umap-js

UMAP-JS

This is a JavaScript reimplementation of UMAP from the python implementation found at https://github.com/lmcinnes/umap.

Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.

There are a few important differences between the python implementation and the JS port.

• The optimization step is seeded with a random embedding rather than a spectral embedding. This gives comparable results for smaller datasets. The spectral embedding computation relies on efficient eigenvalue / eigenvector computations that are not easily done in JS.
• There is no specialized functionality for angular distances or sparse data representations.

Usage

Installation

yarn add umap-js

Synchronous fitting

import { UMAP } from 'umap-js';

const umap = new UMAP();
const embedding = umap.fit(data);

Asynchronous fitting

import { UMAP } from 'umap-js';

const umap = new UMAP();
const embedding = await umap.fitAsync(data, epochNumber => {
  // check progress and give user feedback, or return `false` to stop
});

Step-by-step fitting

import { UMAP } from 'umap-js';

const umap = new UMAP();
const nEpochs = umap.initializeFit(data);
for (let i = 0; i < nEpochs; i++) {
  umap.step();
}
const embedding = umap.getEmbedding();

Supervised projection using labels

import { UMAP } from 'umap-js';

const umap = new UMAP();
umap.setSupervisedProjection(labels);
const embedding = umap.fit(data);

Transforming additional points after fitting

import { UMAP } from 'umap-js';

const umap = new UMAP();
umap.fit(data);
const transformed = umap.transform(additionalData);

Parameters

The UMAP constructor can accept a number of hyperparameters via a UMAPParameters object, with the most common described below. See umap.ts for more details.

Parameter	Description	default
nComponents	The number of components (dimensions) to project the data to	2
nEpochs	The number of epochs to optimize embeddings via SGD	(computed automatically)
nNeighbors	The number of nearest neighbors to construct the fuzzy manifold	15
minDist	The effective minimum distance between embedded points, used with spread to control the clumped/dispersed nature of the embedding	0.1
spread	The effective scale of embedded points, used with minDist to control the clumped/dispersed nature of the embedding	1.0
random	A pseudo-random-number generator for controlling stochastic processes	Math.random
distanceFn	A custom distance function to use	euclidean

const umap = new UMAP({
  nComponents: 2,
  nEpochs: 400,
  nNeighbors: 15,
});

Testing

umap-js uses jest for testing.

yarn test

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