Algorithm discovers dynamic cell structures for better neural network performance.
problem Finding optimal neural network architectures for diverse data samples and time steps.
method Combines recurrent and recursive neural networks to dynamically search for customized cell structures.
result Achieves better prediction accuracy compared to existing models.
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.
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.
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.
Dynamic cell-free networks reduce complexity in serving many devices with distributed APs and DRL.
problem Designing efficient cell-free networks with many devices and APs.
method Dynamic architecture, SIC, DAS, DRL for optimization.
result DRL significantly improves performance in dynamic cell-free networks.
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.
Prototype controls stochastic drug resistance in cells.
problem Emergence of drug-resistant cells from random mutations.
method Deep reinforcement learning for adaptive drug dosing.
result 100% success rate in suppressing cell proliferation.
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.
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.
Chaos in cerebellar cells enhances complexity of neural patterns.
problem Understanding how cerebellar granular layer represents complex information.
method Constructed a model of cerebellar granular layer with gap junctions, evaluated using reservoir computing.
result Chaotic dynamics in the cerebellar granular layer produce complex and diverse output patterns.
Mathematical model describes how red blood cells return to equilibrium.
problem How red blood cells regain equilibrium after deformation.
method Gradient flow of the Canham-Helfrich functional, proving global existence and convergence for spheres and axisymmetric tori.
result Global existence and convergence of smooth solutions for spheres and axisymmetric tori under specific energy conditions.
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 …
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.
In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked …
Multi-StyleGAN simulates live cell microscopy imagery.
problem Costly and complex live cell experiments.
method Generative adversarial network (GAN) synthesizing multi-domain time-lapse images.
result Captures biophysical factors and time dependencies in cell imagery.
Introduces σ-Cell for improved financial volatility forecasting.
problem Improving volatility forecasting in financial markets.
method Combines GARCH and deep learning, incorporating stochastic layers and time-varying parameters.
result Demonstrates superior forecasting accuracy compared to traditional models.
Tree complex linked to polyhedral shapes like associahedra and cyclohedra.
problem Understanding the structure of mapping class groups and complex dynamics.
method Characterizing associahedra and cyclohedra using planar tree embeddings and barycentric subdivision.
result Tree complex is a barycentric subdivision of a polyhedral cell complex made of associahedra and cyclohedra.
Latent variable models have been widely applied for the analysis of time series resulting from experimental neuroscience techniques. In these datasets, observations are relatively smooth and possibly nonlinear. We present Variational Inference for Nonlinear Dynamics (VIND), a variational inference framework that is abl…
TrajectoryNet models dynamic cellular trajectories using optimal transport.
problem Modeling continuous and non-linear paths in dynamic processes.
method Continuous normalizing flows linked to dynamic optimal transport.
result TrajectoryNet improves interpolation of cellular distributions.
Multi-cell cooperative processing with limited backhaul traffic is studied for cellular uplinks. Aiming at reduced backhaul overhead, a sparsity-regularized multi-cell receive-filter design problem is formulated. Both unstructured distributed cooperation as well as clustered cooperation, in which base station groups ar…
A new method for state estimation on complex networks.
problem Reconstructing latent dynamics from multivariate time-series on topological cell complexes.
method Topology-aware state space framework derived from stochastic partial differential equations, with state evolution following heat-like topological diffusion.
result The proposed method successfully recovers latent states and topological structures in real-world networks.
This paper explores non-periodic folding of Spidron units, revealing nonlinear dynamics.
problem Understanding the kinematics and nonlinear phenomena of Spidron units.
method Analysis of single unit cell kinematics and recursive construction of multiple cells.
result Non-periodic folding restricts isotropic folding as the number of unit cells increases.
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.
Enhances forecasting of complex systems using FKMD.
problem Forecasting high-dimensional dynamical systems with unknown features.
method Featurized Koopman Mode Decomposition (FKMD) using delay embedding and learned Mahalanobis distance.
result Improves prediction accuracy for various complex systems.
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.
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.
A novel circuit motif uses sister cells for inference with correlated priors.
problem Structured priors in neural systems pose architectural challenges.
method Proposes a novel circuit motif using sister cells to implement correlated priors without direct interactions.
result Demonstrates the efficacy of correlated priors for inference in noisy environments.
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.
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.
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.
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.
We introduce two tools, dynamical thickening and flow selectors, to overcome the infamous discontinuity of the gradient flow endpoint map near non-degenerate critical points. More precisely, we interpret the stable fibrations of certain Conley pairs (N,L), established in [2,3], as a dynamical thickening of the stable…
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.
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the activation of special proteins called transcription factors (TFs). Due to the difficult …
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.
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.
Matching cells over time has long been the most difficult step in cell tracking. In this paper, we approach this problem by recasting it as a classification problem. We construct a feature set for each cell, and compute a feature difference vector between a cell in the current frame and a cell in a previous frame. Then…
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.
The study identifies all possible vector field structures on specific 2D shapes.
problem Optimal discrete gradient vector fields on surfaces with 1-2 critical cells.
method Analysis of discrete vector fields on 2D shapes with minimal critical cells.
result All possible structures of discrete Morse functions on specified shapes.
In the present work we introduce a stochastic cellular automata model in order to simulate the dynamics of the stock market. A direct percolation method is used to create a hierarchy of clusters of active traders on a two dimensional grid. Active traders are characterised by the decision to buy, (+1), or sell, (-1), a …
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.
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.
Proposes CXNs for neural network computations on cell complexes.
problem Performing neural network computations on complex topological spaces.
method Introduces a message passing scheme and a unified encoder-decoder framework for cell complexes.
result Generalizes message passing to cell complexes and provides a cell2vec representation.
Time series analysis is used to understand and predict dynamic processes, including evolving demands in business, weather, markets, and biological rhythms. Exponential smoothing is used in all these domains to obtain simple interpretable models of time series and to forecast future values. Despite its popularity, expon…
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.
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.