biopython

v1.71.0

biopython v1.71.0 Bio.HMM.Trainer.KnownStateTrainer

Estimate probabilities with known state sequences.

This should be used for direct estimation of emission and transition probabilities when both the state path and emission sequence are known for the training examples.

Link to this section Summary

Functions

__init__()

Initialize

_count_emissions()

Add emissions from the training sequence to the current counts

_count_transitions()

Add transitions from the training sequence to the current counts

train()

Estimate the Markov Model parameters with known state paths

Link to this section Functions

Link to this function __init__()

Initialize.

Link to this function _count_emissions()

Add emissions from the training sequence to the current counts.

Arguments:

  • training_seq — A TrainingSequence with states and emissions to get the counts from
  • emission_counts — The current emission counts to add to.
Link to this function _count_transitions()

Add transitions from the training sequence to the current counts.

Arguments:

  • state_seq — A Seq object with the states of the current training sequence.
  • transition_counts — The current transition counts to add to.
Link to this function train()

Estimate the Markov Model parameters with known state paths.

This trainer requires that both the state and the emissions are known for all of the training sequences in the list of TrainingSequence objects. This training will then count all of the transitions and emissions, and use this to estimate the parameters of the model.