Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: The Highest Expected Reward Decoding for HMMs with Application to
  Recombination Detection   Hidden Markov models are traditionally decoded by the Viterbi algorithm which
finds the highest probability state path in the model. In recent years, several
limitations of the Viterbi decoding have been demonstrated, and new algorithms
have been developed to address them
\citep{Kall2005,Brejova2007,Gross2007,Brown2010}.
  In this paper, we propose a new efficient highest expected reward decoding
algorithm (HERD) that allows for uncertainty in boundaries of individual
sequence features. We demonstrate usefulness of our approach on jumping HMMs
for recombination detection in viral genomes.

31
The categories of this paper are: ao-sci
37
The categories of this paper are: supr-con
14
The categories of this paper are: math-ph
12
The categories of this paper are: nucl-th
18
The categories of this paper are: econ
8
The categories of this paper are: hep-ex
20
The categories of this paper are: acc-phys
3
The categories of this paper are: physics
28
The categories of this paper are: alg-geom
2
The categories of this paper are: math
33
The categories of this paper are: plasm-ph
26
The categories of this paper are: bayes-an
29
The categories of this paper are: funct-an
22
The categories of this paper are: chao-dyn
15
The categories of this paper are: nucl-ex
35
The categories of this paper are: mtrl-th