

In collider-based particle and nuclear physics experiments, data are produced at such extreme rates that only a subset can be recorded for later analysis. Typically, algorithms select individual collision events for preservation and store…

Scanning transmission electron microscopy (STEM) has advanced rapidly in the last decade thanks to the ability to correct the major aberrations of the probe forming lens. Now atomic-sized beams are routine, even at accelerating voltages as…

This study investigates the use of non-linear unsupervised dimensionality reduction techniques to compress a music dataset into a low-dimensional representation which can be used in turn for the synthesis of new sounds. We systematically…

Variational autoencoders (VAEs), that are built upon deep neural networks have emerged as popular generative models in computer vision. Most of the work towards improving variational autoencoders has focused mainly on making the…

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…

Optimal computations under uncertainty require an adequate probabilistic representation about beliefs. Deep generative models, and specifically Variational Autoencoders (VAEs), have the potential to meet this demand by building latent…

Current deep learning-based manifold learning algorithms such as the variational autoencoder (VAE) require fully sampled data to learn the probability density of real-world datasets. Once learned, the density can be used for a variety of…

Different tasks in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM) require enhancing the quality of the highly noisy raw images. To this end, we develop an efficient algorithm for signal enhancement of…

The design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to…

Cryo-electron tomography (cryoET) is a technique that captures images of biological samples at different tilts, preserving their native state as much as possible. Along with the partial tilt series and noise, one of the major challenges in…

Although the variational autoencoder (VAE) and its conditional extension (CVAE) are capable of state-of-the-art results across multiple domains, their precise behavior is still not fully understood, particularly in the context of data (like…

Developing effective representations of protein structures is essential for advancing protein science, particularly for protein generative modeling. Current approaches often grapple with the complexities of the SE(3) manifold, rely on…

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…

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…

Electrospray ion beam deposition (ESIBD) is the intact, chemically selective deposition of molecular ions on surfaces in vacuum. Here, we present a general method and dedicated instrumentation for ESIBD-based cryoEM sample preparation of…

Cryo-electron microscopy (cryo-EM) has recently emerged as a powerful tool for obtaining three-dimensional (3D) structures of biological macromolecules in native states. A minimum cryo-EM image data set for deriving a meaningful…

Microscopy techniques generate vast amounts of complex image data that in principle can be used to discover simpler, interpretable, and parsimonious forms to reveal the underlying physical structures, such as elementary building blocks in…