Changelog

Source: NEWS.md

rnndescent (development version)

rnndescent 0.1.6

CRAN release: 2024-05-14

• This is a patch release to fix an issue that occurred with the recent release of a new version of ‘dqrng’ on CRAN. Unfortunately, version 0.1.5 didn’t quite work out. A fix for incorrect behavior for some metrics is also included (see below).

Bug fixes and minor improvements

• Building an index with the "cosine", "jaccard" or "hellinger" metrics could give incorrect results if maximally-dissimilar items were in the nearest neighbors. Thank you to Maciej Beręsewicz for the report (https://github.com/jlmelville/rnndescent/issues/14).

rnndescent 0.1.5

CRAN release: 2024-04-18

• This is a minor release to change an internal API to support an upcoming release for dqrng. See https://github.com/daqana/dqrng/issues/80. Thank you to Ralf Stubner for the report and a patch.

rnndescent 0.1.4

CRAN release: 2024-03-18

New features

• New parameter: for nnd_knn and rnnd_build: weight_by_degree. If set to TRUE, then the candidate list in nearest neighbor descent is weighted in favor of low-degree items, which should make for a more diverse local join. There is a minor increase in computation but also a minor increase in accuracy.

Bug fixes and minor improvements

• rnnd_build generated an error when preparing the search graph for some metrics (notably cosine and jaccard).
• Fix a factor of 2 error in the TS-SS metric. This does not affect the returned neighbors, just the distances. Thank you to reporter Henry Linder (https://github.com/jlmelville/rnndescent/issues/8).
• New parameter for prepare_search_graph: use_alt_metric. This behaves like the existing use_alt_metric parameters in other functions and may speed up the index preparation step in e.g. rnnd_build.
• New parameter for rnnd_build and prepare_search_graph: prune_reverse. If set to TRUE the reverse graph will be pruned using the pruning_degree_multiplier parameter before any diversification. This can help prevent an excessive amount of time being spent in the diversification step in the case where an item has a large number of neighbors (in the reverse graph this can be as large as the number of items in the dataset). Pruning of the merged graph still occurs, so this is an additional pruning step. This should have little effect on search results, but for backwards compatibility, the default is FALSE.

rnndescent 0.1.3

CRAN release: 2023-12-07

CRAN resubmission to fix lingering UBSAN errors.

rnndescent 0.1.2

Bug fixes and minor improvements

• Some internal Address/Undefined Behavior Sanitizer fixes discovered by CRAN checks on the 0.1.1 submission have been fixed.

rnndescent 0.1.1

CRAN release: 2023-11-27

Initial CRAN submission.

rnndescent 0.0.16

Breaking changes

• rnnd_build now always prepares the search graph.
• The rnnd_prepare function has been removed. The option to not prepare the search graph during index building only made sense if you were only interested in the k-nearest neighbor graph. Now that rnnd_knn exists for that purpose (see below), the logic of index building has been substantially simplified.
• The nn_to_sparse function has been removed.
• The merge_knn function has been removed, and merge_knnl has been renamed to merge_knn. If you were running e.g. merge_knn(nn1, nn2), you must now use merge_knn(list(nn1, nn2)). Also the parameter nn_graphs has been renamed graphs.

New features

• New function: rnnd_knn. Behaves a lot like rnnd_build, but only returns the knn graph with no index built. The index can be very large in size for high dimensional or large datasets, so this function is useful if you only care about the knn graph and won’t ever want to query new data.
• New function: neighbor_overlap. Measures the overlap of two knn graphs via their shared indices. A similar function was used extensively in some vignettes so it may have sufficient utility to be useful to others.
• New parameter for rnnd_query and graph_knn_query: max_search_fraction. This parameter controls the maximum number of nodes that can be searched during querying. If the number of nodes searched exceeds this fraction of the total number of nodes in the graph, the search will be terminated. This can be used in combination with epsilon to avoid excessive search times.

Bug fixes and minor improvements

• The sparse spearmanr distance has been fixed.
• During tree-building with n_threads = 0, progress/interrupt monitoring was not occurring.
• You can provide a user-defined graph to the init parameter of rnnd_query.
• rnnd_query: if verbose = TRUE, a summary of the min, max and average number of distance queries will be logged. This can help tune epsilon and max_search_fraction.

rnndescent 0.0.15

Breaking Changes

• Standalone distance functions have been removed. They hadn’t expanded to match all the distances available in the nearest neighbor functions, nor was sparse support added. Doing so would increase the size of this package’s API even further. They may show up in another package.
• The local_scale_nn has been removed, for similar reasons to the removal of the standalone distance functions. It remains in the localscale branch of the github repo.
• The search graph returned from prepare_search_graph is now transposed. This prevents having to repeatedly transpose inside every call to graph_knn_query if multiple queries are being made. You will need to either regenerate any saved search graphs or transpose them with Matrix::t(search_graph).

New features

• New functions: rnnd_build, rnnd_query and rnnd_prepare. These functions streamline the process of building a k-nearest neighbor graph, preparing a search graph and querying it.

rnndescent 0.0.14

Breaking Changes

• The bhamming metric no longer exists as a specialized metric. Instead, if you pass a logical matrix to data, reference or query parameter (depending on the function) and specify metric = "hamming" you will automatically get the binary-specific version of the hamming metric.

• The hamming and bhamming metrics are now normalized with respect to the number of features, to be consistent with the other binary-style metrics (and PyNNDescent). If you need the old distances, multiply the distance matrix by the number of columns, e.g. do something like:

  
  res <- brute_force_knn(X, metric = "hamming")
  res$dist <- res$dist * ncol(X)

• The metric l2sqr has been renamed sqeuclidean to be consistent with PyNNDescent.

New features

• Metrics? We got ’em! The metric parameter now accepts a much larger number of metrics. See the rdoc for the full list of supported metrics. Currently, most of the metrics from PyNNDescent which don’t require extra parameters are supported. The number of specialized binary metrics has also been expanded.
• New parameter for rpf_knn and rpf_build: max_tree_depth this controls the depth of the tree and was set to 100 internally. This default has been doubled to 200 and can now be user-controlled. If verbose = TRUE and the largest leaf in the forest exceeds the leaf_size parameter, a message warning you about this will be logged and indicates that the maximum tree depth has been exceeded. Increasing max_tree_depth may not be the answer: it’s more likely there is something unusual about the distribution of the distances in your dataset and a random initialization might be a better use of your time.

rnndescent 0.0.13

New features

• Sparse data is now supported. Pass a dgCMatrix to the data, reference or query parameters where you would usually use a dense matrix or data frame. cosine, euclidean, manhattan, hamming and correlation are all available, but alternative versions in the dense case, e.g. cosine-preprocess or the binary-specific bhamming for dense data is not.
• A new init option for graph_knn_query: you can now pass an RP forest and initialize with that, e.g. from rpf_build, or by setting ret_forest = TRUE on nnd_knn or rpf_knn. You may want to cut down the size of the forest used for initialization with rpf_filter first, though (a single tree may be enough). This will also use the metric data in the forest, so setting metric (or use_alt_metric) in the function itself will be ignored.

Bug fixes and minor improvements

• If the knn graph you pass to prepare_search_graph or to graph_knn_query contains missing data, this will no longer cause an error (it still might not be the best idea though).

rnndescent 0.0.12

New features

• New function: rpf_knn. Calculates the approximate k-nearest neighbors using a random partition forest.
• New function: rpf_build. Builds a random partition forest.
• New function: rpf_knn_query. Queries a random partition forest (built with rpf_build to find the approximate nearest neighbors for the query points.
• New function: rpf_filter. Retains only the best “scoring” trees in a forest, where each tree is scored based on how well it reproduces a given knn.
• New initialization method for nnd_knn: init = "tree". Uses the RP Forest initialization method.
• New parameter for nnd_knn: ret_forest. Returns the search forest used if init = "tree" so it can be used for future searching or filtering.
• New parameter for nnd_knn: init_opts. Options that can be passed to the RP forest initialization (same as in rpf_knn).

rnndescent 0.0.11

Bug fixes and minor improvements

• Progess report for nnd_knn with n_threads > 0 was reporting double the actual number of iterations. This made the progress bar way too optimistic.
• A bug with flagging neighbors in 0.0.10 made the nearest neighbor descent inefficient.

rnndescent 0.0.10

New features

• A change to metric: "cosine" and "correlation" have been renamed "cosine-preprocess" and "correlation-preprocess" respectively. This reflects that they do some preprocessing of the data up front to make subsequent distance calculations faster. I have endeavored to avoid unnecessary allocations or copying in this preprocessing, but there is still a chance of more memory usage.
• The cosine and correlation metrics are still available as an option, but now use an implementation that doesn’t do any preprocessing. The preprocessing and non-preprocessing version should give the same numerical results, give or take some minor numerical differences, but when the distance should be zero, the preprocessing versions may give values which are slightly different from zero (e.g. 1e-7).
• New functions: correlation_distance, cosine_distance, euclidean_distance, hamming_distance, l2sqr_distance, manhattan_distance for calculating the distance between two vectors, which may be useful for more arbitrary distance calculations than the nearest neighbor routines here, although they won’t be as efficient (they do call the same C++ code, though). The cosine and correlation calculations here use the non-preprocessing implementations.
• Generalize hamming metric to a standard definition. The old implementation of hamming metric which worked on binary data only was renamed into bhamming. (contributed by Vitalie Spinu)
• New parameter obs has been added to most functions: set obs = "C" and you can pass the input data in column-oriented format.

Bug fixes and minor improvements

• The random_knn function used to always return each item as its own neighbor, so that only n_nbrs - 1 of the returned neighbors were actually selected at random. Even I forgot it did that and it doesn’t make a lot of sense, so now you really do just get back n_nbrs random selections.
• If providing pre-calculated neighbors as the init parameter to nnd_knn or graph_knn_query: previously, if k was specified and larger than the number of neighbors included in init, this gave an error. Now, init will be augmented with random neighbors to reach the desired k. This could be useful as a way to “restart” a neighbor search from a better-than-random location if k has been found to have been too small initially. Note that the random selection does not take into account the identities of the already chosen neighbors, so duplicates may be included in the augmented result, which will reduce the effective size of the initialized number of neighbors.
• Removed the block_size and grain_size parameters from functions. These were related to the amount of work done per thread, but it’s not obvious to an outside user how to set these.
• Most long-running computations should update any progress indicators more frequently (if verbose = TRUE) and respond to user-requested cancellation.

rnndescent 0.0.9 (20 June 2021)

New features

• nnd_knn_query has been renamed to graph_knn_query and now more closely follows the current pynndescent graph search method (including backtracking search).
• New function: prepare_search_graph for preparing a search graph from a neighbor graph for use in graph_knn_query, by using reverse nearest neighbors, occlusion pruning and truncation.
• Sparse graphs are supported as input to graph_knn_query.

rnndescent 0.0.8 (10 October 2020)

There was a major rewrite of the internal organization of the C++ to be less R-specific.

Minor License Change

The license for rnndescent has changed from GPLv3 to GPLv3 or later.

New features

• New metric: "correlation". This is (1 minus) the Pearson correlation.
• New function: k_occur which counts the k-occurrences of each item in the idx matrix, which is the number of times an item appears in the k-nearest neighbor list in the dataset. The distribution of the k-occurrences can be used to diagnose the “hubness” of a dataset. Items with a large k-occurrence (>> k, e.g. 10k), may indicate low accuracy of the approximate nearest neighbor result.

rnndescent 0.0.7 (1 March 2020)

Bug fixes and minor improvements

To avoid undefined behavior issues, rnndescent now uses an internal implementation of RcppParallel’s parallelFor loop that works with std::thread and does not load Intel’s TBB library.

rnndescent 0.0.6 (29 November 2019)

Bug fixes and minor improvements

• For some reason, I thought it would be ok to use the dqrng sample routines from inside a thread, despite it clearly using the R API extensively. It’s not ok and causes lots of crashes. There is now a re-implementation of dqrng’s sample routines using plain std::vectors in src/rnn_sample.h. That file is licensed under the AGPL (rnndescent as a whole remains GPL3).

rnndescent 0.0.5 (23 November 2019)

New features

• New function: merge_knn, to combine two nearest neighbor graphs. Useful for combining the results of multiple runs of nnd_knn or random_knn. Also, merge_knnl, which operates on a list of multiple neighbor graphs, and can provide a speed up over merge_knn if you don’t mind storing multiple graphs in memory at once.

Bug fixes and minor improvements

• There was a thread-locking issue to do with converting R matrices to the internal heap data structure that affected nnd_knn with n_threads > 1 and random_knn with n_threads > 1 and order_by_distance = TRUE.
• Potential minor speed improvement for nnd_knn with n_threads > 1 due to the use of a mutex pool.

rnndescent 0.0.4 (21 November 2019)

Mainly an internal clean-up to reduce duplication.

Bug fixes and minor improvements

• By default, nnd_knn and nnd_knn_query use the same progress bar as the brute force and random neighbor functions. Bring back the old per-iteration logging that also showed the current distance sum of the knn with the progress = "dist" option.
• For random_knn and random_knn_query, when order_by_distance = TRUE and n_threads > 0, the final sorting of the knn graph will be multi-threaded.
• Initialization of the nearest neighbor descent data structures are also multi-threaded if n_threads > 0.
• Progress bar updating and cancellation should now be more consistent and less likely to cause hanging and crashing across the different methods.
• Using Cosine and Hamming distance may take up less memory or run a bit faster.

rnndescent 0.0.3 (15 November 2019)

New features

• There are now “query” versions of the three functions: nnd_knn_query being the most useful, but brute_force_knn_query and random_knn_query are also available. This allows for query data to search reference data, i.e. the returned indices and distances are relative to the reference data, not any other member of query. These methods are also available in multi-threaded mode, and nnd_knn_query has a low and high memory version.

Bug fixes and minor improvements

• Incremental search in nearest neighbor descent didn’t work correctly, because retained new neighbors were marked as new rather than old. This made the search repeat distance calculations unnecessarily.
• Heap initialization ignored existing distances in the input distance matrix.
• The l2 metric has been renamed to l2sqr to more accurately reflect what it is: the square of the L2 (Euclidean) metric.
• New option use_alt_metric. Set to FALSE if you don’t want alternative, faster metrics (which keep the distance ordering of metric) to be used in internal calculations. Currently only applies to metric = "euclidean", where the squared Euclidean distance is used internally. Only worth setting this to FALSE if you think the alternative is causing numerical issues (which is a bug, so please report it!).
• Random and brute force methods will make use of alternative metrics.
• New option block_size for parallel methods, which determines the amount of work done in parallel before checking for user interrupt request and updating any progress.
• random_knn now returns its results in sorted order. You can turn this off with order_distances = FALSE, if you don’t need the sorting (e.g. you are using the results as input to something else).
• Progress bars for the brute_force and random methods should now be correct.

rnndescent 0.0.2 (7 November 2019)

New features

• Brute force nearest neighbor function has been renamed to brute_force_knn.
• Random nearest neighbors has been renamed to random_knn.
• Brute force and random nearest neighbors are now interruptible.
• Progress bar will be shown if verbose = TRUE.
• fast_rand option has been removed, as it only applied to single-threading, and had a negligible effect.

Also, a number of changes inspired by recent work in https://github.com/lmcinnes/pynndescent:

• The parallel nearest neighbor descent should now be faster.
• The rho sampling parameter has been removed. The size of the candidates (general neighbors) list is now controlled entirely by max_candidates.
• Default max_candidates has been reduced to 20.
• The use_set logical flag has been replaced by low_memory, which has the opposite meaning. It now also works when using multiple threads. While it follows the pynndescent implementation, it’s still experimental, so low_memory = TRUE by default for the moment.
• The low_memory = FALSE implementation for n_threads = 0 (originally equivalent to use_set = TRUE) is faster.
• New parameter block_size, which balances interleaving of queuing updates versus applying them to the current graph.

Bug fixes and minor improvements

• In the incremental search, the neighbors were marked as having been selected for the new candidate list even if they were later removed due to the finite size of the candidates heap. Now, only those indices that are still retained after candidate building are marked as new.
• Improved man pages (examples plus link to nearest neighbor descent reference).
• Removed dependency on Boost headers.

rnndescent 0.0.1 (27 October 2019)

• Initial release.

New features

• Nearest Neighbor Descent with the following metrics: Euclidean, Cosine, Manhattan, Hamming.
• Support for multi-threading with RcppParallel.
• Initialization with random neighbors.
• Brute force nearest neighbor calculation.