bh-tsne

Barnes-Hut t-SNE

This code was derived from T-SNE-Java

See LICENSE.md for further information!

Maven coordinates:

<dependency>
    <groupId>de.javagl</groupId>
    <artifactId>bh-tsne</artifactId>
    <version>0.0.1</version>
</dependency>

Project structure

The project consists of two modules:

• bh-tsne: The actual library offering the t-SNE functionality. It has the ejml (Efficient Java Matrix Library) as its only dependency

• bh-tsne-demo: A small application that allows running the t-SNE on different test data sets, and visualizing the results:

Changes done to the original code:

• Replaced the use of ThreadLocalRandom with a Random instance that is initialized with a fixed (but modifiable) random seed. Since t-SNE is often used for scientific publications, having the possibility to create the same result repeatedly is crucial for reproducability. I also used this to verify (empirically) that all subsequent changes did not affect the validity of the results.

• Collected all classes that are required for the BHTSne into a single package - and only these classes!

• Made private what could be private. Made default-visible what could be default-visible. Made static what could be static. Removed all code that was then no longer used (which was most of it)

• Removed unnecessary dependencies (for example, JAMA was used for a single line of code that was not called at all). Specifcially: Removed all dependencies except for the one to EJML, which has been replaced with the proper one in its latest available version.

• Replaced the System.out.print... calls by some (pragmatic) logging and progress report

• Added a trivial parallelization that brought roughly 40% speedup by changing a few lines of code (and seems to be faster than the oddly complicated ParallelBHTsne of the original implementation...)

• Allowed the computation to be interrupted by calling interrupt() on the executing thread

• Significantly reduced the number of memory allocations, mainly by introducing the DoubleArray interface

• Offered the whole functionality in a single public class, with some basic JavaDoc

• Offered the library in Maven Central