Skip to content

In this section, the current design of Turing’s model “compiler” is described which enables Turing to perform various types of Bayesian inference without changing the model definition. The “compiler” is essentially just a macro that rewrites the user’s model definition to a function that generates a Model struct that Julia’s dispatch can operate on and that Julia’s compiler can successfully do type inference on for efficient machine code generation.

Overview

The following terminology will be used in this section:

  • D: observed data variables conditioned upon in the posterior,
  • P: parameter variables distributed according to the prior distributions, these will also be referred to as random variables,
  • Model: a fully defined probabilistic model with input data

Turing’s @model macro rewrites the user-provided function definition such that it can be used to instantiate a Model by passing in the observed data D.

The following are the main jobs of the @model macro:

  1. Parse ~ and .~ lines, e.g. y .~ Normal.(c*x, 1.0)
  2. Figure out if a variable belongs to the data D and or to the parameters P
  3. Enable the handling of missing data variables in D when defining a Model and treating them as parameter variables in P instead
  4. Enable the tracking of random variables using the data structures VarName and VarInfo
  5. Change ~/.~ lines with a variable in P on the LHS to a call to tilde_assume or dot_tilde_assume
  6. Change ~/.~ lines with a variable in D on the LHS to a call to tilde_observe or dot_tilde_observe
  7. Enable type stable automatic differentiation of the model using type parameters

The model

A model::Model is a callable struct that one can sample from by calling

(model::Model)([rng, varinfo, sampler, context])

where rng is a random number generator (default: Random.GLOBAL_RNG), varinfo is a data structure that stores information about the random variables (default: DynamicPPL.VarInfo()), sampler is a sampling algorithm (default: DynamicPPL.SampleFromPrior()), and context is a sampling context that can, e.g., modify how the log probability is accumulated (default: DynamicPPL.DefaultContext()).

Sampling resets the log joint probability of varinfo and increases the evaluation counter of sampler. If context is a LikelihoodContext, only the log likelihood will be accumulated. With the DefaultContext the log joint probability of P and D is accumulated.

The Model struct contains the three internal fields f, args and defaults. When model::Model is called, then the internal function model.f is called as model.f(rng, varinfo, sampler, context, model.args...) (for multithreaded sampling, instead of varinfo a threadsafe wrapper is passed to model.f). The positional and keyword arguments that were passed to the user-defined model function when the model was created are saved as a NamedTuple in model.args. The default values of the positional and keyword arguments of the user-defined model functions, if any, are saved as a NamedTuple in model.defaults. They are used for constructing model instances with different arguments by the logprob and prob string macros.

Example

Let’s take the following model as an example:

@model function gauss(x = missing, y = 1.0, ::Type{TV} = Vector{Float64}) where {TV<:AbstractVector}
    if x === missing
        x = TV(undef, 3)
    end
    p = TV(undef, 2)
    p[1] ~ InverseGamma(2, 3)
    p[2] ~ Normal(0, 1.0)
    @. x[1:2] ~ Normal(p[2], sqrt(p[1]))
    x[3] ~ Normal()
    y ~ Normal(p[2], sqrt(p[1]))
end

The above call of the @model macro defines the function gauss with positional arguments x, y, and ::Type{TV}, rewritten in such a way that every call of it returns a model::Model. Note that only the function body is modified by the @model macro, and the function signature is left untouched. It is also possible to implement models with keyword arguments such as

@model function gauss(::Type{TV} = Vector{Float64}; x = missing, y = 1.0) where {TV<:AbstractVector}
    ...
end

This would allow us to generate a model by calling gauss(; x = rand(3)).

If an argument has a default value missing, it is treated as a random variable. For variables which require an intialization because we need to loop or broadcast over its elements, such as x above, the following needs to be done:

if x === missing
    x = ...
end

Note that since gauss behaves like a regular function it is possible to define additional dispatches in a second step as well. For instance, we could achieve the same behaviour by

@model function gauss(x, y = 1.0, ::Type{TV} = Vector{Float64}) where {TV<:AbstractVector}
    p = TV(undef, 2)
    ...
end

function gauss(::Missing, y = 1.0, ::Type{TV} = Vector{Float64}) where {TV<:AbstractVector}
    return gauss(TV(undef, 3), y, TV)
end

If x is sampled as a whole from a distribution and not indexed, e.g., x ~ Normal(...) or x ~ MvNormal(...), there is no need to initialize it in an if-block.

Step 1: Break up the model definition

First, the @model macro breaks up the user-provided function definition using DynamicPPL.build_model_info. This function returns a dictionary consisting of:

  • allargs_exprs: The expressions of the positional and keyword arguments, without default values.
  • allargs_syms: The names of the positional and keyword arguments, e.g., [:x, :y, :TV] above.
  • allargs_namedtuple: An expression that constructs a NamedTuple of the positional and keyword arguments, e.g., :((x = x, y = y, TV = TV)) above.
  • defaults_namedtuple: An expression that constructs a NamedTuple of the default positional and keyword arguments, if any, e.g., :((x = missing, y = 1, TV = Vector{Float64})) above.
  • modeldef: A dictionary with the name, arguments, and function body of the model definition, as returned by MacroTools.splitdef.

Step 2: Generate the body of the internal model function

In a second step, DynamicPPL.generate_mainbody generates the main part of the transformed function body using the user-provided function body and the provided function arguments, without default values, for figuring out if a variable denotes an observation or a random variable. Hereby the function DynamicPPL.generate_tilde replaces the L ~ R lines in the model and the function DynamicPPL.generate_dot_tilde replaces the @. L ~ R and L .~ R lines in the model.

In the above example, p[1] ~ InverseGamma(2, 3) is replaced with something similar to

#= REPL[25]:6 =#
begin
    var"##tmpright#323" = InverseGamma(2, 3)
    var"##tmpright#323" isa Union{Distribution, AbstractVector{<:Distribution}} || throw(ArgumentError("Right-hand side of a ~ must be subtype of Distribution or a vector of Distributions."))
    var"##vn#325" = (DynamicPPL.VarName)(:p, ((1,),))
    var"##inds#326" = ((1,),)
    p[1] = (DynamicPPL.tilde_assume)(_rng, _context, _sampler, var"##tmpright#323", var"##vn#325", var"##inds#326", _varinfo)
end

Here the first line is a so-called line number node that enables more helpful error messages by providing users with the exact location of the error in their model definition. Then the right hand side (RHS) of the ~ is assigned to a variable (with an automatically generated name). We check that the RHS is a distribution or an array of distributions, otherwise an error is thrown. Next we extract a compact representation of the variable with its name and index (or indices). Finally, the ~ expression is replaced with a call to DynamicPPL.tilde_assume since the compiler figured out that p[1] is a random variable using the following heuristic:

  1. If the symbol on the LHS of ~, :p in this case, is not among the arguments to the model, (:x, :y, :T) in this case, it is a random variable.
  2. If the symbol on the LHS of ~, :p in this case, is among the arguments to the model but has a value of missing, it is a random variable.
  3. If the value of the LHS of ~, p[1] in this case, is missing, then it is a random variable.
  4. Otherwise, it is treated as an observation.

The DynamicPPL.tilde_assume function takes care of sampling the random variable, if needed, and updating its value and the accumulated log joint probability in the _varinfo object. If L ~ R is an observation, DynamicPPL.tilde_observe is called with the same arguments except the random number generator _rng (since observations are never sampled).

A similar transformation is performed for expressions of the form @. L ~ R and L .~ R. For instance, @. x[1:2] ~ Normal(p[2], sqrt(p[1])) is replaced with

#= REPL[25]:8 =#
begin
    var"##tmpright#331" = Normal.(p[2], sqrt.(p[1]))
    var"##tmpright#331" isa Union{Distribution, AbstractVector{<:Distribution}} || throw(ArgumentError("Right-hand side of a ~ must be subtype of Distribution or a vector of Distributions."))
    var"##vn#333" = (DynamicPPL.VarName)(:x, ((1:2,),))
    var"##inds#334" = ((1:2,),)
    var"##isassumption#335" = begin
        let var"##vn#336" = (DynamicPPL.VarName)(:x, ((1:2,),))
            if !((DynamicPPL.inargnames)(var"##vn#336", _model)) || (DynamicPPL.inmissings)(var"##vn#336", _model)
                true
            else
                x[1:2] === missing
            end
        end
    end
    if var"##isassumption#335"
        x[1:2] .= (DynamicPPL.dot_tilde_assume)(_rng, _context, _sampler, var"##tmpright#331", x[1:2], var"##vn#333", var"##inds#334", _varinfo)
    else
        (DynamicPPL.dot_tilde_observe)(_context, _sampler, var"##tmpright#331", x[1:2], var"##vn#333", var"##inds#334", _varinfo)
    end
end

The main difference in the expanded code between L ~ R and @. L ~ R is that the former doesn’t assume L to be defined, it can be a new Julia variable in the scope, while the latter assumes L already exists. Moreover, DynamicPPL.dot_tilde_assume and DynamicPPL.dot_tilde_observe are called instead of DynamicPPL.tilde_assume and DynamicPPL.tilde_observe.

Step 3: Replace the user-provided function body

Finally, we replace the user-provided function body using DynamicPPL.build_output. This function uses MacroTools.combinedef to reassemble the user-provided function with a new function body. In the modified function body an anonymous function is created whose function body was generated in step 2 above and whose arguments are

  • a random number generator _rng,
  • a model _model,
  • a datastructure _varinfo,
  • a sampler _sampler,
  • a sampling context _context,
  • and all positional and keyword arguments of the user-provided model function as positional arguments

without any default values. Finally, in the new function body a model::Model with this anonymous function as internal function is returned.

VarName

In order to track random variables in the sampling process, Turing uses the struct VarName{sym} which acts as a random variable identifier generated at runtime. The VarName of a random variable is generated from the expression on the LHS of a ~ statement when the symbol on the LHS is in P. Every vn::VarName{sym} has a symbol sym which is the symbol of the Julia variable in the model that the random variable belongs to. For example, x[1] ~ Normal() will generate an instance of VarName{:x} assuming x is in P. Every vn::VarName also has a field indexing which stores the indices requires to access the random variable from the Julia variable indicated by sym. For example, x[1] ~ Normal() will generate a vn::VarName{:x} with vn.indexing == "[1]". VarName also supports hierarchical arrays and range indexing. Some more examples:

  • x[1] ~ Normal() will generate a VarName{:x} with indexing == "[1]".
  • x[:,1] ~ MvNormal(zeros(2)) will generate a VarName{:x} with indexing == "[Colon(),1]".
  • x[:,1][2] ~ Normal() will generate a VarName{:x} with indexing == "[Colon(),1][2]".

VarInfo

Overview

VarInfo is the data structure in Turing that facilitates tracking random variables and certain metadata about them that are required for sampling. For instance, the distribution of every random variable is stored in VarInfo because we need to know the support of every random variable when sampling using HMC for example. Random variables whose distributions have a constrained support are transformed using a bijector from Bijectors.jl so that the sampling happens in the unconstrained space. Different samplers require different metadata about the random variables.

The definition of VarInfo in Turing is:

struct VarInfo{Tmeta, Tlogp} <: AbstractVarInfo
    metadata::Tmeta
    logp::Base.RefValue{Tlogp}
    num_produce::Base.RefValue{Int}
end

Based on the type of metadata, the VarInfo is either aliased UntypedVarInfo or TypedVarInfo. metadata can be either a subtype of the union type Metadata or a NamedTuple of multiple such subtypes. Let vi be an instance of VarInfo. If vi isa VarInfo{<:Metadata}, then it is called an UntypedVarInfo. If vi isa VarInfo{<:NamedTuple}, then vi.metadata would be a NamedTuple mapping each symbol in P to an instance of Metadata. vi would then be called a TypedVarInfo. The other fields of VarInfo include logp which is used to accumulate the log probability or log probability density of the variables in P and D. num_produce keeps track of how many observations have been made in the model so far. This is incremented when running a ~ statement when the symbol on the LHS is in D.

Metadata

The Metadata struct stores some metadata about the random variables sampled. This helps query certain information about a variable such as: its distribution, which samplers sample this variable, its value and whether this value is transformed to real space or not. Let md be an instance of Metadata:

  • md.vns is the vector of all VarName instances. Let vn be an arbitrary element of md.vns
  • md.idcs is the dictionary that maps each VarName instance to its index in

md.vns, md.ranges, md.dists, md.orders and md.flags.

  • md.vns[md.idcs[vn]] == vn.
  • md.dists[md.idcs[vn]] is the distribution of vn.
  • md.gids[md.idcs[vn]] is the set of algorithms used to sample vn. This is used in

the Gibbs sampling process.

  • md.orders[md.idcs[vn]] is the number of observe statements before vn is sampled.
  • md.ranges[md.idcs[vn]] is the index range of vn in md.vals.
  • md.vals[md.ranges[md.idcs[vn]]] is the linearized vector of values of corresponding to vn.
  • md.flags is a dictionary of true/false flags. md.flags[flag][md.idcs[vn]] is the

value of flag corresponding to vn.

Note that in order to make md::Metadata type stable, all the md.vns must have the same symbol and distribution type. However, one can have a single Julia variable, e.g. x, that is a matrix or a hierarchical array sampled in partitions, e.g. x[1][:] ~ MvNormal(zeros(2), 1.0); x[2][:] ~ MvNormal(ones(2), 1.0). The symbol x can still be managed by a single md::Metadata without hurting the type stability since all the distributions on the RHS of ~ are of the same type.

However, in Turing models one cannot have this restriction, so we must use a type unstable Metadata if we want to use one Metadata instance for the whole model. This is what UntypedVarInfo does. A type unstable Metadata will still work but will have inferior performance.

To strike a balance between flexibility and performance when constructing the spl::Sampler instance, the model is first run by sampling the parameters in P from their priors using an UntypedVarInfo, i.e. a type unstable Metadata is used for all the variables. Then once all the symbols and distribution types have been identified, a vi::TypedVarInfo is constructed where vi.metadata is a NamedTuple mapping each symbol in P to a specialized instance of Metadata. So as long as each symbol in P is sampled from only one type of distributions, vi::TypedVarInfo will have fully concretely typed fields which brings out the peak performance of Julia.