Sampling is based on simulating the Hamiltonian of a particle with a starting position equal to the current parameter values and an initial momentum (kinetic energy) generated randomly. The potential energy at work on the particle is taken to be the negative log (unnormalized) total probability function defined by the model. In the usual approach to implementing HMC, the Hamiltonian dynamics of the particle is simulated using the leapfrog integrator, which discretizes the smooth path of the particle into a number of small time steps called leapfrog steps.
For each leapfrog step, the negative log probability function and its gradient need to be evaluated at the position corresponding to the current parameter values (a more detailed sketch is provided in the next section). These are used to update the momentum based on the gradient and the position based on the momentum.
For simple models, only a few leapfrog steps with large step sizes are needed. For models with complex posterior geometries, many small leapfrog steps may be needed to accurately model the path of the parameters.
If the user specifies the number of leapfrog steps (i.e., chooses to use standard HMC), that number of leapfrog steps are simulated. If the user has not specified the number of leapfrog steps, the No-U-Turn sampler (NUTS) will determine the number of leapfrog steps adaptively (Hoffman and Gelman 2014).
Log probability and gradient calculation
During each leapfrog step, the log probability function and its gradient must be calculated. This is where most of the time in the Stan algorithm is spent. This log probability function, which is used by the sampling algorithm, is defined over the unconstrained parameters.
The first step of the calculation requires the inverse transform of the unconstrained parameter values back to the constrained parameters in terms of which the model is defined. There is no error checking required because the inverse transform is a total function on every point in whose range satisfies the constraints.
Because the probability statements in the model are defined in terms of constrained parameters, the log Jacobian of the inverse transform must be added to the accumulated log probability.
Next, the transformed parameter statements are executed. After they complete, any constraints declared for the transformed parameters are checked. If the constraints are violated, the model will halt with a diagnostic error message.
The final step in the log probability function calculation is to execute the statements defined in the model block.
As the log probability function executes, it accumulates an in-memory representation of the expression tree used to calculate the log probability. This includes all of the transformed parameter operations and all of the Jacobian adjustments. This tree is then used to evaluate the gradients by propagating partial derivatives backward along the expression graph. The gradient calculations account for the majority of the cycles consumed by a Stan program.
A standard Metropolis accept/reject step is required to retain detailed balance and ensure draws are marginally distributed according to the probability function defined by the model. This Metropolis adjustment is based on comparing log probabilities, here defined by the Hamiltonian, which is the sum of the potential (negative log probability) and kinetic (squared momentum) energies. In theory, the Hamiltonian is invariant over the path of the particle and rejection should never occur. In practice, the probability of rejection is determined by the accuracy of the leapfrog approximation to the true trajectory of the parameters.
If step sizes are small, very few updates will be rejected, but many steps will be required to move the same distance. If step sizes are large, more updates will be rejected, but fewer steps will be required to move the same distance. Thus a balance between effort and rejection rate is required. If the user has not specified a step size, Stan will tune the step size during warmup sampling to achieve a desired rejection rate (thus balancing rejection versus number of steps).
If the proposal is accepted, the parameters are updated to their new values. Otherwise, the sample is the current set of parameter values.
Hoffman, Matthew D., and Andrew Gelman. 2014. “The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo.” Journal of Machine Learning Research 15: 1593–1623. http://jmlr.org/papers/v15/hoffman14a.html.