Genome 540 Homework Assignment 8

Due Sunday Mar 8, 11:59pm

• Using the same HMM and dataset as in homework 7, write a program that implements EM (Baum-Welch) training instead. Use the same starting parameter values, but in contrast to homework 7, you should not hold any parameter values fixed or set to be equivalent-- allow all of them to change with each iteration. Compute the log-likelihood (to the base 2) of the sequence at each iteration, and run the program until the increase in log-likelihood between successive iterations becomes less than 0.1. You should check that the log-likelihood increases with each iteration -- if it doesn't, something is wrong with your program. My program took less than 300 iterations to converge.
• Your output should provide:
  • the name and first line of the .fna file
  • the number of iterations until convergence
  • the final log-likelihood
  • the final initial, emission, and transition probabilities -- please output these in scientific notation, to four significant digits (i.e., 9.000e-1)
• You must turn in your results and your computer program, using this template file. Please put everything into ONE plain text file - do not send an archive of files or a tar file, or a word processing document file. Compress it (using either Unix compress, or gzip -- if you don't have access to either of these programs let us know), and send it as an attachment to both Phil (phg (at) u.washington.edu) and Mitchell(mvollger (at) uw.edu).