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Find *k*-nearest neighbors using searcher object

`Idx = knnsearch(Mdl,Y)`

`Idx = knnsearch(Mdl,Y,Name,Value)`

```
[Idx,D]
= knnsearch(___)
```

searches for the nearest neighbor (i.e., the closest point, row, or observation) in
`Idx`

= knnsearch(`Mdl`

,`Y`

)`Mdl.X`

to each point (i.e., row or observation) in the query
data `Y`

using an exhaustive search or a
*K*d-tree. `knnsearch`

returns
`Idx`

, which is a column vector of the indices in
`Mdl.X`

representing the nearest neighbors.

returns the indices of the closest points in `Idx`

= knnsearch(`Mdl`

,`Y`

,`Name,Value`

)`Mdl.X`

to
`Y`

with additional options specified by one or more
`Name,Value`

pair arguments. For example, specify the number of
nearest neighbors to search for, distance metric different from the one stored in
`Mdl.Distance`

. You can also specify which action to take if
the closest distances are tied.

`[`

additionally returns the matrix `Idx`

,`D`

]
= knnsearch(___)`D`

using any of the input
arguments in the previous syntaxes. `D`

contains the distances
between each observation in `Y`

that correspond to the closest
observations in `Mdl.X`

. By default, the function arranges the
columns of `D`

in ascending order by closeness, with respect to
the distance metric.

`knnsearch`

accepts `ExhaustiveSearcher`

or `KDTreeSearcher`

model objects to search the training data for the nearest neighbors to the query data. An `ExhaustiveSearcher`

model invokes the exhaustive searcher algorithm, and a `KDTreeSearcher`

model defines a *K*d-tree, which `knnsearch`

uses to search for nearest neighbors.

Load Fisher's iris data set. Randomly reserve five observations from the data for query data.

load fisheriris rng(1); % For reproducibility n = size(meas,1); idx = randsample(n,5); X = meas(~ismember(1:n,idx),:); % Training data Y = meas(idx,:); % Query data

The variable `meas`

contains 4 predictors.

Grow a default four-dimensional *K*d-tree.

MdlKDT = KDTreeSearcher(X)

MdlKDT = KDTreeSearcher with properties: BucketSize: 50 Distance: 'euclidean' DistParameter: [] X: [145x4 double]

`MdlKDT`

is a `KDTreeSearcher`

model object. You can alter its writable properties using dot notation.

Prepare an exhaustive nearest neighbor searcher.

MdlES = ExhaustiveSearcher(X)

MdlES = ExhaustiveSearcher with properties: Distance: 'euclidean' DistParameter: [] X: [145x4 double]

`MdlKDT`

is an `ExhaustiveSearcher`

model object. It contains the options, such as the distance metric, to use to find nearest neighbors.

Alternatively, you can grow a *K*d-tree or prepare an exhaustive nearest neighbor searcher using `createns`

.

Search the training data for the nearest neighbors indices that correspond to each query observation. Conduct both types of searches using the default settings. By default, the number of neighbors to search for per query observation is `1`

.

IdxKDT = knnsearch(MdlKDT,Y); IdxES = knnsearch(MdlES,Y); [IdxKDT IdxES]

`ans = `*5×2*
17 17
6 6
1 1
89 89
124 124

In this case, the results of the search are the same.

Grow a *K*d-tree nearest neighbor searcher object by using the `createns`

function. Pass the object and query data to the `knnsearch`

function to find *k*-nearest neighbors.

Load Fisher's iris data set.

`load fisheriris`

Remove five irises randomly from the predictor data to use as a query set.

rng(1); % For reproducibility n = size(meas,1); % Sample size qIdx = randsample(n,5); % Indices of query data tIdx = ~ismember(1:n,qIdx); % Indices of training data Q = meas(qIdx,:); X = meas(tIdx,:);

Grow a four-dimensional *K*d-tree using the training data. Specify the Minkowski distance for finding nearest neighbors.

Mdl = createns(X,'Distance','minkowski')

Mdl = KDTreeSearcher with properties: BucketSize: 50 Distance: 'minkowski' DistParameter: 2 X: [145x4 double]

Because `X`

has four columns and the distance metric is Minkowski, `createns`

creates a `KDTreeSearcher`

model object by default. The Minkowski distance exponent is `2`

by default.

Find the indices of the training data (`Mdl.X`

) that are the two nearest neighbors of each point in the query data (`Q`

).

`IdxNN = knnsearch(Mdl,Q,'K',2)`

`IdxNN = `*5×2*
17 4
6 2
1 12
89 66
124 100

Each row of `IdxNN`

corresponds to a query data observation, and the column order corresponds to the order of the nearest neighbors, with respect to ascending distance. For example, based on the Minkowski distance, the second nearest neighbor of `Q(3,:)`

is `X(12,:)`

.

Load Fisher's iris data set.

`load fisheriris`

Remove five irises randomly from the predictor data to use as a query set.

rng(4); % For reproducibility n = size(meas,1); % Sample size qIdx = randsample(n,5); % Indices of query data X = meas(~ismember(1:n,qIdx),:); Y = meas(qIdx,:);

Grow a four-dimensional *K*d-tree using the training data. Specify the Minkowski distance for finding nearest neighbors.

Mdl = KDTreeSearcher(X);

`Mdl`

is a `KDTreeSearcher`

model object. By default, the distance metric for finding nearest neighbors is the Euclidean metric.

Find the indices of the training data (`X`

) that are the seven nearest neighbors of each point in the query data (`Y`

).

[Idx,D] = knnsearch(Mdl,Y,'K',7,'IncludeTies',true);

`Idx`

and `D`

are five-element cell arrays of vectors, with each vector having at least seven elements.

Display the lengths of the vectors in `Idx`

.

`cellfun('length',Idx)`

`ans = `*5×1*
8
7
7
7
7

Because cell `1`

contains a vector with length greater than *k* = 7, query observation 1 (`Y(1,:)`

) is equally close to at least two observations in `X`

.

Display the indices of the nearest neighbors to `Y(1,:)`

and their distances.

nn5 = Idx{1}

`nn5 = `*1×8*
91 98 67 69 71 93 88 95

nn5d = D{1}

`nn5d = `*1×8*
0.1414 0.2646 0.2828 0.3000 0.3464 0.3742 0.3873 0.3873

Training observations `88`

and `95`

are 0.3873 cm away from query observation `1`

.

Train two `KDTreeSearcher`

models using different distance metrics, and compare *k*-nearest neighbors of query data for the two models.

Load Fisher's iris data set. Consider the petal measurements as predictors.

load fisheriris X = meas(:,3:4); % Predictors Y = species; % Response

Train a `KDTreeSearcher`

model object by using the predictors. Specify the Minkowski distance with exponent 5.

KDTreeMdl = KDTreeSearcher(X,'Distance','minkowski','P',5)

KDTreeMdl = KDTreeSearcher with properties: BucketSize: 50 Distance: 'minkowski' DistParameter: 5 X: [150x2 double]

Find the 10 nearest neighbors from `X`

to a query point (`newpoint`

), first using Minkowski then Chebychev distance metrics. The query point must have the same column dimension as the data used to train the model.

newpoint = [5 1.45]; [IdxMk,DMk] = knnsearch(KDTreeMdl,newpoint,'k',10); [IdxCb,DCb] = knnsearch(KDTreeMdl,newpoint,'k',10,'Distance','chebychev');

`IdxMk`

and `IdxCb`

are 1-by-10 matrices containing the row indices of `X`

corresponding to the nearest neighbors to `newpoint`

using Minkowski and Chebychev distances, respectively. Element (1,1) is the nearest, element (1,2) is the next nearest, and so on.

Plot the training data, query point, and nearest neighbors.

figure; gscatter(X(:,1),X(:,2),Y); title('Fisher''s Iris Data -- Nearest Neighbors'); xlabel('Petal length (cm)'); ylabel('Petal width (cm)'); hold on plot(newpoint(1),newpoint(2),'kx','MarkerSize',10,'LineWidth',2); % Query point plot(X(IdxMk,1),X(IdxMk,2),'o','Color',[.5 .5 .5],'MarkerSize',10); % Minkowski nearest neighbors plot(X(IdxCb,1),X(IdxCb,2),'p','Color',[.5 .5 .5],'MarkerSize',10); % Chebychev nearest neighbors legend('setosa','versicolor','virginica','query point',... 'minkowski','chebychev','Location','Best');

Zoom in on the points of interest.

h = gca; % Get current axis handle. h.XLim = [4.5 5.5]; h.YLim = [1 2]; axis square;

Several observations are equal, which is why only eight nearest neighbors are identified in the plot.

`Mdl`

— Nearest neighbor searcher`ExhaustiveSearcher`

model object | `KDTreeSearcher`

model objectNearest neighbor searcher, specified as an `ExhaustiveSearcher`

or `KDTreeSearcher`

model object, respectively.

If `Mdl`

is an `ExhaustiveSearcher`

model, then
`knnsearch`

searches for nearest neighbors using an exhaustive
search. Otherwise, `knnsearch`

uses the grown
*K*d-tree to search for nearest neighbors.

`Y`

— Query datanumeric matrix

Query data, specified as a numeric matrix.

`Y`

is an *m*-by-*K* matrix.
Rows of `Y`

correspond to observations (i.e., examples),
and columns correspond to predictors (i.e., variables or features). `Y`

must
have the same number of columns as the training data stored in `Mdl.X`

.

**Data Types: **`single`

| `double`

Specify optional
comma-separated pairs of `Name,Value`

arguments. `Name`

is
the argument name and `Value`

is the corresponding value.
`Name`

must appear inside quotes. You can specify several name and value
pair arguments in any order as
`Name1,Value1,...,NameN,ValueN`

.

`'K',2,'Distance','minkowski'`

specifies to find the two
nearest neighbors of `Mdl.X`

to each point in `Y`

and to use the Minkowski distance metric.`'Distance'`

— Distance metric`Mdl.Distance`

(default) | `'cityblock'`

| `'euclidean'`

| `'mahalanobis'`

| `'minkowski'`

| `'seuclidean'`

| function handle | ...Distance metric used to find neighbors of the training data to the query observations,
specified as the comma-separated pair consisting of `'Distance'`

and a
character vector, string scalar, or function handle.

For both types of nearest neighbor searchers, `knnsearch`

supports these
distance metrics.

Value | Description |
---|---|

`'chebychev'` | Chebychev distance (maximum coordinate difference). |

`'cityblock'` | City block distance. |

`'euclidean'` | Euclidean distance. |

`'minkowski'` | Minkowski distance. The default exponent is 2. To specify a different exponent, use the
`'P'` name-value pair argument. |

If `Mdl`

is an `ExhaustiveSearcher`

model object, then
`knnsearch`

also supports these distance metrics.

Value | Description |
---|---|

`'correlation'` | One minus the sample linear correlation between observations (treated as sequences of values). |

`'cosine'` | One minus the cosine of the included angle between observations (treated as row vectors). |

`'hamming'` | Hamming distance, which is the percentage of coordinates that differ. |

`'jaccard'` | One minus the Jaccard coefficient, which is the percentage of nonzero coordinates that differ. |

`'mahalanobis'` | Mahalanobis distance, computed using a positive definite covariance matrix. To change the
value of the covariance matrix, use the
`'Cov'` name-value pair
argument. |

`'seuclidean'` | Standardized Euclidean distance. Each coordinate difference between rows in
`Mdl.X` and the query matrix is
scaled by dividing by the corresponding element of
the standard deviation computed from
`Mdl.X` . To specify another
scaling, use the `'Scale'`
name-value pair argument. |

`'spearman'` | One minus the sample Spearman's rank correlation between observations (treated as sequences of values). |

If `Mdl`

is an `ExhaustiveSearcher`

model object, then you
can also specify a function handle for a custom distance metric
by using `@`

(for example,
`@distfun`

). The custom distance
function must:

Have the form

`function D2 = distfun(ZI,ZJ)`

.Take as arguments:

A 1-by-

*K*vector`ZI`

containing a single row from`Mdl.X`

or`Y`

, where*K*is the number of columns of`Mdl.X`

.An

*m*-by-*K*matrix`ZJ`

containing multiple rows of`Mdl.X`

or`Y`

, where*m*is a positive integer.

Return an

*m*-by-1 vector of distances`D2`

, where`D2(`

is the distance between the observations)`j`

`ZI`

and`ZJ(`

.,:)`j`

For more details, see Distance Metrics.

**Example: **`'Distance','minkowski'`

`'IncludeTies'`

— Flag to include all nearest neighbors`false`

(`0`

) (default) | `true `

(`1`

)Flag to include nearest neighbors that have the same distance from
query observations, specified as the comma-separated pair consisting of
`'IncludeTies'`

and `false`

(`0`

) or `true`

(`1`

).

If `IncludeTies`

is `true`

, then:

`knnsearch`

includes all nearest neighbors whose distances are equal to the*k*th smallest distance in the output arguments, where*k*is the number of searched nearest neighbors specified by the`'K'`

name-value pair argument.`Idx`

and`D`

are*m*-by-`1`

cell arrays such that each cell contains a vector of at least*k*indices and distances, respectively. Each vector in`D`

contains arranged distances in ascending order. Each row in`Idx`

contains the indices of the nearest neighbors corresponding to the distances in`D`

.

If `IncludeTies`

is
`false`

, then `knnsearch`

chooses
the observation with the smallest index among the observations that have
the same distance from a query point.

**Example: **`'IncludeTies',true`

`'K'`

— Number of nearest neighbors`1`

(default) | positive integerNumber of nearest neighbors to search for in the training data per
query observation, specified as the comma-separated pair consisting of
`'K'`

and a positive integer.

**Example: **`'K',2`

**Data Types: **`single`

| `double`

`'P'`

— Exponent for Minkowski distance metric`2`

(default) | positive scalarExponent for the Minkowski distance metric, specified as the comma-separated pair consisting
of `'P'`

and a positive scalar. This argument is valid only if
`'Distance'`

is `'minkowski'`

.

**Example: **`'P',3`

**Data Types: **`single`

| `double`

`'SortIndices'`

— Flag to sort returned indices according to distance`true`

(`1`

) (default) | `false`

(`0`

)Flag to sort returned indices according to distance, specified as the
comma-separated pair consisting of `'SortIndices'`

and
either `true`

(`1`

) or
`false`

(`0`

).

For faster performance, you can set `SortIndices`

to `false`

when the following are true:

`Y`

contains many observations that have many nearest neighbors in`X`

.`Mdl`

is a`KDTreeSearcher`

model object.`IncludeTies`

is`false`

.

In this case, `knnsearch`

returns the
indices of the nearest neighbors in no particular order. When
`SortIndices`

is `true`

, the
function arranges the nearest-neighbor indices in ascending order by
distance.

`SortIndices`

is `true`

by
default. When `Mdl`

is an
`ExhaustiveSearcher`

model object or
`IncludeTies`

is `true`

, the
function always sorts the indices.

**Example: **`'SortIndices',false`

**Data Types: **`logical`

`'Cov'`

— Covariance matrix for Mahalanobis distance metric`nancov(Mdl.X)`

(default) | positive definite matrixCovariance matrix for the Mahalanobis distance metric, specified as the comma-separated pair
consisting of `'Cov'`

and a positive definite matrix.
`Cov`

is a *K*-by-*K* matrix,
where *K* is the number of columns of `Mdl.X`

. If you
specify `Cov`

and do not specify
`'`

`Distance`

`','mahalanobis'`

,
then `knnsearch`

returns an error message.

**Example: **`'Cov',eye(3)`

**Data Types: **`single`

| `double`

`'Scale'`

— Scale parameter value for standardized Euclidean distance metric`nanstd(Mdl.X)`

(default) | nonnegative numeric vectorScale parameter value for the standardized Euclidean distance metric, specified as the
comma-separated pair consisting of `'Scale'`

and a nonnegative numeric
vector. `Scale`

has length *K*, where
*K* is the number of columns of `Mdl.X`

.

The software scales each difference between the training and query data using the
corresponding element of `Scale`

. If you specify
`Scale`

and do not specify
`'`

`Distance`

`','seuclidean'`

,
then `knnsearch`

returns an error message.

**Example: **```
'Scale',quantile(Mdl.X,0.75) -
quantile(Mdl.X,0.25)
```

**Data Types: **`single`

| `double`

If you specify
`'`

`Distance`

`'`

,
`'`

`Cov`

`'`

,
`'`

`P`

`'`

, or
`'`

`Scale`

`'`

, then
`Mdl.Distance`

and `Mdl.DistParameter`

do
not change value.

`Idx`

— Training data indices of nearest neighborsnumeric matrix | cell array of numeric vectors

Training data indices of nearest neighbors, returned as a numeric matrix or cell array of numeric vectors.

If you do not specify

`IncludeTies`

(`false`

by default), then`Idx`

is an*m*-by-*k*numeric matrix, where*m*is the number of rows in`Y`

and*k*is the number of searched nearest neighbors specified by the`'K'`

name-value pair argument.`Idx(j,i)`

indicates that`Mdl.X(Idx(j,i),:)`

is one of the*k*closest observations in`Mdl.X`

to the query observation`Y(j,:)`

.If you specify

`'IncludeTies',true`

, then`Idx`

is an*m*-by-`1`

cell array such that cell`j`

(`Idx{j}`

) contains a vector of at least*k*indices of the closest observations in`Mdl.X`

to the query observation`Y(j,:)`

.

If `SortIndices`

is `true`

, then
`knnsearch`

arranges the indices in ascending order
by distance.

`D`

— Distances of nearest neighborsnumeric matrix | cell array of numeric vectors

Distances of the nearest neighbors to the query data, returned as a numeric matrix or cell array of numeric vectors.

If you do not specify

`IncludeTies`

(`false`

by default), then`D`

is an*m*-by-*k*numeric matrix, where*m*is the number of rows in`Y`

and*k*is the number of searched nearest neighbors specified by the`'K'`

name-value pair argument.`D(j,i)`

is the distance between`Mdl.X(Idx(j,i),:)`

and the query observation`Y(j,:)`

with respect to the distance metric.If you specify

`'IncludeTies',true`

, then`D`

is an*m*-by-`1`

cell array such that cell`j`

(`D{j}`

) contains a vector of at least*k*distances of the closest observations in`Mdl.X`

to the query observation`Y(j,:)`

.

If `SortIndices`

is `true`

, then
`knnsearch`

arranges the distances in ascending
order.

`knnsearch`

finds the *k* (positive integer)
points in `Mdl.X`

that are *k*-nearest for each
`Y`

point. In contrast, `rangesearch`

finds all the points in `Mdl.X`

that are
within distance `r`

(positive scalar) of each `Y`

point.

`knnsearch`

is an object function that requires an`ExhaustiveSearcher`

or a`KDTreeSearcher`

model object and query data. Under equivalent conditions, the`knnsearch`

object function returns the same results as the`knnsearch`

function when you specify the name-value pair argument`'NSMethod','exhaustive'`

or`'NSMethod','kdtree'`

, respectively.For

*k*-nearest neighbors classification, see`fitcknn`

and`ClassificationKNN`

.

[1] Friedman, J. H., Bentely, J., and Finkel, R. A. (1977). “An Algorithm
for Finding Best Matches in Logarithmic Expected Time.” *ACM
Transactions on Mathematical Software* Vol. 3, Issue 3, Sept. 1977, pp.
209–226.

Generate C and C++ code using MATLAB® Coder™.

Usage notes and limitations:

This table contains notes about the arguments of

`knnsearch`

. Arguments not included in this table are fully supported.Argument Notes and Limitations `Mdl`

There are two ways to use

`Mdl`

in code generation. For an example, see Code Generation for Nearest Neighbor Searcher.Use

`saveCompactModel`

,`loadCompactModel`

, and`codegen`

to generate code for the`knnsearch`

function. Save a trained model by using`saveCompactModel`

. Define an entry-point function that loads the saved model by using`loadCompactModel`

and calls the`knnsearch`

function. Then use`codegen`

to generate code for the entry-point function.Include

`coder.Constant(Mdl)`

in the`-args`

value of`codegen`

.

If

`Mdl`

is a`KDTreeSearcher`

object, and the code generation build type is a MEX function, then`codegen`

generates a MEX function using Intel^{®}Threading Building Blocks (TBB) for parallel computation. Otherwise,`codegen`

generates code using`parfor`

.MEX function for the

*k*d-tree search algorithm —`codegen`

generates an optimized MEX function using Intel TBB for parallel computation on multicore platforms. You can use the MEX function to accelerate MATLAB^{®}algorithms. For details on Intel TBB, see https://software.intel.com/en-us/intel-tbb.If you generate the MEX function to test the generated code of the

`parfor`

version, you can disable the usage of Intel TBB. Set the`ExtrinsicCalls`

property of the MEX configuration object to`false`

. For details, see`coder.MexCodeConfig`

.MEX function for the exhaustive search algorithm and standalone C/C++ code for both algorithms — The generated code of

`knnsearch`

uses`parfor`

to create loops that run in parallel on supported shared-memory multicore platforms in the generated code. If your compiler does not support the Open Multiprocessing (OpenMP) application interface or you disable OpenMP library, MATLAB Coder™ treats the`parfor`

-loops as`for`

-loops. To find supported compilers, see Supported Compilers. To disable OpenMP library, set the`EnableOpenMP`

property of the configuration object to`false`

. For details, see`coder.CodeConfig`

.

`'Distance'`

Cannot be a custom distance function.

Must be a compile-time constant; its value cannot change in the generated code.

`'IncludeTies'`

Must be a compile-time constant; its value cannot change in the generated code.

`'SortIndices'`

Not supported. The output arguments are always sorted. Name-value pair arguments Names in name-value pair arguments must be compile-time constants. For example, to allow a user-defined exponent for the Minkowski distance in the generated code, include

`{coder.Constant('Distance'),coder.Constant('Minkowski'),coder.Constant('P'),0}`

in the`-args`

value of`codegen`

.`Idx`

When you specify

`'IncludeTies'`

as`true`

, the sorted order of tied distances in the generated code can be different from the order in MATLAB due to numerical precision.

For more information, see Introduction to Code Generation and Code Generation for Nearest Neighbor Searcher.

`ClassificationKNN`

| `ExhaustiveSearcher`

| `KDTreeSearcher`

| `createns`

| `fitcknn`

| `knnsearch`

| `rangesearch`

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