BiocNeighbors 1.12.0
The BiocNeighbors package provides several algorithms for approximate neighbor searches:
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.
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$index)
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
## [1,] 9439 4415 4050 1824 7530 1765 1809 9042 4664 2563
## [2,] 2790 3423 3782 8726 625 2779 7927 7627 2499 9672
## [3,] 2457 7743 221 1509 7170 4612 357 1104 7804 4335
## [4,] 4969 3827 7582 434 4839 8877 8875 5642 8399 6484
## [5,] 3024 1233 9286 4642 7428 2218 2799 4303 3709 4587
## [6,] 970 8731 5495 8513 3823 1449 582 1072 4587 5913
head(fout$distance)
## [,1] [,2] [,3] [,4] [,5] [,6] [,7]
## [1,] 0.9488623 0.9526768 0.9918012 1.0155424 1.018635 1.038617 1.060869
## [2,] 0.9491687 0.9837804 0.9908242 1.0480871 1.055283 1.068011 1.078402
## [3,] 0.9902376 1.0116328 1.0365927 1.0736140 1.083189 1.086472 1.097179
## [4,] 0.9866520 1.0091648 1.0289248 1.0347098 1.054599 1.058922 1.071430
## [5,] 0.9620222 0.9739777 0.9899967 0.9961459 1.009494 1.019439 1.021883
## [6,] 0.9976924 1.0015095 1.0361325 1.0463392 1.058199 1.059819 1.070786
## [,8] [,9] [,10]
## [1,] 1.061591 1.061877 1.079348
## [2,] 1.106313 1.106321 1.107904
## [3,] 1.113934 1.127635 1.131233
## [4,] 1.075089 1.079372 1.095900
## [5,] 1.036463 1.037183 1.043278
## [6,] 1.081499 1.115437 1.120747
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$index)
## [,1] [,2] [,3] [,4] [,5]
## [1,] 2637 872 1732 1461 4400
## [2,] 1826 156 3000 8512 2001
## [3,] 960 524 3618 2276 5273
## [4,] 84 2483 4965 1349 5243
## [5,] 8038 8264 4906 2087 1823
## [6,] 9085 1358 3541 8958 6405
head(qout$distance)
## [,1] [,2] [,3] [,4] [,5]
## [1,] 0.9116162 0.9471505 0.9820164 0.9885749 1.0134385
## [2,] 0.9471223 1.0264651 1.0276965 1.0382000 1.0838469
## [3,] 0.9862803 1.0282627 1.0421263 1.0499210 1.0595300
## [4,] 0.7931599 0.8482375 0.8868514 0.9529580 0.9833588
## [5,] 0.9192116 0.9710984 0.9776919 0.9884884 1.0078245
## [6,] 0.9002737 1.0350211 1.0597970 1.0611564 1.0645769
It is similarly easy to use the HNSW algorithm by setting BNPARAM=HnswParam().
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.
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/RtmpBdikDR/file2cc07639387048.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.
sessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
##
## 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
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] BiocNeighbors_1.12.0 knitr_1.36 BiocStyle_2.22.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.7 magrittr_2.0.1 BiocGenerics_0.40.0
## [4] BiocParallel_1.28.0 lattice_0.20-45 R6_2.5.1
## [7] rlang_0.4.12 fastmap_1.1.0 stringr_1.4.0
## [10] tools_4.1.1 parallel_4.1.1 grid_4.1.1
## [13] xfun_0.27 jquerylib_0.1.4 htmltools_0.5.2
## [16] yaml_2.2.1 digest_0.6.28 bookdown_0.24
## [19] Matrix_1.3-4 BiocManager_1.30.16 S4Vectors_0.32.0
## [22] sass_0.4.0 evaluate_0.14 rmarkdown_2.11
## [25] stringi_1.7.5 compiler_4.1.1 bslib_0.3.1
## [28] stats4_4.1.1 jsonlite_1.7.2