inference: implement assortative SBMs

src/graph/inference/Makefile.am

@@ -38,6 +38,9 @@ libgraph_tool_inference_la_SOURCES = \
     partition_modes/graph_partition_mode_clustering.cc \
     partition_modes/graph_partition_mode_clustering_mcmc.cc \
     partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc \
+    planted_partition/graph_planted_partition.cc \
+    planted_partition/graph_planted_partition_mcmc.cc \
+    planted_partition/graph_planted_partition_multiflip_mcmc.cc \
     overlap/graph_blockmodel_overlap.cc \
     overlap/graph_blockmodel_overlap_exhaustive.cc \
     overlap/graph_blockmodel_overlap_gibbs.cc \
@@ -110,6 +113,7 @@ nobase_libgraph_tool_inference_la_include_HEADERS = \
     partition_centroid/graph_partition_centroid_rmi.hh \
     partition_modes/graph_partition_mode.hh \
     partition_modes/graph_partition_mode_clustering.hh \
+    planted_partition/graph_planted_partition.hh \
     overlap/graph_blockmodel_overlap.hh \
     overlap/graph_blockmodel_overlap_mcmc_bundled.hh \
     overlap/graph_blockmodel_overlap_util.hh \

src/graph/inference/graph_inference.cc

@@ -134,6 +134,9 @@ extern void export_partition_mode();
 extern void export_mode_cluster_state();
 extern void export_mode_cluster_mcmc();
 extern void export_mode_cluster_multiflip_mcmc();
+extern void export_pp_state();
+extern void export_pp_mcmc();
+extern void export_pp_multiflip_mcmc();
 
 BOOST_PYTHON_MODULE(libgraph_tool_inference)
 {
@@ -204,6 +207,9 @@ BOOST_PYTHON_MODULE(libgraph_tool_inference)
     export_mode_cluster_state();
     export_mode_cluster_mcmc();
     export_mode_cluster_multiflip_mcmc();
+    export_pp_state();
+    export_pp_mcmc();
+    export_pp_multiflip_mcmc();
 
     def("vector_map", vector_map<int32_t>);
     def("vector_map64", vector_map<int64_t>);

src/graph/inference/planted_partition/graph_planted_partition.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2006-2020 Tiago de Paula Peixoto <tiago@skewed.de>
+//
+// This program is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public License
+// as published by the Free Software Foundation; either version 3
+// of the License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+#include "graph_tool.hh"
+#include "random.hh"
+
+#include <boost/python.hpp>
+
+#include "graph_planted_partition.hh"
+#include "../support/graph_state.hh"
+
+using namespace boost;
+using namespace graph_tool;
+
+GEN_DISPATCH(block_state, PPState, BLOCK_STATE_params)
+
+python::object make_pp_state(boost::python::object ostate)
+{
+    python::object state;
+    block_state::make_dispatch(ostate,
+                               [&](auto& s){state = python::object(s);});
+    return state;
+}
+
+void export_pp_state()
+{
+    using namespace boost::python;
+    def("make_pp_state", &make_pp_state);
+
+    block_state::dispatch
+        ([&](auto* s)
+         {
+             typedef typename std::remove_reference<decltype(*s)>::type state_t;
+             void (state_t::*move_vertex)(size_t, size_t) =
+                 &state_t::move_vertex;
+             double (state_t::*virtual_move)(size_t, size_t, size_t,
+                                             const pp_entropy_args_t& ea) =
+                 &state_t::virtual_move;
+
+             class_<state_t>
+                 c(name_demangle(typeid(state_t).name()).c_str(),
+                   no_init);
+             c.def("move_vertex", move_vertex)
+                 .def("virtual_move", virtual_move)
+                 .def("entropy", &state_t::entropy);
+         });
+
+    class_<pp_entropy_args_t>("pp_entropy_args")
+        .def_readwrite("uniform", &pp_entropy_args_t::uniform)
+        .def_readwrite("degree_dl_kind", &pp_entropy_args_t::degree_dl_kind);
+}

src/graph/inference/planted_partition/graph_planted_partition_mcmc.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2006-2020 Tiago de Paula Peixoto <tiago@skewed.de>
+//
+// This program is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public License
+// as published by the Free Software Foundation; either version 3
+// of the License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+#include "graph_tool.hh"
+#include "random.hh"
+
+#include <boost/python.hpp>
+
+#include "graph_planted_partition.hh"
+#include "../blockmodel/graph_blockmodel_mcmc.hh"
+#include "../loops/mcmc_loop.hh"
+
+using namespace boost;
+using namespace graph_tool;
+
+GEN_DISPATCH(block_state, PPState, BLOCK_STATE_params)
+
+template <class State>
+GEN_DISPATCH(mcmc_block_state, MCMC<State>::template MCMCBlockState,
+             MCMC_BLOCK_STATE_params(State))
+
+python::object pp_mcmc_sweep(python::object omcmc_state,
+                             python::object oblock_state,
+                             rng_t& rng)
+{
+    python::object ret;
+    auto dispatch = [&](auto& block_state)
+    {
+        typedef typename std::remove_reference<decltype(block_state)>::type
+            state_t;
+
+        mcmc_block_state<state_t>::make_dispatch
+           (omcmc_state,
+            [&](auto& s)
+            {
+                auto ret_ = mcmc_sweep(s, rng);
+                ret = tuple_apply([&](auto&... args){ return python::make_tuple(args...); }, ret_);
+            });
+    };
+    block_state::dispatch(oblock_state, dispatch);
+    return ret;
+}
+
+void export_pp_mcmc()
+{
+    using namespace boost::python;
+    def("pp_mcmc_sweep", &pp_mcmc_sweep);
+}

src/graph/inference/planted_partition/graph_planted_partition_multiflip_mcmc.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2006-2020 Tiago de Paula Peixoto <tiago@skewed.de>
+//
+// This program is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public License
+// as published by the Free Software Foundation; either version 3
+// of the License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+#include "graph_tool.hh"
+#include "random.hh"
+
+#include <boost/python.hpp>
+
+#include "graph_planted_partition.hh"
+#include "../blockmodel/graph_blockmodel_multiflip_mcmc.hh"
+#include "../loops/mcmc_loop.hh"
+
+using namespace boost;
+using namespace graph_tool;
+
+GEN_DISPATCH(block_state, PPState, BLOCK_STATE_params)
+
+template <class State>
+GEN_DISPATCH(mcmc_block_state, MCMC<State>::template MCMCBlockState,
+             MCMC_BLOCK_STATE_params(State))
+
+python::object pp_multiflip_mcmc_sweep(python::object omcmc_state,
+                                       python::object oblock_state,
+                                       rng_t& rng)
+{
+    python::object ret;
+    auto dispatch = [&](auto& block_state)
+    {
+        typedef typename std::remove_reference<decltype(block_state)>::type
+            state_t;
+
+        mcmc_block_state<state_t>::make_dispatch
+           (omcmc_state,
+            [&](auto& s)
+            {
+                auto ret_ = mcmc_sweep(s, rng);
+                ret = tuple_apply([&](auto&... args){ return python::make_tuple(args...); }, ret_);
+            });
+    };
+    block_state::dispatch(oblock_state, dispatch);
+    return ret;
+}
+
+void export_pp_multiflip_mcmc()
+{
+    using namespace boost::python;
+    def("pp_multiflip_mcmc_sweep", &pp_multiflip_mcmc_sweep);
+}

src/graph_tool/Makefile.am

@@ -77,6 +77,7 @@ graph_tool_inference_PYTHON = \
     inference/modularity.py \
     inference/partition_centroid.py \
     inference/partition_modes.py \
+    inference/planted_partition.py \
     inference/latent_multigraph.py \
     inference/util.py
 graph_tool_inferencedir = $(MOD_DIR)/inference

src/graph_tool/inference/__init__.py

@@ -183,6 +183,7 @@ __all__ = ["minimize_blockmodel_dl",
            "OverlapBlockState",
            "LayeredBlockState",
            "NestedBlockState",
+           "PPBlockState",
            "PartitionCentroidState",
            "PartitionModeState",
            "ModeClusterState",
@@ -252,3 +253,4 @@ from . modularity import *
 from . latent_multigraph import *
 from . partition_centroid import *
 from . partition_modes import *
+from . planted_partition import *