1 Introduction

The BiocNeighbors package provides several algorithms for approximate neighbor searches:

  • The Annoy (Approximate Nearest Neighbors Oh Yeah) method uses C++ code from the RcppAnnoy package. It works by building a tree where a random hyperplane partitions a group of points into two child groups at each internal node. This is repeated to construct a forest of trees where the number of trees determines the accuracy of the search. Given a query data point, we identify all points in the same leaf node for each tree. We then take the union of leaf node sets across trees and search them exactly for the nearest neighbors.
  • The HNSW (Hierarchical Navigable Small Worlds) method uses C++ code from the RcppHNSW package. It works by building a series of nagivable small world graphs containing links between points across the entire data set. The algorithm walks through the graphs where each step is chosen to move closer to a given query point. Different graphs contain links of different lengths, yielding a hierarchy where earlier steps are large and later steps are small. The accuracy of the search is determined by the connectivity of the graphs and the size of the intermediate list of potential neighbors.

These methods complement the exact algorithms described previously. Again, it is straightforward to switch from one algorithm to another by simply changing the BNPARAM argument in findKNN and queryKNN.

2 Identifying nearest neighbors

We perform the k-nearest neighbors search with the Annoy algorithm by specifying BNPARAM=AnnoyParam().

nobs <- 10000
ndim <- 20
data <- matrix(runif(nobs*ndim), ncol=ndim)

fout <- findKNN(data, k=10, BNPARAM=AnnoyParam())
head(fout$index)
##      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
## [1,] 3521 6940 7197 2671  590 6508  649  891 1436  2265
## [2,] 5076 1010 6926 3469  122 2042 6395  778 7022  1902
## [3,] 6755 1777 5789 9447 9730 1215 2609  793 7163  1266
## [4,] 1553 8994 8187 3844 1962 3457  109 8824 7417   939
## [5,] 2426   91 9785 9127 2655 5888 5433 3348 9616  8991
## [6,] 8786 6180 3485 3826 4068 8907 4252 3467 6429  7282
head(fout$distance)
##           [,1]      [,2]      [,3]      [,4]      [,5]     [,6]     [,7]
## [1,] 0.8939867 0.9363595 1.0008545 1.0161842 1.0631888 1.064085 1.077162
## [2,] 0.9608915 0.9682344 1.0185841 1.0358274 1.0508249 1.051615 1.089248
## [3,] 0.8045722 0.9334469 0.9345300 0.9352991 0.9947063 1.039884 1.044366
## [4,] 0.8362793 0.8582160 0.8825148 0.9497098 0.9522839 1.007295 1.007637
## [5,] 0.9503789 1.0751200 1.1055510 1.1151500 1.1241959 1.133050 1.135079
## [6,] 1.0123729 1.0160055 1.0189724 1.0288382 1.0357256 1.050178 1.080513
##          [,8]     [,9]    [,10]
## [1,] 1.094295 1.102976 1.121646
## [2,] 1.094440 1.136807 1.139871
## [3,] 1.053339 1.083925 1.087731
## [4,] 1.007907 1.016277 1.019069
## [5,] 1.136122 1.137514 1.143163
## [6,] 1.101067 1.112083 1.123004

We can also identify the k-nearest neighbors in one dataset based on query points in another dataset.

nquery <- 1000
ndim <- 20
query <- matrix(runif(nquery*ndim), ncol=ndim)

qout <- queryKNN(data, query, k=5, BNPARAM=AnnoyParam())
head(qout$index)
##      [,1] [,2] [,3] [,4] [,5]
## [1,] 2527 1139 2203 9993 6640
## [2,] 3129 4395 6689 4217 6701
## [3,] 9677  385   10 3993 7034
## [4,] 7533 8356 1771   48 5844
## [5,] 1566 6995 2749 9165 3525
## [6,] 4126 7452 6597 6468 9665
head(qout$distance)
##           [,1]      [,2]      [,3]      [,4]      [,5]
## [1,] 0.8259433 0.9379281 0.9428999 0.9689491 0.9751185
## [2,] 0.8221393 0.9631063 1.1422907 1.1520110 1.1591171
## [3,] 0.8956584 0.9790214 1.0144969 1.0156194 1.0178609
## [4,] 0.8217030 1.0031134 1.0049297 1.0262222 1.0467658
## [5,] 0.9914263 1.0444784 1.0719147 1.0735639 1.0821632
## [6,] 0.9146192 1.0163833 1.0326532 1.0444288 1.0478787

It is similarly easy to use the HNSW algorithm by setting BNPARAM=HnswParam().

3 Further options

Most of the options described for the exact methods are also applicable here. For example:

  • subset to identify neighbors for a subset of points.
  • get.distance to avoid retrieving distances when unnecessary.
  • BPPARAM to parallelize the calculations across multiple workers.
  • BNINDEX to build the forest once for a given data set and re-use it across calls.

The use of a pre-built BNINDEX is illustrated below:

pre <- buildIndex(data, BNPARAM=AnnoyParam())
out1 <- findKNN(BNINDEX=pre, k=5)
out2 <- queryKNN(BNINDEX=pre, query=query, k=2)

Both Annoy and HNSW perform searches based on the Euclidean distance by default. Searching by Manhattan distance is done by simply setting distance="Manhattan" in AnnoyParam() or HnswParam().

Users are referred to the documentation of each function for specific details on the available arguments.

4 Saving the index files

Both Annoy and HNSW generate indexing structures - a forest of trees and series of graphs, respectively - that are saved to file when calling buildIndex(). By default, this file is located in tempdir()1 On HPC file systems, you can change TEMPDIR to a location that is more amenable to concurrent access. and will be removed when the session finishes.

AnnoyIndex_path(pre)
## [1] "C:\\Users\\biocbuild\\bbs-3.11-bioc\\tmpdir\\Rtmp6hDGS5\\file2e806c4a418a.idx"

If the index is to persist across sessions, the path of the index file can be directly specified in buildIndex. This can be used to construct an index object directly using the relevant constructors, e.g., AnnoyIndex(), HnswIndex(). However, it becomes the responsibility of the user to clean up any temporary indexing files after calculations are complete.

5 Session information

sessionInfo()
## R version 4.0.0 (2020-04-24)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows Server 2012 R2 x64 (build 9600)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=C                          
## [2] LC_CTYPE=English_United States.1252   
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocNeighbors_1.6.0 knitr_1.28          BiocStyle_2.16.0   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.4.6        bookdown_0.18       lattice_0.20-41    
##  [4] digest_0.6.25       grid_4.0.0          stats4_4.0.0       
##  [7] magrittr_1.5        evaluate_0.14       rlang_0.4.5        
## [10] stringi_1.4.6       S4Vectors_0.26.0    Matrix_1.2-18      
## [13] rmarkdown_2.1       BiocParallel_1.22.0 tools_4.0.0        
## [16] stringr_1.4.0       parallel_4.0.0      xfun_0.13          
## [19] yaml_2.2.1          compiler_4.0.0      BiocGenerics_0.34.0
## [22] BiocManager_1.30.10 htmltools_0.4.0