umap-js

by PAIR-code

PAIR-code / umap-js

JavaScript implementation of UMAP

165 Stars 17 Forks Last release: over 1 year ago (1.2.2) Apache License 2.0 103 Commits 6 Releases

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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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