umap transform fuzzy graph

[PedroMilanezAlmeida]

I was just wondering if umap_transform produces a fuzzy graph (with or without the reference points) and if this "transformed" fuzzy graph is/could be returned as well.

Any help would be much appreciated.

[jlmelville]

It does internally create the fuzzy graph but it doesn't output it, sorry.

It should be possible to add this functionality without too much difficulty though.

[jlmelville]

@PedroMilanezAlmeida I just pushed a change to the master branch so the development version of uwot will now return the fuzzy graph used for transforming if you pass ret_extra = c("fgraph") , e.g.:

iris_train <- iris[1:100, ]
iris_test <- iris[101:150, ]

iris_train_umap <- umap(iris_train, ret_model = TRUE)
iris_test_umap <- umap_transform(iris_test, iris_train_umap, ret_extra = c("fgraph"))

iris_test_umap$embedding # the coordinates
iris_test_umap$fgraph # the fuzzy graph

the returned fuzzy graph has as many rows as there are items in the new data to transform, and as many columns as there were items in the data used to build the model, so in the example above dim(iris_test_umap$fgraph) == c(50, 100).

This will eventually appear in the next CRAN release (which is unlikely to be submitted before the end of the year).

[PedroMilanezAlmeida]

@jlmelville

Thank you very much for your quick reply and solution. I appreciate it! I'll close this for now and, in the unlikely event of running into any issues, I'll let you know. Thanks again!