Fig. 2

Shortest-path principle. A single-cell Hi-C matrix can be represented as a graph, where nodes (circles) correspond to genomic regions and edges (black lines) bear weights corresponding to the three-dimensional (3D) distance between the bins. For pairs of nodes with missing data (dotted line; x), a value can be estimated by finding the shortest possible path (red edges; a + b + c) between the two nodes, traversing the edges with observed distance values