Pheno-GS is a new method for computing scalable, geometry-aware optimal transport distances between large patient cohorts of single‑cell data. It uses graph connectivity regularization, an unbalanced OT formulation with KL marginal penalties, and a batched matrix algorithm that dramatically speeds up pairwise distance calculations. The authors validate the approach on synthetic benchmarks and a CyTOF perturbation dataset.
arXiv:2608. 28262v1 Announce Type: new Abstract: Entropic optimal transport (EOT) has been shown to offer a computationally tractable approximation to exact optimal transport.
arXiv:2607. 06497v1 Announce Type: new Abstract: We introduce EntroPath, a manifold learning method that recovers geodesic geometry from data graphs through ensembles of diffusion paths.
arXiv:2609.25659v1 Announce Type: new Abstract: Many scientific datasets, such as molecular conformational ensembles or single-cell tissue measurements, are naturally modeled as meta-distributions: d...
arXiv:2606. 15760v1 Announce Type: new Abstract: A significant gap exists between theory and practice in deep learning.
arXiv:2606. 16273v1 Announce Type: cross Abstract: We introduce, to our knowledge, the first deep generative modeling framework for probability distributions continuously supported on compact metric graphs.
arXiv:2606. 02047v1 Announce Type: cross Abstract: We introduce Convex Distance Operator Transport (CDOT), the first convex optimal transport framework that aligns distributions across heterogeneous domains by jointly preserving feature correspondence and intrinsic geometric structure.
arXiv:2606. 14334v1 Announce Type: new Abstract: High-dimensional datasets often concentrate near low-dimensional structures, but estimating their geometry from samples typically relies on graphs and kernels that scale poorly with dataset size and dimension.
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.
The paper introduces the Sparse Landmark Embedding (SLE) kernel, a new framework that removes the need for conditionally negative definite (CND) distance measures in kernel methods and Gaussian Processes. By embedding each input into a sparse feature vector using compactly supported bump functions centered at all training points, any standard positive semi-definite (PSD) kernel can be applied in this embedding space, guaranteeing PSD for arbitrary distance measures. The authors provide theoretical guarantees on PSD, sparsity, stability, and universal approximation, and show through experiments with geodesic and Wasserstein distances that the SLE kernel matches or surpasses domain-specific baselines in predictive accuracy and uncertainty quantification.
arXiv:2607. 22381v1 Announce Type: new Abstract: Curvature notions on graphs, particularly Ollivier-Ricci and Forman, have emerged as powerful tools for addressing fundamental issues in Graph Neural Networks (GNNs) such as oversmoothing and oversquashing, but rely almost exclusively on local edge-level comparisons and therefore fail to certify how information actually propagates over long distances.
arXiv:2605. 14981v2 Announce Type: replace Abstract: Gromov--Wasserstein (GW) distances compare graphs, shapes, and point clouds through internal distances, without requiring a common coordinate system.
arXiv:2608. 15306v1 Announce Type: cross Abstract: High-throughput single-cell and spatial transcriptomic technologies provide high-resolution snapshots of heterogeneous cellular states, but their destructive nature prevents repeated measurements of the same cells over time.