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$index)
##      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
## [1,] 8367 8024  412 7452 4986 8059 8767 5863 5568  9170
## [2,] 7505 5084 4941 9248 8300 2767 2588 5815 2414  6779
## [3,] 1423 6033 4754 5243 1063 7402 5736  569 2958  2372
## [4,] 4099 6815 4468 4392 8794 2570 9754 4784 9030  4412
## [5,]  581 2481 8556 6514 4270 6759 2803 4132 5325  7112
## [6,] 8144 6697 3402 9300 5248 3157 7580 2971 1667  1060
head(fout$distance)
##           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]      [,7]
## [1,] 0.9171678 0.9425159 0.9431646 0.9572297 0.9644480 0.9805946 1.0174010
## [2,] 0.9621327 0.9670848 0.9929832 0.9993303 1.0228894 1.0396564 1.0438344
## [3,] 0.8206025 0.8798296 0.8804766 0.9020995 0.9048094 0.9160107 0.9232739
## [4,] 0.8161841 0.8854532 0.9174184 0.9401400 0.9851396 0.9930533 0.9965966
## [5,] 1.0427125 1.0645164 1.0669452 1.0683836 1.1139536 1.1449358 1.1469938
## [6,] 0.7417828 0.9002681 0.9140049 0.9155242 0.9189631 0.9382798 0.9427933
##           [,8]      [,9]     [,10]
## [1,] 1.0249903 1.0295681 1.0335536
## [2,] 1.0509665 1.0897555 1.0998900
## [3,] 0.9412209 0.9614992 0.9652658
## [4,] 1.0189202 1.0367405 1.0378553
## [5,] 1.1491128 1.1525401 1.1539816
## [6,] 0.9929794 0.9986178 1.0044509

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$index)
##      [,1] [,2] [,3] [,4] [,5]
## [1,] 6822 4426 1715 7508 2464
## [2,]  957 5985 2454 2068 3042
## [3,] 9306 7186 6908 9102 7949
## [4,]  866 6060 1349 6982 8261
## [5,] 8861  443  188 3160 1484
## [6,] 9055 4826 3262 5514 6679
head(qout$distance)
##           [,1]      [,2]      [,3]      [,4]      [,5]
## [1,] 0.9289543 1.0253005 1.0686672 1.0935981 1.1488045
## [2,] 0.7525633 0.8865743 0.8985186 0.9768201 0.9948143
## [3,] 0.9024137 0.9536997 1.0628147 1.0737333 1.0961367
## [4,] 0.8370829 0.9533898 0.9977849 1.0355099 1.0538019
## [5,] 0.7983236 0.8354070 0.8403973 0.8904105 0.9825965
## [6,] 0.9309431 1.0334160 1.0844851 1.1001310 1.1003900

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] "/tmp/RtmpesdGhm/fileb34145b0b1486.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 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocNeighbors_1.20.0 knitr_1.44           BiocStyle_2.30.0    
## 
## loaded via a namespace (and not attached):
##  [1] cli_3.6.1           rlang_1.1.1         xfun_0.40          
##  [4] jsonlite_1.8.7      S4Vectors_0.40.0    htmltools_0.5.6.1  
##  [7] stats4_4.3.1        sass_0.4.7          rmarkdown_2.25     
## [10] grid_4.3.1          evaluate_0.22       jquerylib_0.1.4    
## [13] fastmap_1.1.1       yaml_2.3.7          bookdown_0.36      
## [16] BiocManager_1.30.22 compiler_4.3.1      codetools_0.2-19   
## [19] Rcpp_1.0.11         BiocParallel_1.36.0 lattice_0.22-5     
## [22] digest_0.6.33       R6_2.5.1            parallel_4.3.1     
## [25] bslib_0.5.1         Matrix_1.6-1.1      tools_4.3.1        
## [28] BiocGenerics_0.48.0 cachem_1.0.8