Skip to content

CRAN release 0.1.8
Compare
Choose a tag to compare
@jlmelville jlmelville released this 19 Jul 00:29
· 392 commits to master since this release
v0.1.8
72350ef

uwot 0.1.8

Better late than never, here are the release notes for CRAN release 0.1.8. It's a bumper selection due to my failure to get 0.1.6 and 0.1.7 accepted.

New features

  • New parameter, ret_extra, a vector which can contain any combination of: "model" (same as ret_model = TRUE), "nn" (same as ret_nn = TRUE) and fgraph (see below).
  • New return value data: If the ret_extra vector contains "fgraph", the returned list will contain an fgraph item representing the fuzzy simplicial input graph as a sparse N x N matrix. For lvish, use "P" instead of "fgraph" (#47). Note that there is a further sparsifying step where edges with a very low membership are removed if there is no prospect of the edge being sampled during optimization. This is controlled by n_epochs: the smaller the value, the more sparsifying will occur. If you are only interested in the fuzzy graph and not the embedded coordinates, set n_epochs = 0.
  • New function: unload_uwot, to unload the Annoy nearest neighbor indices in a model. This prevents the model from being used in umap_transform, but allows for the temporary working directory created by both save_uwot and load_uwot to be deleted. Previously, both load_uwot and save_uwot were attempting to delete the temporary working directories they used, but would always silently fail because Annoy is making use of files in those directories.
  • An attempt has been made to reduce the variability of results due to different compiler and C++ library versions on different machines. Visually results are unchanged in most cases, but this is a breaking change in terms of numerical output. The best chance of obtaining floating point determinism across machines is to use init = "spca", fixed values of a and b (rather than allowing them to be calculated through setting min_dist and spread) and approx_pow = TRUE. Using the tumap method with init = "spca" is probably the most robust approach.

Big fixes and minor improvements

  • default for n_threads is now NULL to provide a bit more protection from changing dependencies.
  • uwot should no longer trigger undefined behavior in sanitizers, due to replacement of RcppParallel with the standard C++11 implementation of threading (and some code "borrowed" from RcppParallel) (#52).
  • Further sanitizer improvements in the nearest neighbor search code due to the upstream efforts of erikbern and eddelbuettel (#50).
  • New behavior when n_epochs = 0. This used to behave like (n_epochs = NULL) and gave a default number of epochs (dependent on the number of vertices in the dataset). Now it more usefully carries out all calculations except optimization, so the returned coordinates are those specified by the init parameter, so this is an easy way to access e.g. the spectral or PCA initialization coordinates. If you want the input fuzzy graph (ret_extra vector contains "fgraph"), this will also prevent the graph having edges with very low membership being removed.
    You still get the old default epochs behavior by setting n_epochs = NULL or to a negative value.
  • save_uwot and load_uwot have been updated with a verbose parameter so it's easier to see what temporary files are being created.
  • save_uwot has a new parameter, unload, which if set to TRUE will delete the working directory for you, at the cost of unloading the model, i.e. it can't be used with umap_transform until you reload it with load_uwot.
  • save_uwot now returns the saved model with an extra field, mod_dir, which points to the location of the temporary working directory, so you should now assign the result of calling save_uwot to the model you saved, e.g. model <- save_uwot(model, "my_model_file"). This field is intended for use with unload_uwot.
  • load_uwot also returns the model with a mod_dir item for use with unload_uwot.
  • save_uwot and load_uwot were not correctly handling relative paths.
  • A previous bug fix to load_uwot in uwot 0.1.4 to work with newer versions of RcppAnnoy (#31) failed in the typical case of a single metric for the nearest neighbor search using all available columns, giving an error message along the lines of: Error: index size <size> is not a multiple of vector size <size>. This has now been fixed, but required changes to both save_uwot and load_uwot, so existing saved models must be regenerated. Thank you to reporter OuNao.
Assets 2
Loading