# graph_tool.inference - Statistical inference of generative network models¶

This module contains algorithms for the identification of large-scale network structure via the statistical inference of generative models.

Note

An introduction to the concepts used here, as well as a basic HOWTO is included in the cookbook section: Inferring modular network structure.

## Nonparametric stochastic block model inference¶

### High-level functions¶

 minimize_blockmodel_dl Fit the stochastic block model, by minimizing its description length using an agglomerative heuristic. minimize_nested_blockmodel_dl Fit the nested stochastic block model, by minimizing its description length using an agglomerative heuristic.

### State classes¶

 BlockState The stochastic block model state of a given graph. OverlapBlockState The overlapping stochastic block model state of a given graph. LayeredBlockState The (possibly overlapping) block state of a given graph, where the edges are divided into discrete layers. NestedBlockState The nested stochastic block model state of a given graph. TemperingState This class aggregates several state classes and corresponding inverse-temperature values to implement parallel tempering MCMC.

### Sampling and minimization¶

 mcmc_equilibrate Equilibrate a MCMC with a given starting state. mcmc_anneal Equilibrate a MCMC at a specified target temperature by performing simulated annealing. mcmc_multilevel Equilibrate a MCMC from a starting state with a higher order, by performing successive agglomerative initializations and equilibrations until the desired order is reached, such that metastable states are avoided. multicanonical_equilibrate Equilibrate a multicanonical Monte Carlo sampling using the Wang-Landau algorithm. MulticanonicalState The density of states of a multicanonical Monte Carlo algorithm. bisection_minimize Find the best order (number of groups) given an initial set of states by performing a one-dimension minimization, using a Fibonacci (or golden section) search. hierarchy_minimize Attempt to find a fit of the nested stochastic block model that minimizes the description length.

### Auxiliary functions¶

 model_entropy Computes the amount of information necessary for the parameters of the traditional blockmodel ensemble, for B blocks, N vertices, E edges, and either a directed or undirected graph. mf_entropy Compute the “mean field” entropy given the vertex block membership marginals. bethe_entropy Compute the Bethe entropy given the edge block membership marginals. microstate_entropy Compute microstate entropy given a histogram of partitions. half_edge_graph Generate a half-edge graph, where each half-edge is represented by a node, and an edge connects the half-edges like in the original graph. get_block_edge_gradient Get edge gradients corresponding to the block membership at the endpoints of the edges given by the be edge property map.

### Auxiliary classes¶

 PartitionHist Histogram of partitions, implemented in C++. BlockPairHist Histogram of block pairs, implemented in C++.

## Nonparametric network reconstruction¶

### State classes¶

 MeasuredBlockState The inference state of a measured graph, using the stochastic block model as a prior. MixedMeasuredBlockState The inference state of a measured graph with heterogeneous errors, using the stochastic block model as a prior. UncertainBlockState The inference state of an uncertain graph, using the stochastic block model as a prior. UncertainBaseState Base state for uncertain network inference.

## Semiparametric stochastic block model inference¶

### State classes¶

 EMBlockState The parametric, undirected stochastic block model state of a given graph.

### Expectation-maximization Inference¶

 em_infer Infer the model parameters and latent variables using the expectation-maximization (EM) algorithm with initial state given by state.

## Large-scale descriptors¶

 modularity Calculate Newman’s modularity of a network partition.

## Contents¶

class graph_tool.inference.blockmodel.PartitionHist

Histogram of partitions, implemented in C++. Interface supports querying and setting using Vector_int32_t as keys, and ints as values.

asdict()

Return the histogram’s contents as a dict.

class graph_tool.inference.blockmodel.BlockPairHist

Histogram of block pairs, implemented in C++. Interface supports querying and setting using pairs of ints as keys, and ints as values.

asdict()

Return the histogram’s contents as a dict.

class graph_tool.inference.blockmodel.BlockState(g, b=None, B=None, eweight=None, vweight=None, recs=[], rec_types=[], rec_params=[], clabel=None, pclabel=None, bfield=None, deg_corr=True, allow_empty=False, max_BE=1000, **kwargs)[source]

Bases: object

The stochastic block model state of a given graph.

Parameters: Graph to be modelled. b : PropertyMap (optional, default: None) Initial block labels on the vertices. If not supplied, it will be randomly sampled. B : int (optional, default: None) Number of blocks (or vertex groups). If not supplied it will be obtained from the parameter b. eweight : PropertyMap (optional, default: None) Edge multiplicities (for multigraphs or block graphs). vweight : PropertyMap (optional, default: None) Vertex multiplicities (for block graphs). recs : list of PropertyMap instances (optional, default: []) List of real or discrete-valued edge covariates. rec_types : list of edge covariate types (optional, default: []) List of types of edge covariates. The possible types are: "real-exponential", "real-normal", "discrete-geometric", "discrete-poisson" or "discrete-binomial". rec_params : list of dict (optional, default: []) Model hyperparameters for edge covariates. This should be a list of dict instances, or the string “microcanonical” (the default if nothing is specified). The keys depend on the type of edge covariate: "real-exponential" or "discrete-poisson" The parameter list is ["r", "theta"], corresponding to the parameters of the Gamma prior distribution. If unspecified, the default is the “empirical Bayes” choice: r = 1.0 and theta is the global average of the edge covariate. "discrete-geometric" The parameter list is ["alpha", "beta"], corresponding to the parameters of the Beta prior distribution. If unspecified, the default is the noninformative choice: alpha = beta = 1.0 "discrete-binomial" The parameter list is ["N", "alpha", "beta"], corresponding to the number of trials N and the parameters of the Beta prior distribution. If unspecified, the default is the noninformative choice, alpha = beta = 1.0, and N is taken to be the maximum edge covarite value. "real-normal" The parameter list is ["m0", "k0", "v0", "nu0"] corresponding to the normal-inverse-chi-squared prior. If unspecified, the defaults are: m0 = rec.fa.mean(), k0 = 1, v0 = rec.fa.std() ** 2, and nu0 = 3, where rec is the corresponding edge covariate property map. clabel : PropertyMap (optional, default: None) Constraint labels on the vertices. If supplied, vertices with different label values will not be clustered in the same group. pclabel : PropertyMap (optional, default: None) Partition constraint labels on the vertices. This has the same interpretation as clabel, but will be used to compute the partition description length. bfield : PropertyMap (optional, default: None) Local field acting as a prior for the node partition. This should be a vector property map of type vector, and contain the log-probability for each node to be placed in each group. deg_corr : bool (optional, default: True) If True, the degree-corrected version of the blockmodel ensemble will be assumed, otherwise the traditional variant will be used. allow_empty : bool (optional, default: False) If True, partition description length computed will allow for empty groups. max_BE : int (optional, default: 1000) If the number of blocks exceeds this value, a sparse matrix is used for the block graph. Otherwise a dense matrix will be used.
get_rec_params()[source]

Get model hyperparameters for edge covariates.

set_rec_params(params)[source]

Update model hyperparameters for edge covariates.

copy(g=None, eweight=None, vweight=None, b=None, B=None, deg_corr=None, clabel=None, overlap=False, pclabel=None, bfield=None, max_BE=None, **kwargs)[source]

Copies the block state. The parameters override the state properties, and have the same meaning as in the constructor.

get_block_state(b=None, vweight=False, **kwargs)[source]

Returns a BlockState corresponding to the block graph (i.e. the blocks of the current state become the nodes). The parameters have the same meaning as the in the constructor. If vweight == True the nodes of the block state are weighted with the node counts.

get_E()[source]

Returns the total number of edges.

get_N()[source]

Returns the total number of nodes.

get_B()[source]

Returns the total number of blocks.

get_nonempty_B()[source]

Returns the total number of nonempty blocks.

get_bclabel(clabel=None)[source]

Returns a PropertyMap corresponding to constraint labels for the block graph.

get_bpclabel()[source]

Returns a PropertyMap corresponding to partition constraint labels for the block graph.

get_blocks()[source]

Returns the property map which contains the block labels for each vertex.

set_blocks(b)[source]

Sets the internal partition of the state.

get_bg()[source]

Returns the block graph.

get_ers()[source]

Returns the edge property map of the block graph which contains the $$e_{rs}$$ matrix entries. For undirected graphs, the diagonal values (self-loops) contain $$e_{rr}/2$$.

get_er()[source]

Returns the vertex property map of the block graph which contains the number $$e_r$$ of half-edges incident on block $$r$$. If the graph is directed, a pair of property maps is returned, with the number of out-edges $$e^+_r$$ and in-edges $$e^-_r$$, respectively.

get_nr()[source]

Returns the vertex property map of the block graph which contains the block sizes $$n_r$$.

entropy(adjacency=True, dl=True, partition_dl=True, degree_dl=True, degree_dl_kind='distributed', edges_dl=True, dense=False, multigraph=True, deg_entropy=True, recs=True, recs_dl=True, beta_dl=1.0, exact=True, **kwargs)[source]

Calculate the entropy (a.k.a. negative log-likelihood) associated with the current block partition.

Parameters: adjacency : bool (optional, default: True) If True, the adjacency term of the description length will be included. dl : bool (optional, default: True) If True, the description length for the parameters will be included. partition_dl : bool (optional, default: True) If True, and dl == True the partition description length will be included. degree_dl : bool (optional, default: True) If True, and dl == True the degree sequence description length will be included (for degree-corrected models). degree_dl_kind : str (optional, default: "distributed") This specifies the prior used for the degree sequence. It must be one of: "uniform", "distributed" (default) or "entropy". edges_dl : bool (optional, default: True) If True, and dl == True the edge matrix description length will be included. dense : bool (optional, default: False) If True, the “dense” variant of the entropy will be computed. multigraph : bool (optional, default: True) If True, the multigraph entropy will be used. deg_entropy : bool (optional, default: True) If True, the degree entropy term that is independent of the network partition will be included (for degree-corrected models). recs : bool (optional, default: True) If True, the likelihood for real or discrete-valued edge covariates is computed. recs_dl : bool (optional, default: True) If True, and dl == True the edge covariate description length will be included. beta_dl : double (optional, default: 1.) Prior inverse temperature. exact : bool (optional, default: True) If True, the exact expressions will be used. Otherwise, Stirling’s factorial approximation will be used for some terms.

Notes

The “entropy” of the state is the negative log-likelihood of the microcanonical SBM, that includes the generated graph $$\boldsymbol{A}$$ and the model parameters $$\boldsymbol{\theta}$$,

$\begin{split}\Sigma &= - \ln P(\boldsymbol{A},\boldsymbol{\theta}) \\ &= - \ln P(\boldsymbol{A}|\boldsymbol{\theta}) - \ln P(\boldsymbol{\theta}).\end{split}$

This value is also called the description length of the data, and it corresponds to the amount of information required to describe it (in nats).

For the traditional blockmodel (deg_corr == False), the model parameters are $$\boldsymbol{\theta} = \{\boldsymbol{e}, \boldsymbol{b}\}$$, where $$\boldsymbol{e}$$ is the matrix of edge counts between blocks, and $$\boldsymbol{b}$$ is the partition of the nodes into blocks. For the degree-corrected blockmodel (deg_corr == True), we have an additional set of parameters, namely the degree sequence $$\boldsymbol{k}$$.

For the traditional blockmodel, the model likelihood is

$\begin{split}P(\boldsymbol{A}|\boldsymbol{e},\boldsymbol{b}) &= \frac{\prod_{r<s}e_{rs}!\prod_re_{rr}!!}{\prod_rn_r^{e_r}}\times \frac{1}{\prod_{i<j}A_{ij}!\prod_iA_{ii}!!},\\ P(\boldsymbol{A}|\boldsymbol{e},\boldsymbol{b}) &= \frac{\prod_{rs}e_{rs}!}{\prod_rn_r^{e_r}}\times \frac{1}{\prod_{ij}A_{ij}!},\end{split}$

for undirected and directed graphs, respectively, where $$e_{rs}$$ is the number of edges from block $$r$$ to $$s$$ (or the number of half-edges for the undirected case when $$r=s$$), and $$n_r$$ is the number of vertices in block $$r$$ .

For the degree-corrected variant the equivalent expressions are

$\begin{split}P(\boldsymbol{A}|\boldsymbol{e},\boldsymbol{b},\boldsymbol{k}) &= \frac{\prod_{r<s}e_{rs}!\prod_re_{rr}!!}{\prod_re_r!}\times \frac{\prod_ik_i!}{\prod_{i<j}A_{ij}!\prod_iA_{ii}!!},\\ P(\boldsymbol{A}|\boldsymbol{e},\boldsymbol{b},\boldsymbol{k}) &= \frac{\prod_{rs}e_{rs}!}{\prod_re_r^+!\prod_re_r^-!}\times \frac{\prod_ik_i^+!\prod_ik_i^-!}{\prod_{ij}A_{ij}!},\end{split}$

where $$e_r = \sum_se_{rs}$$ is the number of half-edges incident on block $$r$$, and $$e^+_r = \sum_se_{rs}$$ and $$e^-_r = \sum_se_{sr}$$ are the numbers of out- and in-edges adjacent to block $$r$$, respectively.

If exact == False, Stirling’s approximation is used in the above expression.

If dense == True, the likelihood for the non-degree-corrected model becomes instead

$\begin{split}P(\boldsymbol{A}|\boldsymbol{e},\boldsymbol{b})^{-1} &= \prod_{r<s}{n_rn_s\choose e_{rs}}\prod_r{{n_r\choose 2}\choose e_{rr}/2},\\ P(\boldsymbol{A}|\boldsymbol{e},\boldsymbol{b})^{-1} &= \prod_{rs}{n_rn_s\choose e_{rs}}\end{split}$

if multigraph == False, otherwise we replace $${n\choose m}\to\left(\!\!{n\choose m}\!\!\right)$$ above, where $$\left(\!\!{n\choose m}\!\!\right) = {n+m-1\choose m}$$. A “dense” entropy for the degree-corrected model is not available, and if requested will raise a NotImplementedError.

If dl == True, the description length $$\mathcal{L} = -\ln P(\boldsymbol{\theta})$$ of the model will be returned as well. The terms $$P(\boldsymbol{e})$$ and $$P(\boldsymbol{b})$$ are described in described in model_entropy().

For the degree-corrected model we need to specify the prior $$P(\boldsymbol{k})$$ for the degree sequence as well. Here there are three options:

1. degree_dl_kind == "uniform"

$P(\boldsymbol{k}|\boldsymbol{e},\boldsymbol{b}) = \prod_r\left(\!\!{n_r\choose e_r}\!\!\right)^{-1}.$

This corresponds to a noninformative prior, where the degrees are sampled from a uniform distribution.

2. degree_dl_kind == "distributed" (default)

$P(\boldsymbol{k}|\boldsymbol{e},\boldsymbol{b}) = \prod_r\frac{\prod_k\eta_k^r!}{n_r!} \prod_r q(e_r, n_r)^{-1}$

with $$\eta_k^r$$ being the number of nodes with degree $$k$$ in group $$r$$, and $$q(n,m)$$ being the number of partitions of integer $$n$$ into at most $$m$$ parts.

This corresponds to a prior for the degree sequence conditioned on the degree frequencies, which are themselves sampled from a uniform hyperprior. This option should be preferred in most cases.

3. degree_dl_kind == "entropy"

$P(\boldsymbol{k}|\boldsymbol{e},\boldsymbol{b}) \approx \prod_r\exp\left(-n_rH(\boldsymbol{k}_r)\right)$

where $$H(\boldsymbol{k}_r) = -\sum_kp_r(k)\ln p_r(k)$$ is the entropy of the degree distribution inside block $$r$$.

Note that, differently from the other two choices, this represents only an approximation of the description length. It is meant to be used only for comparison purposes, and should be avoided in practice.

For the directed case, the above expressions are duplicated for the in- and out-degrees.

References

 [peixoto-nonparametric-2017175] Tiago P. Peixoto, “Nonparametric Bayesian inference of the microcanonical stochastic block model”, Phys. Rev. E 95 012317 (2017), DOI: 10.1103/PhysRevE.95.012317 [sci-hub, @tor], arXiv: 1610.02703
 [peixoto-hierarchical-2014175] Tiago P. Peixoto, “Hierarchical block structures and high-resolution model selection in large networks “, Phys. Rev. X 4, 011047 (2014), DOI: 10.1103/PhysRevX.4.011047 [sci-hub, @tor], arXiv: 1310.4377.
 [peixoto-weighted-2017175] Tiago P. Peixoto, “Nonparametric weighted stochastic block models”, arXiv: 1708.01432
get_matrix()[source]

Returns the block matrix (as a sparse csr_matrix), which contains the number of edges between each block pair.

Warning

This corresponds to the adjacency matrix of the block graph, which by convention includes twice the amount of edges in the diagonal entries if the graph is undirected.

Examples

>>> g = gt.collection.data["polbooks"]
>>> state = gt.BlockState(g, B=5, deg_corr=True)
>>> state.mcmc_sweep(niter=1000)
(...)
>>> m = state.get_matrix()
>>> figure()
<...>
>>> matshow(m.todense())
<...>
>>> savefig("bloc_mat.pdf")


A 5x5 block matrix.

virtual_vertex_move(v, s, **kwargs)[source]

Computes the entropy difference if vertex v is moved to block s. The remaining parameters are the same as in graph_tool.inference.blockmodel.BlockState.entropy().

move_vertex(v, s)[source]

Move vertex v to block s.

This optionally accepts a list of vertices and blocks to move simultaneously.

remove_vertex(v)[source]

Remove vertex v from its current group.

This optionally accepts a list of vertices to remove.

Warning

This will leave the state in an inconsistent state before the vertex is returned to some other group, or if the same vertex is removed twice.

add_vertex(v, r)[source]

Add vertex v to block r.

This optionally accepts a list of vertices and blocks to add.

Warning

This can leave the state in an inconsistent state if a vertex is added twice to the same group.

merge_vertices(u, v)[source]

Merge vertex u into v.

Warning

This modifies the underlying graph.

sample_vertex_move(v, c=1.0, d=0.1)[source]

Sample block membership proposal of vertex v according to real-valued sampling parameters c and d: For $$c\to 0$$ the blocks are sampled according to the local neighborhood and their connections; for $$c\to\infty$$ the blocks are sampled randomly. With a probability d, a new (empty) group is sampled.

get_move_prob(v, s, c=1.0, d=0.1, reverse=False)[source]

Compute the probability of a move proposal for vertex v to block s according to sampling parameters c and d, as obtained with graph_tool.inference.blockmodel.BlockState.sample_vertex_move(). If reverse == True, the reverse probability of moving the node back from block s to its current one is obtained.

get_edges_prob(missing, spurious=[], entropy_args={})[source]

Compute the joint log-probability of the missing and spurious edges given by missing and spurious (a list of (source, target) tuples, or Edge() instances), together with the observed edges.

More precisely, the log-likelihood returned is

$\ln \frac{P(\boldsymbol G + \delta \boldsymbol G | \boldsymbol b)}{P(\boldsymbol G| \boldsymbol b)}$

where $$\boldsymbol G + \delta \boldsymbol G$$ is the modified graph (with missing edges added and spurious edges deleted).

The values in entropy_args are passed to entropy() to calculate the log-probability.

mcmc_sweep(beta=1.0, c=1.0, d=0.01, niter=1, entropy_args={}, allow_vacate=True, sequential=True, deterministic=False, parallel=False, vertices=None, verbose=False, **kwargs)[source]

Perform niter sweeps of a Metropolis-Hastings acceptance-rejection sampling MCMC to sample network partitions.

Parameters: beta : float (optional, default: 1.) Inverse temperature. c : float (optional, default: 1.) 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. d : float (optional, default: .01) Probability of selecting a new (i.e. empty) group for a given move. niter : int (optional, default: 1) Number of sweeps to perform. During each sweep, a move attempt is made for each node. entropy_args : dict (optional, default: {}) Entropy arguments, with the same meaning and defaults as in graph_tool.inference.blockmodel.BlockState.entropy(). allow_vacate : bool (optional, default: True) Allow groups to be vacated. sequential : bool (optional, default: True) If sequential == True each vertex move attempt is made sequentially, where vertices are visited in random order. Otherwise the moves are attempted by sampling vertices randomly, so that the same vertex can be moved more than once, before other vertices had the chance to move. deterministic : bool (optional, default: False) If sequential == True and deterministic == True the vertices will be visited in deterministic order. parallel : bool (optional, default: False) If parallel == True, vertex movements are attempted in parallel. Warning If parallel == True, the asymptotic exactness of the MCMC sampling is not guaranteed. vertices : list of ints (optional, default: None) If provided, this should be a list of vertices which will be moved. Otherwise, all vertices will. verbose : bool (optional, default: False) If verbose == True, detailed information will be displayed. dS : float Entropy difference after the sweeps. nattempts : int Number of vertex moves attempted. nmoves : int Number of vertices moved.

Notes

This algorithm has an $$O(E)$$ complexity, where $$E$$ is the number of edges (independent of the number of blocks).

References

 [peixoto-efficient-2014178] 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
multiflip_mcmc_sweep(a1=0.99, an=0.9, beta=1.0, c=1.0, d=0.01, niter=1, entropy_args={}, allow_vacate=True, sequential=True, verbose=False, **kwargs)[source]

Perform niter sweeps of a Metropolis-Hastings acceptance-rejection sampling MCMC with multiple simultaneous moves to sample network partitions.

Parameters: a1 : float (optional, default: .9) Probability of single moves. an : float (optional, default: .9) Relative probability of group merges. The complementary probability will correspond to multiple moves within a group. beta : float (optional, default: 1.) Inverse temperature. c : float (optional, default: 1.) 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. d : float (optional, default: .01) Probability of selecting a new (i.e. empty) group for a given move. niter : int (optional, default: 1) Number of sweeps to perform. During each sweep, a move attempt is made for each node. entropy_args : dict (optional, default: {}) Entropy arguments, with the same meaning and defaults as in graph_tool.inference.blockmodel.BlockState.entropy(). allow_vacate : bool (optional, default: True) Allow groups to be vacated. verbose : bool (optional, default: False) If verbose == True, detailed information will be displayed. dS : float Entropy difference after the sweeps. nattempts : int Number of vertex moves attempted. nmoves : int Number of vertices moved.

Notes

This algorithm has an $$O(E)$$ complexity, where $$E$$ is the number of edges (independent of the number of blocks).

gibbs_sweep(beta=1.0, niter=1, entropy_args={}, allow_vacate=True, allow_new_group=True, sequential=True, deterministic=False, parallel=False, vertices=None, verbose=False, **kwargs)[source]

Perform niter sweeps of a rejection-free Gibbs sampling MCMC to sample network partitions.

Parameters: beta : float (optional, default: 1.) Inverse temperature. niter : int (optional, default: 1) Number of sweeps to perform. During each sweep, a move attempt is made for each node. entropy_args : dict (optional, default: {}) Entropy arguments, with the same meaning and defaults as in graph_tool.inference.blockmodel.BlockState.entropy(). allow_vacate : bool (optional, default: True) Allow groups to be vacated. allow_new_group : bool (optional, default: True) Allow the number of groups to increase. sequential : bool (optional, default: True) If sequential == True each vertex move attempt is made sequentially, where vertices are visited in random order. Otherwise the moves are attempted by sampling vertices randomly, so that the same vertex can be moved more than once, before other vertices had the chance to move. deterministic : bool (optional, default: False) If sequential == True and deterministic == True the vertices will be visited in deterministic order. parallel : bool (optional, default: False) If parallel == True, vertex movements are attempted in parallel. Warning If parallel == True, the asymptotic exactness of the MCMC sampling is not guaranteed. vertices : list of ints (optional, default: None) If provided, this should be a list of vertices which will be moved. Otherwise, all vertices will. verbose : bool (optional, default: False) If verbose == True, detailed information will be displayed. dS : float Entropy difference after the sweeps. nattempts : int Number of vertex moves attempted. nmoves : int Number of vertices moved.

Notes

This algorithm has an $$O(E\times B)$$ complexity, where $$B$$ is the number of blocks, and $$E$$ is the number of edges.

multicanonical_sweep(m_state, multiflip=False, **kwargs)[source]

Perform niter sweeps of a non-Markovian multicanonical sampling using the Wang-Landau algorithm.

Parameters: m_state : MulticanonicalState MulticanonicalState instance containing the current state of the Wang-Landau run. multiflip : bool (optional, default: False) If True, multiflip_mcmc_sweep() will be used, otherwise mcmc_sweep(). **kwargs : Keyword parameter list The remaining parameters will be passed to multiflip_mcmc_sweep() or mcmc_sweep(). dS : float Entropy difference after the sweeps. nattempts : int Number of vertex moves attempted. nmoves : int Number of vertices moved.

Notes

This algorithm has an $$O(E)$$ complexity, where $$E$$ is the number of edges (independent of the number of blocks).

References

 [wang-efficient-2001179] Fugao Wang, D. P. Landau, “An efficient, multiple range random walk algorithm to calculate the density of states”, Phys. Rev. Lett. 86, 2050 (2001), DOI: 10.1103/PhysRevLett.86.2050 [sci-hub, @tor], arXiv: cond-mat/0011174
exhaustive_sweep(entropy_args={}, callback=None, density=None, vertices=None, initial_partition=None, max_iter=None)[source]

Perform an exhaustive loop over all possible network partitions.

Parameters: entropy_args : dict (optional, default: {}) Entropy arguments, with the same meaning and defaults as in graph_tool.inference.blockmodel.BlockState.entropy(). callback : callable object (optional, default: None) Function to be called for each partition, with three arguments (S, S_min, b_min) corresponding to the the current entropy value, the minimum entropy value so far, and the corresponding partition, respectively. If not provided, and hist is None an iterator over the same values will be returned instead. density : tuple (optional, default: None) If provided, it should contain a tuple with values (S_min, S_max, n_bins), which will be used to obtain the density of states via a histogram of size n_bins. This parameter is ignored unless callback is None. vertices : iterable of ints (optional, default: None) If provided, this should be a list of vertices which will be moved. Otherwise, all vertices will. initial_partition : iterable of ints (optional, default: None) If provided, this will provide the initial partition for the iteration. max_iter : int (optional, default: None) If provided, this will limit the total number of iterations. states : iterator over (S, S_min, b_min) If callback is None and hist is None, the function will return an iterator over (S, S_min, b_min) corresponding to the the current entropy value, the minimum entropy value so far, and the corresponding partition, respectively. Ss, counts : pair of numpy.ndarray If callback is None and hist is not None, the function will return the values of each bin (Ss) and the state count of each bin (counts). b_min : PropertyMap If callback is not None or hist is not None, the function will also return partition with smallest entropy.

Notes

This algorithm has an $$O(B^N)$$ complexity, where $$B$$ is the number of blocks, and $$N$$ is the number of vertices.

merge_sweep(nmerges=1, niter=10, entropy_args={}, parallel=True, verbose=False, **kwargs)[source]

Perform niter merge sweeps, where block nodes are progressively merged together in a manner that least increases the entropy.

Parameters: nmerges : int (optional, default: 1) Number block nodes to merge. niter : int (optional, default: 1) Number of merge attempts to perform for each block node, before the best one is selected. entropy_args : dict (optional, default: {}) Entropy arguments, with the same meaning and defaults as in graph_tool.inference.blockmodel.BlockState.entropy(). parallel : bool (optional, default: True) If parallel == True, the merge candidates are obtained in parallel. verbose : bool (optional, default: False) If verbose == True, detailed information will be displayed. dS : float Entropy difference after the sweeps. nattempts : int Number of attempted merges. nmoves : int Number of vertices merged.

Notes

This function should only be called for block states, obtained from graph_tool.inference.blockmodel.BlockState.get_block_state().

References

 [peixoto-efficient-2014180] 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
shrink(B, **kwargs)[source]

Reduces the order of current state by progressively merging groups, until only B are left. All remaining keyword arguments are passed to graph_tool.inference.blockmodel.BlockState.merge_sweep().

This function leaves the current state untouched and returns instead a copy with the new partition.

collect_edge_marginals(p=None, update=1)[source]

Collect the edge marginal histogram, which counts the number of times the endpoints of each node have been assigned to a given block pair.

This should be called multiple times, e.g. after repeated runs of the graph_tool.inference.blockmodel.BlockState.mcmc_sweep() function.

Parameters: p : PropertyMap (optional, default: None) Edge property map with edge marginals to be updated. If not provided, an empty histogram will be created. update : float (optional, default: 1) Each call increases the current count by the amount given by this parameter. Edge property map with updated edge marginals.

Examples

>>> g = gt.collection.data["polbooks"]
>>> state = gt.BlockState(g, B=4, deg_corr=True)
>>> pe = None
>>> state.mcmc_sweep(niter=1000)   # remove part of the transient
(...)
>>> for i in range(1000):
...     ret = state.mcmc_sweep(niter=10)
...     pe = state.collect_edge_marginals(pe)
>>> gt.bethe_entropy(g, pe)[0]
-0.901611...

collect_vertex_marginals(p=None, unlabel=False, update=1)[source]

Collect the vertex marginal histogram, which counts the number of times a node was assigned to a given block.

This should be called multiple times, e.g. after repeated runs of the graph_tool.inference.blockmodel.BlockState.mcmc_sweep() function.

Parameters: p : PropertyMap (optional, default: None) Vertex property map with vector-type values, storing the previous block membership counts. If not provided, an empty histogram will be created. unlabel : bool (optional, default: False) If True, a canonical labelling of the groups will be used, so that each partition is uniquely represented. update : int (optional, default: 1) Each call increases the current count by the amount given by this parameter. Vertex property map with vector-type values, storing the accumulated block membership counts.

Examples

>>> g = gt.collection.data["polbooks"]
>>> state = gt.BlockState(g, B=4, deg_corr=True)
>>> pv = None
>>> state.mcmc_sweep(niter=1000)   # remove part of the transient
(...)
>>> for i in range(1000):
...     ret = state.mcmc_sweep(niter=10)
...     pv = state.collect_vertex_marginals(pv)
>>> gt.mf_entropy(g, pv)
26.887021...
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_shape="pie",
...               vertex_pie_fractions=pv, output="polbooks_blocks_soft_B4.pdf")
<...>


“Soft” block partition of a political books network with $$B=4$$.

collect_partition_histogram(h=None, update=1, unlabel=True)[source]

Collect a histogram of partitions.

This should be called multiple times, e.g. after repeated runs of the graph_tool.inference.blockmodel.BlockState.mcmc_sweep() function.

Parameters: h : PartitionHist (optional, default: None) Partition histogram. If not provided, an empty histogram will be created. update : float (optional, default: 1) Each call increases the current count by the amount given by this parameter. unlabel : bool (optional, default: True) If True, a canonical labelling of the groups will be used, so that each partition is uniquely represented. h : PartitionHist (optional, default: None) Updated Partition histogram.

Examples

>>> g = gt.collection.data["polbooks"]
>>> state = gt.BlockState(g, B=4, deg_corr=True)
>>> ph = None
>>> state.mcmc_sweep(niter=1000)   # remove part of the transient
(...)
>>> for i in range(1000):
...     ret = state.mcmc_sweep(niter=10)
...     ph = state.collect_partition_histogram(ph)
>>> gt.microstate_entropy(ph)
129.330077...

draw(**kwargs)[source]

Convenience wrapper to graph_draw() that draws the state of the graph as colors on the vertices and edges.

sample_graph(canonical=False, multigraph=True, self_loops=True)[source]

Sample a new graph from the fitted model.

Parameters: canonical : bool (optional, default: False) If canonical == True, the graph will be sampled from the maximum-likelihood estimate of the canonical stochastic block model. Otherwise, it will be sampled from the microcanonical model. multigraph : bool (optional, default: True) If True, parallel edges will be allowed. self-loops : bool (optional, default: True) If True, self-loops will be allowed. Generated graph.

Notes

This function is just a convenience wrapper to generate_sbm().

Examples

>>> g = gt.collection.data["polbooks"]
>>> state = gt.minimize_blockmodel_dl(g, B_max=3)
>>> u = state.sample_graph(canonical=True, self_loops=False, multigraph=False)
>>> ustate = gt.BlockState(u, b=state.b)
>>> state.draw(pos=g.vp.pos, output="polbooks-sbm.png")
<...>
>>> ustate.draw(pos=u.own_property(g.vp.pos), output="polbooks-sbm-sampled.png")
<...>


Left: Political books network. Right: Sample from the degree-corrected SBM fitted to the original network.

graph_tool.inference.blockmodel.model_entropy(B, N, E, directed=False, nr=None, allow_empty=True)[source]

Computes the amount of information necessary for the parameters of the traditional blockmodel ensemble, for B blocks, N vertices, E edges, and either a directed or undirected graph.

This is equivalently defined as minus the log-likelihood of sampling the parameters from a nonparametric generative model.

A traditional blockmodel is defined as a set of $$N$$ vertices which can belong to one of $$B$$ blocks, and the matrix $$e_{rs}$$ describes the number of edges from block $$r$$ to $$s$$ (or twice that number if $$r=s$$ and the graph is undirected).

For an undirected graph, the number of distinct $$e_{rs}$$ matrices is given by,

$\Omega_m = \left(\!\!{B(B+1)/2 \choose E}\!\!\right)$

and for a directed graph,

$\Omega_m = \left(\!\!{B^2 \choose E}\!\!\right)$

where $$\left(\!{n \choose k}\!\right) = {n+k-1\choose k}$$ is the number of $$k$$ combinations with repetitions from a set of size $$n$$. Hence, we have the description length of the edge counts

$-\ln P(\boldsymbol{e}) = \ln \Omega_m.$

For the node partition $$\boldsymbol{b}$$ we assume a two-level Bayesian hierarchy, where first the group size histogram is generated, and conditioned on it the partition, which leads to a description length:

$-\ln P(\boldsymbol{b}) = \ln\left(\!\!{B \choose N}\!\!\right) + \ln N! - \sum_r \ln n_r!,$

where $$n_r$$ is the number of nodes in block $$r$$. If we forbid empty groups, with allow_empty == False, this changes slightly to

$-\ln P(\boldsymbol{b}) = \ln {N - 1 \choose B - 1} + \ln N! - \sum_r \ln n_r!.$

The total information necessary to describe the model is then,

$-\ln P(\boldsymbol{e}, \boldsymbol{b}) = -\ln P(\boldsymbol{e}) - \ln P(\boldsymbol{b}).$

If nr is None, it is assumed $$n_r=N/B$$. If nr is False, the partition term $$-\ln P(\boldsymbol{b})$$ is omitted entirely.

References

 [peixoto-parsimonious-2013181] Tiago P. Peixoto, “Parsimonious module inference in large networks”, Phys. Rev. Lett. 110, 148701 (2013), DOI: 10.1103/PhysRevLett.110.148701 [sci-hub, @tor], arXiv: 1212.4794.
 [peixoto-nonparametric-2017181] Tiago P. Peixoto, “Nonparametric Bayesian inference of the microcanonical stochastic block model”, Phys. Rev. E 95 012317 (2017), DOI: 10.1103/PhysRevE.95.012317 [sci-hub, @tor], arXiv: 1610.02703
graph_tool.inference.blockmodel.bethe_entropy(g, p)[source]

Compute the Bethe entropy given the edge block membership marginals.

Parameters: The graph. Edge property map with edge marginals. H : float The Bethe entropy value (in nats) Hmf : float The “mean field” entropy value (in nats), as would be returned by the mf_entropy() function. pv : PropertyMap (optional, default: None) Vertex property map with vector-type values, storing the accumulated block membership counts. These are the node marginals, as would be returned by the collect_vertex_marginals() method.

Notes

The Bethe entropy is defined as,

$H = -\sum_{ij}A_{ij}\sum_{rs}\pi_{ij}(r,s)\ln\pi_{ij}(r,s) - \sum_i(1-k_i)\sum_r\pi_i(r)\ln\pi_i(r),$

where $$\pi_{ij}(r,s)$$ is the marginal probability that vertices $$i$$ and $$j$$ belong to blocks $$r$$ and $$s$$, respectively, and $$\pi_i(r)$$ is the marginal probability that vertex $$i$$ belongs to block $$r$$, and $$k_i$$ is the degree of vertex $$i$$ (or total degree for directed graphs).

References

 [mezard-information-2009183] Marc Mézard, Andrea Montanari, “Information, Physics, and Computation”, Oxford Univ Press, 2009. DOI: 10.1093/acprof:oso/9780198570837.001.0001 [sci-hub, @tor]
graph_tool.inference.blockmodel.mf_entropy(g, p)[source]

Compute the “mean field” entropy given the vertex block membership marginals.

Parameters: The graph. Vertex property map with vector-type values, storing the accumulated block membership counts. Hmf : float The “mean field” entropy value (in nats).

Notes

The “mean field” entropy is defined as,

$H = - \sum_{i,r}\pi_i(r)\ln\pi_i(r),$

where $$\pi_i(r)$$ is the marginal probability that vertex $$i$$ belongs to block $$r$$.

References

 [mezard-information-2009184] Marc Mézard, Andrea Montanari, “Information, Physics, and Computation”, Oxford Univ Press, 2009. DOI: 10.1093/acprof:oso/9780198570837.001.0001 [sci-hub, @tor]
graph_tool.inference.blockmodel.microstate_entropy(h, unlabel=True)[source]

Compute microstate entropy given a histogram of partitions.

Parameters: h : PartitionHist (optional, default: None) Partition histogram. unlabel : bool (optional, default: True) If True, a canonical labelling of the groups will be used, so that each partition is uniquely represented. However, the entropy computed will still correspond to the full distribution over labelled partitions, where all permutations are assumed to be equally likely. H : float The microstate entropy value (in nats).

Notes

The microstate entropy is defined as,

$H = - \sum_{\boldsymbol b}p({\boldsymbol b})\ln p({\boldsymbol b}),$

where $$p({\boldsymbol b})$$ is observed frequency of labelled partition $${\boldsymbol b}$$.

References

 [mezard-information-2009185] Marc Mézard, Andrea Montanari, “Information, Physics, and Computation”, Oxford Univ Press, 2009. DOI: 10.1093/acprof:oso/9780198570837.001.0001 [sci-hub, @tor]
class graph_tool.inference.overlap_blockmodel.OverlapBlockState(g, b=None, B=None, recs=[], rec_types=[], rec_params=[], clabel=None, pclabel=None, deg_corr=True, allow_empty=False, max_BE=1000, **kwargs)[source]

The overlapping stochastic block model state of a given graph.

Parameters: Graph to be modelled. b : PropertyMap or numpy.ndarray (optional, default: None) Initial block labels on the vertices or half-edges. If not supplied, it will be randomly sampled. If the value passed is a vertex property map, it will be assumed to be a non-overlapping partition of the vertices. If it is an edge property map, it should contain a vector for each edge, with the block labels at each end point (sorted according to their vertex index, in the case of undirected graphs, otherwise from source to target). If the value is an numpy.ndarray, it will be assumed to correspond directly to a partition of the list of half-edges. B : int (optional, default: None) Number of blocks (or vertex groups). If not supplied it will be obtained from the parameter b. recs : list of PropertyMap instances (optional, default: []) List of real or discrete-valued edge covariates. rec_types : list of edge covariate types (optional, default: []) List of types of edge covariates. The possible types are: "real-exponential", "real-normal", "discrete-geometric", "discrete-poisson" or "discrete-binomial". rec_params : list of dict (optional, default: []) Model hyperparameters for edge covariates. This should a list of dict instances. See BlockState for more details. clabel : PropertyMap (optional, default: None) Constraint labels on the vertices. If supplied, vertices with different label values will not be clustered in the same group. deg_corr : bool (optional, default: True) If True, the degree-corrected version of the blockmodel ensemble will be assumed, otherwise the traditional variant will be used. allow_empty : bool (optional, default: False) If True, partition description length computed will allow for empty groups. max_BE : int (optional, default: 1000) If the number of blocks exceeds this number, a sparse representation of the block graph is used, which is slightly less efficient, but uses less memory,
copy(g=None, b=None, B=None, deg_corr=None, clabel=None, pclabel=None, **kwargs)[source]

Copies the block state. The parameters override the state properties, and have the same meaning as in the constructor. If overlap=False an instance of BlockState is returned. This is by default a shallow copy.

get_E()[source]

Returns the total number of edges.

get_N()[source]

Returns the total number of nodes.

get_B()[source]

Returns the total number of blocks.

get_nonempty_B()[source]

Returns the total number of nonempty blocks.

get_edge_blocks()[source]

Returns an edge property map which contains the block labels pairs for each edge.

get_overlap_blocks()[source]

Returns the mixed membership of each vertex.

Returns: A vector-valued vertex property map containing the block memberships of each node. bc_in : PropertyMap The labelled in-degrees of each node, i.e. how many in-edges belong to each group, in the same order as the bv property above. bc_out : PropertyMap The labelled out-degrees of each node, i.e. how many out-edges belong to each group, in the same order as the bv property above. bc_total : PropertyMap The labelled total degrees of each node, i.e. how many incident edges belong to each group, in the same order as the bv property above.
get_nonoverlap_blocks()[source]

Returns a scalar-valued vertex property map with the block mixture represented as a single number.

get_majority_blocks()[source]

Returns a scalar-valued vertex property map with the majority block membership of each node.

entropy(adjacency=True, dl=True, partition_dl=True, degree_dl=True, degree_dl_kind='distributed', edges_dl=True, dense=False, multigraph=True, deg_entropy=True, recs=True, recs_dl=True, beta_dl=1.0, exact=True, **kwargs)[source]

Calculate the entropy associated with the current block partition.

Parameters: adjacency : bool (optional, default: True) If True, the adjacency term of the description length will be included. dl : bool (optional, default: True) If True, the description length for the parameters will be included. partition_dl : bool (optional, default: True) If True, and dl == True the partition description length will be included. degree_dl : bool (optional, default: True) If True, and dl == True the degree sequence description length will be included (for degree-corrected models). degree_dl_kind : str (optional, default: "distributed") This specifies the prior used for the degree sequence. It must be one of: "uniform", "distributed" (default) or "entropy". edges_dl : bool (optional, default: True) If True, and dl == True the edge matrix description length will be included. dense : bool (optional, default: False) If True, the “dense” variant of the entropy will be computed. multigraph : bool (optional, default: True) If True, the multigraph entropy will be used. deg_entropy : bool (optional, default: True) If True, the degree entropy term that is independent of the network partition will be included (for degree-corrected models). recs : bool (optional, default: True) If True, the likelihood for real or discrete-valued edge covariates is computed. recs_dl : bool (optional, default: True) If True, and dl == True the edge covariate description length will be included. beta_dl : double (optional, default: 1.) Prior inverse temperature. exact : bool (optional, default: True) If True, the exact expressions will be used. Otherwise, Stirling’s factorial approximation will be used for some terms.

Notes

The “entropy” of the state is minus the log-likelihood of the microcanonical SBM, that includes the generated graph $$\boldsymbol{A}$$ and the model parameters $$\boldsymbol{\theta}$$,

$\begin{split}\mathcal{S} &= - \ln P(\boldsymbol{A},\boldsymbol{\theta}) \\ &= - \ln P(\boldsymbol{A}|\boldsymbol{\theta}) - \ln P(\boldsymbol{\theta}).\end{split}$

This value is also called the description length of the data, and it corresponds to the amount of information required to describe it (in nats).

For the traditional blockmodel (deg_corr == False), the model parameters are $$\boldsymbol{\theta} = \{\boldsymbol{e}, \boldsymbol{b}\}$$, where $$\boldsymbol{e}$$ is the matrix of edge counts between blocks, and $$\boldsymbol{b}$$ is the overlapping partition of the nodes into blocks. For the degree-corrected blockmodel (deg_corr == True), we have an additional set of parameters, namely the labelled degree sequence $$\boldsymbol{k}$$.

The model likelihood $$P(\boldsymbol{A}|\theta)$$ is given analogously to the non-overlapping case, as described in graph_tool.inference.blockmodel.BlockState.entropy().

If dl == True, the description length $$\mathcal{L} = -\ln P(\boldsymbol{\theta})$$ of the model will be returned as well. The edge-count prior $$P(\boldsymbol{e})$$ is described in described in model_entropy(). For the overlapping partition $$P(\boldsymbol{b})$$, we have

$-\ln P(\boldsymbol{b}) = \ln\left(\!\!{D \choose N}\!\!\right) + \sum_d \ln {\left(\!\!{{B\choose d}\choose n_d}\!\!\right)} + \ln N! - \sum_{\vec{b}}\ln n_{\vec{b}}!,$

where $$d \equiv |\vec{b}|_1 = \sum_rb_r$$ is the mixture size, $$n_d$$ is the number of nodes in a mixture of size $$d$$, $$D$$ is the maximum value of $$d$$, $$n_{\vec{b}}$$ is the number of nodes in mixture $$\vec{b}$$.

For the degree-corrected model we need to specify the prior $$P(\boldsymbol{k})$$ for the labelled degree sequence as well:

$-\ln P(\boldsymbol{k}) = \sum_r\ln\left(\!\!{m_r \choose e_r}\!\!\right) - \sum_{\vec{b}}\ln P(\boldsymbol{k}|{\vec{b}}),$

where $$m_r$$ is the number of non-empty mixtures which contain type $$r$$, and $$P(\boldsymbol{k}|{\vec{b}})$$ is the likelihood of the labelled degree sequence inside mixture $$\vec{b}$$. For this term we have three options:

1. degree_dl_kind == "uniform"

$P(\boldsymbol{k}|\vec{b}) = \prod_r\left(\!\!{n_{\vec{b}}\choose e^r_{\vec{b}}}\!\!\right)^{-1}.$
2. degree_dl_kind == "distributed"

$P(\boldsymbol{k}|\vec{b}) = \prod_{\vec{b}}\frac{\prod_{\vec{k}}\eta_{\vec{k}}^{\vec{b}}!}{n_{\vec{b}}!} \prod_r q(e_{\vec{b}}^r - n_{\vec{b}}, n_{\vec{b}})$

where $$n^{\vec{b}}_{\vec{k}}$$ is the number of nodes in mixture $$\vec{b}$$ with labelled degree $$\vec{k}$$, and $$q(n,m)$$ is the number of partitions of integer $$n$$ into at most $$m$$ parts.

3. degree_dl_kind == "entropy"

$P(\boldsymbol{k}|\vec{b}) = \prod_{\vec{b}}\exp\left(-n_{\vec{b}}H(\boldsymbol{k}_{\vec{b}})\right)$

where $$H(\boldsymbol{k}_{\vec{b}}) = -\sum_{\vec{k}}p_{\vec{b}}(\vec{k})\ln p_{\vec{b}}(\vec{k})$$ is the entropy of the labelled degree distribution inside mixture $$\vec{b}$$.

Note that, differently from the other two choices, this represents only an approximation of the description length. It is meant to be used only for comparison purposes, and should be avoided in practice.

For the directed case, the above expressions are duplicated for the in- and out-degrees.

mcmc_sweep(bundled=False, **kwargs)[source]

Perform sweeps of a Metropolis-Hastings rejection sampling MCMC to sample network partitions. If bundled == True, the half-edges incident of the same node that belong to the same group are moved together. All remaining parameters are passed to graph_tool.inference.blockmodel.BlockState.mcmc_sweep().

shrink(B, **kwargs)[source]

Reduces the order of current state by progressively merging groups, until only B are left. All remaining keyword arguments are passed to graph_tool.inference.blockmodel.BlockState.merge_sweep().

This function leaves the current state untouched and returns instead a copy with the new partition.

draw(**kwargs)[source]

Convenience wrapper to graph_draw() that draws the state of the graph as colors on the vertices and edges.

graph_tool.inference.overlap_blockmodel.half_edge_graph(g, b=None, B=None, rec=None)[source]

Generate a half-edge graph, where each half-edge is represented by a node, and an edge connects the half-edges like in the original graph.

graph_tool.inference.overlap_blockmodel.augmented_graph(g, b, node_index, eweight=None)[source]

Generates an augmented graph from the half-edge graph g partitioned according to b, where each half-edge belonging to a different group inside each node forms a new node.

graph_tool.inference.overlap_blockmodel.get_block_edge_gradient(g, be, cmap=None)[source]

Get edge gradients corresponding to the block membership at the endpoints of the edges given by the be edge property map.

Parameters: The graph. Vector-valued edge property map with the block membership at each endpoint. cmap : matplotlib.colors.Colormap (optional, default: default_cm) Color map used to construct the gradient. A vector-valued edge property map containing a color gradient.
class graph_tool.inference.layered_blockmodel.LayeredBlockState(g, ec, eweight=None, vweight=None, recs=[], rec_types=[], rec_params=[], b=None, B=None, clabel=None, pclabel=False, layers=False, deg_corr=True, overlap=False, allow_empty=False, **kwargs)[source]

The (possibly overlapping) block state of a given graph, where the edges are divided into discrete layers.

Parameters: Graph to be modelled. containing discrete edge covariates that will split the network in discrete layers. recs : list of PropertyMap instances (optional, default: []) List of real or discrete-valued edge covariates. rec_types : list of edge covariate types (optional, default: []) List of types of edge covariates. The possible types are: "real-exponential", "real-normal", "discrete-geometric", "discrete-poisson" or "discrete-binomial". rec_params : list of dict (optional, default: []) Model hyperparameters for edge covariates. This should a list of dict instances. See BlockState for more details. eweight : PropertyMap (optional, default: None) Edge multiplicities (for multigraphs or block graphs). vweight : PropertyMap (optional, default: None) Vertex multiplicities (for block graphs). b : PropertyMap or numpy.ndarray (optional, default: None) Initial block labels on the vertices or half-edges. If not supplied, it will be randomly sampled. B : int (optional, default: None) Number of blocks (or vertex groups). If not supplied it will be obtained from the parameter b. clabel : PropertyMap (optional, default: None) Constraint labels on the vertices. If supplied, vertices with different label values will not be clustered in the same group. pclabel : PropertyMap (optional, default: None) Partition constraint labels on the vertices. This has the same interpretation as clabel, but will be used to compute the partition description length. layers : bool (optional, default: False) If layers == True, the “independent layers” version of the model is used, instead of the “edge covariates” version. deg_corr : bool (optional, default: True) If True, the degree-corrected version of the blockmodel ensemble will be assumed, otherwise the traditional variant will be used. overlap : bool (optional, default: False) If True, the overlapping version of the model will be used. allow_empty : bool (optional, default: True) If True, partition description length computed will allow for empty groups. max_BE : int (optional, default: 1000) If the number of blocks exceeds this value, a sparse matrix is used for the block graph. Otherwise a dense matrix will be used.
get_N()[source]

Returns the total number of edges.

get_E()[source]

Returns the total number of nodes.

get_B()[source]

Returns the total number of blocks.

get_nonempty_B()[source]

Returns the total number of nonempty blocks.

copy(g=None, eweight=None, vweight=None, b=None, B=None, deg_corr=None, clabel=None, pclabel=None, bfield=None, overlap=None, layers=None, ec=None, **kwargs)[source]

Copies the block state. The parameters override the state properties, and have the same meaning as in the constructor.

get_bg()[source]

Returns the block graph.

get_block_state(b=None, vweight=False, deg_corr=False, overlap=False, layers=None, **kwargs)[source]

Returns a LayeredBlockState corresponding to the block graph. The parameters have the same meaning as the in the constructor.

get_edge_blocks()[source]

Returns an edge property map which contains the block labels pairs for each edge.

get_overlap_blocks()[source]

Returns the mixed membership of each vertex.

Returns: A vector-valued vertex property map containing the block memberships of each node. bc_in : PropertyMap The labelled in-degrees of each node, i.e. how many in-edges belong to each group, in the same order as the bv property above. bc_out : PropertyMap The labelled out-degrees of each node, i.e. how many out-edges belong to each group, in the same order as the bv property above. bc_total : PropertyMap The labelled total degrees of each node, i.e. how many incident edges belong to each group, in the same order as the bv property above.
get_nonoverlap_blocks()[source]

Returns a scalar-valued vertex property map with the block mixture represented as a single number.

get_majority_blocks()[source]

Returns a scalar-valued vertex property map with the majority block membership of each node.

entropy(adjacency=True, dl=True, partition_dl=True, degree_dl=True, degree_dl_kind='distributed', edges_dl=True, dense=False, multigraph=True, deg_entropy=True, exact=True, **kwargs)[source]

Calculate the entropy associated with the current block partition. The meaning of the parameters are the same as in graph_tool.inference.blockmodel.BlockState.entropy().

get_edges_prob(missing, spurious=[], entropy_args={})[source]

Compute the joint log-probability of the missing and spurious edges given by missing and spurious (a list of (source, target, layer) tuples, or Edge() instances), together with the observed edges.

More precisely, the log-likelihood returned is

$\ln \frac{P(\boldsymbol G + \delta \boldsymbol G | \boldsymbol b)}{P(\boldsymbol G| \boldsymbol b)}$

where $$\boldsymbol G + \delta \boldsymbol G$$ is the modified graph (with missing edges added and spurious edges deleted).

The values in entropy_args are passed to graph_tool.inference.blockmodel.BlockState.entropy() to calculate the log-probability.

mcmc_sweep(bundled=False, **kwargs)[source]

Perform sweeps of a Metropolis-Hastings rejection sampling MCMC to sample network partitions. If bundled == True and the state is an overlapping one, the half-edges incident of the same node that belong to the same group are moved together. All remaining parameters are passed to graph_tool.inference.blockmodel.BlockState.mcmc_sweep().

shrink(B, **kwargs)[source]

Reduces the order of current state by progressively merging groups, until only B are left. All remaining keyword arguments are passed to graph_tool.inference.blockmodel.BlockState.shrink() or graph_tool.inference.overlap_blockmodel.OverlapBlockState.shrink(), as appropriate.

This function leaves the current state untouched and returns instead a copy with the new partition.

draw(**kwargs)[source]

Convenience function to draw the current state. All keyword arguments are passed to graph_tool.inference.blockmodel.BlockState.draw() or graph_tool.inference.overlap_blockmodel.OverlapBlockState.draw(), as appropriate.

class graph_tool.inference.nested_blockmodel.NestedBlockState(g, bs, base_type=<class 'graph_tool.inference.blockmodel.BlockState'>, state_args={}, hstate_args={}, hentropy_args={}, sampling=False, **kwargs)[source]

Bases: object

The nested stochastic block model state of a given graph.

Parameters: Graph to be modeled. bs : list of PropertyMap or numpy.ndarray Hierarchical node partition. base_type : type (optional, default: BlockState) State type for lowermost level (e.g. BlockState, OverlapBlockState or LayeredBlockState) hstate_args : dict (optional, default: {}) Keyword arguments to be passed to the constructor of the higher-level states. hentropy_args : dict (optional, default: {}) Keyword arguments to be passed to the entropy() method of the higher-level states. sampling : bool (optional, default: False) If True, the state will be properly prepared for MCMC sampling (as opposed to minimization). state_args : dict (optional, default: {}) Keyword arguments to be passed to base type constructor. **kwargs : keyword arguments Keyword arguments to be passed to base type constructor. The state_args parameter overrides this.
copy(g=None, bs=None, state_args=None, hstate_args=None, hentropy_args=None, sampling=None, **kwargs)[source]

Copies the block state. The parameters override the state properties, and have the same meaning as in the constructor.

get_bs()[source]

Get hierarchy levels as a list of numpy.ndarray objects with the group memberships at each level.

get_levels()[source]

Get hierarchy levels as a list of BlockState instances.

project_partition(j, l)[source]

Project partition of level j onto level l, and return it.

propagate_clabel(l)[source]

Project base clabel to level l.

get_clabel(l)[source]

Get clabel for level l.

replace_level(l, b)[source]

Replace level l given the new partition b

delete_level(l)[source]

Delete level l.

duplicate_level(l)[source]

Duplicate level l.

level_entropy(l, bstate=None, **kwargs)[source]

Compute the entropy of level l.

entropy(**kwargs)[source]

Compute the entropy of whole hierarchy.

The keyword arguments are passed to the entropy() method of the underlying state objects (e.g. graph_tool.inference.blockmodel.BlockState.entropy, graph_tool.inference.overlap_blockmodel.OverlapBlockState.entropy, or graph_tool.inference.layered_blockmodel.LayeredBlockState.entropy).

move_vertex(v, s)[source]

Move vertex v to block s.

remove_vertex(v)[source]

Remove vertex v from its current group.

This optionally accepts a list of vertices to remove.

Warning

This will leave the state in an inconsistent state before the vertex is returned to some other group, or if the same vertex is removed twice.

add_vertex(v, r)[source]

Add vertex v to block r.

This optionally accepts a list of vertices and blocks to add.

Warning

This can leave the state in an inconsistent state if a vertex is added twice to the same group.

get_edges_prob(missing, spurious=[], entropy_args={})[source]

Compute the joint log-probability of the missing and spurious edges given by missing and spurious (a list of (source, target) tuples, or Edge() instances), together with the observed edges.

More precisely, the log-likelihood returned is

$\ln \frac{P(\boldsymbol G + \delta \boldsymbol G | \boldsymbol b)}{P(\boldsymbol G| \boldsymbol b)}$

where $$\boldsymbol G + \delta \boldsymbol G$$ is the modified graph (with missing edges added and spurious edges deleted).

The values in entropy_args are passed to graph_tool.inference.blockmodel.BlockState.entropy() to calculate the log-probability.

get_bstack()[source]

Return the nested levels as individual graphs.

This returns a list of Graph instances representing the inferred hierarchy at each level. Each graph has two internal vertex and edge property maps named “count” which correspond to the vertex and edge counts at the lower level, respectively. Additionally, an internal vertex property map named “b” specifies the block partition.

project_level(l)[source]

Project the partition at level l onto the lowest level, and return the corresponding state.

print_summary()[source]

Print a hierarchy summary.

find_new_level(l, bisection_args={}, B_min=None, B_max=None, b_min=None, b_max=None)[source]

Attempt to find a better network partition at level l, using bisection_minimize() with arguments given by bisection_args.

mcmc_sweep(**kwargs)[source]

Perform niter sweeps of a Metropolis-Hastings acceptance-rejection MCMC to sample hierarchical network partitions.

The arguments accepted are the same as in graph_tool.inference.blockmodel.BlockState.mcmc_sweep().

If the parameter c is a scalar, the values used at each level are c * 2 ** l for l in the range [0, L-1]. Optionally, a list of values may be passed instead, which specifies the value of c[l] to be used at each level.

multiflip_mcmc_sweep(**kwargs)[source]

Perform niter sweeps of a Metropolis-Hastings acceptance-rejection MCMC with multiple moves to sample hierarchical network partitions.

The arguments accepted are the same as in graph_tool.inference.blockmodel.BlockState.multiflip_mcmc_sweep().

If the parameter c is a scalar, the values used at each level are c * 2 ** l for l in the range [0, L-1]. Optionally, a list of values may be passed instead, which specifies the value of c[l] to be used at each level.

multicanonical_sweep(**kwargs)[source]

Perform niter sweeps of a non-Markovian multicanonical sampling using the Wang-Landau algorithm.

The arguments accepted are the same as in graph_tool.inference.blockmodel.BlockState.multicanonical_sweep().

collect_partition_histogram(h=None, update=1)[source]

Collect a histogram of partitions.

This should be called multiple times, e.g. after repeated runs of the graph_tool.inference.nested_blockmodel.NestedBlockState.mcmc_sweep() function.

Parameters: h : PartitionHist (optional, default: None) Partition histogram. If not provided, an empty histogram will be created. update : float (optional, default: 1) Each call increases the current count by the amount given by this parameter. h : PartitionHist (optional, default: None) Updated Partition histogram.
draw(**kwargs)[source]

Convenience wrapper to draw_hierarchy() that draws the hierarchical state.

graph_tool.inference.nested_blockmodel.hierarchy_minimize(state, B_min=None, B_max=None, b_min=None, b_max=None, frozen_levels=None, bisection_args={}, epsilon=1e-08, verbose=False)[source]

Attempt to find a fit of the nested stochastic block model that minimizes the description length.

Parameters: The nested block state. B_min : int (optional, default: None) The minimum number of blocks. B_max : int (optional, default: None) The maximum number of blocks. b_min : PropertyMap (optional, default: None) The partition to be used with the minimum number of blocks. b_max : PropertyMap (optional, default: None) The partition to be used with the maximum number of blocks. frozen_levels : sequence of int values (optional, default: None) List of hierarchy levels that are kept constant during the minimization. bisection_args : dict (optional, default: {}) Arguments to be passed to bisection_minimize(). epsilon: float (optional, default: 1e-8) Only replace levels if the description length difference is above this threshold. verbose : bool or tuple (optional, default: False) If True, progress information will be shown. Optionally, this accepts arguments of the type tuple of the form (level, prefix) where level is a positive integer that specifies the level of detail, and prefix is a string that is prepended to the all output messages. min_state : NestedBlockState Nested state with minimal description length.

Notes

This algorithms moves along the hierarchical levels, attempting to replace, delete or insert partitions that minimize the description length, until no further progress is possible.

See [peixoto-hierarchical-2014186] for details on the algorithm.

This algorithm has a complexity of $$O(V \ln^2 V)$$, where $$V$$ is the number of nodes in the network.

References

 [peixoto-hierarchical-2014186] (1, 2) Tiago P. Peixoto, “Hierarchical block structures and high-resolution model selection in large networks “, Phys. Rev. X 4, 011047 (2014), DOI: 10.1103/PhysRevX.4.011047 [sci-hub, @tor], arXiv: 1310.4377.
graph_tool.inference.nested_blockmodel.get_hierarchy_tree(state, empty_branches=True)[source]

Obtain the nested hierarchical levels as a tree.

This transforms a NestedBlockState instance into a single Graph instance containing the hierarchy tree.

Parameters: Nested block model state. empty_branches : bool (optional, default: True) If empty_branches == False, dangling branches at the upper layers will be pruned. tree : Graph A directed graph, where vertices are blocks, and a directed edge points to an upper to a lower level in the hierarchy. label : PropertyMap A vertex property map containing the block label for each node. order : PropertyMap A vertex property map containing the relative ordering of each layer according to the total degree of the groups at the specific levels.
class graph_tool.inference.uncertain_blockmodel.UncertainBaseState(g, nested=True, state_args={}, bstate=None, self_loops=False, init_empty=False)[source]

Bases: object

Base state for uncertain network inference.

get_block_state()[source]

Return the underlying block state, which can be either BlockState or NestedBlockState.

entropy(latent_edges=True, density=True, **kwargs)[source]

Return the entropy, i.e. negative log-likelihood.

mcmc_sweep(r=0.5, **kwargs)[source]

Perform sweeps of a Metropolis-Hastings acceptance-rejection sampling MCMC to sample network partitions and latent edges. The parameter r controls the probability with which edge move will be attempted, instead of partition moves. The remaining keyword parameters will be passed to mcmc_sweep().

multiflip_mcmc_sweep(r=0.5, **kwargs)[source]

Perform sweeps of a multiflip Metropolis-Hastings acceptance-rejection sampling MCMC to sample network partitions and latent edges. The parameter r controls the probability with which edge move will be attempted, instead of partition moves. The remaining keyword parameters will be passed to multiflip_mcmc_sweep().

get_edge_prob(u, v, entropy_args={}, epsilon=1e-08)[source]

Return conditional posterior probability of edge $$(u,v)$$.

get_edges_prob(elist, entropy_args={}, epsilon=1e-08)[source]

Return conditional posterior probability of an edge list, with shape $$(E,2)$$.

get_graph()[source]

Return the current inferred graph.

collect_marginal(g=None)[source]

Collect marginal inferred network during MCMC runs.

Parameters: g : Graph (optional, default: None) Previous marginal graph. New marginal graph, with internal edge PropertyMap "eprob", containing the marginal probabilities for each edge.

Notes

The posterior marginal probability of an edge $$(i,j)$$ is defined as

$\pi_{ij} = \sum_{\boldsymbol A}A_{ij}P(\boldsymbol A|\boldsymbol D)$

where $$P(\boldsymbol A|\boldsymbol D)$$ is the posterior probability given the data.

class graph_tool.inference.uncertain_blockmodel.UncertainBlockState(g, q, q_default=0.0, aE=nan, nested=True, state_args={}, bstate=None, self_loops=False, **kwargs)[source]

The inference state of an uncertain graph, using the stochastic block model as a prior.

Parameters: Measured graph. Edge probabilities in range $$[0,1]$$. q_default : float (optional, default: 0.) Non-edge probability in range $$[0,1]$$. aE : float (optional, default: NaN) Expected total number of edges used in prior. If NaN, a flat prior will be used instead. nested : boolean (optional, default: True) If True, a NestedBlockState will be used, otherwise BlockState. state_args : dict (optional, default: {}) Arguments to be passed to NestedBlockState or BlockState. bstate : NestedBlockState or BlockState (optional, default: None) If passed, this will be used to initialize the block state directly. self_loops : bool (optional, default: False) If True, it is assumed that the uncertain graph can contain self-loops.

References

 [peixoto-reconstructing-2018187] Tiago P. Peixoto, “Reconstructing networks with unknown and heterogeneous errors” arXiv: 1806.07956
copy(**kwargs)[source]

Return a copy of the state.

class graph_tool.inference.uncertain_blockmodel.MeasuredBlockState(g, n, x, n_default=1, x_default=0, fn_params={'alpha': 1, 'beta': 1}, fp_params={'mu': 1, 'nu': 1}, aE=nan, nested=True, state_args={}, bstate=None, self_loops=False, **kwargs)[source]

The inference state of a measured graph, using the stochastic block model as a prior.

Parameters: Measured graph. Edge property map of type int, containing the total number of measurements for each edge. Edge property map of type int, containing the number of positive measurements for each edge. n_default : int (optional, default: 1) Total number of measurements for each non-edge. x_default : int (optional, default: 1) Total number of positive measurements for each non-edge. fn_params : dict (optional, default: dict(alpha=1, beta=1)) Beta distribution hyperparameters for the probability of missing edges (false negatives). fp_params : dict (optional, default: dict(mu=1, nu=1)) Beta distribution hyperparameters for the probability of spurious edges (false positives). aE : float (optional, default: NaN) Expected total number of edges used in prior. If NaN, a flat prior will be used instead. nested : boolean (optional, default: True) If True, a NestedBlockState will be used, otherwise BlockState. state_args : dict (optional, default: {}) Arguments to be passed to NestedBlockState or BlockState. bstate : NestedBlockState or BlockState (optional, default: None) If passed, this will be used to initialize the block state directly. self_loops : bool (optional, default: False) If True, it is assumed that the uncertain graph can contain self-loops.

References

 [peixoto-reconstructing-2018188] Tiago P. Peixoto, “Reconstructing networks with unknown and heterogeneous errors” arXiv: 1806.07956
copy(**kwargs)[source]

Return a copy of the state.

set_hparams(alpha, beta, mu, nu)[source]

Set edge and non-edge hyperparameters.

get_p_posterior()[source]

Get beta distribution parameters for the posterior probability of missing edges.

get_q_posterior()[source]

Get beta distribution parameters for the posterior probability of spurious edges.

class graph_tool.inference.uncertain_blockmodel.MixedMeasuredBlockState(g, n, x, n_default=1, x_default=0, fn_params={'alpha': 1, 'beta': 10}, fp_params={'mu': 1, 'nu': 10}, aE=nan, nested=True, state_args={}, bstate=None, self_loops=False, **kwargs)[source]

The inference state of a measured graph with heterogeneous errors, using the stochastic block model as a prior.

Parameters: Measured graph. Edge property map of type int, containing the total number of measurements for each edge. Edge property map of type int, containing the number of positive measurements for each edge. n_default : int (optional, default: 1) Total number of measurements for each non-edge. x_default : int (optional, default: 1) Total number of positive measurements for each non-edge. fn_params : dict (optional, default: dict(alpha=1, beta=10)) Beta distribution hyperparameters for the probability of missing edges (false negatives). fp_params : dict (optional, default: dict(mu=1, nu=10)) Beta distribution hyperparameters for the probability of spurious edges (false positives). aE : float (optional, default: NaN) Expected total number of edges used in prior. If NaN, a flat prior will be used instead. nested : boolean (optional, default: True) If True, a NestedBlockState will be used, otherwise BlockState. state_args : dict (optional, default: {}) Arguments to be passed to NestedBlockState or BlockState. bstate : NestedBlockState or BlockState (optional, default: None) If passed, this will be used to initialize the block state directly. self_loops : bool (optional, default: False) If True, it is assumed that the uncertain graph can contain self-loops.

References

 [peixoto-reconstructing-2018189] Tiago P. Peixoto, “Reconstructing networks with unknown and heterogeneous errors” arXiv: 1806.07956
set_hparams(alpha, beta, mu, nu)[source]

Set edge and non-edge hyperparameters.

copy(**kwargs)[source]

Return a copy of the state.

graph_tool.inference.mcmc.mcmc_equilibrate(state, wait=1000, nbreaks=2, max_niter=inf, force_niter=None, epsilon=0, gibbs=False, multiflip=False, mcmc_args={}, entropy_args={}, history=False, callback=None, verbose=False)[source]

Equilibrate a MCMC with a given starting state.

Parameters: state : Any state class (e.g. BlockState) Initial state. This state will be modified during the algorithm. wait : int (optional, default: 1000) Number of iterations to wait for a record-breaking event. nbreaks : int (optional, default: 2) Number of iteration intervals (of size wait) without record-breaking events necessary to stop the algorithm. max_niter : int (optional, default: numpy.inf) Maximum number of iterations. force_niter : int (optional, default: None) If given, will force the algorithm to run this exact number of iterations. epsilon : float (optional, default: 0) Relative changes in entropy smaller than epsilon will not be considered as record-breaking. gibbs : bool (optional, default: False) If True, each step will call state.gibbs_sweep instead of state.mcmc_sweep. multiflip : bool (optional, default: False) If True, each step will call state.multiflip_mcmc_sweep instead of state.mcmc_sweep. mcmc_args : dict (optional, default: {}) Arguments to be passed to state.mcmc_sweep (or state.gibbs_sweep). history : bool (optional, default: False) If True, a list of tuples of the form (nattempts, nmoves, entropy) will be kept and returned, where entropy is the current entropy and nmoves is the number of vertices moved. callback : function (optional, default: None) If given, this function will be called after each iteration. The function must accept the current state as an argument, and its return value must be either None or a (possibly empty) list of values that will be append to the history, if history == True. verbose : bool or tuple (optional, default: False) If True, progress information will be shown. Optionally, this accepts arguments of the type tuple of the form (level, prefix) where level is a positive integer that specifies the level of detail, and prefix is a string that is prepended to the all output messages. history : list of tuples of the form (nattempts, nmoves, entropy) Summary of the MCMC run. This is returned only if history == True. entropy : float Current entropy value after run. This is returned only if history == False. nattempts : int Number of node move attempts. nmoves : int Number of node moves.

Notes

The MCMC equilibration is attempted by keeping track of the maximum and minimum values, and waiting sufficiently long without a record-breaking event.

This function calls state.mcmc_sweep (or state.gibbs_sweep) at each iteration (e.g. graph_tool.inference.blockmodel.BlockState.mcmc_sweep() and graph_tool.inference.blockmodel.BlockState.gibbs_sweep()), and keeps track of the value of state.entropy(**args) with args corresponding to mcmc_args["entropy_args"].

References

 [peixoto-efficient-2014190] 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
graph_tool.inference.mcmc.mcmc_anneal(state, beta_range=(1.0, 10.0), niter=100, history=False, mcmc_equilibrate_args={}, verbose=False)[source]

Equilibrate a MCMC at a specified target temperature by performing simulated annealing.

Parameters: state : Any state class (e.g. BlockState) Initial state. This state will be modified during the algorithm. beta_range : tuple of two floats (optional, default: (1., 10.)) Inverse temperature range. niter : int (optional, default: 100) Number of steps (in logspace) from the starting temperature to the final one. history : bool (optional, default: False) If True, a list of tuples of the form (nattempts, nmoves, beta, entropy) mcmc_equilibrate_args : dict (optional, default: {}) Arguments to be passed to mcmc_equilibrate(). verbose : bool or tuple (optional, default: False) If True, progress information will be shown. Optionally, this accepts arguments of the type tuple of the form (level, prefix) where level is a positive integer that specifies the level of detail, and prefix is a string that is prepended to the all output messages. history : list of tuples of the form (nattempts, nmoves, beta, entropy) Summary of the MCMC run. This is returned only if history == True. entropy : float Current entropy value after run. This is returned only if history == False. nattempts : int Number of node move attempts. nmoves : int Number of node moves.

Notes

This algorithm employs exponential cooling, where the value of beta is multiplied by a constant at each iteration, so that starting from beta_range[0] the value of beta_range[1] is reached after niter iterations.

At each iteration, the function mcmc_equilibrate() is called with the current value of beta (via the mcmc_args parameter).

References

 [peixoto-efficient-2014191] 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
graph_tool.inference.mcmc.mcmc_multilevel(state, B, r=2, b_cache=None, anneal=False, mcmc_equilibrate_args={}, anneal_args={}, shrink_args={}, verbose=False)[source]

Equilibrate a MCMC from a starting state with a higher order, by performing successive agglomerative initializations and equilibrations until the desired order is reached, such that metastable states are avoided.

Parameters: state : Any state class (e.g. BlockState) Initial state. This state will not be modified during the algorithm. B : int Desired model order (i.e. number of groups). r : int (optional, default: 2) Greediness of agglomeration. At each iteration, the state order will be reduced by a factor r. b_cache : dict (optional, default: None) If specified, this should be a dictionary with key-value pairs of the form (B, state) that contain pre-computed states of the specified order. This dictionary will be modified during the algorithm. anneal : bool (optional, default: False) If True, the equilibration steps will use simulated annealing, by calling mcmc_anneal(), instead of mcmc_equilibrate(). mcmc_equilibrate_args : dict (optional, default: {}) Arguments to be passed to mcmc_equilibrate(). mcmc_anneal_args : dict (optional, default: {}) Arguments to be passed to mcmc_anneal(). shrink_args : dict (optional, default: {}) Arguments to be passed to state.shrink (e.g. graph_tool.inference.blockmodel.BlockState.shrink()). verbose : bool or tuple (optional, default: False) If True, progress information will be shown. Optionally, this accepts arguments of the type tuple of the form (level, prefix) where level is a positive integer that specifies the level of detail, and prefix is a string that is prepended to the all output messages. state : The same type as parameter state This is the final state after the MCMC run.

Notes

This algorithm alternates between equilibrating the MCMC state and reducing the state order (via calls to state.shrink, e.g. graph_tool.inference.blockmodel.BlockState.shrink()).

This greatly reduces the changes of getting trapped in metastable states if the starting point if far away from equilibrium, as discussed in [peixoto-efficient-2014192].

References

 [peixoto-efficient-2014192] (1, 2) 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
class graph_tool.inference.mcmc.MulticanonicalState(g, S_min, S_max, nbins=1000)[source]

Bases: object

The density of states of a multicanonical Monte Carlo algorithm. It is used by graph_tool.inference.mcmc.multicanonical_equilibrate().

Parameters: Graph to be modelled. S_min : float Minimum energy. S_max : float Maximum energy. nbins : int (optional, default: 1000) Number of bins.
get_energies()[source]

Get energy bounds.

get_allowed_energies()[source]

Get allowed energy bounds.

get_range()[source]

Get energy range.

get_density(B=None)[source]

Get density of states, normalized so that total sum is $$B^N$$, where $$B$$ is the number of groups, and $$N$$ is the number of nodes. If not supplied $$B=N$$ is assumed.

get_hist()[source]

Get energy histogram.

get_perm_hist()[source]

Get permanent energy histogram.

get_flatness(h=None, allow_gaps=True)[source]

Get energy histogram flatness.

get_posterior(N=None)[source]

Get posterior probability.

reset_hist()[source]

Reset energy histogram.

graph_tool.inference.mcmc.multicanonical_equilibrate(state, m_state, f_range=(1.0, 1e-06), r=2, flatness=0.95, allow_gaps=True, callback=None, multicanonical_args={}, verbose=False)[source]

Equilibrate a multicanonical Monte Carlo sampling using the Wang-Landau algorithm.

Parameters: state : Any state class (e.g. BlockState) Initial state. This state will be modified during the algorithm. m_state : MulticanonicalState Initial multicanonical state, where the state density will be stored. f_range : tuple of two floats (optional, default: (1., 1e-6)) Range of density updates. r : float (optional, default: 2.) Greediness of convergence. At each iteration, the density updates will be reduced by a factor r. flatness : float (optional, default: .95) Sufficient histogram flatness threshold used to continue the algorithm. allow_gaps : bool (optional, default: True) If True, gaps in the histogram (regions with zero count) will be ignored when computing the flatness. callback : function (optional, default: None) If given, this function will be called after each iteration. The function must accept the current state and m_state as arguments. multicanonical_args : dict (optional, default: {}) Arguments to be passed to state.multicanonical_sweep (e.g. graph_tool.inference.blockmodel.BlockState.multicanonical_sweep()). verbose : bool or tuple (optional, default: False) If True, progress information will be shown. Optionally, this accepts arguments of the type tuple of the form (level, prefix) where level is a positive integer that specifies the level of detail, and prefix is a string that is prepended to the all output messages. niter : int Number of iterations required for convergence.

References

 [wang-efficient-2001193] Fugao Wang, D. P. Landau, “An efficient, multiple range random walk algorithm to calculate the density of states”, Phys. Rev. Lett. 86, 2050 (2001), DOI: 10.1103/PhysRevLett.86.2050 [sci-hub, @tor], arXiv: cond-mat/0011174
 [belardinelli-wang-2007193] R. E. Belardinelli, V. D. Pereyra, “Wang-Landau algorithm: A theoretical analysis of the saturation of the error”, J. Chem. Phys. 127, 184105 (2007), DOI: 10.1063/1.2803061 [sci-hub, @tor], arXiv: cond-mat/0702414
class graph_tool.inference.mcmc.TemperingState(states, betas, idx=None)[source]

Bases: object

This class aggregates several state classes and corresponding inverse-temperature values to implement parallel tempering MCMC.

This is meant to be used with mcmc_equilibrate().

Parameters: states : list of state objects (e.g. BlockState) Initial parallel states. betas : list of floats Inverse temperature values.
entropy(**kwargs)[source]

Returns the sum of the entropy of the parallel states. All keyword arguments are propagated to the individual states’ entropy() method.

entropies(**kwargs)[source]

Returns the entropies of the parallel states. All keyword arguments are propagated to the individual states’ entropy() method.

states_swap(adjacent=True, **kwargs)[source]

Perform a full sweep of the parallel states, where swaps are attempted. All relevant keyword arguments are propagated to the individual states’ entropy() method.

states_move(sweep_algo, **kwargs)[source]

Perform a full sweep of the parallel states, where state moves are attempted by calling sweep_algo(state, beta=beta, **kwargs).

mcmc_sweep(**kwargs)[source]

Perform a full mcmc sweep of the parallel states, where swap or moves are chosen randomly. It accepts an keyword argument r (default: 0.1) specifying the relative probability with which state swaps is performed with respect to node moves. All remaining keyword arguments are propagated to the individual states’ mcmc_sweep() method.

multiflip_mcmc_sweep(**kwargs)[source]

Perform a full mcmc sweep of the parallel states, where swap or moves are chosen randomly. It accepts an keyword argument r (default: 0.1) specifying the relative probability with which state swaps is performed with respect to node moves. All remaining keyword arguments are propagated to the individual states’ mcmc_sweep() method.

gibbs_sweep(**kwargs)[source]

Perform a full Gibbs mcmc sweep of the parallel states, where swap or moves are chosen randomly. It accepts an keyword argument r (default: 0.1) specifying the relative probability with which state swaps is performed with respect to node moves. All remaining keyword arguments are propagated to the individual states’ gibbs_sweep() method.

graph_tool.inference.bisection.bisection_minimize(init_states, random_bisection=False, mcmc_multilevel_args={}, verbose=False)[source]

Find the best order (number of groups) given an initial set of states by performing a one-dimension minimization, using a Fibonacci (or golden section) search.

Parameters: init_states : Any state class (e.g. BlockState) List with two or more states that will be used to bracket the search. random_bisection : bool (optional, default: False) If True, the bisection will be done randomly in the interval, instead of using the golden rule. mcmc_multilevel_args : dict (optional, default: {}) Arguments to be passed to mcmc_multilevel(). verbose : bool or tuple (optional, default: False) If True, progress information will be shown. Optionally, this accepts arguments of the type tuple of the form (level, prefix) where level is a positive integer that specifies the level of detail, and prefix is a string that is prepended to the all output messages. min_state : Any state class (e.g. BlockState) State with minimal entropy in the interval.

Notes

This function calls mcmc_multilevel() to reduce the order of a given state, and uses the value of state.entropy(**args) for the minimization, with args obtained from mcmc_multilevel_args.

References

 [golden-section-search195] “Golden section search”, https://en.wikipedia.org/wiki/Golden_section_search
 [peixoto-efficient-2014195] 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
graph_tool.inference.minimize.minimize_blockmodel_dl(g, B_min=None, B_max=None, b_min=None, b_max=None, deg_corr=True, overlap=False, nonoverlap_init=True, layers=False, state_args={}, bisection_args={}, mcmc_args={}, anneal_args={}, mcmc_equilibrate_args={}, shrink_args={}, mcmc_multilevel_args={}, verbose=False)[source]

Fit the stochastic block model, by minimizing its description length using an agglomerative heuristic.

Parameters: The graph. B_min : int (optional, default: None) The minimum number of blocks. B_max : int (optional, default: None) The maximum number of blocks. b_min : PropertyMap (optional, default: None) The partition to be used with the minimum number of blocks. b_max : PropertyMap (optional, default: None) The partition to be used with the maximum number of blocks. deg_corr : bool (optional, default: True) If True, the degree-corrected version of the model will be used. overlap : bool (optional, default: False) If True, the overlapping version of the model will be used. nonoverlap_init : bool (optional, default: True) If True, and overlap == True a non-overlapping initial state will be used. layers : bool (optional, default: False) If True, the layered version of the model will be used. state_args : dict (optional, default: {}) Arguments to be passed to appropriate state constructor (e.g. BlockState, OverlapBlockState or LayeredBlockState) bisection_args : dict (optional, default: {}) Arguments to be passed to bisection_minimize(). mcmc_args : dict (optional, default: {}) mcmc_equilibrate_args : dict (optional, default: {}) Arguments to be passed to mcmc_equilibrate(). shrink_args : dict (optional, default: {}) mcmc_multilevel_args : dict (optional, default: {}) Arguments to be passed to mcmc_multilevel(). verbose : bool or tuple (optional, default: False) If True, progress information will be shown. Optionally, this accepts arguments of the type tuple of the form (level, prefix) where level is a positive integer that specifies the level of detail, and prefix is a string that is prepended to the all output messages. State with minimal description length.

Notes

This function is a convenience wrapper around bisection_minimize().

See [peixoto-efficient-2014197] for details on the algorithm.

This algorithm has a complexity of $$O(V \ln^2 V)$$, where $$V$$ is the number of nodes in the network.

References

 [holland-stochastic-1983197] Paul W. Holland, Kathryn Blackmond Laskey, Samuel Leinhardt, “Stochastic blockmodels: First steps”, Carnegie-Mellon University, Pittsburgh, PA 15213, U.S.A., DOI: 10.1016/0378-8733(83)90021-7 [sci-hub, @tor].
 [faust-blockmodels-1992197] Katherine Faust, and Stanley Wasserman. “Blockmodels: Interpretation and Evaluation.” Social Networks 14, no. 1-2 (1992): 5-61, DOI: 10.1016/0378-8733(92)90013-W [sci-hub, @tor].
 [karrer-stochastic-2011197] Brian Karrer, and M. E. J. Newman. “Stochastic Blockmodels and Community Structure in Networks.” Physical Review E 83, no. 1 (2011): 016107, DOI: 10.1103/PhysRevE.83.016107 [sci-hub, @tor].
 [peixoto-entropy-2012197] Tiago P. Peixoto “Entropy of Stochastic Blockmodel Ensembles.” Physical Review E 85, no. 5 (2012): 056122, DOI: 10.1103/PhysRevE.85.056122 [sci-hub, @tor], arXiv: 1112.6028.
 [peixoto-parsimonious-2013197] Tiago P. Peixoto, “Parsimonious module inference in large networks”, Phys. Rev. Lett. 110, 148701 (2013), DOI: 10.1103/PhysRevLett.110.148701 [sci-hub, @tor], arXiv: 1212.4794.
 [peixoto-efficient-2014197] (1, 2) 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.
 [peixoto-model-2016197] Tiago P. Peixoto, “Model selection and hypothesis testing for large-scale network models with overlapping groups”, Phys. Rev. X 5, 011033 (2016), DOI: 10.1103/PhysRevX.5.011033 [sci-hub, @tor], arXiv: 1409.3059.
 [peixoto-inferring-2016197] Tiago P. Peixoto, “Inferring the mesoscale structure of layered, edge-valued and time-varying networks”, Phys. Rev. E 92, 042807 (2015), DOI: 10.1103/PhysRevE.92.042807 [sci-hub, @tor], arXiv: 1504.02381.

Examples

>>> g = gt.collection.data["polbooks"]
>>> state = gt.minimize_blockmodel_dl(g)
>>> state.draw(pos=g.vp["pos"], vertex_shape=state.get_blocks(),
...            output="polbooks_blocks_mdl.pdf")
<...>


Block partition of a political books network, which minimizes the description length of the network according to the degree-corrected stochastic blockmodel.

>>> g = gt.collection.data["polbooks"]
>>> state = gt.minimize_blockmodel_dl(g, overlap=True)
>>> state.draw(pos=g.vp["pos"], output="polbooks_overlap_blocks_mdl.pdf")
<...>


Overlapping partition of a political books network, which minimizes the description length of the network according to the overlapping degree-corrected stochastic blockmodel.

graph_tool.inference.minimize.minimize_nested_blockmodel_dl(g, B_min=None, B_max=None, b_min=None, b_max=None, Bs=None, bs=None, deg_corr=True, overlap=False, nonoverlap_init=True, layers=False, hierarchy_minimize_args={}, state_args={}, bisection_args={}, mcmc_args={}, anneal_args={}, mcmc_equilibrate_args={}, shrink_args={}, mcmc_multilevel_args={}, verbose=False)[source]

Fit the nested stochastic block model, by minimizing its description length using an agglomerative heuristic.

Parameters: The graph. B_min : int (optional, default: None) The minimum number of blocks. B_max : int (optional, default: None) The maximum number of blocks. b_min : PropertyMap (optional, default: None) The partition to be used with the minimum number of blocks. b_max : PropertyMap (optional, default: None) The partition to be used with the maximum number of blocks. Bs : list of ints (optional, default: None) If provided, it will correspond to the sizes of the initial hierarchy. bs : list of integer-valued numpy.ndarray objects (optional, default: None) If provided, it will correspond to the initial hierarchical partition. deg_corr : bool (optional, default: True) If True, the degree-corrected version of the model will be used. overlap : bool (optional, default: False) If True, the overlapping version of the model will be used. nonoverlap_init : bool (optional, default: True) If True, and overlap == True a non-overlapping initial state will be used. layers : bool (optional, default: False) If True, the layered version of the model will be used. hierarchy_minimize_args : dict (optional, default: {}) Arguments to be passed to hierarchy_minimize(). state_args : dict (optional, default: {}) Arguments to be passed to appropriate state constructor (e.g. BlockState, OverlapBlockState or LayeredBlockState) bisection_args : dict (optional, default: {}) Arguments to be passed to bisection_minimize(). mcmc_args : dict (optional, default: {}) mcmc_equilibrate_args : dict (optional, default: {}) Arguments to be passed to mcmc_equilibrate(). shrink_args : dict (optional, default: {}) mcmc_multilevel_args : dict (optional, default: {}) Arguments to be passed to mcmc_multilevel(). verbose : bool or tuple (optional, default: False) If True, progress information will be shown. Optionally, this accepts arguments of the type tuple of the form (level, prefix) where level is a positive integer that specifies the level of detail, and prefix is a string that is prepended to the all output messages. min_state : NestedBlockState Nested state with minimal description length.

Notes

This function is a convenience wrapper around hierarchy_minimize().

See [peixoto-hierarchical-2014205] for details on the algorithm.

This algorithm has a complexity of $$O(V \ln^2 V)$$, where $$V$$ is the number of nodes in the network.

References

 [peixoto-hierarchical-2014205] (1, 2) Tiago P. Peixoto, “Hierarchical block structures and high-resolution model selection in large networks “, Phys. Rev. X 4, 011047 (2014), DOI: 10.1103/PhysRevX.4.011047 [sci-hub, @tor], arXiv: 1310.4377.
 [peixoto-efficient-2014205] 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.
 [peixoto-model-2016205] Tiago P. Peixoto, “Model selection and hypothesis testing for large-scale network models with overlapping groups”, Phys. Rev. X 5, 011033 (2016), DOI: 10.1103/PhysRevX.5.011033 [sci-hub, @tor], arXiv: 1409.3059.
 [peixoto-inferring-2016205] Tiago P. Peixoto, “Inferring the mesoscale structure of layered, edge-valued and time-varying networks”, Phys. Rev. E 92, 042807 (2015), DOI: 10.1103/PhysRevE.92.042807 [sci-hub, @tor], arXiv: 1504.02381.

Examples

>>> g = gt.collection.data["power"]
>>> state = gt.minimize_nested_blockmodel_dl(g, deg_corr=True)
>>> state.draw(output="power_nested_mdl.pdf")
(...)


Hierarchical Block partition of a power-grid network, which minimizes the description length of the network according to the nested (degree-corrected) stochastic blockmodel.

>>> g = gt.collection.data["celegansneural"]
>>> state = gt.minimize_nested_blockmodel_dl(g, deg_corr=True, overlap=True)
>>> state.draw(output="celegans_nested_mdl_overlap.pdf")
(...)


Overlapping block partition of the C. elegans neural network, which minimizes the description length of the network according to the nested overlapping degree-corrected stochastic blockmodel.

class graph_tool.inference.blockmodel_em.EMBlockState(g, B, init_state=None)[source]

Bases: object

The parametric, undirected stochastic block model state of a given graph.

Parameters: Graph to be modelled. B : int Number of blocks (or vertex groups). init_state : BlockState (optional, default: None) Optional block state used for initialization.

Notes

This class is intended to be used with em_infer() to perform expectation maximization with belief propagation. See [decelle_asymptotic_2011209] for more details.

References

 [decelle_asymptotic_2011209] (1, 2) Aurelien Decelle, Florent Krzakala, Cristopher Moore, and Lenka Zdeborová, “Asymptotic analysis of the stochastic block model for modular networks and its algorithmic applications”, Phys. Rev. E 84, 066106 (2011), DOI: 10.1103/PhysRevE.84.066106 [sci-hub, @tor], arXiv: 1109.3041
get_vertex_marginals()[source]

Return the vertex marginals.

get_group_sizes()[source]

Return the group sizes.

get_matrix()[source]

Return probability matrix.

get_MAP()[source]

Return the maximum a posteriori (MAP) estimate of the node partition.

get_fe()[source]

Return the Bethe free energy.

get_ak()[source]

Return the model’s average degree.

e_iter(max_iter=1000, epsilon=0.001, verbose=False)[source]

Perform ‘expectation’ iterations, using belief propagation, where the vertex marginals and edge messages are updated, until convergence according to epsilon or the maximum number of iterations given by max_iter. If verbose == True, convergence information is displayed.

The last update delta is returned.

m_iter()[source]

Perform a single ‘maximization’ iteration, where the group sizes and connection probability matrix are updated.

The update delta is returned.

learn(epsilon=0.001)[source]

Perform ‘maximization’ iterations until convergence according to epsilon.

The last update delta is returned.

draw(**kwargs)[source]

Convenience wrapper to graph_draw() that draws the state of the graph as colors on the vertices and edges.

graph_tool.inference.blockmodel_em.em_infer(state, max_iter=1000, max_e_iter=1, epsilon=0.001, learn_first=False, verbose=False)[source]

Infer the model parameters and latent variables using the expectation-maximization (EM) algorithm with initial state given by state.

Parameters: state : model state State object, e.g. of type graph_tool.inference.blockmodel_em.EMBlockState. max_iter : int (optional, default: 1000) Maximum number of iterations. max_e_iter : int (optional, default: 1) Maximum number of ‘expectation’ iterations inside the main loop. epsilon : float (optional, default: 1e-3) Convergence criterion. learn_first : bool (optional, default: False) If True, the maximization (a.k.a parameter learning) is converged before the main loop is run. verbose : bool (optional, default: True) If True, convergence information is displayed. delta : float The last update delta. niter : int The total number of iterations.

References

 [wiki-EM210] “Expectation–maximization algorithm”, https://en.wikipedia.org/wiki/Expectation%E2%80%93maximization_algorithm

Examples

>>> g = gt.collection.data["polbooks"]
>>> state = gt.EMBlockState(g, B=3)
>>> delta, niter = gt.em_infer(state)
>>> state.draw(pos=g.vp["pos"], output="polbooks_EM_B3.pdf")
<...>


“Soft” block partition of a political books network with $$B=3$$.

class graph_tool.inference.util.DictState(d)[source]

Bases: dict

Dictionary with (key,value) pairs accessible via attributes.

graph_tool.inference.util.dmask(d, ks)[source]

Copy dictionary d and remove key list ks.

graph_tool.inference.util.lbinom(n, k)[source]

Return log of binom(n, k).

graph_tool.inference.util.pmap(prop, value_map)[source]

Maps all the values of prop to the values given by value_map, which is indexed by the values of prop.

graph_tool.inference.util.reverse_map(prop, value_map)[source]

Modify value_map such that the positions indexed by the values in prop correspond to their index in prop.

graph_tool.inference.util.continuous_map(prop)[source]

Remap the values of prop in the continuous range $$[0, N-1]$$.

graph_tool.inference.modularity.modularity(g, b, weight=None)[source]

Calculate Newman’s modularity of a network partition.

Parameters: Graph to be used. Vertex property map with the community partition. weight : PropertyMap (optional, default: None) Edge property map with the optional edge weights. Q : float Newman’s modularity.

Notes

Given a specific graph partition specified by prop, Newman’s modularity [newman-modularity-2006211] is defined as:

$Q = \frac{1}{2E} \sum_r e_{rr}- \frac{e_r^2}{2E}$

where $$e_{rs}$$ is the number of edges which fall between vertices in communities s and r, or twice that number if $$r = s$$, and $$e_r = \sum_s e_{rs}$$.

If weights are provided, the matrix $$e_{rs}$$ corresponds to the sum of edge weights instead of number of edges, and the value of $$E$$ becomes the total sum of edge weights.

References

 [newman-modularity-2006211] (1, 2) M. E. J. Newman, “Modularity and community structure in networks”, Proc. Natl. Acad. Sci. USA 103, 8577-8582 (2006), DOI: 10.1073/pnas.0601602103 [sci-hub, @tor], arXiv: physics/0602124

Examples

>>> g = gt.collection.data["football"]
>>> gt.modularity(g, g.vp.value_tsevans)
0.5744393497...