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Compute undirected UMAP weights from directed distance graph. UMAP is a layout algorithm that usually takes as input a directed distance graph, for instance a k nearest neighbor graph based on Euclidean distance between points in a vector space. The graph is directed because vertex v1 might consider vertex v2 a close neighbor, but v2 itself might have many neighbors that are closer than v1. This function computes the symmetrized weights from the distance graph using union as the symmetry operator. In simple terms, if either vertex considers the other a close neighbor, they will be treated as close neighbors.

This function can be used as a separate preprocessing step to Graph.layout_umap(). For efficiency reasons, the returned weights have the same length as the input distances, however because of the symmetryzation some information is lost. Therefore, the weight of one of the edges is set to zero whenever edges in opposite directions are found in the input distance graph. You can pipe the output of this function directly into Graph.layout_umap() as follows: weights = igraph.umap_compute_weights(graph, dist) layout = graph.layout_umap(weights=weights)