@saehrimnir/druidjs / UMAP

Class: UMAP<T>

Defined in: dimred/UMAP.js:41

Uniform Manifold Approximation and Projection (UMAP)

A novel manifold learning technique for dimensionality reduction. UMAP is constructed from a theoretical framework based on Riemannian geometry and algebraic topology. It is often faster than t-SNE while preserving more of the global structure.

Template

See

• Paper
• TSNE for a similar visualization technique

Example

import * as druid from "@saehrimnir/druidjs";

const X = [[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12]];
const umap = new druid.UMAP(X, {
    n_neighbors: 15,
    min_dist: 0.1,
    d: 2,
    seed: 42
});

const Y = umap.transform(500); // 500 iterations
// [[x1, y1], [x2, y2], [x3, y3]]

Extends

• DR

Type Parameters

Type Parameter	Description
T extends InputType

Constructors

Constructor

new UMAP<T>(X: T, parameters?: Partial<ParametersUMAP>): UMAP<T>;

Defined in: dimred/UMAP.js:46

Parameters

Parameter	Type	Description
X	T	The high-dimensional data.
parameters?	Partial<ParametersUMAP>	Object containing parameterization of the DR method.

Returns

UMAP<T>

Overrides

DR.constructor

Properties

Property	Type	Inherited from	Defined in
__input	T	DR.__input	dimred/DR.js:38
_a	number | undefined	-	dimred/UMAP.js:331
_alpha	number | undefined	-	dimred/UMAP.js:479
_b	number | undefined	-	dimred/UMAP.js:332
_D	number	DR._D	dimred/DR.js:20
_epoch_of_next_negative_sample	Float32Array<ArrayBuffer> | undefined	-	dimred/UMAP.js:341
_epoch_of_next_sample	Float32Array<ArrayBuffer> | undefined	-	dimred/UMAP.js:340
_epochs_per_negative_sample	Float32Array<ArrayBuffer> | undefined	-	dimred/UMAP.js:339
_epochs_per_sample	Float32Array<ArrayBufferLike> | undefined	-	dimred/UMAP.js:338
_graph	Matrix | undefined	-	dimred/UMAP.js:333
_head	number[] | undefined	-	dimred/UMAP.js:335
_is_initialized	boolean	DR._is_initialized	dimred/DR.js:26
_iter	number	-	dimred/UMAP.js:82
_N	number	DR._N	dimred/DR.js:22
_parameters	ParametersUMAP	DR._parameters	dimred/DR.js:41
_randomizer	Randomizer	DR._randomizer	dimred/DR.js:24
_tail	number[] | undefined	-	dimred/UMAP.js:336
_type	"array" | "matrix" | "typed"	DR._type	dimred/DR.js:46
_weights	number[] | undefined	-	dimred/UMAP.js:337
X	Matrix	DR.X	dimred/DR.js:48
Y	Matrix	DR.Y	dimred/UMAP.js:84

Accessors

projection

Get Signature

get projection(): T;

Defined in: dimred/DR.js:211

Returns

T

The projection in the type of input X.

Inherited from

DR.projection

Methods

check_init()

check_init(): DR<T, ParametersUMAP>;

Defined in: dimred/DR.js:202

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

Returns

DR<T, ParametersUMAP>

Inherited from

DR.check_init

---

generator()

generator(iterations?: number): Generator<T, T, void>;

Defined in: dimred/UMAP.js:370

Parameters

Parameter	Type	Default value	Description
iterations?	number	350	Number of iterations. Default is 350

Returns

Generator<T, T, void>

Overrides

DR.generator

---

graph()

graph(): {
  cols: number[] | undefined;
  rows: number[] | undefined;
  weights: number[] | undefined;
};

Defined in: dimred/UMAP.js:345

Returns

{
  cols: number[] | undefined;
  rows: number[] | undefined;
  weights: number[] | undefined;
}

Name	Type	Defined in
cols	number[] | undefined	dimred/UMAP.js:347
rows	number[] | undefined	dimred/UMAP.js:347
weights	number[] | undefined	dimred/UMAP.js:347

---

init()

init(): UMAP<T>;

Defined in: dimred/UMAP.js:324

Computes all necessary

Returns

UMAP<T>

Overrides

DR.init

---

parameter()

Call Signature

parameter(): ParametersUMAP;

Defined in: dimred/DR.js:74

Get all Parameters.

Returns

ParametersUMAP

Inherited from

DR.parameter

Call Signature

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

Defined in: dimred/DR.js:80

Get value of given parameter.

Type Parameters

Type Parameter	Description
K extends keyof ParametersUMAP

Parameters

Parameter	Type	Description
name	K	Name of the parameter.

Returns

ParametersUMAP[K]

Inherited from

DR.parameter

Call Signature

parameter<K>(name: K, value: ParametersUMAP[K]): UMAP<T>;

Defined in: dimred/DR.js:87

Set value of given parameter.

Type Parameters

Type Parameter	Description
K extends keyof ParametersUMAP

Parameters

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

Returns

UMAP<T>

Inherited from

DR.parameter

---

transform()

transform(iterations?: number): T;

Defined in: dimred/UMAP.js:354

Parameters

Parameter	Type	Default value	Description
iterations?	number	350	Number of iterations. Default is 350

Returns

T

Overrides

DR.transform

---

transform_async()

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

Defined in: dimred/DR.js:233

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

DR.transform_async

---

generator()

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

Defined in: dimred/UMAP.js:502

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

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

Returns

Generator<T, T, void>

Overrides

DR.generator

---

transform()

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

Defined in: dimred/UMAP.js:491

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

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

Returns

T

Overrides

DR.transform

---

transform_async()

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

Defined in: dimred/UMAP.js:514

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

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

Returns

Promise<T>

Overrides

DR.transform_async