Just after I had been through a bit of a posting slump due to some fading tuits, it would seem as if they have magically returned. This week brings the start of the Fall 2009 semester and I have seemingly sprung back to life. With the new semester comes new opportunities to use perl!

First, I wanted to mention the one bit of news that made my summer, maybe even the last 2 years, seem as if I haven’t been running in circles. I noticed that my new department head at the university posted the final new rules regarding the qualification exams. The change is that there is a list of approved courses that will be offering the QE, passing any 3 is sufficient, and there is still no marginal grade. The last exam I took, Data / Text Mining in Bioinformatics, was not listed in the blessed course list. Turns out, the department would still accept the score, so I now only lack 1 remaining pass to be an official “phd candidate“.

This semester I am taking the Design & Analysis of Computer Algorithms course. The down side is this course tends to be theory-centric, so I won’t have many chances to flex my Perl muscles. There are tons of modules on CPAN though that might help understanding the basics. There are plenty of graph, tree, and dynamic programming solutions available.

Interestingly enough, while sifting though those modules, I discovered a module of personal interest. I stumbled across the Algorithm::Viterbi module. I have studied Markov models, Markov chains, and Hidden Markov models a bunch in the last 2 years. One algorithm that keeps showing up is the Viterbi algorithm. I’ll leave it as an exercise to the reader as to how this algorithm is used, but I will point out that the Wikipedia page has Python code. Ironically, “Python’s answer to CPAN” isn’t quite all it’s cracked up to be; it lacks any packages pertaining to “viterbi” and no generic Markov package.

Perl: Automatically tested, student approved.