The Incorporation of Latent Variables in Causal Discovery Using Experimental Data
By Chris Fell
Supervised by Kevin Korb
Thesis available in pdf, html (HTML version may have rendering errors in formulae, images, etc), or LaTeX. Note that in order to compile the LaTeX, the entire images directory will need to be in the same directory as the LaTeX source.
Program source is available here (requires Java 5), plus some sample networks to try it out with here.