@saehrimnir/druidjs / KKMDS

Class: KKMDS<T>

Defined in: dimred/KKMDS.js:22

Kamada-Kawai Multidimensional Scaling (KKMDS)

StressMDS fixed at weights: -2, weighting each pair by 1 / d_ij². That is the Kamada-Kawai energy from graph drawing, known in the MDS literature as elastic scaling.

Its classic use is laying out a graph from its shortest-path distances — pass those as a "precomputed" matrix, as MINFOTree does.

Template

T

See

• https://doi.org/10.1016/0020-0190(89)90102-6
• StressMDS for other weightings.

Extends

• StressMDS

Type Parameters

Type Parameter	Description
T extends InputType

Constructors

Constructor

new KKMDS<T>(X: T, parameters?: Partial<ParametersKKMDS>): KKMDS<T>;

Defined in: dimred/KKMDS.js:30

Kamada-Kawai weighted MDS.

Parameters

Parameter	Type	Description
X	T	The high-dimensional data, or a precomputed distance matrix.
parameters?	Partial<ParametersKKMDS>	Object containing parameterization of the DR method. weights is not among them; it is fixed at -2.

Returns

KKMDS<T>

Overrides

StressMDS.constructor

Properties

Property	Type	Default value	Description	Inherited from	Defined in
__input	T	undefined	-	StressMDS.__input	dimred/DR.js:46
_D	number	undefined	-	StressMDS._D	dimred/DR.js:28
_energy	number	Infinity	-	StressMDS._energy	dimred/StressMDS.js:63
_is_initialized	boolean	undefined	-	StressMDS._is_initialized	dimred/DR.js:34
_N	number	undefined	-	StressMDS._N	dimred/DR.js:30
_parameters	ParametersStressMDS	undefined	-	StressMDS._parameters	dimred/DR.js:49
_randomizer	Randomizer	undefined	-	StressMDS._randomizer	dimred/DR.js:32
_target_distances	Matrix | undefined	undefined	The target distances. Named apart from the base class's _D, which is the input dimensionality of X, not a matrix.	StressMDS._target_distances	dimred/StressMDS.js:57
_type	"array" | "matrix" | "typed"	undefined	-	StressMDS._type	dimred/DR.js:54
_weights	Matrix | undefined	undefined	-	StressMDS._weights	dimred/StressMDS.js:60
X	Matrix	undefined	-	StressMDS.X	dimred/DR.js:56
Y	Matrix	undefined	-	StressMDS.Y	dimred/DR.js:58

Accessors

energy

Get Signature

get energy(): number;

Defined in: dimred/StressMDS.js:103

The weighted stress σ(Y) of the current embedding.

Returns

number

Inherited from

StressMDS.energy

---

projection

Get Signature

get projection(): T;

Defined in: dimred/DR.js:219

Returns

T

The projection in the type of input X.

Inherited from

StressMDS.projection

---

weights

Get Signature

get weights(): Matrix;

Defined in: dimred/StressMDS.js:113

The weight matrix actually in use, whatever form weights was given in.

Returns

Matrix

Inherited from

StressMDS.weights

Methods

[dispose]()

dispose: void;

Defined in: dimred/DR.js:320

Alias of release for the using declaration, so a hand-driven run frees its buffers when the block exits. Note that transform and a completed or break-ed generator() already release on their own — this only matters for a generator abandoned part way.

using tsne = new TSNE(X, { d: 2 });
const steps = tsne.generator(500);
steps.next(); // buffers released when the enclosing block exits

Returns

void

Inherited from

StressMDS.[dispose]

---

check_init()

check_init(): DR<T, ParametersStressMDS>;

Defined in: dimred/DR.js:210

If the respective DR method has an init function, call it before transform.

Returns

DR<T, ParametersStressMDS>

Inherited from

StressMDS.check_init

---

generator()

generator(): Generator<T, T, void>;

Defined in: dimred/StressMDS.js:326

Computes the projection.

Returns

Generator<T, T, void>

A generator yielding the intermediate steps of the projection.

Inherited from

StressMDS.generator

---

init()

init(): KKMDS<T>;

Defined in: dimred/StressMDS.js:186

Computes the target distances, the weights, and the starting configuration.

Returns

KKMDS<T>

Inherited from

StressMDS.init

---

parameter()

Call Signature

parameter(): ParametersStressMDS;

Defined in: dimred/DR.js:82

Get all Parameters.

Returns

ParametersStressMDS

Inherited from

StressMDS.parameter

Call Signature

parameter<K>(name: K): ParametersStressMDS[K];

Defined in: dimred/DR.js:88

Get value of given parameter.

Type Parameters

Type Parameter	Description
K extends keyof ParametersStressMDS

Parameters

Parameter	Type	Description
name	K	Name of the parameter.

Returns

ParametersStressMDS[K]

Inherited from

StressMDS.parameter

Call Signature

parameter<K>(name: K, value: ParametersStressMDS[K]): KKMDS<T>;

Defined in: dimred/DR.js:95

Set value of given parameter.

Type Parameters

Type Parameter	Description
K extends keyof ParametersStressMDS

Parameters

Parameter	Type	Description
name	K	Name of the parameter.
value	ParametersStressMDS[K]	Value of the parameter to set.

Returns

KKMDS<T>

Inherited from

StressMDS.parameter

---

release()

release(): KKMDS<T>;

Defined in: dimred/DR.js:302

Hands back the WASM buffers this instance is holding.

Only needed after driving generator() by hand and stopping early — a plain transform(), or a for…of over generator() (including one you break), already releases when it ends. It frees only this method's buffers, never another running instance's, and the next run simply reallocates, so it is safe to call at any time, more than once, and while other instances are mid-run.

Returns

KKMDS<T>

Example

const tsne = new TSNE(X, { d: 2 });
const steps = tsne.generator(500);
steps.next();
tsne.release(); // stop early and give the buffers back

Inherited from

StressMDS.release

---

transform()

transform(): T;

Defined in: dimred/StressMDS.js:386

Computes the projection.

Returns

T

Inherited from

StressMDS.transform

---

transform_async()

transform_async(...args: unknown[]): Promise<T>;

Defined in: dimred/DR.js:241

Computes the projection.

Parameters

Parameter	Type	Description
...args	unknown[]	Arguments the transform method of the respective DR method takes.

Returns

Promise<T>

The dimensionality reduced dataset.

Inherited from

StressMDS.transform_async

---

generator()

static generator<T>(X: T, parameters?: Partial<ParametersKKMDS>): Generator<T, T, void>;

Defined in: dimred/KKMDS.js:51

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

Parameter	Type	Description
X	T	-
parameters?	Partial<ParametersKKMDS>	-

Returns

Generator<T, T, void>

Overrides

StressMDS.generator

---

transform()

static transform<T>(X: T, parameters?: Partial<ParametersKKMDS>): T;

Defined in: dimred/KKMDS.js:40

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

Parameter	Type	Description
X	T	-
parameters?	Partial<ParametersKKMDS>	-

Returns

T

Overrides

StressMDS.transform

---

transform_async()

static transform_async<T>(X: T, parameters?: Partial<ParametersKKMDS>): Promise<T>;

Defined in: dimred/KKMDS.js:63

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

Parameter	Type	Description
X	T	-
parameters?	Partial<ParametersKKMDS>	-

Returns

Promise<T>

Overrides

StressMDS.transform_async