Detailed API for AdvancedHMC.jl

An important design goal of AdvancedHMC.jl is modularity; we would like to support algorithmic research on HMC. This modularity means that different HMC variants can be easily constructed by composing various components, such as preconditioning metric (i.e., mass matrix), leapfrog integrators, trajectories (static or dynamic), adaption schemes, etc. In this section, we will explain the detailed usage of different modules in AdancedHMC.jl to provide a comprehensive udnerstanding of how AdvancedHMC.jl can achieve both modularity and efficiency. The section highlights the key components of AdvancedHMC.jl, with a complete documentation provided at the end.

Hamiltonian mass matrix (`metric`)

Unit metric: UnitEuclideanMetric(dim)
Diagonal metric: DiagEuclideanMetric(dim)
Dense metric: DenseEuclideanMetric(dim)

where dim is the dimensionality of the sampling space.

Integrator (`integrator`)

Ordinary leapfrog integrator: Leapfrog(ϵ)
Jittered leapfrog integrator with jitter rate n: JitteredLeapfrog(ϵ, n)
Tempered leapfrog integrator with tempering rate a: TemperedLeapfrog(ϵ, a)

where ϵ is the step size of leapfrog integration.

Kernel (`kernel`)

Static HMC with a fixed number of steps (n_steps) from Neal [1]: HMCKernel(Trajectory{EndPointTS}(integrator, FixedNSteps(integrator)))
HMC with a fixed total trajectory length (trajectory_length) from Neal [1]: HMCKernel(Trajectory{EndPointTS}(integrator, FixedIntegrationTime(trajectory_length)))
Original NUTS with slice sampling from Hoffman et al. [2]: HMCKernel(Trajectory{SliceTS}(integrator, ClassicNoUTurn()))
Generalised NUTS with slice sampling from Betancourt [3]: HMCKernel(Trajectory{SliceTS}(integrator, GeneralisedNoUTurn()))
Original NUTS with multinomial sampling from Betancourt [3]: HMCKernel(Trajectory{MultinomialTS}(integrator, ClassicNoUTurn()))
Generalised NUTS with multinomial sampling from Betancourt [3]: HMCKernel(Trajectory{MultinomialTS}(integrator, GeneralisedNoUTurn()))

Adaptor (`adaptor`)

Adapt the mass matrix metric of the Hamiltonian dynamics: mma = MassMatrixAdaptor(metric)
- This is lowered to UnitMassMatrix, WelfordVar or WelfordCov based on the type of the mass matrix metric
Adapt the step size of the leapfrog integrator integrator: ssa = StepSizeAdaptor(δ, integrator)
- It uses Nesterov's dual averaging with δ as the target acceptance rate.
Combine the two above naively: NaiveHMCAdaptor(mma, ssa)
Combine the first two using Stan's windowed adaptation: StanHMCAdaptor(mma, ssa)

The `sample` functions

sample(
    rng::Union{AbstractRNG,AbstractVector{<:AbstractRNG}},
    h::Hamiltonian,
    κ::HMCKernel,
    θ::AbstractVector{<:AbstractFloat},
    n_samples::Int;
    adaptor::AbstractAdaptor=NoAdaptation(),
    n_adapts::Int=min(div(n_samples, 10), 1_000),
    drop_warmup=false,
    verbose::Bool=true,
    progress::Bool=false,
)

Draw n_samples samples using the kernel κ under the Hamiltonian system h

The randomness is controlled by rng.
- If rng is not provided, the default random number generator (Random.default_rng()) will be used.
The initial point is given by θ.
The adaptor is set by adaptor, for which the default is no adaptation.
- It will perform n_adapts steps of adaptation, for which the default is 1_000 or 10% of n_samples, whichever is lower.
drop_warmup specifies whether to drop samples.
verbose controls the verbosity.
progress controls whether to show the progress meter or not.

Note that the function signature of the sample function exported by AdvancedHMC.jl differs from the sample function used by Turing.jl. We refer to the documentation of Turing.jl for more details on the latter.

Full documentation of APIs in AdvancedHMC.jl

AdvancedHMC.AbstractIntegrator — Type

abstract type AbstractIntegrator

Represents an integrator used to simulate the Hamiltonian system.

Implementation

A AbstractIntegrator is expected to have the following implementations:

stat(@ref)
nom_step_size(@ref)
step_size(@ref)

Detailed API for AdvancedHMC.jl

Hamiltonian mass matrix (metric)

Integrator (integrator)

Kernel (kernel)