Single-cell RNA sequencing (scRNA-seq) is a fast growing approach to measure the genome-wide transcriptome of many individual cells in parallel, but results in noisy data with many dropout events. Existing methods to learn molecular signatures from bulk transcriptomic data may therefore not be adapted to scRNA-seq data…
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32 results for “scRNA-seq”
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.
SimCD simultaneously clusters cells and identifies differential gene expression in scRNA-seq data.
problem Separate clustering and differential expression analysis for scRNA-seq data leads to suboptimal results.
method Develops SimCD, a unified hierarchical gamma-negative binomial model for simultaneous cell clustering and differential expression analysis.
result SimCD outperforms existing methods in discovering cell clusters and capturing dynamic expression changes.
New hypergraph method improves scRNA-seq clustering.
problem Loss of higher-order information and overestimation in coexpression networks.
method Conceptualizing scRNA-seq data as hypergraphs and proposing novel clustering methods.
result Proposed methods outperform existing methods on simulated and real datasets.
Spatial studies of transcriptome provide biologists with gene expression maps of heterogeneous and complex tissues. However, most experimental protocols for spatial transcriptomics suffer from the need to select beforehand a small fraction of genes to be quantified over the entire transcriptome. Standard single-cell RN…
DIMM-SC: A Dirichlet mixture model for clustering droplet-based single cell transcriptomic datastat.ML
Motivation: Single cell transcriptome sequencing (scRNA-Seq) has become a revolutionary tool to study cellular and molecular processes at single cell resolution. Among existing technologies, the recently developed droplet-based platform enables efficient parallel processing of thousands of single cells with direct coun…
A Large-Scale Comparative Analysis of Imputation Methods for Single-Cell RNA Sequencing Dataq-bio.GN
A comprehensive benchmark of 15 scRNA-seq imputation methods across various datasets and analyses.
problem Imputation of single-cell RNA sequencing data to recover latent transcriptional signals.
method Evaluation of 15 imputation methods across 30 datasets and 6 downstream analyses.
result Traditional methods generally outperform DL-based methods in scRNA-seq data analysis.
Linear classifiers in product space forms improve scRNA-seq data classification.
problem Linear classification in products of Euclidean, spherical, and hyperbolic spaces.
method Novel formulations of linear classifiers on Riemannian manifolds, proving expressive power, and formalizing perceptron and SVM classifiers.
result Linear classifiers in product space forms have the same expressive power as in Euclidean space of the same dimension.
Robust Bayesian Tensor Factorization with Zero-Inflated Poisson Model and Consensus Aggregationstat.ML
Paper introduces ZIPTF and C-ZIPTF for better tensor factorization of zero-inflated count data.
problem Inefficient tensor factorization for zero-inflated count data, especially in scRNA-seq.
method Zero Inflated Poisson Tensor Factorization (ZIPTF) and Consensus Zero Inflated Poisson Tensor Factorization (C-ZIPTF).
result ZIPTF and C-ZIPTF improve tensor factorization accuracy and consistency for zero-inflated count data.
New metrics improve scRNA-seq perturbation modeling by reducing mode collapse.
problem Outperformed by simple mean prediction in scRNA-seq perturbation modeling.
method Introduce DEG-aware metrics (WMSE, ) and negative/positive baselines.
result WMSE loss function reduces mode collapse and improves model performance.
Scalable GPLVM reduces complexity in scRNA-seq data, accounting for technical and biological confounders.
problem Complexity and confounders in scRNA-seq data hamper interpretation.
method Extended Gaussian process latent variable model (GPLVM) to handle large datasets.
result Framework reconstructs latent signatures and captures disease-specific gene expression.
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.
VampPrior Mixture Model improves clustering in DLVMs.
problem Simplicity of standard priors in DLVMs leads to poor clustering performance.
method Leverages VampPrior concepts to fit a Bayesian GMM prior in a VAE.
result VMM achieves highly competitive clustering performance on benchmark datasets.
New methods improve analysis of single cell RNA sequencing data.
problem High dimensionality and complexity of scRNA-seq data.
method Topological Nonnegative Matrix Factorization (TNMF) and Robust Topological NMF (rTNMF).
result TNMF and rTNMF significantly outperform other NMF-based methods.
Generative Intervention Models predict perturbation effects without knowing the underlying mechanisms.
problem Predicting perturbation effects when the mechanisms are unknown.
method Generative Intervention Models (GIM) that map perturbation features to distributions over atomic interventions in a causal model.
result GIMs achieve robust out-of-distribution predictions and infer underlying perturbation mechanisms.
Proposes CCCVAE for better single-cell clustering with cell-cell communication.
problem Improving single-cell RNA sequencing clustering by incorporating cell-cell communication.
method Integrates cell-cell communication into a variational autoencoder framework.
result Empirical results show CCCVAE outperforms standard VAEs in clustering performance.
Flow Matching for Count Datastat.ML
Flow Matching for count data improves sample quality and efficiency.
problem Mapping between count distributions across batches or time points in high-dimensional count data.
method count-FM, a flow-matching framework based on a continuous-time birth-death process with local unit jumps.
result count-FM achieves better sample quality than representative baselines while using fewer parameters.
Approximating mutual information of high-dimensional variables using learned representationsq-bio.QM
LMI approximates mutual information in high dimensions using learned low-dimensional representations.
problem Estimating mutual information between high-dimensional variables is challenging due to sample size limitations.
method Developed a method called latent MI (LMI) approximation that applies a nonparametric MI estimator to low-dimensional representations learned by a simple model architecture.
result LMI can approximate MI well for variables with >10^3 dimensions if their dependence structure has low intrinsic dimensionality.
Graph Attention Networks predict disease state from single-cell data.
problem Predicting disease state from single-cell data.
method Graph Attention Networks (GAT) for learning from both features and graph structures.
result Achieved 92% accuracy in predicting MS from single-cell data.
Parameterizing the approximate posterior of a generative model with neural networks has become a common theme in recent machine learning research. While providing appealing flexibility, this approach makes it difficult to impose or assess structural constraints such as conditional independence. We propose a framework f…
DiSC detects feature clusters that differentiate between conditions.
problem Identifying subsets of features that differentiate between two conditions.
method Construct feature graphs, compute connectivity differences using spectral clustering.
result DiSC uncovers features that better differentiate between conditions.
Tree-SNE combines t-SNE and hierarchical clustering for data visualization.
problem Data visualization and clustering in complex datasets.
method Stacked one-dimensional t-SNE embeddings and alpha-clustering.
result Effective hierarchical clustering and visualization of various datasets.
Harmonic Alignmentcs.LG
We propose a novel framework for combining datasets via alignment of their intrinsic geometry. This alignment can be used to fuse data originating from disparate modalities, or to correct batch effects while preserving intrinsic data structure. Importantly, we do not assume any pointwise correspondence between datasets…
TrajectoryNet models dynamic cellular trajectories using optimal transport.
problem Modeling continuous and non-linear paths in dynamic processes.
method Continuous normalizing flows linked to dynamic optimal transport.
result TrajectoryNet improves interpolation of cellular distributions.
CT-OT Flow estimates continuous-time dynamics from discrete snapshots.
problem Estimating continuous-time dynamics from temporally aggregated snapshots with noisy or uncertain timestamps.
method Two-stage framework: aligning neighboring intervals via partial optimal transport (POT) and reconstructing a continuous-time distribution through temporal kernel smoothing.
result Reduces distributional and trajectory errors compared with existing methods across synthetic and real datasets.
DEN creates interpretable visualizations using Siamese networks.
problem Creating interpretable visualizations of complex datasets.
method Differentiating Embedding Networks (DEN) using Siamese neural networks and loss functions.
result DEN outperforms existing techniques on FashionMNIST and interpretable features are identified.
ContrastiveVI+ models CRISPR screens with noisy guide efficiency.
problem Noisy guide efficiency in CRISPR screens.
method Generative modeling framework that disentangles perturbation-induced from shared variations.
result ContrastiveVI+ better recovers perturbation-induced variations and identifies cells without edits.
A method for fast estimation of Wasserstein distances using sliced Wasserstein distances.
problem Efficiently computing Wasserstein distances for multiple pairs of distributions.
method Regression on sliced Wasserstein distances to predict true Wasserstein distances.
result The proposed method provides a better approximation of Wasserstein distance than state-of-the-art models, especially in low-data regimes.
New method learns complex cell networks from millions of cells.
problem Existing methods fail to scale to large datasets.
method Multi-axis Gaussian graphical models.
result Method scales to millions of cells in minutes.
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.
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.
New method handles correlated genes for better genomic prediction.
problem Technical issues with highly correlated genes in prediction models.
method Grouping algorithm that treats correlated genes as a group and uses their common patterns.
result Significantly outperforms standard models in prediction and feature selection.