Todd Johnson

In February 2012 I completed a PhD in computer science at the University of California, Irvine. My advisor was Eric Mjolsness. The main webpage for Eric's research group is Computable Plant.
My research interests are in machine learning, artificial intelligence, and computational biology.

My PhD thesis focused on two novel approaches in probabilistic graphical models. Each of these is described on its own page. Each page also includes links to download software packages for the Mathematica programming langauge, and example notebooks.

Dependency Diagrams extend factor graphs (a superset of Bayesian networks and Markov random fields). I used them to implement a package that, among other things, automatically generates runnable source code for the process of performing Metropolis-Hastings sampling on arbitrary distributions.

Graph-Constrained Correlation Dynamics formalizes a method of representing probability distributions that evolve continuously in time. The software package leverages Dependency Diagrams to optimize GCCD models.

My thesis is also available as a PDF.
selected side projects
I read, when I can; my Goodreads page is here. I can be found on Facebook here. I am lucky enough to be married to Ruth Barrett, an excptionally talented neuroscientist. We have a weblog, where we post pictures and occassional goings-on, for friends and family. I also maintain a weblog with some friends from college.

Coincidentally, all of the males in my immediate family-in-law are also computer scientists. Sorted by the degree to which our research is related, these fine fellows are: