A new dataset for denoising real fluorescence microscopy images.
problem Noisy real fluorescence microscopy images.
method Constructed a dataset of 12,000 real fluorescence microscopy images with different noise levels.
result Deep learning methods perform best on the denoising of the FMD dataset.
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.
A deep model learns to infer fluorescence labels from unlabeled microscopy images.
problem Challenges in obtaining high quality images of cellular structures due to complex environments and label staining limitations.
method Developed a novel deep model using global pixel transformer layers and dense blocks, incorporating multi-scale input strategy.
result Significantly outperforms state-of-the-art methods in fluorescence image prediction 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.
Super-resolution fluorescence microscopy, with a resolution beyond the diffraction limit of light, has become an indispensable tool to directly visualize biological structures in living cells at a nanometer-scale resolution. Despite advances in high-density super-resolution fluorescent techniques, existing methods stil…
In this paper, we propose a novel application of Generative Adversarial Networks (GAN) to the synthesis of cells imaged by fluorescence microscopy. Compared to natural images, cells tend to have a simpler and more geometric global structure that facilitates image generation. However, the correlation between the spatial…
Unified method for multi-defect microscopy image restoration with limited training data.
problem Challenges in applying deep learning methods due to limited training data for multi-defect microscopy images.
method Two-stage approach: data augmentation with GAN and conditional GAN training.
result Proposed method gives comparable or superior results to existing methods in image quality restoration.
Imaging fluorescent disease biomarkers in tissues and skin is a non-invasive method to screen for health conditions. We report an automated process that combines intraoral fluorescent porphyrin biomarker imaging, clinical examinations and machine learning for correlation of systemic health conditions with periodontal d…
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.
Bayesian method detects neuron spike activities from noisy fluorescence data.
problem Detecting neuron spike activities from noisy fluorescence data.
method Random finite set (RFS) based Bayesian approach.
result Gains 12% extra detection accuracy compared to MLSpike method.
We present a conditional generative model to learn variation in cell and nuclear morphology and the location of subcellular structures from microscopy images. Our model generalizes to a wide range of subcellular localization and allows for a probabilistic interpretation of cell and nuclear morphology and structure loca…
TUNet improves protein classification in cell images.
problem Classifying specific proteins in human cells using microscopy images.
method TUNet model incorporating segmentation maps for improved classification.
result TUNet achieves competitive performance in protein classification.
A fundamental challenge in calcium imaging has been to infer the timing of action potentials from the measured noisy calcium fluorescence traces. We systematically evaluate a range of spike inference algorithms on a large benchmark dataset recorded from varying neural tissue (V1 and retina) using different calcium indi…
Enhances high-throughput imaging of microtubule networks, improving clarity and consistency.
problem Fluorescence noise obscures microtubule structures in high-throughput imaging.
method CycleGAN learning to enhance low-resolution images of microtubule networks.
result CycleGAN effectively identifies microtubules with high accuracy (0.93+ AUC-ROC).
MarmoNet automates analysis of marmoset brain axonal projections.
problem Automatically detect and segment axonal tracer signals in noisy, cluttered images.
method Uses machine learning, specifically CNNs and image registration, to process and map axonal projections.
result Automated pipeline extracts and maps axonal projections robustly.
Researchers create a simulator to infer worm brain states from calcium imaging data.
problem Impute C. elegans membrane potentials from calcium imaging data.
method Developed a stochastic whole-brain simulator and used SMC method for imputation.
result First to infer worm brain states from partial calcium imaging observations.
We present a probabilistic modeling framework and adaptive sampling algorithm wherein unsupervised generative models are combined with black box predictive models to tackle the problem of input design. In input design, one is given one or more stochastic "oracle" predictive functions, each of which maps from the input …
New method optimizes protein design by sampling from realistic inputs.
problem Optimizing properties of interest in design problems, especially with black box predictive models.
method Conditioning by Adaptive Sampling, using model-based adaptive sampling to estimate conditional input distributions.
result Achieves state-of-the-art results on protein fluorescence problem.
Calcium imaging permits optical measurement of neural activity. Since intracellular calcium concentration is an indirect measurement of neural activity, computational tools are necessary to infer the true underlying spiking activity from fluorescence measurements. Bayesian model inversion can be used to solve this prob…
We present a sparse knowledge gradient (SpKG) algorithm for adaptively selecting the targeted regions within a large RNA molecule to identify which regions are most amenable to interactions with other molecules. Experimentally, such regions can be inferred from fluorescence measurements obtained by binding a complement…
New method classifies reticulocytes from red blood cells without labels.
problem Classifying reticulocytes from mature red blood cells without fluorescent labels.
method Unsupervised machine learning on morpho-rheological markers.
result Promising results in classifying reticulocytes from mature red blood cells.
We consider factoring low-rank tensors in the presence of outlying slabs. This problem is important in practice, because data collected in many real-world applications, such as speech, fluorescence, and some social network data, fit this paradigm. Prior work tackles this problem by iteratively selecting a fixed number …
Deep learning improves single-molecule localization for super-resolution microscopy.
problem Accurate and efficient localization of single molecules for super-resolution microscopy.
method A novel deep learning network architecture that uses temporal context to simultaneously detect and localize molecules.
result Achieves state-of-the-art performance on the SMLM2016 challenge, excels at high densities.
A new method avoids noise amplification when subtracting or dividing stochastic signals.
problem Noise amplification when subtracting or dividing stochastic signals.
method Normalizing flows to approximate the distribution of the signal of interest.
result Normalizing flows can generate an approximation of the probability distribution over the signal of interest, avoiding subtraction or division.
We describe a probabilistic PARAFAC/CANDECOMP (CP) factorization for multiway (i.e., tensor) data that incorporates auxiliary covariates, SupCP. SupCP generalizes the supervised singular value decomposition (SupSVD) for vector-valued observations, to allow for observations that have the form of a matrix or higher-order…
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.
Hippocampal dentate granule cells are among the few neuronal cell types generated throughout adult life in mammals. In the normal brain, new granule cells are generated from progenitors in the subgranular zone and integrate in a typical fashion. During the development of epilepsy, granule cell integration is profoundly…
Researchers infer gene activity in dividing cells, accounting for protein inheritance and division history.
problem Inferring protein production kinetics in dividing cells due to protein inheritance and division history.
method Adapted conditional normalizing flows to approximate intractable likelihoods from simulated data.
result Glc3 gene is mostly inactive under stress, with brief and transient expression.
BNNs enhance reservoir computing by acting as generalization filters.
problem Understanding how BNNs integrate with reservoir computing.
method Optogenetics and calcium imaging to record BNNs, reservoir computing framework.
result BNNs improve reservoir computing performance through generalization.
Optimizes tensor completion using geodesics on Segre manifolds.
problem Incomplete tensor data in recommender systems and spectroscopy.
method Riemannian conjugate gradient optimization with explicit geodesic expressions.
result Recovery of tensor decomposition from as little as 10% of data.
This paper presents a novel method for the reconstruction of a neural network connectivity using calcium fluorescence data. We introduce a fast unsupervised method to integrate different networks that reconstructs structural connectivity from neuron activity. Our method improves the state-of-the-art reconstruction meth…
New CNN method improves deconvolution microscopy without PSF measurement.
problem Computational expense and blind estimation in conventional deconvolution microscopy.
method Cycle consistent CNN with explicit PSF modeling layers for blind deconvolution.
result Algorithm robustness and efficacy confirmed through experimental results.
We address the problem of analyzing sets of noisy time-varying signals that all report on the same process but confound straightforward analyses due to complex inter-signal heterogeneities and measurement artifacts. In particular we consider single-molecule experiments which indirectly measure the distinct steps in a b…
LaMBO optimizes biological sequences using autoencoders and Bayesian optimization.
problem Bayesian optimization for drug design is limited by discrete, high-dimensional decision variables.
method Jointly trains denoising autoencoder with a Gaussian process head for gradient-based optimization in latent space.
result LaMBO outperforms genetic optimizers and requires no large pretraining corpus.
Study shows how numerical discretization affects reconstructions and parameter distributions in nano metrology.
problem Impact of numerical discretization on parameter reconstructions and model parameter distributions.
method Bayesian target vector optimization, finite element model, Gaussian process, stochastic machine learning surrogate models, Markov chain Monte Carlo sampler.
result Numerical discretization parameters impact the accuracy and distribution of reconstructed model parameters.
The PARAFAC2 is a multimodal factor analysis model suitable for analyzing multi-way data when one of the modes has incomparable observation units, for example because of differences in signal sampling or batch sizes. A fully probabilistic treatment of the PARAFAC2 is desirable in order to improve robustness to noise an…
Flow cytometry is often used to characterize the malignant cells in leukemia and lymphoma patients, traced to the level of the individual cell. Typically, flow cytometric data analysis is performed through a series of 2-dimensional projections onto the axes of the data set. Through the years, clinicians have determined…
High-dimensional spectroscopy data makes ML models achieve near-perfect accuracy, even when chemical distinctions are absent.
problem Why machine learning models achieve near-perfect accuracy in spectroscopic classification tasks without chemically meaningful features.
method Theoretical analysis grounded in the Feldman-Hajek theorem and concentration of measure, combined with specific experiments on synthetic and real fluorescence spectra.
result Infinitesimal distributional differences in high-dimensional spaces can lead to perfect separability, making models achieve near-perfect accuracy in spectroscopy.
Reactmine infers chemical reactions from time series data, overcoming sparse model limitations.
problem Inferring chemical reaction networks from time series data, especially when initial conditions are not varied.
method Sequential reaction inference in a search tree, ranking and re-optimizing kinetics.
result Reactmine successfully infers preponderant regulations in real datasets, matching model-based analyses.
Improved prediction of soil parameters using Multi-target Stacked Generalisation on EDXRF spectra.
problem Challenges in predicting multiple soil parameters accurately from EDXRF spectra.
method Multi-target Stacked Generalisation (MTSG) method combining multiple regression models.
result MTSG significantly improved prediction accuracy for multiple soil parameters, reducing average error from 0.67 to 0.64.
A new approach to protein language models combines latent space prediction with masked language modeling.
problem Improving protein language models by predicting amino acid identities at masked positions.
method A variant of masked language modeling that predicts latent targets only at masked positions, retaining the MLM cross-entropy.
result The new approach outperforms pure masked language modeling on 11 out of 16 downstream tasks.
We derive generalized estimators for a number of spatial statistics that have been used in the analysis of spatially resolved omics data, such as Ripley's K, H and L functions, clustering index, and degree of clustering, which allow these statistics to be calculated on data modelled by arbitrary random measures (RMs). …
CatSIM measures image similarity robustly to small changes.
problem Measuring similarity between images, especially with small perturbations.
method Uses structural similarity image quality paradigm, robust to small location changes.
result Structural similarity between images rated higher when not entirely overlapping.
Develops statistical guarantees for image-to-image regression models.
problem Current image-to-image regression models lack statistical guarantees for model mistakes and hallucinations.
method Uncertainty quantification techniques with rigorous statistical guarantees for image-to-image regression problems.
result Derives uncertainty intervals around each pixel with formal mathematical guarantees.
The study forecasts water quality from satellite data using machine learning.
problem Predicting future water quality from satellite data for coastal regions.
method Decomposed time series into components and used machine learning models (SARIMA, regression, neural network).
result Regression and neural network models are best at predicting Chl-a, SARIMA model best at FLH and SST.
AugurOne trains single image generators without GANs using image warps.
problem Training end-to-end single image generators without GANs.
method Non-affine augmentations of single input images for training an upscaling neural network.
result End-to-end training yields state-of-the-art performance on conditional generation tasks.
Paper analyzes learning from ghost imaging without reconstruction bottleneck.
problem High-speed cell classification bottleneck in ghost cytometry.
method Theoretical analysis of learning from ghost imaging without reconstruction.
result Theoretical analysis supports learning from ghost imaging without reconstruction.
Total variation denoising improves image quality adaptively.
problem Improving image quality from noisy data.
method Total variation regularization for image denoising.
result Denoised images converge to true images at a parametric rate.