arXiv:2605. 00545v2 Announce Type: replace-cross Abstract: Inferring cellular trajectories from destructive snapshots is complicated by the challenges of stochasticity and non-conservative mass dynamics such as cell proliferation and apoptosis.
arXiv:2606. 11286v1 Announce Type: cross Abstract: High-content imaging assays quantify cellular responses to chemical and genetic perturbations, yet continuous trajectories of individual cells are unobservable because cells are chemically fixed at acquisition.
The paper introduces SUDO, a simulation‑free framework for unbalanced dynamic optimal transport (UDOT) that supports general convex growth penalties beyond the quadratic Wasserstein‑Fisher‑Rao case. By showing that concave penalties lead to degenerate solutions, the authors focus on convex penalties, learning conditional paths and transport costs to solve a semi‑coupling problem and then applying unbalanced flow matching. On benchmark datasets, SUDO matches the accuracy of analytical WFR solvers while being faster than simulation‑based methods, and it also handles asymmetric penalties that better reflect proliferation‑dominant biological priors.
CRNDiff is a new count‑native diffusion framework that uses stochastic chemical reaction networks to model nonnegative integer data such as single‑cell RNA sequencing. It provides a closed‑form forward‑noising kernel, enabling efficient reverse sampling via forward‑filtering backward‑sampling and data‑driven selection of the terminal noising time. The method also introduces tilted Feynman–Kac steering to sample rare subpopulations without retraining, and demonstrates superior conditional fidelity and marker‑level preservation on human heart scRNA‑seq data.
arXiv:2607. 06583v1 Announce Type: cross Abstract: DNA methylation (DNAm) serves as one of the most robust molecular biomarkers of biological aging.
arXiv:2609.23290v1 Announce Type: cross Abstract: High-dimensional count data are common in scientific applications, but most diffusion and flow models are designed for continuous or categorical data...
arXiv:2510.16656v2 Announce Type: replace Abstract: Modeling dynamical systems and unraveling their underlying structural dependencies is central to many domains in the natural sciences. Various phys...
arXiv:2506. 22228v2 Announce Type: replace-cross Abstract: Single-cell sequencing is revolutionizing biology by enabling detailed investigations of cell-state transitions.
arXiv:2608.21070v1 Announce Type: cross Abstract: Inferring continuous system evolution from sparse temporal snapshots is a key challenge in generative modeling and single-cell omics. While Optimal T...
arXiv:2602. 24201v2 Announce Type: replace Abstract: Estimating density ratios between pairs of intractable data distributions is a core problem in probabilistic modeling, enabling principled comparisons of sample likelihoods under different data-generating processes across conditions.
arXiv:2510. 01894v3 Announce Type: replace Abstract: Many natural dynamic processes -- such as in vivo cellular differentiation or disease progression -- can only be observed through the lens of static sample snapshots.
arXiv:2607. 04738v1 Announce Type: cross Abstract: Reconstructing population dynamics is a central problem in the physical and data sciences.
arXiv:2607. 16987v1 Announce Type: cross Abstract: Over the past few years, diffusion-based Schr\"odinger bridge models have been proposed to approximate optimal transport dynamics between two prescribed boundary distributions, with successful applications to generative modeling.