Related papers: The Highest Expected Reward Decoding for HMMs with…
The classic algorithm of Viterbi computes the most likely path in a Hidden Markov Model (HMM) that results in a given sequence of observations. It runs in time $O(Tn^2)$ given a sequence of $T$ observations from a HMM with $n$ states.…
Recombination is an important event in the evolution of HIV. It affects the global spread of the pandemic as well as evolutionary escape from host immune response and from drug therapy within single patients. Comprehensive computational…
We consider the maximum likelihood (Viterbi) alignment of a hidden Markov model (HMM). In an HMM, the underlying Markov chain is usually hidden and the Viterbi alignment is often used as the estimate of it. This approach will be referred to…
An algorithm used to extract HMM parameters is revisited. Most parts of the extraction process are taken from implemented Hidden Markov Toolkit (HTK) program under name HInit. The algorithm itself shows a few variations compared to another…
Hidden semi-Markov models (HSMMs) are latent variable models which allow latent state persistence and can be viewed as a generalization of the popular hidden Markov models (HMMs). In this paper, we introduce a novel spectral algorithm to…
We consider a bivariate, possibly non-homogeneous, finite-state Markov chain $(X,U)=\{(X_t,U_t)\}_{t=1}^n$. We are interested in the marginal process $X$, which typically is not a Markov chain. The goal is to find a realization (path)…
Two major tasks in applications of hidden Markov models are to (i) compute distributions of summary statistics of the hidden state sequence, and (ii) decode the hidden state sequence. We describe finite Markov chain imbedding (FMCI) and…
In this paper, we advance a recently-proposed uncertainty decoding scheme for DNN-HMM (deep neural network - hidden Markov model) hybrid systems. This numerical sampling concept averages DNN outputs produced by a finite set of feature…
A hidden Markov model (HMM) solved recursively by the Viterbi algorithm can be configured to search for persistent, quasimonochromatic gravitational radiation from an isolated or accreting neutron star, whose rotational frequency is unknown…
Hidden Markov models provide a natural statistical framework for the detection of the copy number variations (CNV) in genomics. In this paper, we consider a Hidden Markov Model involving several correlated hidden processes at the same time.…
For hidden Markov models one of the most popular estimates of the hidden chain is the Viterbi path -- the path maximising the posterior probability. We consider a more general setting, called the pairwise Markov model (PMM), where the joint…
The hidden Markov model (HMM) is a generative model that treats sequential data under the assumption that each observation is conditioned on the state of a discrete hidden variable that evolves in time as a Markov chain. In this paper, we…
As deep neural networks continue to revolutionize various application domains, there is increasing interest in making these powerful models more understandable and interpretable, and narrowing down the causes of good and bad predictions. We…
Effective and efficient malware detection is at the forefront of research into building secure digital systems. As with many other fields, malware detection research has seen a dramatic increase in the application of machine learning…
Hidden Markov models (HMMs) are characterized by an unobservable Markov chain and an observable process -- a noisy version of the hidden chain. Decoding the original signal from the noisy observations is one of the main goals in nearly all…
Hidden Markov models (HMMs) are popular models to identify a finite number of latent states from sequential data. However, fitting them to large data sets can be computationally demanding because most likelihood maximization techniques…
The paper studies optimal coding of hidden Markov sources (HMS), which represent a broad class of practical sources obtained through noisy acquisition processes, beside their explicit modeling use in speech processing and recognition, image…
We demonstrate the application of pattern recognition algorithms via hidden Markov models (HMM) for qubit readout. This scheme provides a state-path trajectory approach capable of detecting qubit state transitions and makes for a robust…
Inferring a state sequence from a sequence of measurements is a fundamental problem in bioinformatics and natural language processing. The Viterbi and the Beam Search (BS) algorithms are popular inference methods, but they have limitations…
Hidden Markov models and their variants are the predominant sequential classification method in such domains as speech recognition, bioinformatics and natural language processing. Being generative rather than discriminative models, however,…