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.
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.
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.
MSBM extends SB for multi-marginal trajectory inference.
problem Trajectory inference from multiple discrete snapshots.
method Multi-Marginal Schrödinger Bridge Matching (MSBM) using iterative Markovian fitting (IMF).
result MSBM effectively captures complex trajectories and respects intermediate distributions.
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.
Active learning selects optimal measurement times for inferring continuous paths from sparse data.
problem Inferring continuous probability paths from sparse snapshots in high-fidelity domains like single-cell biology.
method Extends active experimentation to the space of measures using Linearized Optimal Transport (LOT) for probabilistic surrogate modeling.
result Empirical results show that the proposed strategy outperforms uncertainty-agnostic baselines.
SnapMMD forecasts cell differentiation outcomes from snapshot data.
problem Forecasting cell differentiation outcomes from limited snapshot data.
method SnapMMD learns dynamics by directly fitting the joint distribution of state measurements and observation time with MMD loss, allowing for unknown and state-dependent volatilities.
result SnapMMD delivers accurate forecasts and an R2-style statistic for diagnosing fit.
New method infers population dynamics from snapshots using path space optimization.
problem Recover dynamics of a population from its temporal marginals.
method Grid-free algorithm using Schrödinger bridges coupled via noisy gradient descent in mean-field limit.
result Global convergence to min-entropy estimator with end-to-end theoretical guarantees.
3MSBM learns smooth trajectories from multiple snapshots.
problem Capturing long-range temporal dependencies in complex systems.
method Lifts dynamics to phase space, generalizes stochastic bridges to multi-marginal conditional problems, learns transport maps preserving intermediate marginals.
result Significantly improves convergence and scalability in capturing complex dynamics.
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…
A new algorithm reconstructs population dynamics from coarse samples.
problem Reconstructing population dynamics from unlabeled samples at coarse time intervals.
method Deep Momentum Multi-Marginal Schrödinger Bridge (DMSB) framework.
result Significantly outperforms baselines in synthetic and real-world 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.
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.
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.
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.
DDD reformulated for sparse matrices, integrating trajectory and snapshot time series data.
problem Efficiently integrate trajectory and snapshot time series data.
method Reformulate DDD to use compact basis functions, reducing parameter scaling.
result Inference of sparse matrices reduces the number of parameters in DDD.
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.
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.
A neural network improves DOA estimation from a single snapshot.
problem Estimating DOAs from a single snapshot with limited aperture.
method Deep learning architecture trained to generate high-resolution spatial spectrum.
result Our (SP)2-Net outperforms classical methods. Physics-informed methods infer spatial dynamics from static snapshots, but limits exist.
problem Inferring spatial dynamics from static molecular patterns.
method Combining flexible representations with mechanistic constraints, analyzing structural identifiability, and adapting physics-informed schemes.
result Static spatial patterns can identify spatially varying dynamics, but limits exist due to modeling choices.
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.
Unified framework for discrete diffusion modeling with flexible noising processes.
problem Efficient modeling of large discrete state spaces with arbitrary corruption dynamics.
method Generalized Discrete Diffusion from Snapshots (GDDS) framework that supports uniformization for fast noising and snapshot-based ELBO for reverse process.
result GDDS outperforms existing discrete diffusion methods in training efficiency and generation quality.
Direction of arrival (DOA) estimation is a classical problem in signal processing with many practical applications. Its research has recently been advanced owing to the development of methods based on sparse signal reconstruction. While these methods have shown advantages over conventional ones, there are still difficu…
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 neural network, IHT-Net, improves DOA estimation with sparse arrays.
problem Single-snapshot DOA estimation with sparse arrays in dynamic settings.
method IHT-inspired neural network with recurrent neural network and autoencoders.
result IHT-Net achieves faster convergence and higher accuracy in DOA estimation.
New method identifies SDE drift and diffusion from temporal data.
problem Learning SDE parameters from temporal data, especially in noisy or incomplete data.
method Entropy-regularized optimal transport, APPEX algorithm.
result Can almost always recover drift and diffusion from temporal marginals.
Bayesian method predicts future network configurations from past snapshots.
problem Reconstructing evolving networks from partial observations.
method Bayesian approach using past network snapshots to inform future predictions.
result Method accurately predicts link probabilities and network structure.
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…
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.
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…
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.
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 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.
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.
Recently a variety of LSTM-based conditional language models (LM) have been applied across a range of language generation tasks. In this work we study various model architectures and different ways to represent and aggregate the source information in an end-to-end neural dialogue system framework. A method called snaps…
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…
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.
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.
We study the inference of a model of dynamic networks in which both communities and links keep memory of previous network states. By considering maximum likelihood inference from single snapshot observations of the network, we show that link persistence makes the inference of communities harder, decreasing the detectab…
TURB-Rot provides a large database of turbulent rotating flow snapshots for research.
problem Lack of large-scale, high-resolution datasets for turbulent rotating flows.
method Direct Numerical Simulations of Navier-Stokes equations with rotation.
result Provides a diverse set of 300K complex images and fields for testing.
Study characterizes spike deconvolution basin for noisy data.
problem Recover spike locations from noisy convolution with PSF across multiple snapshots.
method Variable-projection formulation, explicit basin of convexity characterization, local convergence guarantees.
result Consistent estimator within basin of convexity under stochastic noise, complementary error bound under adversarial noise.
New algorithm optimizes matrix reordering for noisy disordered matrices.
problem Optimizing matrix reordering for noisy disordered matrices in single-cell biology and metagenomics.
method Proposed a polynomial-time adaptive sorting algorithm to improve upon spectral seriation.
result Our algorithm achieves superior performance compared to existing methods in real datasets.
Paper improves DOA estimation in sparse arrays using Siamese neural networks.
problem Challenges in DOA estimation with limited snapshots in sparse linear arrays.
method Introduces a Siamese neural network with a sparse augmentation layer for enhanced signal feature embedding.
result Demonstrates improved DOA estimation accuracy in sparse arrays.
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.