hmmmm 🤔

Yet another aptly-named Hidden-Markov Model library for Rust.

Important Note: This crate depends on the feature generic_const_exprs. For now, usage of this crate is limited to use with the nightly Rust channel.

Usage

Installation

cargo add hmmmm --features derive

States + Observations

To create a Hmm, we first need two enums corresponding to the states and observations of the hidden Markov model. This can be done by using the #[derive(State)] and #[derive(Observation)] proc macros in the hmmmm_derive crate:

#[repr(u8)]
#[derive(State)]
enum Condition {
  Healthy,
  Fever,
}

#[repr(u8)]
#[derive(Observation)]
enum Feeling {
  Normal,
  Cold,
  Dizzy,
}

Note that the attribute repr(u8) is required for both enums definitions, as we need to have the enums be: a) as small as possible for efficient computation and b) easily cast between itself and u8 / usize. The derive macros will throw a compilation error if this attribute is not present on the enum.

Probabilities

A Hmm requires 3 different probability matrices:

1. Initial (state) probabilities - [f64; N]
2. Transition probabilities - [[f64; N]; N]
3. Emission probabilities - [[f64; M]; N]

...where N is the number of possible states and O is the number of possible observations.

These can be:

• Manualy declared, e.g.:

let pr_initial: [f64; 2] = [0.6, 0.4]; // [Healthy, Fever]

• Declared via the methods in hmmmm::utils, e.g.:

let pr_initial: [f64; 2] = pr_i(|cond| match cond {
  Condition::Healthy => 0.6,
  Condition::Fever => 0.4,
});

Constructing the HMM

Now that we have our states, observations, and corresponding probability matrices we can construct our Hmm:

let pr_initial: [f64; 2] = [0.6, 0.4];
let pr_transition: [[f64; 2]; 2] = [
  [0.7, 0.3],
  [0.4, 0.6]
];
let pr_emission: [[f64; 3]; 2] = [
  [0.5, 0.4, 0.1],
  [0.1, 0.3, 0.6]
]

let hmm = Hmm::<Condition, Feeling>::new(
  pr_initial,
  pr_transition,
  pr_emission
);

Algorithms

Viterbi

Wikipedia

The Viterbi algorithm obtains the maximum a posteriori estimate (MAP) of the most likely sequence of hidden states given an input sequence of observations.

Input: the sequence of observations - &Vec<O>

Output: a tuple containing the log (base 2) probability of the MAP hidden state sequence and the corresponding hidden state sequence - (f64, Vec<S>)

Example:

/* Using the HMM `hmm` from the previous section */

let signal = vec![Feeling::Normal, Feeling::Cold, Feeling::Dizzy];
let (pr, sequence) = hmm.map_estimate::<Viterbi>(&signal);

/*

pr = −6.04739805022
sequence = [Condition::Healthy, Condition::Healthy, Condition::Fever]

*/