This page summarizes some of ForneyLab's internal structures. It is mainly tailored for software developers interested in a high-level overview of the inner workings of the package. Coding style conventions can be found in

Directory structure

ForneyLab's directories and files are structured as follows:

  • /demo/: demos in Jupyter (iJulia) notebook format (.ipynb)
  • /docs/: documentation source and build location
  • /src/: ForneyLab source files
    • algorithms/: inference algorithm implementations
    • engines/: rendering of message passing schedules to executable code
      • julia/: Julia engine and update rule implementations
    • factor_nodes/: all node-specific files
    • update_rules/: message passing update rules
  • /test/: test files with directory structure similar to /src/.

InferenceAlgorithm data structure

A ForneyLab InferenceAlgorithm is structured as follows:

  • algorithm::InferenceAlgorithm: specifies everything required for algorithm generation
    • posterior_factorization::PosteriorFactorization: specifies factorization of the posterior
      • posterior_factors::Vector{PosteriorFactor} (per item):
        • id::Symbol: posterior factor id
        • optimize::Bool: require optimization block
        • initialize::Bool: require initialization block
        • schedule::Schedule (per ScheduleEntry item):
          • schedule_index::Int: position of entry in schedule
          • message_update_rule::Type: update rule type for message computation
          • initialize::Bool: require message initialization
          • family::FactorFunction: family of message distribution (for initialization)
          • dimensionality::Tuple: dimensionality of message distribution (for initialization)
          • inbounds::Vector (per item):
            • inbound::Union: inbound, see below
        • marginal_table::MarginalTable (per MarginalEntry item):
          • marginal_id::Symbol: identifier for the marginal
          • marginal_update_rule::Union{Nothing, Product, Type}: update rule type for marginal computation
          • inbounds::Vector (per item):
            • inbound::Union: inbound, see below
    • average_energies::Dict (per item):
      • node::Type: node type for average energy computation
      • counting_number::Int64: counting number for average energy
      • inbounds::Vector (per item):
        • inbound::Union: inbound, see below
    • entropies::Dict (per item):
      • counting_number::Int64: counting number for (joint) entropy
      • inbound::Union: inbound, see below

Inbounds are of type Union{Nothing, ScheduleEntry, MarginalEntry, Dict, Clamp}.

Update rules naming convention

The name of an update rule is composed of several parts:

  1. The word rule
  2. Type of algorithm
    • SP: sum-product
    • VB: variational Bayes
    • SVB: structured variational Bayes
    • M: marginal (joint)
  3. Type of factor node
  4. Interface of the outgoing message
  5. Types of incoming messages (absent for VB rules)
    • N: Nothing
    • P: point mass
    • D: distribution
    • [I]: first letter of the message's probability distribution
Example 1: ruleSPGaussianPrecisionMPNP
  1. rule : update rule
  2. SP : sum-product algorithm
  3. GaussianPrecision: Gaussian mean-precision parameterized factor node
  4. M: outgoing message through 'Mean' interface
  5. PNP: incoming message types are: point mass, Nothing and point mass
Example 2: ruleVBBernoulliOut
  1. rule: update rule
  2. VB: variational Bayes algorithm
  3. Bernoulli: Bernoulli factor node
  4. Out: outgoing message through 'Out' interface
  5. -
Example 3: ruleEPProbitIn1BG
  1. rule: update rule
  2. EP: expectation propagation algorithm
  3. Probit: probit factor node
  4. In1: outgoing message through 'in1' interface
  5. GB: incoming message types are: Gaussian and Bernoulli
  • Note that EP update rules do not have N (nothing) in the set of incoming messages given that in EP there is an incoming message through the interface of the outgoing message that is being calculated.