Class DP

  • Direct Known Subclasses:
    PairwiseDP, SingleDP

    public abstract class DP
    extends Object

    Objects that can perform dymamic programming operations upon sequences with HMMs.

    The three main DP operations are Forwards, Backwards and Viterbi. Forwards and Backwards calculate the probability of the sequences having been made in any way by the model. Viterbi finds the most supported way that the sequence could have been made.

    Each of the functions can return the dynamic-programming matrix containing the intermediate results. This may be useful for model training, or for visualisation.

    Each of the funcitons can be calculated using the model probabilities, the null-model probabilities or the odds (ratio between the two). For Forwards and Backwards, the odds calculations produce numbers with questionable basis in reality. For Viterbi with odds, you will recieve the path through the model that is most different from the null model, and supported by the probabilities.

    Matthew Pocock, Thomas Down