Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the three-dimensional structure of a macromolecule from noisy and randomly orien…
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27 results for “cryo-em”
A new diffusion model improves cryo-EM structure sampling.
problem Gaussian prior in VAE fails to match approximate posterior in cryo-EM data.
method Train a diffusion model as an expressive, learnable prior in cryoDRGN framework.
result Samples accurately follow the data distribution, not the VAE prior.
Method recovers particle orientations from cryo-EM projections.
problem Unknown orientations in cryo-EM images.
method Two-step process: estimating distances and recovering orientations.
result Accurate orientation recovery from noisy projections.
Cryo-electron microscopy (cryo-EM) is capable of producing reconstructed 3D images of biomolecules at near-atomic resolution. As such, it represents one of the most promising imaging techniques in structural biology. However, raw cryo-EM images are only highly corrupted - noisy and band-pass filtered - 2D projections o…
Cryo-EM reconstruction is reformulated as a stochastic inverse problem to handle structural heterogeneity.
problem Handling structural heterogeneity in cryo-EM 3D reconstruction.
method Formulated as a stochastic inverse problem over probability measures, using variational discrepancy and Wasserstein gradient flow.
result Validated approach using synthetic examples, demonstrating recovery of continuous structural distributions.
Sequence-guided protein structure determination using graph convolutional and recurrent networksq-bio.BM
Automated protein structure prediction from cryo-EM data.
problem Challenging to build atomic models from cryo-EM densities without prior structure.
method Uses GCN and LSTM to automate model building from amino acid identities and candidate locations.
result Automated approach reduces time and eliminates human intervention for protein structure determination.
Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural biologists to perform 6D translation-rotation searching, which is extremely comput…
VAEs help in learning latent variables for cryo-EM applications.
problem Learning latent variables for cryo-EM data.
method Used VAEs for latent variable learning, focusing on the encoder's role.
result The encoder of the VAE in cryo-EM applications resembles traditional latent variable representations.
SOLVAR efficiently analyzes cryo-EM data's structural variability.
problem Analyzing continuous heterogeneity in cryo-EM data.
method Low-rank assumption on covariance matrix for tractable estimation.
result Accurately captures dominant components of structural variability.
A method improves Cryo-EM 3D map refinement by regularizing rotation estimation.
problem Noise-robustness vs. data-consistency in Cryo-EM 3D map reconstruction.
method Ellipsoidal support lifting (ESL) for regularizing and approximating the global minimizer over Riemannian manifolds.
result The induced bias due to regularizing effect of ESL estimates better rotations than global optimisation.
A new algorithm for cryo-EM data collection that balances reward and latency.
problem Optimizing data collection in cryo-EM experiments with action delays.
method Latency-aware contextual bandit framework and COAF algorithm.
result The COAF algorithm efficiently maximizes reward over time in cryo-EM experiments.
Single particle reconstruction (SPR) from cryo-electron microscopy (EM) is a technique in which the 3D structure of a molecule needs to be determined from its contrast transfer function (CTF) affected, noisy 2D projection images taken at unknown viewing directions. One of the main challenges in cryo-EM is the typically…
The problem of image restoration in cryo-EM entails correcting for the effects of the Contrast Transfer Function (CTF) and noise. Popular methods for image restoration include `phase flipping', which corrects only for the Fourier phases but not amplitudes, and Wiener filtering, which requires the spectral signal to noi…
Geometric shape matching for recovering protein conformations from single-particle Cryo-EM dataq-bio.BM
Researchers use shape analysis to recover protein structures from Cryo-EM data.
problem Recovering the three-dimensional backbone structure of single polypeptide proteins from noisy tomographic projections.
method Shape analysis and matrix Lie group actions to deform point clouds to match 2D tomography data.
result Optimal deformations are computed to recover the three-dimensional backbone structure of proteins.
Determining the 3D structures of biological molecules is a key problem for both biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising technique for structure estimation which relies heavily on computational methods to reconstruct 3D structures from 2D images. This paper introduces the challenging Cryo-…
Cryo-electron microscopy (cryo-EM) is an emerging experimental method to characterize the structure of large biomolecular assemblies. Single particle cryo-EM records 2D images (so-called micrographs) of projections of the three-dimensional particle, which need to be processed to obtain the three-dimensional reconstruct…
Cryo-em images are found to be low-dimensional.
problem Understanding the geometric structure of cryo-em data.
method Applied manifold learning techniques to CryoSBI representations.
result Cryo-em data inherently populate low-dimensional manifolds.
Motivated by the task of 2-D classification in single particle reconstruction by cryo-electron microscopy (cryo-EM), we consider the problem of heterogeneous multireference alignment of images. In this problem, the goal is to estimate a (typically small) set of target images from a (typically large) collection of obser…
Automatic post-picking using MAPPOS improves particle image detection from Cryo-EM micrographsstat.ML
Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron microscopes automatically acquire thousands of high-quality micrographs. Particles are…
Novel higher-order group synchronization for noisy local measurements on hypergraphs.
problem Synchronizing higher-order local measurements on hyperedges to global estimates on nodes.
method Message passing algorithm for global synchronization of higher-order measurements.
result Higher-order method outperforms standard pairwise synchronization methods in certain applications.
Single-particle electron cryomicroscopy is an essential tool for high-resolution 3D reconstruction of proteins and other biological macromolecules. An important challenge in cryo-EM is the reconstruction of non-rigid molecules with parts that move and deform. Traditional reconstruction methods fail in these cases, resu…
Particle picking is currently a critical step in the cryo-EM single particle reconstruction pipeline. Despite extensive work on this problem, for many data sets it is still challenging, especially for low SNR micrographs. We present the KLT (Karhunen Loeve Transform) picker, which is fully automatic and requires as an …
New findings show sparse signals in MRA model require fewer measurements than previously thought.
problem Learning an unknown signal from repeated noisy images under group actions.
method Enhanced probabilistic method and analysis of uniform uncertainty principles.
result Sparse signals exhibit intermediate sample complexity, improving over traditional .
We develop methods to learn dictionaries invariant under group symmetries, useful in cryo-EM and tracking.
problem Learning dictionaries invariant under group symmetries.
method Representation theory, non-abelian Fourier analysis, matrix orbitopes, alternating minimization.
result Effective dictionary learning for SO(3) symmetries with guarantees.
Data augmentation is a widely used trick when training deep neural networks: in addition to the original data, properly transformed data are also added to the training set. However, to the best of our knowledge, a clear mathematical framework to explain the performance benefits of data augmentation is not available. In…
This work optimizes signal estimation for sparse MRA with collision-free signals.
problem Recovering an unknown signal from repeated observations under cyclic isometries with high noise.
method Investigates minimax optimality for collision-free signals in the MRA model.
result The minimax optimal rate of estimation is \( \sigma^2/\sqrt{n} \) for sparse MRA.
Recent years have witnessed a trend that advanced mathematical tools, such as algebraic topology, differential geometry, graph theory, and partial differential equations, have been developed for describing biological macromolecules. These tools have considerably strengthened our ability to understand the molecular mech…