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.
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…
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.
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.
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.
Stem uses diffusion models to infer gene expression from H&E images.
problem Inference of gene expression from H&E stained images is time-consuming and expensive.
method Conditional diffusion generative model to infer gene expression.
result Stem achieves state-of-the-art performance in spatial gene expression prediction.
New algorithm balances spatial data approximation and prediction accuracy.
problem Lack of methods considering spatial correlation and downstream modeling in dimension reduction.
method Formalizes approximation and modeling utility as metrics, proposes a balanced algorithm.
result Optimal trade-off between approximation accuracy and downstream modeling utility.
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.
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.
Sparse neural networks visualize paired transcriptomic and electrophysiological data.
problem Efficiently analyzing and visualizing paired multivariate neuroscientific data.
method Sparse deep neural networks with a two-dimensional bottleneck and group lasso penalty.
result Biologically interpretable two-dimensional visualizations of paired data.
With the advent of deep generative models in computational chemistry, in silico anticancer drug design has undergone an unprecedented transformation. While state-of-the-art deep learning approaches have shown potential in generating compounds with desired chemical properties, they disregard the genetic profile and prop…
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate identification of lncRNAs in RNA-seq datasets is crucial for exploring their char…
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…
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.
Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological observations might be heterogeneous and correspond to different biological mechanisms. Seco…
DET unifies geometric and functional alignment for high-dimensional scientific data.
problem Challenges in nonrigid registration for high-dimensional, irregular data.
method Domain Elastic Transform (DET) treats data as functions on irregular domains, using a Bayesian framework for elastic motion registration.
result DET achieves 92% topological preservation on MERFISH data and successfully registers whole-embryo Stereo-seq atlases.
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…
Constructing gene regulatory networks is a critical step in revealing disease mechanisms from transcriptomic data. In this work, we present NO-BEARS, a novel algorithm for estimating gene regulatory networks. The NO-BEARS algorithm is built on the basis of the NOTEARS algorithm with two improvements. First, we propose …
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.
A new method infers causal gene regulatory networks from parallel CRISPR interventions and transcriptomic data.
problem Learning causal gene regulatory networks from observational data is complicated by lack of identifiability and a combinatorial solution space.
method A continuous optimization framework that leverages observational and interventional data to infer a single causal structure, assuming a linear Structural Equation Model (SEM).
result A provably consistent estimator of the true DAG under mild assumptions.
Proposes a robust similarity measure for sparse time series data.
problem Sparse time course data in biological settings.
method Gaussian processes (GP) similarity measure based on log-likelihood ratio.
result Enhanced robustness to noise compared to Euclidean distance.
New method optimizes clustering with better log-likelihood landscape.
problem Nonconvex log-likelihood optimization in model-based clustering.
method Entropic optimal transport loss for Sinkhorn-EM algorithm.
result New loss function avoids spurious local optima.
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 …
In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a reference genome. The approach uses an RNN to transform kmers of the RNA-seq reads into a 2 dimensional representation that is used to predict abundance of each kmer. We report that our…
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…
Structured Nonparametric Variational Inference for Dependent Latent Modeling
problem Approximating posterior distributions with complex dependencies among latent variables
method Structured Nonparametric Variational Inference (SN-VI)
result Flexible and accurate posterior approximation with arbitrary shapes
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.
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.
New algorithm speeds up large-scale statistical inference.
problem Efficiently solving large-scale mean-field variational inference problems.
method Developed a novel primal-dual algorithm (PD-VI) and a block-preconditioned extension (P2D-VI) for mean-field variational inference. result PD-VI and P2D-VI achieve faster convergence and better solution quality compared to existing methods. Deep learning with Convolutional Neural Networks has shown great promise in various areas of image-based classification and enhancement but is often unsuitable for predictive modeling involving non-image based features or features without spatial correlations. We present a novel approach for representation of high dime…
New algorithm for low-rank optimal transport with improved interpretability and efficiency.
problem Quadratic scaling of optimal transport coupling matrix for massive datasets.
method Factor Relaxation with Latent Coupling (FRLC) algorithm.
result Superior performance on diverse applications including graph clustering and spatial transcriptomics.
Sparse Convex Biclustering improves accuracy and robustness in high-dimensional datasets.
problem Challenges in clustering rows and columns of large-scale datasets due to noise and computational complexity.
method Sparse Convex Biclustering (SpaCoBi) using convex optimization and stability-based tuning.
result Significantly outperforms state-of-the-art methods in accuracy for high-dimensional datasets.
A method selects key genes from tumor transcriptomics data using kernel methods and improves classification performance.
problem Feature selection for tumor classification using gene expression data.
method Multiple Kernel Learning with latent regularization and non-linear dimensionality reduction.
result Improved tumor classification performance on unseen test samples.
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.
Motivation: With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to understanding many biological processes. While state-of-the-art clustering methods have been…
Evaluating, explaining, and visualizing high-level concepts in generative models, such as variational autoencoders (VAEs), is challenging in part due to a lack of known prediction classes that are required to generate saliency maps in supervised learning. While saliency maps may help identify relevant features (e.g., p…
Study repurposes open data to find potential COVID-19 drugs.
problem Developing effective treatments for COVID-19.
method Deep learning network-based approach using large scientific corpus.
result Identified 41 repurposable drugs for COVID-19.
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 …
Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Networks (DNNs) that is capable of simultaneous inference of various properti…
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…
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. Unified framework for variable selection in model-based clustering with missing data.
problem Challenges in identifying relevant variables and handling missing data in model-based clustering.
method Unified framework incorporating a data-driven penalty matrix and a mechanism for missingness modeling.
result Achieves both asymptotic consistency and selection consistency in the presence of missing 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.
GIDS reduces high-dimensional response and predictor spaces, improving interpretability and computational efficiency.
problem Challenges in modeling interactions among high-dimensional multimodal data.
method Graph Independence Dual Screening (GIDS) framework that reduces both response and predictor dimensions.
result GIDS reduces feature space to 9,000 CpGs and 2,000 transcripts, revealing coordinated regulatory mechanisms.
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.
Spatial blind source separation simplifies multivariate spatial prediction.
problem Predicting multivariate measurements at unobserved locations with spatial dependencies.
method Spatial blind source separation as a pre-processing tool compared to Cokriging and neural networks.
result Spatial blind source separation simplifies spatial prediction by avoiding cross-dependencies.
The paper introduces groupoid racks for spatial surfaces.
problem Coloring diagrams of spatial surfaces for invariant calculation.
method Introduces groupoid racks with universal properties.
result Groupoid racks provide an invariant for spatial surfaces.
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.