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

This project has been refacored into two separate Maven projects, one for the core tsne and one for the demos.

T-SNE-Java is now in version 1.0 (tsne-core is 1.0.1) It has been in development version long enough.

If you just want to use TSne as a command line tool, you should use TSneCsv which is by far the most flexible alternative.

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

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-1.0.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-1.0.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-1.0.jar --nohdr --nolbls --label_file=src/main/resources/datasets/iris_X_labels.txt src/main/resources/datasets/iris_X.txt

To see graphs generated with this implementation, Klick here

For some tips working with t-sne [Klick here] (http://lejon.github.io)

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

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
    
  }
}

Demo: 1.0 Core: 1.0.1

Enjoy! -Leif