t-SNE Visualization

Data visualizaiton with t-SNE with higher dimensional data.

t-Distributed Stochastic Neighbor Embedding (t-SNE) is a data-visualization tool created by Laurens van der Maaten at Delft University of Technology.

While it can be used for any data, t-SNE (pronounced Tee-Snee) is only really meaningful with labeled data, which clarify how the input is clustering. Below, you can see the kind of graphic you can generate in DL4J with t-SNE working on MNIST data.

Alt text

Look closely and you can see the numerals clustered near their likes, alongside the dots.

Here's how t-SNE appears in Deeplearning4j code.

public class TSNEStandardExample {
private static Logger log = LoggerFactory.getLogger(TSNEStandardExample.class);
public static void main(String[] args) throws Exception {
//STEP 1: Initialization
int iterations = 100;
//create an n-dimensional array of doubles
DataTypeUtil.setDTypeForContext(DataBuffer.Type.DOUBLE);
List<String> cacheList = new ArrayList<>(); //cacheList is a dynamic array of strings used to hold all words
//STEP 2: Turn text input into a list of words
log.info("Load & Vectorize data....");
File wordFile = new ClassPathResource("words.txt").getFile(); //Open the file
//Get the data of all unique word vectors
Pair<InMemoryLookupTable,VocabCache> vectors = WordVectorSerializer.loadTxt(wordFile);
VocabCache cache = vectors.getSecond();
INDArray weights = vectors.getFirst().getSyn0(); //seperate weights of unique words into their own list
for(int i = 0; i < cache.numWords(); i++) //seperate strings of words into their own list
cacheList.add(cache.wordAtIndex(i));
//STEP 3: build a dual-tree tsne to use later
log.info("Build model....");
BarnesHutTsne tsne = new BarnesHutTsne.Builder()
.setMaxIter(iterations).theta(0.5)
.normalize(false)
.learningRate(500)
.useAdaGrad(false)
// .usePca(false)
.build();
//STEP 4: establish the tsne values and save them to a file
log.info("Store TSNE Coordinates for Plotting....");
String outputFile = "target/archive-tmp/tsne-standard-coords.csv";
(new File(outputFile)).getParentFile().mkdirs();
tsne.plot(weights,2,cacheList,outputFile);
//This tsne will use the weights of the vectors as its matrix, have two dimensions, use the words strings as
//labels, and be written to the outputFile created on the previous line
}
}

Here is an image of the tsne-standard-coords.csv file plotted using gnuplot.

Tsne data plot