A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
A deep model learns to infer fluorescence labels from unlabeled microscopy images.
Determining the localization of specific protein in human cells is important for understanding cellular functions and biological processes of underlying diseases. Among imaging techniques, high-throughput fluorescence microscopy imaging is an efficient biotechnology to stain the protein of interest in a cell. In this w…
Histopathology tissue samples are widely available in two states: paraffin-embedded unstained and non-paraffin-embedded stained whole slide RGB images (WSRI). Hematoxylin and eosin stain (H&E) is one of the principal stains in histology but suffers from several shortcomings related to tissue preparation, staining proto…
An important part of Digital Pathology is the analysis of multiple digitised whole slide images from differently stained tissue sections. It is common practice to mount consecutive sections containing corresponding microscopic structures on glass slides, and to stain them differently to highlight specific tissue compon…
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…
Stem uses diffusion models to infer gene expression from H&E images.
Machine learning speeds up FLIM analysis in biomedical research.
Deep learning improves 3D microscopy resolution without matched target images.
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…
Study proposes deep learning techniques to diagnose and differentiate Celiac Disease and Environmental Enteropathy from biopsy images.
We present a new method for design problems wherein the goal is to maximize or specify the value of one or more properties of interest. For example, in protein design, one may wish to find the protein sequence that maximizes fluorescence. We assume access to one or more, potentially black box, stochastic "oracle" predi…
Multi-StyleGAN simulates live cell microscopy imagery.
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…
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…
New method classifies reticulocytes from red blood cells without labels.
Unified method for multi-defect microscopy image restoration with limited training data.
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…
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 …
A new method avoids noise amplification when subtracting or dividing stochastic signals.
Extracting and detecting spike activities from the fluorescence observations is an important step in understanding how neuron systems work. The main challenge lies in that the combination of the ambient noise with dynamic baseline fluctuation, often contaminates the observations, thereby deteriorating the reliability o…
A novel approach for augmenting histopathological images by blending Gaussian-Laplacian pyramids.
Automatization of the diagnosis of any kind of disease is of great importance and it's gaining speed as more and more deep learning solutions are applied to different problems. One of such computer aided systems could be a decision support too able to accurately differentiate between different types of breast cancer hi…
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…
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.
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…
Optimizes tensor completion using geodesics on Segre manifolds.
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 method reduces word embedding storage space by 100x.
This paper proposes synthetic augmentation for nuclei image segmentation in medical pathology.
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 …
Evaluates deep learning models in histopathology for robustness and classification strategies.
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…
Recent studies have shown promising results in using Deep Learning to detect malignancy in whole slide imaging. However, they were limited to just predicting positive or negative finding for a specific neoplasm. We attempted to use Deep Learning with a convolutional neural network algorithm to build a lymphoma diagnost…
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.
Study shows how numerical discretization affects reconstructions and parameter distributions in nano metrology.
Researchers create a simulator to infer worm brain states from calcium imaging data.
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.
Study uses image analysis to predict MSI status in tumors.
Malaria is a serious infectious disease that is responsible for over half million deaths yearly worldwide. The major cause of these mortalities is late or inaccurate diagnosis. Manual microscopy is currently considered as the dominant diagnostic method for malaria. However, it is time consuming and prone to human error…
Unified framework for semi-supervised learning reduces annotation needs.
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…
AI enhances cancer diagnostics using spectroscopy.
CNN-based prostate cancer grading improves accuracy and efficiency.
High-dimensional spectroscopy data makes ML models achieve near-perfect accuracy, even when chemical distinctions are absent.