### Add network reconstruction to inference HOWTO

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 Background: Nonparametric statistical inference ----------------------------------------------- A common task when analyzing networks is to characterize their structures in simple terms, often by dividing the nodes into modules or "communities" __. A principled approach to perform this task is to formulate generative models _ that include the idea of "modules" in their descriptions, which then can be detected by inferring _ the model parameters from data. More precisely, given the partition :math:\boldsymbol b = \{b_i\} of the network into :math:B groups, where :math:b_i\in[0,B-1] is the group membership of node :math:i, we define a model that generates a network :math:\boldsymbol G with a probability .. math:: :label: model-likelihood P(\boldsymbol G|\boldsymbol\theta, \boldsymbol b) where :math:\boldsymbol\theta are additional model parameters that control how the node partition affects the structure of the network. Therefore, if we observe a network :math:\boldsymbol G, the likelihood that it was generated by a given partition :math:\boldsymbol b is obtained via the Bayesian _ posterior probability .. math:: :label: model-posterior-sum P(\boldsymbol b | \boldsymbol G) = \frac{\sum_{\boldsymbol\theta}P(\boldsymbol G|\boldsymbol\theta, \boldsymbol b)P(\boldsymbol\theta, \boldsymbol b)}{P(\boldsymbol G)} where :math:P(\boldsymbol\theta, \boldsymbol b) is the prior probability _ of the model parameters, and .. math:: :label: model-evidence P(\boldsymbol G) = \sum_{\boldsymbol\theta,\boldsymbol b}P(\boldsymbol G|\boldsymbol\theta, \boldsymbol b)P(\boldsymbol\theta, \boldsymbol b) is called the evidence, and corresponds to the total probability of the data summed over all model parameters. The particular types of model that will be considered here have "hard constraints", such that there is only one choice for the remaining parameters :math:\boldsymbol\theta that is compatible with the generated network, such that Eq. :eq:model-posterior-sum simplifies to .. math:: :label: model-posterior P(\boldsymbol b | \boldsymbol G) = \frac{P(\boldsymbol G|\boldsymbol\theta, \boldsymbol b)P(\boldsymbol\theta, \boldsymbol b)}{P(\boldsymbol G)} with :math:\boldsymbol\theta above being the only choice compatible with :math:\boldsymbol G and :math:\boldsymbol b. The inference procedures considered here will consist in either finding a network partition that maximizes Eq. :eq:model-posterior, or sampling different partitions according its posterior probability. As we will show below, this approach also enables the comparison of different models according to statistical evidence (a.k.a. model selection). Minimum description length (MDL) ++++++++++++++++++++++++++++++++ We note that Eq. :eq:model-posterior can be written as .. math:: P(\boldsymbol b | \boldsymbol G) = \frac{\exp(-\Sigma)}{P(\boldsymbol G)} where .. math:: :label: model-dl \Sigma = -\ln P(\boldsymbol G|\boldsymbol\theta, \boldsymbol b) - \ln P(\boldsymbol\theta, \boldsymbol b) is called the **description length** of the network :math:\boldsymbol G. It measures the amount of information _ required to describe the data, if we encode _ it using the particular parametrization of the generative model given by :math:\boldsymbol\theta and :math:\boldsymbol b, as well as the parameters themselves. Therefore, if we choose to maximize the posterior distribution of Eq. :eq:model-posterior it will be fully equivalent to the so-called minimum description length _ method. This approach corresponds to an implementation of Occam's razor _, where the simplest model is selected, among all possibilities with the same explanatory power. The selection is based on the statistical evidence available, and therefore will not overfit _, i.e. mistake stochastic fluctuations for actual structure. In particular this means that we will not find modules in networks if they could have arisen simply because of stochastic fluctuations, as they do in fully random graphs [guimera-modularity-2004]_. The stochastic block model (SBM) -------------------------------- The stochastic block model _ is arguably the simplest generative process based on the notion of groups of nodes [holland-stochastic-1983]_. The microcanonical _ formulation [peixoto-nonparametric-2017]_ of the basic or "traditional" version takes as parameters the partition of the nodes into groups :math:\boldsymbol b and a :math:B\times B matrix of edge counts :math:\boldsymbol e, where :math:e_{rs} is the number of edges between groups :math:r and :math:s. Given these constraints, the edges are then placed randomly. Hence, nodes that belong to the same group possess the same probability of being connected with other nodes of the network. An example of a possible parametrization is given in the following figure. .. testcode:: sbm-example :hide: import os try: os.chdir("demos/inference") except FileNotFoundError: pass g = gt.load_graph("blockmodel-example.gt.gz") gt.graph_draw(g, pos=g.vp.pos, vertex_size=10, vertex_fill_color=g.vp.bo, vertex_color="#333333", edge_gradient=g.new_ep("vector", val=), output="sbm-example.svg") ers = g.gp.w from pylab import * figure() matshow(log(ers)) xlabel("Group $r$") ylabel("Group $s$") gca().xaxis.set_label_position("top") savefig("sbm-example-ers.svg") .. table:: :class: figure +----------------------------------+------------------------------+ |.. figure:: sbm-example-ers.svg |.. figure:: sbm-example.svg | | :width: 300px | :width: 300px | | :align: center | :align: center | | | | | Matrix of edge counts | Generated network. | | :math:\boldsymbol e between | | | groups. | | +----------------------------------+------------------------------+ .. note:: We emphasize that no constraints are imposed on what kind of modular structure is allowed, as the matrix of edge counts :math:e is unconstrained. Hence, we can detect the putatively typical pattern of "community structure" _, i.e. when nodes are connected mostly to other nodes of the same group, if it happens to be the most likely network description, but we can also detect a large multiplicity of other patterns, such as bipartiteness _, core-periphery, and many others, all under the same inference framework. Although quite general, the traditional model assumes that the edges are placed randomly inside each group, and because of this the nodes that belong to the same group tend to have very similar degrees. As it turns out, this is often a poor model for many networks, which possess highly heterogeneous degree distributions. A better model for such networks is called the degree-corrected stochastic block model [karrer-stochastic-2011]_, and it is defined just like the traditional model, with the addition of the degree sequence :math:\boldsymbol k = \{k_i\} of the graph as an additional set of parameters (assuming again a microcanonical formulation [peixoto-nonparametric-2017]_). The nested stochastic block model +++++++++++++++++++++++++++++++++ The regular SBM has a drawback when applied to large networks. Namely, it cannot be used to find relatively small groups, as the maximum number of groups that can be found scales as :math:B_{\text{max}}=O(\sqrt{N}), where :math:N is the number of nodes in the network, if Bayesian inference is performed [peixoto-parsimonious-2013]_. In order to circumvent this, we need to replace the noninformative priors used by a hierarchy of priors and hyperpriors, which amounts to a nested SBM, where the groups themselves are clustered into groups, and the matrix :math:e of edge counts are generated from another SBM, and so on recursively [peixoto-hierarchical-2014]_, as illustrated below. .. figure:: nested-diagram.* :width: 400px :align: center Example of a nested SBM with three levels. With this model, the maximum number of groups that can be inferred scales as :math:B_{\text{max}}=O(N/\log(N)). In addition to being able to find small groups in large networks, this model also provides a multilevel hierarchical description of the network. With such a description, we can uncover structural patterns at multiple scales, representing different levels of coarse-graining.
 .. _weights: Edge weights and covariates --------------------------- Very often networks cannot be completely represented by simple graphs, but instead have arbitrary "weights" :math:x_{ij} on the edges. Edge weights can be continuous or discrete numbers, and either strictly positive or positive or negative, depending on context. The SBM can be extended to cover these cases by treating edge weights as covariates that are sampled from some distribution conditioned on the node partition [aicher-learning-2015]_ [peixoto-weighted-2017]_, i.e. .. math:: P(\boldsymbol x,\boldsymbol G|\boldsymbol b) = P(\boldsymbol x|\boldsymbol G,\boldsymbol b) P(\boldsymbol G|\boldsymbol b), where :math:P(\boldsymbol G|\boldsymbol b) is the likelihood of the unweighted SBM described previously, and :math:P(\boldsymbol x|\boldsymbol G,\boldsymbol b) is the integrated likelihood of the edge weights .. math:: P(\boldsymbol x|\boldsymbol G,\boldsymbol b) = \prod_{r\le s}\int P({\boldsymbol x}_{rs}|\gamma)P(\gamma)\,\mathrm{d}\gamma, where :math:P({\boldsymbol x}_{rs}|\gamma) is some model for the weights :math:{\boldsymbol x}_{rs} between groups :math:(r,s), conditioned on some parameter :math:\gamma, sampled from its prior :math:P(\gamma). A hierarchical version of the model can also be implemented by replacing this prior by a nested sequence of priors and hyperpriors, as described in [peixoto-weighted-2017]_. The posterior partition distribution is then simply .. math:: P(\boldsymbol b | \boldsymbol G,\boldsymbol x) = \frac{P(\boldsymbol x|\boldsymbol G,\boldsymbol b) P(\boldsymbol G|\boldsymbol b) P(\boldsymbol b)}{P(\boldsymbol G,\boldsymbol x)}, which can be sampled from, or maximized, just like with the unweighted case, but will use the information on the weights to guide the partitions. A variety of weight models is supported, reflecting different kinds of edge covariates: .. csv-table:: :header: "Name", "Domain", "Bounds", "Shape" :widths: 10, 5, 5, 5 :delim: | :align: center "real-exponential" | Real :math:(\mathbb{R}) | :math:[0,\infty] | Exponential _ "real-normal" | Real :math:(\mathbb{R}) | :math:[-\infty,\infty] | Normal _ "discrete-geometric" | Natural :math:(\mathbb{N}) | :math:[0,\infty] | Geometric _ "discrete-binomial" | Natural :math:(\mathbb{N}) | :math:[0,M] | Binomial _ "discrete-poisson" | Natural :math:(\mathbb{N}) | :math:[0,\infty] | Poisson _ In fact, the actual model implements microcanonical _ versions of these distributions that are asymptotically equivalent, as described in [peixoto-weighted-2017]_. These can be combined with arbitrary weight transformations to achieve a large family of associated distributions. For example, to use a log-normal _ weight model for positive real weights :math:\boldsymbol x, we can use the transformation :math:y_{ij} = \ln x_{ij} together with the "real-normal" model for :math:\boldsymbol y. To model weights that are positive or negative integers in :math:\mathbb{Z}, we could either subtract the minimum value, :math:y_{ij} = x_{ij} - x^*, with :math:x^*=\operatorname{min}_{ij}x_{ij}, and use any of the above models for non-negative integers in :math:\mathbb{N}, or alternatively, consider the sign as an additional covariate, i.e. :math:s_{ij} = [\operatorname{sign}(x_{ij})+1]/2 \in \{0,1\}, using the Binomial distribution with :math:M=1 (a.k.a. the Bernoulli distribution _), and any of the other discrete distributions for the magnitude, :math:y_{ij} = \operatorname{abs}(x_{ij}). The support for weighted networks is activated by passing the parameters recs and rec_types to :class:~graph_tool.inference.blockmodel.BlockState (or :class:~graph_tool.inference.overlap_blockmodel.OverlapBlockState), that specify the edge covariates (an edge :class:~graph_tool.PropertyMap) and their types (a string from the table above), respectively. Note that these parameters expect *lists*, so that multiple edge weights can be used simultaneously. For example, let us consider a network of suspected terrorists involved in the train bombing of Madrid on March 11, 2004 [hayes-connecting-2006]_. An edge indicates that a connection between the two persons have been identified, and the weight of the edge (an integer in the range :math:[0,3]) indicates the "strength" of the connection. We can apply the weighted SBM, using a Binomial model for the weights, as follows: .. testsetup:: weighted-model import os try: os.chdir("demos/inference") except FileNotFoundError: pass gt.seed_rng(42) .. testcode:: weighted-model g = gt.collection.konect_data["moreno_train"] # This network contains an internal edge property map with name # "weight" that contains the strength of interactions. The values # integers in the range [0, 3]. state = gt.minimize_nested_blockmodel_dl(g, state_args=dict(recs=[g.ep.weight], rec_types=["discrete-binomial"])) state.draw(edge_color=g.ep.weight, ecmap=(matplotlib.cm.inferno, .6), eorder=g.ep.weight, edge_pen_width=gt.prop_to_size(g.ep.weight, 1, 4, power=1), edge_gradient=[], output="moreno-train-wsbm.svg") .. figure:: moreno-train-wsbm.* :align: center :width: 350px Best fit of the Binomial-weighted degree-corrected SBM for a network of terror suspects, using the strength of connection as edge covariates. The edge colors and widths correspond to the strengths. Model selection +++++++++++++++ In order to select the best weighted model, we proceed in the same manner as described in Sec. :ref:model_selection. However, when using transformations on continuous weights, we must include the associated scaling of the probability density, as described in [peixoto-weighted-2017]_. For example, consider a food web _ between species in south Florida [ulanowicz-network-2005]_. A directed link exists from species :math:i to :math:j if a energy flow exists between them, and a weight :math:x_{ij} on this edge indicates the magnitude of the energy flow (a positive real value, i.e. :math:x_{ij}\in [0,\infty]). One possibility, therefore, is to use the "real-exponential" model, as follows: .. testsetup:: food-web import os try: os.chdir("demos/inference") except FileNotFoundError: pass gt.seed_rng(44) .. testcode:: food-web g = gt.collection.konect_data["foodweb-baywet"] # This network contains an internal edge property map with name # "weight" that contains the biomass flow between species. The values # are continuous in the range [0, infinity]. state = gt.minimize_nested_blockmodel_dl(g, state_args=dict(recs=[g.ep.weight], rec_types=["real-exponential"])) state.draw(edge_color=gt.prop_to_size(g.ep.weight, power=1, log=True), ecmap=(matplotlib.cm.inferno, .6), eorder=g.ep.weight, edge_pen_width=gt.prop_to_size(g.ep.weight, 1, 4, power=1, log=True), edge_gradient=[], output="foodweb-wsbm.svg") .. figure:: foodweb-wsbm.* :align: center :width: 350px Best fit of the exponential-weighted degree-corrected SBM for a food web, using the biomass flow as edge covariates (indicated by the edge colors and widths). Alternatively, we may consider a transformation of the type .. math:: :label: log_transform y_{ij} = \ln x_{ij} so that :math:y_{ij} \in [-\infty,\infty]. If we use a model "real-normal" for :math:\boldsymbol y, it amounts to a log-normal _ model for :math:\boldsymbol x. This can be a better choice if the weights are distributed across many orders of magnitude, or show multi-modality. We can fit this alternative model simply by using the transformed weights: .. testcode:: food-web # Apply the weight transformation y = g.ep.weight.copy() y.a = log(y.a) state_ln = gt.minimize_nested_blockmodel_dl(g, state_args=dict(recs=[y], rec_types=["real-normal"])) state_ln.draw(edge_color=gt.prop_to_size(g.ep.weight, power=1, log=True), ecmap=(matplotlib.cm.inferno, .6), eorder=g.ep.weight, edge_pen_width=gt.prop_to_size(g.ep.weight, 1, 4, power=1, log=True), edge_gradient=[], output="foodweb-wsbm-lognormal.svg") .. figure:: foodweb-wsbm-lognormal.* :align: center :width: 350px Best fit of the log-normal-weighted degree-corrected SBM for a food web, using the biomass flow as edge covariates (indicated by the edge colors and widths). At this point, we ask ourselves which of the above models yields the best fit of the data. This is answered by performing model selection via posterior odds ratios just like in Sec. :ref:model_selection. However, here we need to take into account the scaling of the probability density incurred by the variable transformation, i.e. .. math:: P(\boldsymbol x | \boldsymbol G, \boldsymbol b) = P(\boldsymbol y(\boldsymbol x) | \boldsymbol G, \boldsymbol b) \prod_{ij}\left[\frac{\mathrm{d}y_{ij}}{\mathrm{d}x_{ij}}(x_{ij})\right]^{A_{ij}}. In the particular case of Eq. :eq:log_transform, we have .. math:: \prod_{ij}\left[\frac{\mathrm{d}y_{ij}}{\mathrm{d}x_{ij}}(x_{ij})\right]^{A_{ij}} = \prod_{ij}\frac{1}{x_{ij}^{A_{ij}}}. Therefore, we can compute the posterior odds ratio between both models as: .. testcode:: food-web L1 = -state.entropy() L2 = -state_ln.entropy() - log(g.ep.weight.a).sum() print(u"ln \u039b: ", L2 - L1) .. testoutput:: food-web :options: +NORMALIZE_WHITESPACE ln Λ: -70.145685... A value of :math:\Lambda \approx \mathrm{e}^{-70} \approx 10^{-30} in favor the exponential model indicates that the log-normal model does not provide a better fit for this particular data. Based on this, we conclude that the exponential model should be preferred in this case. Posterior sampling ++++++++++++++++++ The procedure to sample from the posterior distribution is identical to what is described in Sec. :ref:sampling, but with the appropriate initialization, i.e. .. testcode:: weighted-model state = gt.BlockState(g, B=20, recs=[g.ep.weight], rec_types=["discrete-poisson"]) or for the nested model .. testcode:: weighted-model state = gt.NestedBlockState(g, bs=[np.random.randint(0, 20, g.num_vertices())] + [zeros(1)] * 10, state_args=dict(recs=[g.ep.weight], rec_types=["discrete-poisson"]))
 Layered networks ---------------- The edges of the network may be distributed in discrete "layers", representing distinct types if interactions [peixoto-inferring-2015]_. Extensions to the SBM may be defined for such data, and they can be inferred using the exact same interface shown above, except one should use the :class:~graph_tool.inference.layered_blockmodel.LayeredBlockState class, instead of :class:~graph_tool.inference.blockmodel.BlockState. This class takes two additional parameters: the ec parameter, that must correspond to an edge :class:~graph_tool.PropertyMap with the layer/covariate values on the edges, and the Boolean layers parameter, which if True specifies a layered model, otherwise one with categorical edge covariates (not to be confused with the weighted models in Sec. :ref:weights). If we use :func:~graph_tool.inference.minimize.minimize_blockmodel_dl, this can be achieved simply by passing the option layers=True as well as the appropriate value of state_args, which will be propagated to :class:~graph_tool.inference.layered_blockmodel.LayeredBlockState's constructor. As an example, let us consider a social network of tribes, where two types of interactions were recorded, amounting to either friendship or enmity [read-cultures-1954]_. We may apply the layered model by separating these two types of interactions in two layers: .. testsetup:: layered-model import os try: os.chdir("demos/inference") except FileNotFoundError: pass gt.seed_rng(42) .. testcode:: layered-model g = gt.collection.konect_data["ucidata-gama"] # The edge types are stored in the edge property map "weights". # Note the different meanings of the two 'layers' parameters below: The # first enables the use of LayeredBlockState, and the second selects # the 'edge layers' version (instead of 'edge covariates'). state = gt.minimize_nested_blockmodel_dl(g, layers=True, state_args=dict(ec=g.ep.weight, layers=True)) state.draw(edge_color=g.ep.weight, edge_gradient=[], ecmap=(matplotlib.cm.coolwarm_r, .6), edge_pen_width=5, output="tribes-sbm-edge-layers.svg") .. figure:: tribes-sbm-edge-layers.* :align: center :width: 350px Best fit of the degree-corrected SBM with edge layers for a network of tribes, with edge layers shown as colors. The groups show two enemy tribes. It is possible to perform model averaging of all layered variants exactly like for the regular SBMs as was shown above.
 Inferring the best partition ---------------------------- The simplest and most efficient approach is to find the best partition of the network by maximizing Eq. :eq:model-posterior according to some version of the model. This is obtained via the functions :func:~graph_tool.inference.minimize.minimize_blockmodel_dl or :func:~graph_tool.inference.minimize.minimize_nested_blockmodel_dl, which employs an agglomerative multilevel Markov chain Monte Carlo (MCMC) _ algorithm [peixoto-efficient-2014]_. We focus first on the non-nested model, and we illustrate its use with a network of American football teams, which we load from the :mod:~graph_tool.collection module: .. testsetup:: football import os try: os.chdir("demos/inference") except FileNotFoundError: pass gt.seed_rng(7) .. testcode:: football g = gt.collection.data["football"] print(g) which yields .. testoutput:: football we then fit the degree-corrected model by calling .. testcode:: football state = gt.minimize_blockmodel_dl(g) This returns a :class:~graph_tool.inference.blockmodel.BlockState object that includes the inference results. .. note:: The inference algorithm used is stochastic by nature, and may return a different answer each time it is run. This may be due to the fact that there are alternative partitions with similar probabilities, or that the optimum is difficult to find. Note that the inference problem here is, in general, NP-Hard _, hence there is no efficient algorithm that is guaranteed to always find the best answer. Because of this, typically one would call the algorithm many times, and select the partition with the largest posterior probability of Eq. :eq:model-posterior, or equivalently, the minimum description length of Eq. :eq:model-dl. The description length of a fit can be obtained with the :meth:~graph_tool.inference.blockmodel.BlockState.entropy method. See also Sec. :ref:sec_model_selection below. We may perform a drawing of the partition obtained via the :mod:~graph_tool.inference.blockmodel.BlockState.draw method, that functions as a convenience wrapper to the :func:~graph_tool.draw.graph_draw function .. testcode:: football state.draw(pos=g.vp.pos, output="football-sbm-fit.svg") which yields the following image. .. figure:: football-sbm-fit.* :align: center :width: 400px Stochastic block model inference of a network of American college football teams. The colors correspond to inferred group membership of the nodes. We can obtain the group memberships as a :class:~graph_tool.PropertyMap on the vertices via the :mod:~graph_tool.inference.blockmodel.BlockState.get_blocks method: .. testcode:: football b = state.get_blocks() r = b # group membership of vertex 10 print(r) which yields: .. testoutput:: football 3 We may also access the matrix of edge counts between groups via :mod:~graph_tool.inference.blockmodel.BlockState.get_matrix .. testcode:: football e = state.get_matrix() matshow(e.todense()) savefig("football-edge-counts.svg") .. figure:: football-edge-counts.* :align: center Matrix of edge counts between groups. We may obtain the same matrix of edge counts as a graph, which has internal edge and vertex property maps with the edge and vertex counts, respectively: .. testcode:: football bg = state.get_bg() ers = state.mrs # edge counts nr = state.wr # node counts .. _sec_model_selection: Hierarchical partitions +++++++++++++++++++++++ The inference of the nested family of SBMs is done in a similar manner, but we must use instead the :func:~graph_tool.inference.minimize.minimize_nested_blockmodel_dl function. We illustrate its use with the neural network of the C. elegans _ worm: .. testsetup:: celegans gt.seed_rng(47) .. testcode:: celegans g = gt.collection.data["celegansneural"] print(g) which has 297 vertices and 2359 edges. .. testoutput:: celegans A hierarchical fit of the degree-corrected model is performed as follows. .. testcode:: celegans state = gt.minimize_nested_blockmodel_dl(g) The object returned is an instance of a :class:~graph_tool.inference.nested_blockmodel.NestedBlockState class, which encapsulates the results. We can again draw the resulting hierarchical clustering using the :meth:~graph_tool.inference.nested_blockmodel.NestedBlockState.draw method: .. testcode:: celegans state.draw(output="celegans-hsbm-fit.svg") .. figure:: celegans-hsbm-fit.* :align: center Most likely hierarchical partition of the neural network of the *C. elegans* worm according to the nested degree-corrected SBM. .. note:: If the output parameter to :meth:~graph_tool.inference.nested_blockmodel.NestedBlockState.draw is omitted, an interactive visualization is performed, where the user can re-order the hierarchy nodes using the mouse and pressing the r key. A summary of the inferred hierarchy can be obtained with the :meth:~graph_tool.inference.nested_blockmodel.NestedBlockState.print_summary method, which shows the number of nodes and groups in all levels: