Kernel testing compares cell states in single-cell data.
problem Comparing non-linear cell states in single-cell data.
method Kernel-based testing framework for non-linear distribution comparison.
result Identifies subtle population variations in cell states.
This study reviews and evaluates clustering methods for single-cell RNA-seq data.
problem Identifying and characterizing novel cell types from single-cell RNA-seq data.
method Review and performance comparison of clustering methods.
result Performance comparison experiments on two datasets.
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 new parallel clustering method improves speed and accuracy for single cell transcriptomic data.
problem Challenges in clustering single cell transcriptomic data, including poor quality, lack of prior knowledge, and slow computation.
method Parallel Split Merge Sampling on Dirichlet Process Mixture Model (Para-DPMM).
result The Para-DPMM model outperforms existing methods in clustering quality and computational speed.
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.
ChemCPA predicts cellular responses to novel drugs using transfer learning.
problem Scaling high-throughput screens to measure cellular responses for many drugs is costly and challenging.
method ChemCPA, a new encoder-decoder architecture combined with transfer learning.
result Training on existing bulk RNA HTS datasets improves generalization performance, reducing the need for extensive single-cell screens.
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.
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…
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.
A model to fill in missing gene data from spatial studies and scRNA-seq.
problem Imputing missing gene expression measurements from spatial transcriptomics.
method A deep generative model (gimVI) for integrating spatial transcriptomic and scRNA-seq data.
result gimVI outperforms existing methods in imputing missing 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.
Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across thousands or millions of individual cells in parallel. This new type of data has …
TransST improves spatial transcriptomics data analysis by identifying cell clusters and biomarkers.
problem Low resolution and insufficient sequencing depth in spatial transcriptomics data.
method Transfer learning framework to adaptively leverage external cell-labeled information.
result TransST successfully identifies five biologically meaningful cell clusters and separates adipose tissues from connective issues.
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.
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.
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.
Study of SK-N-AS cells' response to methamidophos using transcriptomics.
problem Understanding the transcriptional response of SK-N-AS cells to methamidophos exposure.
method Combination of statistical and machine learning methods for anomaly detection and causal network inference.
result Identification of key processes and transcripts involved in the response to methamidophos.
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.
Generative model tailors anticancer drugs based on transcriptomic data.
problem Designing effective anticancer drugs considering genetic profiles.
method RL framework using pretrained VAEs to generate compounds conditioned on transcriptomic data.
result Generative model produces molecules with high predicted inhibitory effects.
PerturBench benchmarks ML models for cellular perturbation analysis.
problem Standardizing benchmarking in modeling single cell transcriptomic responses to perturbations.
method Modular platform, diverse datasets, metrics, extensive evaluation, rank metrics.
result Simpler models are competitive and scale well with larger datasets.
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-sets are characteristically large, and previously modelling frameworks …
Generative Distribution Embeddings learn multiscale representations of distributions.
problem Learning representations of entire distributions for multiscale reasoning.
method Introducing GDE framework that lifts autoencoders to the space of distributions, using conditional generative models and distributional invariance.
result GDEs learn predictive sufficient statistics embedded in Wasserstein space, recovering distances and trajectories for Gaussian and Gaussian mixture distributions.
This study benchmarks transcriptomics models for perturbation analysis, finding scVI and PCA superior.
problem Limited evaluation of transcriptomics foundation models for perturbation analysis.
method Developed a novel evaluation framework using diverse public datasets from different sequencing techniques and cell lines.
result scVI and PCA identified as superior models for understanding biological perturbations.
A new method improves data representation for diverse tasks.
problem Learning meaningful representations for tasks like batch correction and counterfactual inference.
method Contrastive Mixture of Posteriors (CoMP) method using misalignment penalties.
result CoMP achieves state-of-the-art performance on challenging tasks.
A method uses autoencoders to align multi-modal neuron data.
problem Inconsistent cell type definitions across different data modalities.
method Coupled training of autoencoders for cross-modal alignment.
result Representations learned by coupled autoencoders can identify single-modality sampled cell types.
Large datasets represented by multidimensional data point clouds often possess non-trivial distributions with branching trajectories and excluded regions, with the recent single-cell transcriptomic studies of developing embryo being notable examples. Reducing the complexity and producing compact and interpretable repre…
STARK improves denoising of low-depth spatial transcriptomics images.
problem Denoising spatial transcriptomics images at ultra-low sequencing depths.
method Adaptive regularization with kernel ridge regression and graph Laplacian.
result STARK optimizes denoising performance over competing methods.
A new method matches measures across different spaces using cost-regularized optimal transport.
problem Matching measures in different spaces without aligned data.
method Cost-regularized optimal transport formulation to match measures across two Euclidean spaces.
result Demonstrated applicability to single-cell spatial transcriptomics/multiomics matching tasks.
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient sharing of research material through community databases have opened up new view…
A new method uncovers discrete and continuous factors in gene expression data.
problem Jointly identifying discrete and continuous factors of variability without supervision.
method cpl-mixVAE framework using multiple interacting networks.
result The method successfully uncovers discrete and continuous factors in gene expression data.
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.
Cluster LOCO: A model-agnostic feature importance score for interpreting cluster outputs
problem Interpreting and auditing cluster outputs
method Cluster LOCO (Leave-One-Covariate-Out)
result More reliably recovers informative features than existing methods
The study compares different scRNA sequencing methods using a high-dimensional dataset.
problem To identify unique characteristics of different scRNA sequencing methods.
method Quantitative comparison through clustering analysis of a high-dimensional dataset.
result Identifies unique characteristics associated with different scRNA sequencing methods.
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.
HSSE framework embeds single-cell RNA-seq data at multiple scales.
problem Capturing heterogeneous local structure in single-cell RNA-seq data.
method Hierarchical sheaf spectral embedding (HSSE) framework.
result HSSE achieves competitive or improved performance in single-cell RNA-seq data representation learning.
A model learns causal graphs from summary statistics of synthetic data.
problem Causal discovery algorithms are brittle with large sets of variables and limited data.
method A supervised model trained on synthetic data predicts causal graphs from summary statistics.
result The model generalizes well beyond its training set and runs on large graphs.
New model generates realistic single-cell gene expression data.
problem Generating realistic single-cell gene expression profiles is challenging.
method scLDM, a latent diffusion model using Diffusion Transformers and linear interpolants.
result Superior performance in generating realistic single-cell gene expression data.
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.
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.
Proposes BGNN for tumor heterogeneity prediction using graph neural networks.
problem Tumor classification limitations and heterogeneity assessment challenges.
method Artificial data generation, tumor heterogeneity estimation, and BGNN model development.
result BGNN achieves 89.67% accuracy in predicting tumor heterogeneity. 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…
Single-cell gene expression data provide invaluable resources for systematic characterization of cellular hierarchy in multi-cellular organisms. However, cell lineage reconstruction is still often associated with significant uncertainty due to technological constraints. Such uncertainties have not been taken into accou…
New method learns cell trajectories from multiple snapshots.
problem Inferring cell trajectories from limited, single-time-point data.
method Multi-marginal Schrödinger Bridges with iterative reference refinement.
result Effective in capturing long-term dependencies and learning from multiple time points.
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.
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.
Efficiently infers gene regulatory networks from spatial data.
problem Inferring spatially-varying gene regulatory networks.
method Proposed an efficient optimization problem for SV-GMRFs.
result Solves large-scale SV-GMRF problems in minutes.
PCA++ improves robustness to background noise in contrastive learning.
problem Recovering shared signal subspaces from positive pairs in high-dimensional data with structured background noise.
method PCA++ uses hard uniformity-constrained contrastive learning to enforce identity covariance on projected features.
result PCA++ outperforms standard PCA and alignment-only PCA+ in simulations and real-world datasets.
Wavelets model complex interactions in spatial transcriptomics.
problem Capturing higher-order relationships in spatial transcriptomics data.
method Hypergraph diffusion wavelets for representing hyperedges.
result Wavelets effectively represent disease-relevant cellular niches in Alzheimer's disease.