# Tagged Questions

Hidden Markov Models are used for modelling systems that are assumed to be Markov processes with hidden (i.e. unobserved) states.

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### Impulse Response Analysis for Markov-Switching Models

I've estimated a bivariate Markov-Switching VAR(1). I am interesting in understanding how an error/ 'shock' would propagate through the system. I've been stuck on how this could be done? Thank you!
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### Markov models that with several active states

Are there any Markov-like models that can have several active states? So say if trying to determine (the chance) when the person will wake up based on two variables (weather and the time the person ...
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### How to choose between VOMs and Predictive models, e.g., ARIMA?

In time series prediction, there is a lot of work that uses predictive models (e.g., ARIMA). On the other hand, there's also a lot of work that uses Variable Order Markov models (e.g., context ...
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### Reference request: EM algorithm and hidden Markov model books with solutions

I am studying missing data problems and the applications of the EM algorithm to missing data problems, like mixture models and hidden Markov models. We have been using Schafer's book Analysis of ...
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### What are good tutorial on Weighted Finite Automata?

I would especially appreciate papers, books or tutorials with source code already available. Currently I'm reading "Spectral Learning Techniques for Weighted Automata, Transducers, and Grammars" by ...
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### Hidden markov model multivariate regression with time-series data

I am working with a dataset that includes the trajectories of various car trips and would like to be able to predict their destinations using only a subset of the trip trajectory. For instance, if in ...
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### How to use a Hidden Markov Model to detect state in a time series?

Questions Am I right in assuming that the emission probabilities will not be following a gaussian distribution for my particular problem? Obviously, I will need to train the model for state ...
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### disease progression R markov chains

hello i have a dataframe, some of the columns include: remission,height,weight,time from diagnosis, age ethnicity, age, patient id remission is 1 or 0 just to be clear i want to fit an appropriate ...
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### Markov chains vs. HMM

Markov chains makes sense to me, I can use them to model probabilistic state changes in real life problems. Then comes the HMM. HMMs are said to be more suitable to model many problems than MCs. ...
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### Estimate core state transition probability matrix in partially observable Markov decision processes

I have a longitudinal data set of patients who have been monitored by a medical test over a year. The results of this test have false positive and false negative, so the system is partially ...
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### Implications of using fixed effects to account for hierarchical data structure

I am currently implementing a hidden Markov model in R, using the msm package. The data I am using are drawn from a cluster-randomized trial; i.e. there is a ...
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### Hidden Markov model question; pseudo time series?

I apologize that the title of this question isn't super specific, but I am having a very difficult time exactly and succinctly describing the problem I am facing in my implementation of a hidden ...
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### Implementation of bag-of-features HMM?

I'm trying implement a word-spotting paper that uses a Hidden Markov Model where the emissions are a bag of words/features. I have found HMM implementations, but I haven't seen functionality to ...
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### time series based classification

I want to classify some data. Basically the data is time series in nature. The target variable is categorical. I know there are so many algorithms for predicting the time series model. However, I have ...
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### Observation Likelihood in hidden Markov models

As far as I understand, in discrete HMM, the observation symbol probability distribution $b_{i}(O_{t})$ is always a probability less than 1, e.g. $\frac{1}{6}$ for each side when rolling a dice. But ...
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### Values of PDF in Bayes Classifier

I'm new here and also a beginner in statistics. I'm implementing a Bayes classifier for two classes but get confused with the value of likelihood (pdf). $$P(c|o) = p(o|c)\cdot P(c)/p(o);$$ Here ...
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### Good library for Switching Autoregressive Hidden Markov Model (SAR-HMM)

can you recommend a good library for SAR-HMM? (Switching Autoregressive Hidden Markov Model) Apparently only MATLAB can be recommended. ...
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### Hidden Markov models with state transitions conditioned on some node

I'm lacking some clarity related to HMM's Suppose I have a binomial state node and another binomial observation node, In this node the conditional probability table will be state transition matrix ...
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### How to Format Data for Structured Learning Problem?

I'm working on a project classifying discussion forum posts into various pre-defined categories, and would like to use a sequential learning model such as CRF's. I code mostly in Python and have found ...
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### Train HMM with multiple sequences in R

I have multiple sequences and I want to train one HMM model. Is there a way to do it in R? I looked into 'HMM' package and there is only a way to train for 1 sequence of observations Thanks!
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### How long does it take two identical hidden Markov models run on same observations to forget their initial distributions (if ever)?

Let $H_1$ and $H_2$ be two instances of a finite Hidden Markov Model (HMM) $H$. That is, $H_1$ and $H_2$ have identical state spaces $Q$ as well as identical transition $A$ and emission probabilities ...
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### Hidden Markov Model vs Markov Transition Model vs State-Space Model…?

For my master's thesis, I am working on developing a statistical model for the transitions between different states, defined by serological status. For now, I won't give too many details into this ...
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### Is this a job for mixture of experts regression or semi-hidden markov models or something else?

Data I have several thousand timeseries each comprising around 365 data points. Browsing through a few of them, it looks like each timeseries consists of several regimes (different number f regimes ...
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### make prediction with HMM

I want to use HMM to make some prediction. say $O$ is the observation, $S$ is the hidden states, and I know how to train the model with forward-backward algorithm. I just get confused with how to ...
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### Finding occurrences of specific patterns in time series

I have to locate occurrences of Cyllinder, Bell and Funnel patterns in univariate time series $X$ of gamma-ray sensoring. This is a specific case of the general CBF synthetic problem found in a few ...
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### Flow of influence in a v-structure for Probabilistic Graphical Models

I'm not very sure I understand why an observed v-structure have different flow of influence behaviour for a directed and an undirected graph. What is the intuition behind the actual definition for ...
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### Hidden Markov Model to fill missing elements in a sequence

In my project I have a set of sequences (elements are letters from English alphabet) and some of the sequences have missing elements. I need to fill them with the most probable elements. I've been ...
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### Can Hidden Markov Models be used to predict next observation?

I am reading up on Hidden Markov Models (HMMs) for my research and would like to know if it is applicable to the problem I wish to tackle. My problem is to detect/estimate the next value of a ...
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### HMCM vs Viterbi algorithm for calculating most likely path of an HMM [duplicate]

My expertise in machine learning and statistics is probably at a sophomore level. But anyway, my question is this: Given a Hidden Markov Model returned over a sequence of events with some states, how ...
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### Use of Hidden Markov Models for Clustering

I would like to ask whether Hidden Markov Models can be used for clustering and if so, in what cases. I have found somewhere, references like this but practically I haven't found a way to do this. Is ...
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### Calculate probability distribution $p\left(\left.X_{1:T}\right|Z_{1:T},y_{1:T}\right)$ in linear- non-Gaussian state space model

I have a linear, non-Gaussian state space model. Observation equation: $y_{t}=a+bX_{t}+cZ_{t}+\epsilon_{t}$ $\,\,\,\,$ $\epsilon_{t}\sim\mathcal{N}\left(0,\omega^{2}\right)$ Transition equations: ...
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### loglikelihood for HMM with continuous emissions

I have a HMM and that has continuous valued emissions. I model the emissions using Weibull distributions. After I run the HMM I get the states, transition probabilities, priors and shape,scale ...
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### How do you find mathematical expressions for the posterior marginals i.e. $P(x_n|y_0, … , y_n)$ in an HMM?

My goal is to find closed form equations for posterior marginals $P(x_n|y_0, ... , y_n)$ in a general HMM. I was told that we can calculate it exactly via BP (belief propagation, thought not sure how ...
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### What are the states and observation in HMM speech recognition?

For example: Given a two state HMM a and b If I define a -> b = # a -> a = # b -> b = # b -> a = # Pr(A|a) = # Pr(A|b) = # Pr(B|a) = # Pr(B|b) = # ...
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### HMM walk through for backward algorithm with given example

This pdf file is a resource that walk through a simple HMM algorithm of two states http://www.indiana.edu/~iulg/moss/hmmcalculations.pdf, I have question in step 4.1 of the algorithm Specifically ...
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### Step training Baum-welch HMM

Referred to Baum–Welch algorithm, http://cs.au.dk/~cstorm/courses/MLiB_f14/slides/hidden-markov-models-4.pdf Is this formular correct ? I spend a couple days to figure out which part is wrong. I'm ...
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### EM convergence when using em.hmm from PLIS

I use em.hmm function from PLIS package. I tried it on dimensions in range from 2 to 6. In every case of provided data (z-values) EM algorithm does not converge for dimensions 2, 5, 6. So, I wonder ...
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### In Hidden Markov Model (HMM), is the transition matrix known, inferred, or assumed?

I'm reading Kevin Murphy's Probabilistic Machine Learning, which explains the forward algorithm to do filtering in HMM as follows (pp 610): The very first line says that the transition matrices ...
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### Softmax factorization for a hidden markov model

I'm trying to formulate a hidden markov model where the transition and emission probabilities are governed by a softmax distribution. I'm not sure if this is a good idea, but I thought it could be ...
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### HMMFit underlying algorithms

After reading article "Hidden Markov Models for Controlling False Discovery Rate in Genome-Wide Association Analysis" by Zhi Wei I am trying to use it in my project. I am using R and I have found out ...
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### Embedding Markov Matrix

A stochastic matrix with states $S_1$, $S_2$, $S_3$, $S_4$ is given, now we would like to build up another stochastic matrix with finer states, meaning that the states $S_1$ will be considered as ...
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### a joint probability distribution that passes through all markov network graph without being filtered

from filter view of the Markov Network where only those distributions can pass that satisfy all conditional independence statements given by the graph. • Can we think of distribution that can pass ...