Method estimates section thickness and XY anisotropy in ssEM images.
problem Accurate 3D reconstructions require precise section thickness and XY anisotropy estimates.
method Non-parametric Bayesian regression of image statistics.
result Method has lower estimation error compared to existing methods.
Four-dimensional scanning transmission electron microscopy (4D-STEM) of local atomic diffraction patterns is emerging as a powerful technique for probing intricate details of atomic structure and atomic electric fields. However, efficient processing and interpretation of large volumes of data remain challenging, especi…
Scanning Transmission Electron Microscopy (STEM) has become the main stay for materials characterization on atomic level, with applications ranging from visualization of localized and extended defects to mapping order parameter fields. In the last several years, attention was attracted by potential of STEM to explore b…
Improved CG force-field learning from all-atom data.
problem Training accurate coarse-grained models from all-atom simulations is challenging.
method Optimized force mapping to improve statistical efficiency of force-field learning.
result Substantially improved CG force-fields can be learned from the same simulation data.
New algorithm efficiently trains machine learning models to atomic forces data.
problem Efficiently training machine learning models to large amounts of force data.
method Developed an efficient algorithm for training machine learning models to all available force data.
result Training to all available force data is only a few times more expensive than training to energies alone.
We present a variational Bayesian method of joint image reconstruction and point spread function (PSF) estimation when the PSF of the imaging device is only partially known. To solve this semi-blind deconvolution problem, prior distributions are specified for the PSF and the 3D image. Joint image reconstruction and PSF…
AniDS improves molecular force field modeling by learning anisotropic noise.
problem Molecular force field modeling suffers from oversimplified assumptions about atomic motions.
method AniDS introduces anisotropic noise generation for better modeling of directional and structural variability.
result AniDS outperforms existing methods on benchmarks, achieving significant improvements in force prediction accuracy.
Proposes linking energy and force uncertainty in deep learning potentials.
problem Uncertainty in predicted energies and forces in machine learning models.
method Introduces a spatially correlated noise process to link energy and force uncertainty.
result Demonstrates the approach on molecular datasets, linking energy and force uncertainties.
GDML learns effective CG models from all-atom data.
problem Learning effective coarse-grained force fields efficiently.
method Ensemble learning with stratified sampling and GDML.
result GDML yields smaller free energy error than neural networks.
Local minimax analysis for Poisson deconvolution of discrete signals.
problem Estimating a discrete uniform signal from Poisson convolutions.
method Local minimax risk analysis of a broad class of kernels.
result Sharp estimation rates as a function of signal clustering.
Signal processing is rich in inherently continuous and often nonlinear applications, such as spectral estimation, optical imaging, and super-resolution microscopy, in which sparsity plays a key role in obtaining state-of-the-art results. Coping with the infinite dimensionality and non-convexity of these problems typica…
New method uses normalizing flows to improve force fields for coarse-grained molecular dynamics.
problem Lack of reference atomistic forces makes force matching infeasible for MLCG force fields.
method Introduces noise-based kernels adapted to low-data regimes using normalizing flows.
result Flow-based kernels reduce local distortions while preserving global accuracy.
Neural network learns atomic coordinates from Patterson maps in a simplified case.
problem Training a neural network to infer atomic coordinates from Patterson maps.
method Synthetic data training, centering output maps, removing centrosymmetric inversion, and adding empty space.
result The network can generalize to infer atom positions from Patterson maps not in the training set.
A new machine-learned CG model predicts protein structures efficiently.
problem Developing a universal, computationally efficient protein simulation model.
method Combining deep learning with all-atom protein simulations to create a transferable CG force field.
result The model predicts protein structures, intermediates, and fluctuations efficiently.
NucleusDiff models atomic nuclei interactions to prevent separation violations in drug design.
problem Maintaining minimum pairwise distance between atoms to avoid separation violations in drug design.
method Enforces distance constraint between atomic nuclei and manifolds in a diffusion model.
result Reduces separation violations by up to 100.00% and enhances binding affinity by up to 22.16%.
Large GNNs trained with Graph Parallelism improve atomic simulation accuracy.
problem Training memory-intensive GNNs for high-order atomic interactions.
method Graph Parallelism to distribute graphs across GPUs.
result Graph-parallelized models achieve state-of-the-art results on catalyst datasets.
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.
Fluorescence microscopy has enabled a dramatic development in modern biology. Due to its inherently weak signal, fluorescence microscopy is not only much noisier than photography, but also presented with Poisson-Gaussian noise where Poisson noise, or shot noise, is the dominating noise source. To get clean fluorescence…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a drug-like molecule to a given target. These models require expert-level knowled…
Deep learning improves 3D microscopy resolution without matched target images.
problem Anisotropic resolution in volumetric fluorescence microscopy.
method Cycle-consistent generative adversarial network trained on unpaired 2D images.
result Enhanced axial resolution and restored details between imaging planes.
TACE unifies scalar and tensorial modeling in Cartesian space for accurate, stable, and efficient atomistic predictions.
problem Complexity and challenges in equivariant atomistic machine learning models.
method Tensor Atomic Cluster Expansion (TACE) in Cartesian space, decomposing local environments into irreducible Cartesian tensors (ICT).
result Universal invariant and equivariant embeddings, enabling explicit control at inference.
Convolutional neural networks (CNN) have achieved state of the art performance on both classification and segmentation tasks. Applying CNNs to microscopy images is challenging due to the lack of datasets labeled at the single cell level. We extend the application of CNNs to microscopy image classification and segmentat…
Machine learning generates coarse-grained force fields for molecular dynamics.
problem Creating thermodynamically consistent coarse-grained models for larger systems.
method Hybrid architecture using graph neural networks to learn molecular features.
result Framework reproduces thermodynamics for small biomolecular systems.
We discuss recently emerging applications of the state-of-art deep learning methods on optical microscopy and microscopic image reconstruction, which enable new transformations among different modes and modalities of microscopic imaging, driven entirely by image data. We believe that deep learning will fundamentally ch…
BoostMD accelerates molecular dynamics simulations by 8x with ML force fields.
problem Long inference times of ML force fields limit practical use in molecular dynamics.
method BoostMD uses previous time-step features to predict energies and forces, reducing complexity and computational cost.
result BoostMD achieves an 8-fold speedup and accurately samples the Boltzmann distribution.
Paper uses VAEs and GANs to estimate cryo-EM image orientation and camera parameters.
problem Estimating orientation and camera parameters from noisy cryo-EM images.
method Combines VAEs and GANs to learn latent representation, then designs estimation method.
result Geometric approach for fast cryo-EM biomolecule reconstruction.
We propose a solution to the image deconvolution problem where the convolution kernel or point spread function (PSF) is assumed to be only partially known. Small perturbations generated from the model are exploited to produce a few principal components explaining the PSF uncertainty in a high dimensional space. Unlike …
Rapid overlay of chemical structures (ROCS) is a standard tool for the calculation of 3D shape and chemical ("color") similarity. ROCS uses unweighted sums to combine many aspects of similarity, yielding parameter-free models for virtual screening. In this report, we decompose the ROCS color force field into "color com…
Minimum energy paths for transitions such as atomic and/or spin rearrangements in thermalized systems are the transition paths of largest statistical weight. Such paths are frequently calculated using the nudged elastic band method, where an initial path is iteratively shifted to the nearest minimum energy path. The co…
A dataset of 10 molecule types for machine learning studies.
problem Lack of suitable datasets for machine learning in molecular imaging.
method Generated 2D cross-sectional projections of 10 molecule types from Molecular Dynamics trajectories.
result Benchmark dataset for machine learning, deep learning, and image processing in scattering, imaging, and microscopy.
MACE architecture outperforms alternatives in various molecular and materials science tasks.
problem Improving machine learning force fields for diverse molecular and materials science applications.
method Evaluation of MACE architecture on various datasets and tasks, demonstrating data efficiency and excellent performance.
result MACE architecture generally outperforms alternatives across a wide range of systems, including amorphous carbon, universal materials modelling, and organic chemistry.
Machine learning classifies colorectal tissue using photoacoustic microscopy.
problem Traditional diagnostic methods for colorectal cancer are limited in detail and painful.
method Machine learning applied to acoustic resolution photoacoustic microscopy.
result Machine learning accurately classified benign and malignant tissue.
DISPR uses diffusion models to predict 3D cell shapes from 2D images.
problem Predicting 3D cell shapes from 2D microscopy images.
method Diffusion model trained to predict 3D shapes from 2D microscopy images as a prior.
result Adding DISPR predictions to minority cell classes improves classification accuracy.
Deep models store facts in geometric embeddings, not just associative memory.
problem Understanding how deep models store and utilize atomic facts.
method Identified geometric memory, contrasting with associative lookup.
result Geometric memory transforms hard reasoning into easy tasks.
Machine learning speeds up FLIM analysis in biomedical research.
problem Complex, slow, and computationally expensive FLIM analysis.
method Machine learning techniques for faster and smarter FLIM data extraction and interpretation.
result Higher accuracy in classifying and segmenting FLIM images compared to conventional methods.
Deconvolution microscopy has been extensively used to improve the resolution of the widefield fluorescent microscopy. Conventional approaches, which usually require the point spread function (PSF) measurement or blind estimation, are however computationally expensive. Recently, CNN based approaches have been explored a…
Multi-StyleGAN simulates live cell microscopy imagery.
problem Costly and complex live cell experiments.
method Generative adversarial network (GAN) synthesizing multi-domain time-lapse images.
result Captures biophysical factors and time dependencies in cell imagery.
Malaria is a life-threatening disease affecting millions. Microscopy-based assessment of thin blood films is a standard method to (i) determine malaria species and (ii) quantitate high-parasitemia infections. Full automation of malaria microscopy by machine learning (ML) is a challenging task because field-prepared sli…
New method extracts biological concepts from cell microscopy images.
problem Extracting meaningful concepts from vision foundation models trained on cell microscopy images.
method Sparse dictionary learning (DL) combined with PCA whitening pre-processing.
result Successfully retrieved biologically meaningful concepts like cell types and genetic perturbations.
Study improves pollen detection in optical and holographic images using deep learning.
problem Improving pollen detection accuracy in holographic microscopy images.
method Used YOLOv8s for detection and MobileNetV3L for classification, addressing performance gaps through dataset expansion and automated labeling.
result Significant improvement in detection and classification performance on holographic images.
Prototype for adaptive electron microscopy scans reduces dose and time.
problem Reduce electron microscopy scan time and dose with minimal loss.
method Adaptive partial scanning with reinforcement learning.
result Reinforcement learning trained neural network optimizes scan paths.
UDVD uses deep learning to denoise videos without supervision.
problem Lack of clean video data for training deep learning models.
method UDVD is a CNN trained solely on noisy video data, adapting to local motion.
result UDVD performs as well as supervised methods, even with limited training data.
A novel method detects multiple mitosis events and mitigates annotation gaps in phase-contrast microscopy.
problem Detecting multiple mitosis events and handling annotation gaps in closely placed cells.
method Estimating a spatiotemporal likelihood map via 3DCNN to detect multiple mitosis events and mitigate annotation gaps.
result Our method outperformed compared methods in terms of F1-score using a challenging dataset.
Deep learning methods are becoming widely used for restoration of defects associated with fluorescence microscopy imaging. One of the major challenges in application of such methods is the availability of training data. In this work, we propose a unified method for reconstruction of multi-defect fluorescence microscopy…
Improves spline quality and accuracy in computational microscopy.
problem Detecting slender, overlapping structures in microscopy images.
method Differentiable rendering approach for spline refinement.
result Achieves high reliability and sub-pixel accuracy.
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and spatial scales involved in thermodynamic and kinetic phenomena in materials, atomis…
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 104−7 noisy and randomly orien…
Unified theory linking atom-centered and message-passing models for molecular properties.
problem Combining atom-centered and message-passing models for accurate molecular property prediction.
method Generalizing ACDC framework to include multi-centered information, providing a complete linear basis for regression.
result Unified understanding of atom-centered and message-passing models, providing a coherent foundation.