# Hamiltonian Monte Carlo (HMC)¶

Implementation of the Hybrid Monte Carlo (also known as Hamiltonian Monte Carlo) of Duane [21]. The sampler simulates autocorrelated draws from a distribution that can be specified up to a constant of proportionality. Code is derived from Neal’s implementation [62].

## Model-Based Constructors¶

`HMC`(params::ElementOrVector{Symbol}, epsilon::Real, L::Integer; dtype::Symbol=:forward)
`HMC`(params::ElementOrVector{Symbol}, epsilon::Real, L::Integer, Sigma::Matrix{T<:Real}; dtype::Symbol=:forward)

Construct a `Sampler` object for HMC sampling. Parameters are assumed to be continuous, but may be constrained or unconstrained.

Arguments

• `params` : stochastic node(s) to be updated with the sampler. Constrained parameters are mapped to unconstrained space according to transformations defined by the Stochastic `unlist()` function.

• `epsilon` : step size.

• `L` : number of steps to take in the Leapfrog algorithm.

• `Sigma` : covariance matrix for the multivariate normal proposal distribution. The covariance matrix is relative to the unconstrained parameter space, where candidate draws are generated. If omitted, the identity matrix is assumed.

• `dtype` : type of differentiation for gradient calculations. Options are
• `:central` : central differencing.
• `:forward` : forward differencing.

Value

Returns a `Sampler{HMCTune}` type object.

Example

See the Dyes and other Examples.

## Stand-Alone Functions¶

`hmc!`(v::HMCVariate, epsilon::Real, L::Integer, logfgrad::Function)
`hmc!`(v::HMCVariate, epsilon::Real, L::Integer, SigmaF::Cholesky{Float64}, logfgrad::Function)

Simulate one draw from a target distribution using the HMC sampler. Parameters are assumed to be continuous and unconstrained.

Arguments

• `v` : current state of parameters to be simulated.
• `epsilon` : step size.
• `L` : number of steps to take in the Leapfrog algorithm.
• `SigmaF` : Cholesky factorization of the covariance matrix for the multivariate normal proposal distribution. If omitted, the identity matrix is assumed.
• `logfgrad` : function that takes a single `DenseVector` argument at which to compute the log-transformed density (up to a normalizing constant) and gradient vector, and returns the respective results as a tuple.

Value

Returns `v` updated with simulated values and associated tuning parameters.

Example

The following example samples parameters in a simple linear regression model. Details of the model specification and posterior distribution can be found in the Supplement.

```################################################################################
## Linear Regression
##   y ~ N(b0 + b1 * x, s2)
##   b0, b1 ~ N(0, 1000)
##   s2 ~ invgamma(0.001, 0.001)
################################################################################

using Mamba

## Data
data = Dict(
:x => [1, 2, 3, 4, 5],
:y => [1, 3, 3, 3, 5]
)

## Log-transformed Posterior(b0, b1, log(s2)) + Constant and Gradient Vector
b0 = x[1]
b1 = x[2]
logs2 = x[3]
r = data[:y] - b0 - b1 * data[:x]
logf = (-0.5 * length(data[:y]) - 0.001) * logs2 -
(0.5 * dot(r, r) + 0.001) / exp(logs2) -
0.5 * b0^2 / 1000 - 0.5 * b1^2 / 1000
sum(r) / exp(logs2) - b0 / 1000,
sum(data[:x] .* r) / exp(logs2) - b1 / 1000,
-0.5 * length(data[:y]) - 0.001 + (0.5 * dot(r, r) + 0.001) / exp(logs2)
]
end

## MCMC Simulation with Hamiltonian Monte Carlo
## Without (1) and with (2) a user-specified proposal covariance matrix
n = 5000
sim1 = Chains(n, 3, names = ["b0", "b1", "s2"])
sim2 = Chains(n, 3, names = ["b0", "b1", "s2"])
theta1 = HMCVariate([0.0, 0.0, 0.0])
theta2 = HMCVariate([0.0, 0.0, 0.0])
epsilon = 0.1
L = 50
SigmaF = cholfact(eye(3))
for i in 1:n
sim1[i, :, 1] = [theta1[1:2]; exp(theta1[3])]
sim2[i, :, 1] = [theta2[1:2]; exp(theta2[3])]
end
describe(sim1)
describe(sim2)
```

## HMCVariate Type¶

### Declaration¶

`typealias HMCVariate SamplerVariate{HMCTune}`

### Fields¶

• `value::Vector{Float64}` : simulated values.
• `tune::HMCTune` : tuning parameters for the sampling algorithm.

### Constructors¶

`HMCVariate`(x::AbstractVector{T<:Real})
`HMCVariate`(x::AbstractVector{T<:Real}, tune::HMCTune)

Construct a `HMCVariate` object that stores simulated values and tuning parameters for HMC sampling.

Arguments

• `x` : simulated values.
• `tune` : tuning parameters for the sampling algorithm. If not supplied, parameters are set to their defaults.

Value

Returns a `HMCVariate` type object with fields set to the values supplied to arguments `x` and `tune`.

## HMCTune Type¶

### Declaration¶

`type HMCTune <: SamplerTune`

### Fields¶

• `epsilon::Float64` : step size.
• `L::Int` : number of steps to take in the Leapfrog algorithm.
• `SigmaF::Cholesky{Float64}` : Cholesky factorization of the covariance matrix for the multivariate normal proposal distribution.