@saehrimnir/druidjs / PaCMAP

Class: PaCMAP<T, P>

Defined in: dimred/PaCMAP.js:50

Pairwise Controlled Manifold Approximation Projection (PaCMAP)

A dimensionality reduction technique that uses three types of point pairs — nearest neighbor (NN), mid-near (MN), and further (FP) pairs — with a dynamic three-phase weight schedule and Adam optimization to preserve both local and global structure. Neighbours are scaled by a local density estimate before selection, which is what separates the NN set from a plain KNN graph.

Template

T

Template

P

Widened by LocalMAP, which adds a parameter.

See

• Paper
• GitHub
• UMAP for a related graph-based technique
• LocalMAP for the local-refinement variant

Example

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

const X = [[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12]];
const pacmap = new druid.PaCMAP(X, {
    n_neighbors: 10,
    MN_ratio: 0.5,
    FP_ratio: 2.0,
    seed: 42
});

const Y = pacmap.transform(); // 450 iterations (default)
// [[x1, y1], [x2, y2], [x3, y3]]

Extends

• DR

Extended by

• LocalMAP

Type Parameters

Type Parameter	Default type	Description
T extends InputType	-
P extends ParametersPaCMAP	ParametersPaCMAP	Widened by LocalMAP, which adds a parameter.

Constructors

Constructor

new PaCMAP<T, P>(X: T, parameters?: Partial<P>): PaCMAP<T, P>;

Defined in: dimred/PaCMAP.js:55

Parameters

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

Returns

PaCMAP<T, P>

Overrides

DR.constructor

Properties

Property	Type	Inherited from	Defined in
__input	T	DR.__input	dimred/DR.js:46
_adam_m	Float64Array<ArrayBuffer> | undefined	-	dimred/PaCMAP.js:528
_adam_t	any	-	dimred/PaCMAP.js:452
_adam_v	Float64Array<ArrayBuffer> | undefined	-	dimred/PaCMAP.js:529
_D	number	DR._D	dimred/DR.js:28
_fp_pairs	Int32Array<ArrayBufferLike> | undefined	-	dimred/PaCMAP.js:525
_grad	Float64Array<ArrayBuffer> | undefined	-	dimred/PaCMAP.js:531
_is_initialized	boolean	DR._is_initialized	dimred/DR.js:34
_iter	number	-	dimred/PaCMAP.js:79
_mn_pairs	Int32Array<ArrayBufferLike> | undefined	-	dimred/PaCMAP.js:524
_N	number	DR._N	dimred/DR.js:30
_nn_pairs	Int32Array<ArrayBufferLike> | undefined	-	dimred/PaCMAP.js:520
_parameters	P	DR._parameters	dimred/DR.js:49
_randomizer	Randomizer	DR._randomizer	dimred/DR.js:32
_type	"array" | "matrix" | "typed"	DR._type	dimred/DR.js:54
_X_knn	Matrix | undefined	-	dimred/PaCMAP.js:511
X	Matrix	DR.X	dimred/DR.js:56
Y	Matrix	DR.Y	dimred/DR.js:58

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, P>;

Defined in: dimred/DR.js:210

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

Returns

DR<T, P>

Inherited from

DR.check_init

---

generator()

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

Defined in: dimred/PaCMAP.js:605

Parameters

Parameter	Type	Description
iterations?	number	Total number of iterations. Defaults to sum of num_iters.

Returns

Generator<T, T, void>

Overrides

DR.generator

---

init()

init(): PaCMAP<T, P>;

Defined in: dimred/PaCMAP.js:474

Initializes PaCMAP: preprocessing, PCA embedding, NN, MN and FP pairs, and Adam state.

Returns

PaCMAP<T, P>

Overrides

DR.init

---

next()

next(): Matrix;

Defined in: dimred/PaCMAP.js:570

Performs one optimization step.

Returns

Matrix

---

parameter()

Call Signature

parameter(): P;

Defined in: dimred/DR.js:82

Get all Parameters.

Returns

P

Inherited from

DR.parameter

Call Signature

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

Defined in: dimred/DR.js:88

Get value of given parameter.

Type Parameters

Type Parameter	Description
K extends string | number | symbol

Parameters

Parameter	Type	Description
name	K	Name of the parameter.

Returns

P[K]

Inherited from

DR.parameter

Call Signature

parameter<K>(name: K, value: P[K]): PaCMAP<T, P>;

Defined in: dimred/DR.js:95

Set value of given parameter.

Type Parameters

Type Parameter	Description
K extends string | number | symbol

Parameters

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

Returns

PaCMAP<T, P>

Inherited from

DR.parameter

---

release()

release(): PaCMAP<T, P>;

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

PaCMAP<T, P>

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/PaCMAP.js:591

Parameters

Parameter	Type	Description
iterations?	number	Total number of iterations. Defaults to sum of num_iters.

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<ParametersPaCMAP>): Generator<T, T, void>;

Defined in: dimred/PaCMAP.js:633

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

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

Returns

Generator<T, T, void>

Overrides

DR.generator

---

transform()

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

Defined in: dimred/PaCMAP.js:622

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

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

Returns

T

Overrides

DR.transform

---

transform_async()

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

Defined in: dimred/PaCMAP.js:645

Type Parameters

Type Parameter	Description
T extends InputType

Parameters

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

Returns

Promise<T>

Overrides

DR.transform_async