The posterior-Viterbi: a new decoding algorithm for hidden Markov models

Background: Hidden Markov models (HMM) are powerful machine learning tools successfully applied to problems of computational Molecular Biology. In a predictive task, the HMM is endowed with a decoding algorithm in order to assign the most probable state path, and in turn the class labeling, to an unknown sequence. The Viterbi and the posterior decoding algorithms are the most common. The former is very efficient when one path dominates, while the latter, even though does not guarantee to preserve the automaton grammar, is more effective when several concurring paths have similar probabilities. A third good alternative is 1-best, which was shown to perform equal or better than Viterbi. Results: In this paper we introduce the posterior-Viterbi (PV) a new decoding which combines the posterior and Viterbi algorithms. PV is a two step process: first the posterior probability of each state is computed and then the best posterior allowed path through the model is evaluated by a Viterbi algorithm. Conclusions: We show that PV decoding performs better than other algorithms first on toy models and then on the computational biological problem of the prediction of the topology of beta-barrel membrane proteins.Comment: 23 pages, 3 figure

Short Block-length Codes for Ultra-Reliable Low-Latency Communications

This paper reviews the state of the art channel coding techniques for ultra-reliable low latency communication (URLLC). The stringent requirements of URLLC services, such as ultra-high reliability and low latency, have made it the most challenging feature of the fifth generation (5G) mobile systems. The problem is even more challenging for the services beyond the 5G promise, such as tele-surgery and factory automation, which require latencies less than 1ms and failure rate as low as $10^{-9}$. The very low latency requirements of URLLC do not allow traditional approaches such as re-transmission to be used to increase the reliability. On the other hand, to guarantee the delay requirements, the block length needs to be small, so conventional channel codes, originally designed and optimised for moderate-to-long block-lengths, show notable deficiencies for short blocks. This paper provides an overview on channel coding techniques for short block lengths and compares them in terms of performance and complexity. Several important research directions are identified and discussed in more detail with several possible solutions.Comment: Accepted for publication in IEEE Communications Magazin