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.
The paper develops methods for causal inference from single-cell RNA sequencing data with multiple outcomes.
problem Causal inference from single-cell RNA sequencing data with multiple heterogeneous outcomes.
method Generic semiparametric inference framework for doubly robust estimation with multiple derived outcomes.
result Demonstrates the use of semiparametric inferential results for estimating causal effects in genomics.
GENOT matches cells across data modalities using neural OT solvers.
problem Scalability, privacy, and out-of-sample estimation issues in traditional OT solvers.
method Learn stochastic maps, parameterize OT maps, relax mass conservation, integrate quadratic solvers.
result Demonstrates significant potential for enhancing therapeutic strategies.
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.
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.
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.
Paper develops statistical tests for covariance matrix regression on manifold.
problem Regression with random covariance matrices in Fréchet space.
method Develops Wasserstein F-tests for Bures-Wasserstein manifold.
result Asymptotic null distribution and power of the test.
The paper proposes a method to infer differentiation trees from RNA velocity data.
problem Reconstructing dynamic cellular processes from sequencing data.
method Defining varifold distances between RNA velocity curves to approximate shortest-path distances in a tree.
result The varifold distance method approximates the shortest-path distance in a tree isomorphic to the target differentiation tree.
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.
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…
PolyILR: A Tree-Structured Orthonormal Decomposition of Compositional Data
problem Representing compositional data with hierarchical structure
method PolyILR: A canonical orthonormal decomposition of the Aitchison tangent space aligned with any tree topology
result PolyILR yields stable, interpretable features and enables inference at multiscale tree resolution
Federated learning improves bioinformatics by sharing data legally.
problem Lack of access to diverse data in bioinformatics.
method Combines data from multiple institutions legally.
result Federated learning accelerates clinical discovery and robust exploration.
Paper proposes dp-VAE for preserving spatial context in gene expression data.
problem Inaccessibility of spatial context in single-cell gene expression data.
method Generic representation learning and transfer learning framework with a distance-preserving regularizer.
result dp-VAE effectively reconstructs and imputes spatial context from gene expression data.
BasisVAE combines VAE and clustering for tabular data analysis.
problem Lack of insights in tabular high-dimensional data analysis.
method Combines VAE with probabilistic clustering prior for joint dimensionality reduction and clustering.
result Learned one-hot basis function representation for translation-invariant features.
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…
GAGA learns a warped metric for geometry-aware data generation and interpolation.
problem Challenges in generating data with meaningful geometry in high-dimensional datasets.
method Combines manifold learning with generative modeling to learn a warped Riemannian metric.
result GAGA improves trajectory inference by 30% in single-cell population-level data.
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…
Random small feature subsets outperform FS in diverse datasets.
problem The significance of selected features in high-dimensional datasets is questionable.
method Analysis of 28 diverse datasets (microarray, RNA-Seq, etc.).
result Any arbitrary set of features performs as well as or better than selected features across datasets.
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.
GROOVE learns representations for weakly paired multimodal data.
problem Learning representations for high-content perturbation data with weakly paired samples.
method GroupCLIP contrastive loss integrated with an autoencoder framework.
result GROOVE performs on par with or outperforms existing approaches for cross-modal tasks.
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.
ECV method optimizes ensemble parameters for randomized ensembles.
problem Efficient tuning of ensemble parameters in randomized ensembles.
method ECV (Extrapolated Cross-Validation) method for tuning ensemble and subsample sizes.
result ECV yields δ-optimal ensembles for squared prediction risk.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various lea…
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.
BanditPAM clusters data faster than traditional methods.
problem Efficiently clustering large datasets with arbitrary distance metrics.
method Inspired by multi-armed bandits, reduces PAM complexity from O(n2) to O(nlogn). result Matches state-of-the-art clustering loss with up to 4x faster results and 200x fewer distance computations.
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.
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.
Kernel method embeds noisy datasets, capturing shared structures.
problem Limited power in capturing nonlinear structures, noisiness, high-dimensionality, and interpretability issues.
method Kernel spectral joint embeddings using duo-landmark integral operators.
result Consistent recovery of low-dimensional noiseless signals and convergence to eigenfunctions of integral operators.
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.
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.
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…
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.
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.
EB-PCA reduces noise in high-dimensional PCA by estimating a joint prior distribution.
problem High-dimensional PCA noise in samples comparable to or larger than data.
method Empirical Bayes PCA using Kiefer-Wolfowitz MLE, random matrix theory, and AMP algorithm.
result EB-PCA achieves Bayes-optimal accuracy in spiked models and significantly improves over PCA in simulations and real data.
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.
Tutorial on using neural networks for single cell data analysis.
problem Handling large sequencing datasets efficiently.
method Single cell variational inference using variational auto-encoder.
result Model learns data distribution for insights.
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…
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 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.
Paper uses genome Markov structure for outlier detection and read classification.
problem Identifying outliers and classifying reads in genome databases.
method Applying second-order Markov models to triplet base distributions.
result Improved accuracy in outlier identification and read classification.
sgdGMF efficiently estimates generalized matrix factorization models for single-cell RNA sequencing data.
problem Challenges in dimensionality reduction for large single-cell RNA sequencing datasets.
method Scalable adaptive stochastic gradient descent algorithm for generalized matrix factorization models.
result sgdGMF outperforms existing methods in scalability and accuracy for large datasets.
Single-cell RNA sequencing (scRNA-seq) has revolutionized biological discovery, providing an unbiased picture of cellular heterogeneity in tissues. While scRNA-seq has been used extensively to provide insight into both healthy systems and diseases, it has not been used for disease prediction or diagnostics. Graph Atten…
New method learns cell trajectories and network interactions from single-cell data.
problem Network inference in systems biology from steady-state data.
method Min-entropy estimation for stochastic dynamics, leveraging both temporal and perturbational data.
result Jointly learns cellular trajectories and network interactions.
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design architectures to suit it. As such, architectures that fit the structure of genomics should …
Estimates unknown population sizes using the hypergeometric distribution.
problem Estimating discrete distributions with unknown population sizes and category sizes.
method Proposes a novel solution using the hypergeometric likelihood, accounting for a data generating process with a latent variable.
result Empirically demonstrates superior performance in estimating population sizes and learning latent spaces compared to other methods.
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.
TNDE quantifies dynamic gene drivers from single-cell snapshots.
problem Reconstructing time-resolved regulatory effects in biological processes.
method Time-varying Network Driver Estimation (TNDE) using shared graph attention encoder and partial optimal transport.
result TNDE identifies stage-specific driver genes in mouse erythropoiesis.
Genomic models learn DNA sequences to predict functions.
problem Understanding complex genetic interactions.
method Training LLMs on DNA sequences to predict functions.
result gLMs can predict functions of DNA elements.