Hidden Markov Model

Submitted by:

Maheen Fatima(718)
Saba Tasneem (710)

Submitted to:

Ms. Tahira Noor

Department of Bioinformatics
Faculty of Computing
International Islamic University Islamabad
 Hidden Markov Model

Definition:
A Hidden Markov Model (HMM) is a statistical model used to represent systems with
unobserved (hidden) states that generate a sequence of observable events
(observations).
It assumes that the system transitions between hidden states probabilistically, and
each state has a distinct probability of producing each possible observation.

These models work especially well with sequential data, where the underlying states
output observable data but are not directly observable.

Components:

HMMs comprise hidden states, observable states, transition probabilities, and

emission probabilities. The transitions between hidden states are modeled
probabilistically, and each hidden state emits observable data according to emission
probabilities.

Architecture of Hidden Markov Models:

States:
Hidden States:
These represent the unobservable, underlying states of the system. For example,
hidden states might represent weather conditions in a weather forecasting application.
Observable States:
Observable states are the states that emit data. In the weather example, observable
states could represent observed weather parameters like temperature and humidity.
Transition Probabilities:
Define the likelihood of transitioning from one hidden state to another. These
probabilities capture the dynamics of the system.
Emission Probabilities:
Determine the likelihood of an observable state emitting specific data. In our weather
example, emission probabilities would describe the chance of observing particular
weather conditions given the hidden state.
Application and Usage:
Speech Recognition: To accurately convert speech to text, speech recognition
systems make considerable use of HMMs to represent the transition between
phonemes.

Bioinformatics: HMMs are used in bioinformatics to predict genes, analyse protein

sequences, and find conserved themes in DNA sequences.

Economics and Finance: To capture changes between various market states and aid
in the prediction of market trends, HMMs are used in financial market modeling.

Usage in Bioinformatics:
Gene Prediction:
HMMs are used for gene prediction, where hidden states represent coding and non-
coding regions, aiding in identifying potential genes in DNA sequences.

Protein Structure Prediction:

HMMs assist in predicting protein secondary and tertiary structures by modeling the
transitions between different structural states.

Phylogenetic Analysis:
HMMs are applied to model evolutionary processes, helping in constructing
phylogenetic trees and understanding the relationships between species.

Pros of Hidden Markov Models:

Biological Relevance: By identifying structural motifs and evolutionary patterns in
sequences, HMMs offer a biologically meaningful method of representing and
analysing sequences.

Modeling Variability: Because HMMs are probabilistic, they can represent

biological sequence variability and take into account the innate diversity of living
things.

Interpretability: By giving probabilities to various biological states, HMMs provide

interpretability, assisting researchers in deciphering the functional relevance of
observed sequences.
Cons of Hidden Markov Models:
Sensitivity to Model Parameters:
Similar to general HMMs, the performance of HMMs in Bioinformatics is sensitive to
the accurate estimation of model parameters, which can be challenging.

Complexity of Biological Processes:

Biological processes often involve intricate interactions that may not be fully captured
by HMMs, and oversimplified models may lead to inaccurate predictions.

Data Quality Dependency:

The effectiveness of HMMs is dependent on the quality and completeness of the
biological sequence data available.

Reference:
1. A Systematic Review of Hidden Markov Models and Their
Applications | Archives of Computational Methods in Engineering
(springer.com)
2. https://www.researchgate.net/figure/Graphical-representation-of-HMM-and-CHMM-
rolled-out-in-time-of-the-technical-details_fig4_2369443
3. Disaggregated Homes: The pros and cons of using HMMs to model appliances
(oliverparson.co.uk)
4. Advantages and disadvantages of hidden markov model | PPT
(slideshare.net)