New metric scores perturbations across populations, not cells, improving model comparison.
problem Single-cell perturbation data overlaps, making per-cell accuracy unreliable.
method Average per-cell probability vectors over all cells of a perturbation to form a population profile and rank candidate perturbations.
result Classifier Discrimination Score (CDS) identifies true perturbation more reliably than pseudobulk-based scores.
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.
Method learns cell interaction rules from individual trajectories.
problem Inferring interaction rules from heterogeneous cellular data.
method WSINDy for second order IPSs, learning individual cell models.
result Efficiently identifies different species and best-fit models for each.
High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history and population frequency of the subclonal lineages of tumor cells present in the sample can be reconstructed from…
CLSB models system dynamics from cross-sectional data with population-level regularization.
problem Challenges in modeling system dynamics from limited cross-sectional samples and heterogeneous individual behaviors.
method Introduces CLSB framework for learning dynamics, regularized for population-level temporal variations.
result Empirically superior in single-cell sequencing data analyses, e.g., simulating cell development and drug response.
Model predicts urban population using mobile data traffic.
problem Estimating urban population dynamics from mobile data.
method Data-driven approach combining NetMob 2023 and ENACT datasets.
result NetMob 2023 data can estimate urban population with XGBoost models.
In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While c…
MFM integrates multiple evolving populations using Wasserstein manifold flows.
problem Learning dynamics of multiple interacting populations evolving over time.
method Meta Flow Matching (MFM) integrates vector fields on Wasserstein manifold using amortized flow models and GNN embeddings.
result MFM improves prediction of individual treatment responses on multi-patient single-cell drug screen data.
Flow cytometry is a high-throughput technology used to quantify multiple surface and intracellular markers at the level of a single cell. This enables to identify cell sub-types, and to determine their relative proportions. Improvements of this technology allow to describe millions of individual cells from a blood samp…
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.
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.
We introduce principal differences analysis (PDA) for analyzing differences between high-dimensional distributions. The method operates by finding the projection that maximizes the Wasserstein divergence between the resulting univariate populations. Relying on the Cramer-Wold device, it requires no assumptions about th…
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 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.
Tissue heterogeneity is a major confounding factor in studying individual populations that cannot be resolved directly by global profiling. Experimental solutions to mitigate tissue heterogeneity are expensive, time consuming, inapplicable to existing data, and may alter the original gene expression patterns. Here we a…
Feature selection predicts immune state changes in RA mouse model.
problem Predicting the immune state change after RA immunotherapy.
method Feature selection algorithms applied to mouse CIA model data.
result Selected features predict both T cell markers and treatment efficacy.
Model place cells as spatial embeddings for efficient path planning and cognitive map construction.
problem Encoding spatial navigation in the hippocampus.
method Model place cells using spectral decomposition of multi-step random walk transition kernels, inducing sparsity and adjacency.
result Place cells encode spatial information through non-negativity and inner-product structure, forming a cognitive map.
Hexagon grid patterns emerge from conformal isometry in grid cell neural networks.
problem Understanding the algebraic, geometric, and topological properties of grid cells.
method Investigating recurrent neural network models of grid cells, focusing on Lie group and Lie algebra representations, conformal isometry, and hexagon periodic patterns.
result Conformal isometry leads to hexagon periodic patterns in grid cell responses and accurate path integration.
New method learns population dynamics from snapshots, outperforming existing models.
problem Capturing periodic and other dynamical properties of population dynamics.
method Wasserstein Lagrangian Mechanics (WLM) for learning second-order dynamics from observed marginals.
result WLM outperforms existing methods across various dynamics, including vortex dynamics, embryonic development, and flocking.
OptimalFlow uses optimal transport to handle flow cytometry variability.
problem Flow cytometry variability due to biological and technical causes.
method Combines similarity distance and Wasserstein barycenters to cluster and prototype cytometries.
result Supervised learning on new groups performs better than on whole collection.
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.
Essential to each other, growth and exploration are jointly observed in populations, be it alive such as animals and cells or inanimate such as goods and money. But their ability to move, crucial to cope with uncertainty and optimize returns, is tempered by the space/time properties of the environment. We investigate h…
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.
A new method preserves useful information in data rows with outlying cells.
problem Preserving useful information in data rows with outlying cells.
method Cellwise robust Minimum Covariance Determinant (cellMCD) method using observed likelihood and a penalty term on cellwise outliers.
result The cellMCD method performs well in simulations and on real data.
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.
Bayesian approach for multivariate density regression of complex data.
problem Regression of multivariate density-valued responses on predictors.
method Bayesian inference using sliced Wasserstein barycenter and SW distance.
result Accurate fits and reliable predictions for complex data.
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.
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.
The aim of this paper is to construct a natural Riemann-Lagrange differential geometry on 1-jet spaces, in the sense of nonlinear connections, generalized Cartan connections, d-torsions, d-curvatures, jet electromagnetic fields and jet electromagnetic Yang-Mills energies, starting from some given nonlinear evolution OD…
Improves Gaussian process factor models for multi-population recordings.
problem Cubic runtime scaling with trial length and group number limits application to large-scale recordings.
method Two approximate approaches: inducing variables and frequency domain.
result Achieved orders of magnitude speed-up with minimal statistical performance impact.
The challenge in controlling stochastic systems in which low-probability events can set the system on catastrophic trajectories is to develop a robust ability to respond to such events without significantly compromising the optimality of the baseline control policy. This paper presents CelluDose, a stochastic simulatio…
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…
Improved neural population modeling using shared features and ensemble detection.
problem Missing shared coding properties in neural latent variable models.
method Feature sharing across tuning curves and soft clustering of neurons.
result More interpretable and better-performing neural population models.
USP test improves on Pearson's chi-squared and G-test for independence.
problem Deficiencies in Pearson's chi-squared and G-test for independence. method USP test based on U-statistic estimator of population dependence measure. result USP test controls size, handles small cell counts, and detects minimal violations of independence.
Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the …
Model predicts phytoplankton subpopulations based on environmental factors.
problem Predicting phytoplankton dynamics under changing environmental conditions.
method Sparse mixture of multivariate regressions model.
result Identifies environmental covariates influencing phytoplankton subpopulations.
Study evaluates information leakage in Polymarket markets, finding limited applicability and resolution ambiguity.
problem Limited applicability of ILS-dl framework across Polymarket markets.
method Scaling from single-case to population-scale evaluation using ILS-dl framework.
result Only 0.7% of candidate markets yield computable ILS-dl values, and resolution semantics are the main obstacle.
Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutation…
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.
CAST models time-varying treatment effects in cancer patients.
problem Estimating treatment effects at fixed time points limits understanding of dynamic changes over time.
method CAST combines parametric and non-parametric methods to model continuous time-varying treatment effects.
result CAST reveals how treatment effects rise, peak, and decline over the follow-up period.
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 identifies drift and diffusivity from SDE marginals.
problem Challenging task to identify drift and diffusion from SDE population dynamics.
method Proposes nn-APPEX, a Schrodinger Bridge-based inference method.
result Gradient-flow drift and Brownian diffusivity jointly identifiable from marginals.
Framework detects and classifies multi-label RBC images from microscopic images.
problem Challenges in separating touching or overlapping cells for classification.
method Region proposal model + CNN feature extraction + multi-label prediction networks.
result Framework achieves good performance in automatic cell detection and classification.
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.
Stable random variables are motivated by the central limit theorem for densities with (potentially) unbounded variance and can be thought of as natural generalizations of the Gaussian distribution to skewed and heavy-tailed phenomenon. In this paper, we introduce stable graphical (SG) models, a class of multivariate st…
Robustly infers manifold density and geometry under high-dimensional noise.
problem Inaccurate kernel density estimation under high-dimensional noise.
method Doubly stochastic normalization of Gaussian kernel.
result Robust tools for density estimation, noise magnitude estimation, and distance approximation.
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.
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.