MultilevelMCMCState#

class graph_tool.inference.MultilevelMCMCState(entropy_args={})[source]#

Bases: EntropyState

Base state that implements multilevel agglomerative MCMC sweeps.

Methods

get_entropy_args()

Return the current default values for the parameters of the function entropy(), together with other operations that depend on them.

multilevel_mcmc_sweep([niter, beta, c, d, ...])

Perform niter sweeps of a multilevel agglomerative acceptance-rejection pseudo-MCMC (i.e. detailed balance is not preserved) to sample network partitions, that uses a bisection search on the number of groups, together with group merges and singe-node moves.

reset_entropy_args()

Reset the current default values for the parameters of the function entropy(), together with other operations that depend on them.

update_entropy_args(**kwargs)

Update the default values for the parameters of the function entropy() from the keyword arguments, in a stateful way, together with other operations that depend on them.

get_entropy_args()#

Return the current default values for the parameters of the function entropy(), together with other operations that depend on them.

multilevel_mcmc_sweep(niter=1, beta=inf, c=0.5, d=0.01, r=0.9, random_bisect=True, merge_sweeps=10, mh_sweeps=10, init_r=0.99, init_min_iter=5, init_beta=1.0, gibbs=False, B_min=1, B_max=18446744073709551615, b_min=None, b_max=None, M=None, cache_states=True, force_accept=False, parallel=False, entropy_args={}, verbose=False, **kwargs)[source]#

Perform niter sweeps of a multilevel agglomerative acceptance-rejection pseudo-MCMC (i.e. detailed balance is not preserved) to sample network partitions, that uses a bisection search on the number of groups, together with group merges and singe-node moves.

Parameters:
niterint (optional, default: 1)

Number of sweeps to perform. During each sweep, a move attempt is made for each node, on average.

betafloat (optional, default: numpy.inf)

Inverse temperature.

cfloat (optional, default: .5)

Sampling parameter c for move proposals: For \(c\to 0\) the blocks are sampled according to the local neighborhood of a given node and their block connections; for \(c\to\infty\) the blocks are sampled randomly. Note that only for \(c > 0\) the MCMC is guaranteed to be ergodic.

dfloat (optional, default: .01)

Probability of selecting a new (i.e. empty) group for a given single-node move.

rfloat (optional, default: 0.9)

Group shrink ratio. The number of groups is reduced by this fraction at each merge sweep.

random_bisectbool (optional, default: True)

If True, bisections are done at randomly chosen intervals. Otherwise a Fibonacci sequence is used.

merge_sweepsint (optional, default: 10)

Number of sweeps spent to find good merge proposals.

mh_sweepsint (optional, default: 10)

Number of single-node Metropolis-Hastings sweeps between merge splits.

init_rdouble (optional, default: 0.99)

Stopping criterion for the intialization phase, after each node is put in their own group, to set the initial upper bound of the bisection search. A number of single-node Metropolis-Hastings sweeps is done until the number of groups is shrunk by a factor that is larger than this parameter.

init_min_iterint (optional, default: 5)

Minimum number of iterations at the intialization phase.

init_betafloat (optional, default: 1.)

Inverse temperature to be used for the very first sweep of the initialization phase.

gibbsbool (optional, default: False)

If True, the single node moves use (slower) Gibbs sampling, rather than Metropolis-Hastings.

B_minint (optional, default: 1)

Minimum number of groups to be considered in the search.

b_minVertexPropertyMap (optional, default: None)

If provided, this will be used for the partition corresponding to B_min.

B_maxint (optional, default: 1)

Maximum number of groups to be considered in the search.

b_maxVertexPropertyMap (optional, default: None)

If provided, this will be used for the partition corresponding to B_max.

Mint (optional, default: None)

Maximum number of groups to select for the multilevel move. If None is provided, then all groups are always elected.

cache_statesbool (optional, default: True)

If True, intermediary states will be cached during the bisection search.

force_acceptbool (optional, default: False)

If True, new state will be accepted even if it does not improve the objective function.

parallelbool (optional, default: False)

If True, the algorithm will run in parallel (if enabled during compilation).

entropy_argsdict (optional, default: {})

Entropy arguments, with the same meaning and defaults as in graph_tool.inference.BlockState.entropy().

verbosebool (optional, default: False)

If verbose == True, detailed information will be displayed.

Returns:
dSfloat

Entropy difference after the sweeps.

nattemptsint

Number of vertex moves attempted.

nmovesint

Number of vertices moved.

Notes

This algorithm has an \(O(E\ln^2 N)\) complexity, where \(E\) is the number of edges and \(N\) is the number of nodes (independently of the number of groups).

References

[peixoto-efficient-2014]

Tiago P. Peixoto, “Efficient Monte Carlo and greedy heuristic for the inference of stochastic block models”, Phys. Rev. E 89, 012804 (2014), DOI: 10.1103/PhysRevE.89.012804 [sci-hub, @tor], arXiv: 1310.4378

reset_entropy_args()#

Reset the current default values for the parameters of the function entropy(), together with other operations that depend on them.

update_entropy_args(**kwargs)#

Update the default values for the parameters of the function entropy() from the keyword arguments, in a stateful way, together with other operations that depend on them.

Values updated in this manner are preserved by the copying or pickling of the state.