ExhaustiveParam: The ExhaustiveParam class

In LTLA/BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages

The ExhaustiveParam class

Description

A class to hold parameters for the exhaustive algorithm for exact nearest neighbor identification.

Usage

ExhaustiveParam(distance = c("Euclidean", "Manhattan", "Cosine"))

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

Arguments

distance	String specifying the distance metric to use. Cosine distances are implemented as Euclidean distances on L2-normalized coordinates.
BNPARAM	An ExhaustiveParam instance.

Details

The exhaustive search computes all pairwise distances between data and query points to identify nearest neighbors of the latter. It has quadratic complexity and is theoretically the worst-performing method; however, it has effectively no overhead from constructing or querying indexing structures, making it faster for in situations where indexing provides little benefit. This includes queries against datasets with few data points or very high dimensionality.

All that said, this algorithm is largely provided as a baseline for comparing against the other algorithms.

Value

The ExhaustiveParam constructor returns an instance of the ExhaustiveParam class.

The defineBuilder method returns an external pointer that can be used in buildIndex to construct an exhaustive index.

Author(s)

Allison Vuong

See Also

BiocNeighborParam, for the parent class and its available methods.

Examples

(out <- ExhaustiveParam())

LTLA/BiocNeighbors documentation built on Oct. 22, 2024, 11:42 p.m.