Reference for pgm input file format

This documents the input format used by PGM to compute inference. The work of the Matlab M-files is to generate a file in this format.

<method>

• (tree_partition)
  This does not perform inference, but only computes a tree partition.
• (tree_mcmc) (number_steps)
  This perform inference using Tree Sampling with Rao-Blackwellization, with the given number of steps.
• (tree_mcmc_no_rb) (number_steps)
  This perform inference using Tree Sampling WITHOUT Rao-Blackwellization, with the given number of steps.

<all potential tables>

• (all-random)
  This will create all the potentials at random, and the potentials will all be different from each other.
• (all-random-strongly-diagonal-uniform-noise) (a)
  This will create an unique potential table, used for all potentials, with uniform noise and strongly diagonal coefficients. a will be used as the strongly diagonal coefficient.

<timer>

This instructs the inference engine to use a timer; e.g., the computational time will be measured with real seconds instead of steps.

<monitor>

This activates monitoring, allowing errors to be computed at each step/second.

<number of runs> (a)

This will make the requested number of runs (specified by a), instead of a single run.

<observations> (a b) ... (a b)

The variables represented by the indexes a will be set observed to the values b.

<internal potentials> (a) ( x ... z ) ... (a) ( x ... z )

The variables represented by the indexes a will get their priors (internal potentials) set to the vector given by values x ... z.