Comments (1)
Unfortunately, there are no trustworthiness and continuity functions in uwot
. I wrote some evaluation functions at https://github.com/jlmelville/quadra but I am not sure how valuable they are.
Personally, I find that evaluating the nearest neighbor preservation at a handful of nearest neighbor values (e.g. 15, 50, 150) works well enough for me. If you are prepared to install https://github.com/jlmelville/rnndescent then it's not too hard to evaluate the overlap at whatever value of n_neighbors
you used e.g.:
library(uwot)
library(rnndescent)
n_neighbors <- 10
res <- umap(iris, ret_nn = TRUE, n_neighbors = n_neighbors)
high_dim_nn <- res$nn$euclidean
# brute_force_knn and neighbor_overlap both come from rnndescent
low_dim_nn <-
brute_force_knn(res$embedding, k = n_neighbors, n_threads = 6)
neighbor_overlap(high_dim_nn, low_dim_nn)
from uwot.
Related Issues (20)
- Add general_simplicial_set_intersection to the uwot API HOT 3
- umap_transform causes R Studio to abort (R encountered a fatal error.) HOT 4
- umap_transform can give odd results with dens_scale HOT 17
- umap transform fuzzy graph HOT 3
- Citing {uwot} HOT 1
- Weird looking UMAP for spectral flow data HOT 3
- What C++ version should CXX_STD have? HOT 16
- devtools can no longer build uwot on Windows HOT 5
- I can not load the saved model, an example from the help HOT 9
- Reproducibility issue with the same data and OS HOT 17
- umap_transform with seurat umap coordinate HOT 2
- dgCMatrix_colSums' not found error when using a binary matrix HOT 2
- irlba as_cholmod_sparse problems HOT 1
- maybe unintended data use in examples HOT 2
- umap_transform uses a different distance metric if loaded in HOT 5
- if batch = TRUE in training, fgraph of umap_transform is transposed if n_epoch is set to 0 HOT 4
- Found more than one class "dist" in cache HOT 4
- Error on installing uwot under Microsoft R-4.1.2 HOT 2
- Error installing uwot into R-4.3.3 of centos-7.9 HOT 1
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from uwot.