Given that t-SNE is an highly demanding algorithm, the development team at De Novo Software made a great effort to improve the speed of running the algorithm with FCS Express.

 

To give you an idea of how t-SNE is performing within FCS Express, a performance test has been run comparing FCS Express and the independent R package in running both the exact tSNE algorithm and the Barnes-Hut approximation.

 

Here is a brief description of how the test was run:

 

 

 

 

The graph below (Figure 29.59) show the elapsed time (in minutes) for t-SNE calculation (using both the exact t-SNE and the Burnes-Hut Approximation (Amount of Approximation = 0.5)) in both FCS Express and R. A fixed number of parameters (i.e. n=20) and different numbers of events have been used. t-SNE was not estimated for unsampled events. Please refer to the Defining a tSNE transformation chapter for more information about all the above mentioned options.