Semantics and Ambiguity of Stochastic RNA Family Models

@article{Giegerich2011SemanticsAA,
  title={Semantics and Ambiguity of Stochastic RNA Family Models},
  author={Robert Giegerich and Christian H{\"o}ner zu Siederdissen},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year={2011},
  volume={8},
  pages={499-516}
}
Stochastic models, such as hidden Markov models or stochastic context-free grammars (SCFGs) can fail to return the correct, maximum likelihood solution in the case of semantic ambiguity. This problem arises when the algorithm implementing the model inspects the same solution in different guises. It is a difficult problem in the sense that proving semantic nonambiguity has been shown to be algorithmically undecidable, while compensating for it (by coalescing scores of equivalent solutions) has… CONTINUE READING