optimal transport

Label-free flow operators and stability operators from single-cell time courses: what local dynamical operators can and cannot identify

This paper introduces scJDO2, a method to separate score and flow operators from single-cell time courses, evaluating their ability to identify unstable cells and bifurcations in hematopoiesis.

Unified cell segmentation for spatial transcriptomics via transcript reassignment

Tracel improves cell segmentation in spatial transcriptomics by assigning transcripts to cells using optimal transport, enhancing cell-type separation and reducing contamination.

LOTUS: lineage-aware optimal transport reconstructs continuous clonal fate dynamics

LOTUS reconstructs continuous clonal fate dynamics using lineage-aware optimal transport, improving lineage consistency and fate prediction in single-cell data.

Inferring scaling laws of branching networks from their geometry by global optimization

This paper uses global optimization to infer scaling laws of branching networks from their geometry, revealing type-specific signatures and outperforming existing laws in vascular systems.

Optimal Conservation Prioritization for Waterfowl and Other Birds in Eastern Canada

The paper presents an optimized geospatial prioritization scheme for bird conservation in Eastern Canada using linear programming to maximize population coverage.