Contents

• Why estimate amino acid distributions?
• Quantitative measure for regularizers
  • Encoding cost
  • More efficient computation of encoding cost
• Estimation methods
  • Zero-offset
  • Pseudocounts
  • Gribskov average-score method
  • Substitution matrices
  • Substitution matrices plus pseudocounts
  • Substitution matrices plus pseudocounts plus scaled counts
  • Feature alphabets
  • Dirichlet mixtures
• Optimizing parameters of estimation methods
• Experimental method
• Results for training and testing on full database
  • Zero-offset
  • Pseudocounts
  • Gribskov average score
  • Substitution matrices
  • Substitution matrices plus pseudocounts
  • Feature alphabets
  • Dirichlet mixtures
• Results for separate training and testing
• Conclusions and future research
• References
• Partial derivatives for Dirichlet mixtures
• Bayesian interpretation of pseudocount regularizers
• Bayesian interpretation of Dirichlet mixture regularizers
• About this document ...