T-SNE-Java

NEWS 2016-11-02!

T-SNE-Java now have support for Barnes Hut which makes it possible to run the amazing t-SNE on much larger data sets (or much faster on small data sets:) )!

The Barnes Hut version can also be run in parallel! We have seen from 40 % performance improvements on moderate datasets (ca 10 000 samples) to 100 % improvements on larger datasets (MNIST 60000 samples) compared to standard Barnes Hut.

The t-SNE part of running the parallel Barnes Hut t-SNE on MNIST 60000 takes 18.3 minutes on a 2013 Macbook Pro (theta=0.5, perplexity = 50, 1000 iterations)

Both standard and parallel Barnes Hut is of course magnitudes faster than vanilla t-SNE.

Great research by Dr. Maaten!!

About

Pure Java implementation of Van Der Maaten and Hinton's t-SNE clustering algorithm.

This project is divided into two separate Maven projects, one for the core t-SNE and one for the demos (stand-alone executables that can be run from command line).

Basic command line usage

If you just want to use TSne as a command line tool, you should use BarnesHutTSneCsv for the Barnes Hut version or TSneCsv for the classic version.

You must then first build and install 'tsne' and 'tsne-demos' (mvn install). Then use the tsne-demos JAR you just build according to the examples below.

You can also download the pre-build binary JAR from the release page.

Examples:

Run TSne on file without headers and no labels.

java -jar target/tsne-demos-2.4.0.jar -nohdr -nolbls src/main/resources/datasets/iris_X.txt 

Run TSne on CSV file with headers and label column nr. 5.

java -jar target/tsne-demos-2.4.0.jar --lblcolno 5 src/main/resources/datasets/iris.csv

Run TSne on file without headers and no labels but supply a separate label file (with the same ordering as the data file).

java -jar target/tsne-demos-2.4.0.jar --nohdr --nolbls --label_file=src/main/resources/datasets/iris_X_labels.txt src/main/resources/datasets/iris_X.txt

Same as above but using parallelization.

java -jar target/tsne-demos-2.4.0.jar --parallel --nohdr --nolbls --label_file=src/main/resources/datasets/iris_X_labels.txt src/main/resources/datasets/iris_X.txt

Example graph of the MNIST data set (60000 samples) generated with Barnes Hut implementation of t-SNE:

For some tips working with t-sne [Klick here] (http://lejon.github.io) or [here] (https://lvdmaaten.github.io/tsne/#faq) (observe that the last link discusses some implementation details of Laurens implementation of t-SNE and not this Java version, but also some general tips and tricks which applies to t-SNE in general) .

To use the Barnes Hut version (recommended):

import java.io.File;

import com.jujutsu.tsne.barneshut.BHTSne;
import com.jujutsu.tsne.barneshut.BarnesHutTSne;
import com.jujutsu.tsne.barneshut.ParallelBHTsne;
import com.jujutsu.utils.MatrixOps;
import com.jujutsu.utils.MatrixUtils;

public class TSneTest {
  public static void main(String [] args) {
    int initial_dims = 55;
    double perplexity = 20.0;
    double [][] X = MatrixUtils.simpleRead2DMatrix(new File("src/main/resources/datasets/mnist2500_X.txt"), "   ");
    System.out.println(MatrixOps.doubleArrayToPrintString(X, ", ", 50,10));
    BarnesHutTSne tsne;
    boolean parallel = false;
	if(parallel) {			
		tsne = new ParallelBHTsne();
	} else {
		tsne = new BHTSne();
	}
    double [][] Y = tsne.tsne(X, 2, initial_dims, perplexity);   
    
    // Plot Y or save Y to file and plot with some other tool such as for instance R
  }
}

Basic code usage (not recommended, slow standard t-SNE (yes, well it was fast at the time. :)):

import java.io.File;

import com.jujutsu.tsne.FastTSne;
import com.jujutsu.tsne.TSne;
import com.jujutsu.utils.MatrixOps;
import com.jujutsu.utils.MatrixUtils;

public class TSneTest {
  public static void main(String [] args) {
    int initial_dims = 55;
    double perplexity = 20.0;
    double [][] X = MatrixUtils.simpleRead2DMatrix(new File("src/main/resources/datasets/mnist2500_X.txt"), "   ");
    System.out.println(MatrixOps.doubleArrayToPrintString(X, ", ", 50,10));
    TSne tsne = new FastTSne();
    double [][] Y = tsne.tsne(X, 2, initial_dims, perplexity);   

    // Plot Y or save Y to file and plot with some other tool such as for instance R

  }
}

Version

Demo: 2.4.0 Core: 2.3.0

Acknowledgements

I'm a very satisfied user of the YourKit profiler. A Great product with great support. It has been sucessfully used for profiling in this project.

YourKit supports open source projects with its full-featured Java Profiler. YourKit, LLC is the creator of YourKit Java Profiler and YourKit .NET Profiler, innovative and intelligent tools for profiling Java and .NET applications.

Enjoy! -Leif