Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of individual neurons and to categorize neurons based on their gene expression profil…
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48 results for “cell types”
Forest Fire Clustering discovers cell types from single-cell data.
problem Discovering cell types from large-scale single-cell sequencing data.
method Iterative label propagation and parallelized Monte Carlo simulation.
result Forest Fire Clustering outperforms state-of-the-art methods on diverse benchmarks.
New model identifies cell-specific genes for cancer prognosis.
problem No statistical model to integrate multiscale cancer data.
method Bayesian generalized promotion time cure models (GPTCMs).
result Improves cancer prognosis by identifying cell-specific genes.
MarkerMap selects key genes for cell type analysis in single-cell RNA-seq.
problem Selecting informative genes from large single-cell RNA-seq datasets is challenging and computationally intensive.
method MarkerMap is a generative model that identifies minimal gene sets explaining cell type variability.
result MarkerMap outperforms existing methods in both supervised and unsupervised marker selection.
New model clusters cells and individuals, revealing genetic influences on cell types.
problem Clustering nested data with group-level and observation-level variables.
method Nested Atoms Model (NAM), Bayesian nonparametric approach.
result Identifies clusters of genetically similar individuals with homogeneous cell-type profiles.
Understanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A second approach is to use machine learning to discriminate cell types based on th…
Cell detection and cell type classification from biomedical images play an important role for high-throughput imaging and various clinical application. While classification of single cell sample can be performed with standard computer vision and machine learning methods, analysis of multi-label samples (region containi…
New system constructs cell-type taxonomy across multiple samples.
problem Challenges in matching clusters from different datasets.
method Combines Optimal Transport with Relaxed Marginal Constraints (OT-RMC) for simultaneous alignment of clusters across multiple samples.
result Highly accurate annotation of cell types and sample-level feature extraction.
Review of Single-cell RNA-seq Data Clustering for Cell Type Identification and Characterizationq-bio.GN
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become the central component to identify and characterize novel cell types and gene exp…
We present a Bayesian hierarchical multi-view mixture model termed Symphony that simultaneously learns clusters of cells representing cell types and their underlying gene regulatory networks by integrating data from two views: single-cell gene expression data and paired epigenetic data, which is informative of gene-gen…
We develop a latent variable model and an efficient spectral algorithm motivated by the recent emergence of very large data sets of chromatin marks from multiple human cell types. A natural model for chromatin data in one cell type is a Hidden Markov Model (HMM); we model the relationship between multiple cell types by…
Few-shot cell segmentation from diverse sources to target domain.
problem Efficient cell segmentation from limited annotated images.
method Meta-learning combining cross-domain tasks and invariant representation.
result Promising results from 1-10-shot learning on public databases.
Improved GPLVM model for single-cell RNA-seq data.
problem Lack of effective scalable models for clustering cell types in large-scale single-cell RNA-seq data.
method Introduces amortized stochastic variational Bayesian GPLVM (BGPLVM) tailored for single-cell RNA-seq.
result Matches the performance of scVI on synthetic and real-world datasets and reveals more interpretable latent structures.
Advances combinatorial complexes for better modeling of hierarchical and set-type relations.
problem Lack of effective modeling for complex hierarchical and set-type relations in high-dimensional data.
method Introduces combinatorial complexes as a bridge between cell complexes and hypergraphs, emphasizing their different types of relations.
result Combining set-type and hierarchical relations in a single model can be advantageous in learning tasks.
Random walks on cell complexes link to Laplacians and Novikov-Shubin invariants.
problem Computing Novikov-Shubin invariants for complex cell structures.
method Construct random walks on cell complexes, relate to Laplacians, and use return probabilities.
result Novikov-Shubin invariants can be recovered from random walk return probabilities.
We focus on the problem of unsupervised cell outlier detection and repair in mixed-type tabular data. Traditional methods are concerned only with detecting which rows in the dataset are outliers. However, identifying which cells are corrupted in a specific row is an important problem in practice, and the very first ste…
TIMELY improves consistency in labeling blood cell images.
problem Inconsistent labeling of blood cells in microscopy images leads to unreliable diagnoses.
method TIMELY combines pseudotime inference and hidden Markov trees to correct labeling mistakes.
result TIMELY outperforms baseline methods in identifying and correcting inconsistent labels.
A Deep Autoencoder System for Differentiation of Cancer Types Based on DNA Methylation Stateq-bio.QM
A Deep Autoencoder based content retrieval algorithm is proposed for prediction and differentiation of cancer types based on the presence of epigenetic patterns of DNA methylation identified in genetic regions known as CpG islands. The developed deep learning system uses a CpG island state classification sub-system to …
Establishing criteria for top cell inertness in complexes.
problem Criteria for top cell inertness in Poincaré duality complexes.
method Algebraic intersection theory, homotopy fibrations, surgery, homogeneous spaces.
result Established various criteria for top cell inertness.
There are time series that are amenable to recurrent neural network (RNN) solutions when treated as sequences, but some series, e.g. asynchronous time series, provide a richer variation of feature types than current RNN cells take into account. In order to address such situations, we introduce a unified RNN that handle…
Proposes CXNs for neural network computations on cell complexes.
problem Performing neural network computations on complex topological spaces.
method Introduces a message passing scheme and a unified encoder-decoder framework for cell complexes.
result Generalizes message passing to cell complexes and provides a cell2vec representation.
scICML integrates multi-omics data from single cells using co-clustering.
problem High noise and sparsity in multi-omics data from single cells.
method Information-theoretic co-clustering-based multi-view learning.
result Improves clustering performance and provides biological insights.
Elastic co-clustering improves clustering of single-cell genomic data.
problem Improving clustering performance of single-cell genomic datasets.
method Elastic coupled co-clustering in an unsupervised transfer learning framework.
result Our algorithm significantly improves clustering performance over traditional methods.
Quantization on even-dimensional compact manifolds using cell decomposition.
problem Quantization of compact even-dimensional manifolds.
method Cell decomposition and embedding in CP^d, inducing local Poisson structure and star product.
result Achieved Berezin-type quantization on compact even-dimensional manifolds.
Recent developments in high throughput profiling of individual neurons have spurred data driven exploration of the idea that there exist natural groupings of neurons referred to as cell types. The promise of this idea is that the immense complexity of brain circuits can be reduced, and effectively studied by means of i…
Deep learning identifies transcriptomic patterns and cell types associated with SARS-CoV-2 infection and COVID-19 severity.
problem Understanding how SARS-CoV-2 varies in infecting and causing severe COVID-19.
method Developed a new approach to generating self-supervised edge features, using Graph Attention Networks (GAT) and Set Transformer.
result Achieved state-of-the-art performance in predicting disease state of individual cells using single-cell RNA sequencing data.
JojoSCL improves scRNA-seq clustering by reducing intra-cluster dispersion.
problem High dimensionality and sparsity of scRNA-seq data challenge clustering models.
method Integrates shrinkage estimator and contrastive learning for improved clustering.
result JojoSCL outperforms existing methods on ten scRNA-seq datasets.
New method improves clustering accuracy in noisy single-cell data.
problem Challenges in clustering single-cell RNA sequencing data due to noise and variability.
method Latent plug-and-play diffusion framework with input-space steering.
result Improved clustering accuracy on synthetic and real-world single-cell data.
In this paper we present the Ricci curvature on cell-complexes and show the Gauss-Bonnnet type theorem on graphs and 2-complex that decomposes closed surface. The defferential forms on a cell complex is defined as linear maps on chain complex, and Laplacian operates this defferential forms. Then we construct the Bochne…
Short proofs for complex Tverberg theorems using prime powers.
problem Proving Tverberg-type theorems for cell complexes.
method Short proofs using prime powers and continuous maps.
result Pairwise disjoint faces of a complex intersect under continuous maps.
Improved LSTM cell for high-frequency trading forecasts.
problem Precise stock price forecasting with minimal lags.
method Revised long short-term memory (LSTM) cell with optimal gate/state selection.
result Lower forecasting error compared to other recurrent neural networks.
New methods detect continuous variation in single-cell data.
problem Continuous variation within and between cell types not detected by discrete analyses.
method Three topologically motivated mathematical methods for unsupervised feature selection.
result Detect additional biologically meaningful genes with coherent expression patterns.
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…
With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical investigations. In the study, we will be using the dataset collected by the authors of Sys…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. Here, we suggest a set of …
The paper improves Fisher-Pitman tests for Poisson mixtures, detecting autism-related genes.
problem Detecting differentially expressed genes between autism and control subjects.
method Nonparametric Poisson mixtures and Fisher-Pitman permutation tests.
result The tests reveal genes missed by common methods, demonstrating rate optimality.
Cellina uses supervised disentanglement to predict cell behavior in tissues.
problem Querying counterfactuals on tissue graphs
method Cellina framework using supervised disentanglement
result Outperforms spatially-informed and non-spatial competitors
NESS improves neighbor embedding for smooth cell-state transitions in single-cell data.
problem Challenges in extracting smooth, low-dimensional representations from noisy single-cell data.
method Builds on PCS framework to develop NESS, a stable machine learning approach.
result NESS consistently yields useful biological insights across diverse single-cell datasets.
IH-GAN models cellular structures accurately and improves structural performance.
problem Optimizing variable-density cellular structures with multiscale design challenges.
method Conditional deep generative model (IH-GAN) for property-to-geometry mapping using implicit function parameterization.
result Generates unit cells with high accuracy and improves structural performance.
We propose a new deep learning approach for medical imaging that copes with the problem of a small training set, the main bottleneck of deep learning, and apply it for classification of healthy and cancer cells acquired by quantitative phase imaging. The proposed method, called transferring of pre-trained generative ad…
Donor-aware scRNA-seq benchmarks improve classification accuracy in inflammatory bowel disease.
problem Influenza disease classification from scRNA-seq data is prone to donor-level confounding.
method Developed and evaluated three feature representations across two IBD cohorts.
result Compartment-stratified CLR composition and GatedStructuralCFN embeddings outperform linear models in classification accuracy.
Modeling curvature-sensitive cells in visual cortex with geometric structures.
problem Understanding the functional architecture of curvature-sensitive cells in the visual cortex.
method Geometric model based on Engel structure and SIM(2) symmetry.
result Identified SIM(2) as the natural symmetry group for curvature-sensitive cells.
Using Apple Machine Learning Algorithms to Detect and Subclassify Non-Small Cell Lung Cancerq-bio.QM
Lung cancer continues to be a major healthcare challenge with high morbidity and mortality rates among both men and women worldwide. The majority of lung cancer cases are of non-small cell lung cancer type. With the advent of targeted cancer therapy, it is imperative not only to properly diagnose but also sub-classify …
SMAI framework tests and integrates single-cell data alignability.
problem Lack of a rigorous statistical test for alignability and distortion during alignment.
method Spectral manifold alignment and inference (SMAI) framework.
result SMAI outperforms existing methods in alignability testing and integration.
Counting and classifying blood cells is an important diagnostic tool in medicine. Support Vector Machines are increasingly popular and efficient and could replace artificial neural network systems. Here a method to classify blood cells is proposed using SVM. A set of statistics on images are implemented in C++. The MPE…
LSTMs and GRUs are the most common recurrent neural network architectures used to solve temporal sequence problems. The two architectures have differing data flows dealing with a common component called the cell state (also referred to as the memory). We attempt to enhance the memory by presenting a modification that w…
Bayesian approach for multivariate density regression of complex data.
problem Regression of multivariate density-valued responses on predictors.
method Bayesian inference using sliced Wasserstein barycenter and SW distance.
result Accurate fits and reliable predictions for complex data.
GraphDINO learns neuronal morphologies from unlabeled data.
problem Unsupervised learning of neuronal morphologies from unlabeled data.
method Transformer-based approach with novel attention mechanism and data augmentation.
result GraphDINO yields morphological clusterings on par with expert classification.