@saehrimnir/druidjs / UMAP

Class: UMAP<T>

Defined in: dimred/UMAP.js:48

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.

A given seed reproduces an embedding exactly within one engine and library build, but not across browsers or Node versions: the gradient descent is chaotic, so a last-bit difference grows into a visibly different — though equally valid — layout. See DR for why.

Template

T

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:58

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:46
_a	number | undefined	-	dimred/UMAP.js:356
_alpha	number | undefined	-	dimred/UMAP.js:591
_b	number | undefined	-	dimred/UMAP.js:357
_D	number	DR._D	dimred/DR.js:28
_epoch_of_next_negative_sample	Float32Array<ArrayBuffer> | undefined	-	dimred/UMAP.js:366
_epoch_of_next_sample	Float32Array<ArrayBuffer> | undefined	-	dimred/UMAP.js:365
_epochs_per_negative_sample	Float32Array<ArrayBuffer> | undefined	-	dimred/UMAP.js:364
_epochs_per_sample	Float32Array<ArrayBufferLike> | undefined	-	dimred/UMAP.js:363
_graph	Matrix | undefined	-	dimred/UMAP.js:358
_head	number[] | undefined	-	dimred/UMAP.js:360
_head_int32	Int32Array<ArrayBuffer> | undefined	-	dimred/UMAP.js:545
_is_initialized	boolean	DR._is_initialized	dimred/DR.js:34
_iter	number	-	dimred/UMAP.js:94
_N	number	DR._N	dimred/DR.js:30
_parameters	ParametersUMAP	DR._parameters	dimred/DR.js:49
_randomizer	Randomizer	DR._randomizer	dimred/DR.js:32
_tail	number[] | undefined	-	dimred/UMAP.js:361
_tail_int32	Int32Array<ArrayBuffer> | undefined	-	dimred/UMAP.js:546
_type	"array" | "matrix" | "typed"	DR._type	dimred/DR.js:54
_weights	number[] | undefined	-	dimred/UMAP.js:362
X	Matrix	DR.X	dimred/DR.js:56
Y	Matrix	DR.Y	dimred/UMAP.js:96

Accessors

projection

Get Signature

get projection(): T;

Defined in: dimred/DR.js:219

Returns

T

The projection in the type of input X.

Inherited from

DR.projection

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

DR.[dispose]

---

check_init()

check_init(): DR<T, ParametersUMAP>;

Defined in: dimred/DR.js:210

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:399

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:370

Returns

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

Name	Type	Defined in
cols	number[] | undefined	dimred/UMAP.js:372
rows	number[] | undefined	dimred/UMAP.js:372
weights	number[] | undefined	dimred/UMAP.js:372

---

init()

init(): UMAP<T>;

Defined in: dimred/UMAP.js:349

Computes all necessary

Returns

UMAP<T>

Overrides

DR.init

---

parameter()

Call Signature

parameter(): ParametersUMAP;

Defined in: dimred/DR.js:82

Get all Parameters.

Returns

ParametersUMAP

Inherited from

DR.parameter

Call Signature

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

Defined in: dimred/DR.js:88

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:95

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

---

release()

release(): UMAP<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

UMAP<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

DR.release

---

transform()

transform(iterations?: number): T;

Defined in: dimred/UMAP.js:379

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: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

DR.transform_async

---

generator()

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

Defined in: dimred/UMAP.js:614

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:603

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:626

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

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

Returns

Promise<T>

Overrides

DR.transform_async