KmknnParam: The KmknnParam class

In LTLA/kmknn: Nearest Neighbor Detection for Bioconductor Packages

The KmknnParam class

Description

A class to hold parameters for the k-means k-nearest-neighbors (KMKNN) algorithm for exact nearest neighbor identification.

Usage

KmknnParam(..., distance = c("Euclidean", "Manhattan", "Cosine"))

## S4 method for signature 'KmknnParam'
defineBuilder(BNPARAM)

Arguments

...	Further arguments, ignored.
distance	String specifying the distance metric to use. Cosine distances are implemented as Euclidean distances on L2-normalized coordinates.
BNPARAM	A KmknnParam instance.

Details

In the KMKNN algorithm (Wang, 2012), k-means clustering is first applied to the data points using the square root of the number of points as the number of cluster centers. The cluster assignment and distance to the assigned cluster center for each point represent the KMKNN indexing information. This speeds up the nearest neighbor search by exploiting the triangle inequality between cluster centers, the query point and each point in the cluster to narrow the search space. The advantage of the KMKNN approach is its simplicity and minimal overhead, resulting in performance improvements over conventional tree-based methods for high-dimensional data where most points need to be searched anyway. It is also trivially extended to find all neighbors within a threshold distance from a query point.

Note that KMKNN operates much more naturally with Euclidean distances. Computational efficiency may not be optimal when using it with other choices of distance, though the results will still be exact.

Value

The KmknnParam constructor returns an instance of the KmknnParam class.

The defineBuilder method returns a list that can be used in buildIndex to construct a KMKNN index.

Author(s)

Aaron Lun, using code from the cydar package.

References

Wang X (2012). A fast exact k-nearest neighbors algorithm for high dimensional search using k-means clustering and triangle inequality. Proc Int Jt Conf Neural Netw, 43, 6:2351-2358.

See Also

BiocNeighborParam, for the parent class and its available methods.

Examples

(out <- KmknnParam(iter.max=100))

LTLA/kmknn documentation built on Oct. 18, 2024, 9:01 p.m.