Math::Nearest

Raku package with algorithms for finding nearest neighbors for different sets of objects.

Math::Nearest

Raku package for various algorithm for finding Nearest Neighbors (NNs)

The implementation is tested for correctness against Mathematica's Nearest. (See the resource files.)

Features

Finds both top-k Nearest Neighbors (NNs).
Finds NNs within a ball with a given radius.
Can return distances, indexes, and labels for the found NNs.
- The result shape is controlled with the option :prop.
Works with arrays of numbers, arrays of arrays of numbers, and arrays of pairs.
Utilizes distance functions from "Math::DistanceFunctions".
- Which can be specified by their string names, like, "bray-curtis" or "cosine-distance".
Allows custom distance functions to be used.
Currently has two algorithms (simple) Scan and K-Dimensional Tree (KDTree).

Installation

From Zef ecosystem:

zef install Math::Nearest

From GitHub:

zef install https://github.com/antononcube/Raku-Math-Nearest.git

Usage examples

Setup

use Math::Nearest;
use Data::TypeSystem;
use Text::Plot;

# (Any)

Set of points

Make a random set of points:

my @points = ([(^100).rand, (^100).rand] xx 30).unique;
deduce-type(@points);

# Vector(Vector(Atom((Numeric)), 2), 30)

Create the K-dimensional tree object

my &finder = nearest(@points);

say &finder;

# Math::Nearest::Finder(Algorithm::KDimensionalTree(points => 30, distance-function => &euclidean-distance))

Nearest k-neighbors

Use as a search point one from the points set:

my @searchPoint = |@points.head;

# [82.7997137400612 51.815911977937425]

Find 4 nearest neighbors:

my @res = &finder(@searchPoint, 4);
.say for @res;

# [82.7997137400612 51.815911977937425]
# [76.74690048700612 45.30314548421236]
# [93.76468756535048 53.45047592032191]
# [71.62175684954694 55.56128771507127]

Instead of using the "finder" object as a callable (functor) we can use nearest:

.say for nearest(&finder, @searchPoint, count => 4)

# [82.7997137400612 51.815911977937425]
# [76.74690048700612 45.30314548421236]
# [93.76468756535048 53.45047592032191]
# [71.62175684954694 55.56128771507127]

Find nearest neighbors within a ball with radius 30:

.say for &finder(@searchPoint, (Whatever, 30))

# [93.76468756535048 53.45047592032191]
# [82.7997137400612 51.815911977937425]
# [68.66354164361587 52.25273427733615]
# [67.1439347976243 51.678609421192775]
# [76.74690048700612 45.30314548421236]
# [71.62175684954694 55.56128771507127]
# [58.6565707908774 67.61014125155556]
# [80.23300662613086 80.49154195793962]
# [82.92996945428985 71.0086509061165]
# [54.30669960433475 57.177447534448724]

Plot

Plot the points, the found nearest neighbors, and the search point:

my @point-char =  <* ⏺ ▲>;
say <data nns search> Z=> @point-char;
say text-list-plot(
[@points, @res, [@searchPoint,]],
:@point-char,
x-limit => (0, 100),
y-limit => (0, 100),
width => 60,
height => 20);

# (data => * nns => ⏺ search => ▲)
# ++----------+-----------+----------+-----------+----------++
# +                                                    *     + 100.00
# |                                                          |
# |      *                                                   |
# +*   *                      *    *   *         *           +  80.00
# |      *                                                   |
# |    *                                          *          |
# |                                 *                        |
# +                               *                          +  60.00
# |                         *            ** ⏺     ▲     ⏺    |
# |                                            ⏺             |
# + *                                                        +  40.00
# |*   *                                                     |
# |                                                          |
# |                           *                              |
# +                                               *          +  20.00
# |                       *                       *          |
# |              *               *                           |
# +                                                          +   0.00
# ++----------+-----------+----------+-----------+----------++
#  0.00       20.00       40.00      60.00       80.00      100.00

TODO

TODO Implementation
- TODO Implement the Octree nearest neighbors algorithm.
- TODO Make the nearest methods work with strings
  - For example, using Hamming distance over a collection of words.
  - Requires using the distance function as a comparator for the splitting hyperplanes.
  - This means, any objects can be used as long as they provide a distance function.
TODO Documentation
- DONE Basic usage examples with text plots
- TODO More extensive documentation with a Jupyter notebook
  - Using "JavaScript::D3".
- TODO Corresponding blog post
- MAYBE Corresponding video