Initial implementation of partition modes

src/graph/inference/Makefile.am

@@ -31,6 +31,10 @@ libgraph_tool_inference_la_SOURCES = \
     partition_centroid/graph_partition_centroid.cc \
     partition_centroid/graph_partition_centroid_mcmc.cc \
     partition_centroid/graph_partition_centroid_multiflip_mcmc.cc \
+    partition_modes/graph_partition_mode.cc \
+    partition_modes/graph_partition_mode_clustering.cc \
+    partition_modes/graph_partition_mode_clustering_mcmc.cc \
+    partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc \
     overlap/graph_blockmodel_overlap.cc \
     overlap/graph_blockmodel_overlap_exhaustive.cc \
     overlap/graph_blockmodel_overlap_gibbs.cc \
@@ -100,6 +104,8 @@ libgraph_tool_inference_la_include_HEADERS = \
     blockmodel/graph_blockmodel_util.hh \
     blockmodel/graph_blockmodel_weights.hh \
     partition_centroid/graph_partition_centroid.hh \
+    partition_modes/graph_partition_mode.hh \
+    partition_modes/graph_partition_mode_clustering.hh \
     overlap/graph_blockmodel_overlap.hh \
     overlap/graph_blockmodel_overlap_mcmc_bundled.hh \
     overlap/graph_blockmodel_overlap_util.hh \

src/graph/inference/blockmodel/graph_blockmodel.hh

@@ -2584,6 +2584,12 @@ public:
             assert(size_t(_wr[r]) == wr[r]);
     }
 
+    template <class V>
+    void push_state(V&) {}
+    void pop_state() {}
+    void store_next_state(size_t) {}
+    void clear_next_state() {}
+
 //private:
     typedef typename
         std::conditional<is_directed_::apply<g_t>::type::value,

src/graph/inference/blockmodel/graph_blockmodel_multiflip_mcmc.hh

@@ -130,6 +130,7 @@ struct MCMC
             auto& back = _bstack.back();
             for (auto v : vs)
                 back.emplace_back(v, _state._b[v]);
+            _state.push_state(vs);
             _push_b_dispatch(std::forward<Vs>(vvs)...);
         }
 
@@ -150,6 +151,7 @@ struct MCMC
                 move_vertex(v, s);
             }
             _bstack.pop_back();
+            _state.pop_state();
         }
 
         std::vector<size_t> _rlist;
@@ -214,10 +216,10 @@ struct MCMC
         void move_vertex(size_t v, size_t r)
         {
             size_t s = _state._b[v];
+            _state.move_vertex(v, r);
             if (s == r)
                 return;
             remove_element(_groups[s], _vpos, v);
-            _state.move_vertex(v, r);
             add_element(_groups[r], _vpos, v);
             _nmoves++;
         }
@@ -281,11 +283,11 @@ struct MCMC
         stage_split_random(std::vector<size_t>& vs, size_t r, size_t s, RNG& rng)
         {
             std::array<size_t, 2> rt = {null_group, null_group};
-            std::array<double, 2> ps;
             double dS = 0;
 
             std::uniform_real_distribution<> unit(0, 1);
-            double p = unit(rng);
+            double p0 = unit(rng);
+            std::bernoulli_distribution sample(p0);
 
             std::shuffle(vs.begin(), vs.end(), rng);
             for (auto v : vs)
@@ -311,12 +313,6 @@ struct MCMC
                     continue;
                 }
 
-                ps[0] = log(p);
-                ps[1] = log1p(-p);
-
-                double Z = log_sum(ps[0], ps[1]);
-                double p0 = ps[0] - Z;
-                std::bernoulli_distribution sample(exp(p0));
                 if (sample(rng))
                 {
                     dS += _state.virtual_move(v, _state._b[v], rt[0],
@@ -417,8 +413,7 @@ struct MCMC
         }
 
         template <class RNG, bool forward=true>
-        std::tuple<size_t, double, double> split(size_t r, size_t s,
-                                                 RNG& rng)
+        std::tuple<size_t, double, double> split(size_t r, size_t s, RNG& rng)
         {
             auto vs = _groups[r];
 
@@ -602,6 +597,7 @@ struct MCMC
             _dS = _a = 0;
             _vs.clear();
             _nmoves = 0;
+            _state.clear_next_state();
 
             move_t move = _move_sampler.sample(rng);
 
@@ -668,7 +664,10 @@ struct MCMC
                              << " " << -_dS + pb - pf << endl;
 
                     for (auto v : _vs)
+                    {
                         _bnext[v] = _state._b[v];
+                        _state.store_next_state(v);
+                    }
                     pop_b();
 
                     _state._egroups_update = true;
@@ -699,7 +698,10 @@ struct MCMC
                     _dS = merge(r, s);
 
                     for (auto v : _vs)
+                    {
                         _bnext[v] = _state._b[v];
+                        _state.store_next_state(v);
+                    }
                     pop_b();
 
                     _state._egroups_update = true;
@@ -748,6 +750,7 @@ struct MCMC
                             auto v = get<0>(vb);
                             _vs.push_back(v);
                             _bnext[v] = _state._b[v];
+                            _state.store_next_state(v);
                         }
 
                     while (!_bstack.empty())

src/graph/inference/graph_inference.cc

@@ -127,6 +127,10 @@ extern void export_pseudo_ising_mcmc_h();
 extern void export_vi_center_state();
 extern void export_vi_center_mcmc();
 extern void export_vi_multiflip_mcmc();
+extern void export_partition_mode();
+extern void export_mode_cluster_state();
+extern void export_mode_cluster_mcmc();
+extern void export_mode_cluster_multiflip_mcmc();
 
 BOOST_PYTHON_MODULE(libgraph_tool_inference)
 {
@@ -190,6 +194,10 @@ BOOST_PYTHON_MODULE(libgraph_tool_inference)
     export_vi_center_state();
     export_vi_center_mcmc();
     export_vi_multiflip_mcmc();
+    export_partition_mode();
+    export_mode_cluster_state();
+    export_mode_cluster_mcmc();
+    export_mode_cluster_multiflip_mcmc();
 
     def("vector_map", vector_map<int32_t>);
     def("vector_map64", vector_map<int64_t>);

src/graph/inference/overlap/graph_blockmodel_overlap.hh

@@ -1262,6 +1262,11 @@ public:
     void coupled_resize_vertex(size_t) { }
     void update_block_edge(const GraphInterface::edge_t&,
                            const std::vector<double>&) { }
+    template <class V>
+    void push_state(V&) {}
+    void pop_state() {}
+    void store_next_state(size_t) {}
+    void clear_next_state() {}
 
 //private:
     typedef typename

src/graph/inference/partition_centroid/graph_partition_centroid.hh

@@ -36,7 +36,7 @@ typedef multi_array_ref<int32_t,2> bs_t;
 typedef multi_array_ref<int32_t,1> b_t;
 
 #define BLOCK_STATE_params                                                     \
-    ((g, &, all_graph_views, 1))                                               \
+    ((g, &, always_directed_never_reversed, 1))                                \
     ((_abg, &, boost::any&, 0))                                                \
     ((bs,, bs_t, 0))                                                           \
     ((b,, b_t, 0))
@@ -283,6 +283,12 @@ public:
         return true;
     }
 
+    template <class V>
+    void push_state(V&) {}
+    void pop_state() {}
+    void store_next_state(size_t) {}
+    void clear_next_state() {}
+
 };
 
 } // graph_tool namespace

src/graph/inference/partition_modes/graph_partition_mode.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2006-2019 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 "numpy_bind.hh"
+
+#include <boost/python.hpp>
+
+#include "graph_partition_mode.hh"
+
+using namespace boost;
+using namespace graph_tool;
+
+void export_partition_mode()
+{
+    using namespace boost::python;
+
+    class_<PartitionModeState>
+        ("PartitionModeState", init<size_t>())
+        .def("add_partition",
+             +[](PartitionModeState& state, object ob, bool relabel)
+              {
+                  auto b = get_array<int32_t, 1>(ob);
+                  state.add_partition(b, relabel);
+              })
+        .def("remove_partition",
+             +[](PartitionModeState& state, size_t i)
+              {
+                  state.remove_partition(i);
+              })
+        .def("replace_partitions", &PartitionModeState::replace_partitions)
+        .def("get_marginal",
+             +[](PartitionModeState& state,
+                 GraphInterface& gi, boost::any obm)
+              {
+                  run_action<>()
+                      (gi, [&](auto& g, auto bm)
+                      {
+                          state.get_marginal(g, bm);
+                      }, vertex_scalar_vector_properties())(obm);
+              })
+        .def("get_partition",
+             +[](PartitionModeState& state, size_t i)
+              {
+                  auto b = state.get_partition(i);
+                  return wrap_multi_array_not_owned(b);
+              })
+        .def("get_partitions",
+             +[](PartitionModeState& state)
+              {
+                  python::dict obs;
+                  auto& bs = state.get_partitions();
+                  for (auto& kb : bs)
+                  {
+                      auto b = state.get_partition(kb.first);
+                      obs[kb.first] = wrap_multi_array_not_owned(b);
+                  }
+                  return obs;
+              })
+        .def("relabel", &PartitionModeState::relabel)
+        .def("entropy", &PartitionModeState::entropy)
+        .def("posterior_entropy", &PartitionModeState::posterior_entropy);
+}

src/graph/inference/partition_modes/graph_partition_mode_clustering.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2006-2019 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_partition_mode_clustering.hh"
+#include "../support/graph_state.hh"
+
+using namespace boost;
+using namespace graph_tool;
+
+GEN_DISPATCH(block_state, ModeClusterState, BLOCK_STATE_params)
+
+python::object make_mode_cluster_state(boost::python::object ostate)
+{
+    python::object state;
+    block_state::make_dispatch(ostate,
+                               [&](auto& s){state = python::object(s);});
+    return state;
+}
+
+void export_mode_cluster_state()
+{
+    using namespace boost::python;
+    def("make_mode_cluster_state", &make_mode_cluster_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) =
+                 &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)
+                 .def("posterior_entropy", &state_t::posterior_entropy)
+                 .def("relabel_modes", &state_t::relabel_modes)
+                 .def("replace_partitions", &state_t::replace_partitions)
+                 .def("get_mode",
+                      +[](state_t& state, size_t r)
+                       {
+                           return state.get_mode(r);
+                       });
+         });
+}

src/graph/inference/partition_modes/graph_partition_mode_clustering_mcmc.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2006-2019 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_partition_mode_clustering.hh"
+#include "../blockmodel/graph_blockmodel_mcmc.hh"
+#include "../loops/mcmc_loop.hh"
+
+using namespace boost;
+using namespace graph_tool;
+
+GEN_DISPATCH(block_state, ModeClusterState, BLOCK_STATE_params)
+
+template <class State>
+GEN_DISPATCH(mcmc_block_state, MCMC<State>::template MCMCBlockState,
+             MCMC_BLOCK_STATE_params(State))
+
+python::object mode_clustering_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_mode_cluster_mcmc()
+{
+    using namespace boost::python;
+    def("mode_clustering_mcmc_sweep", &mode_clustering_mcmc_sweep);
+}

src/graph/inference/partition_modes/graph_partition_mode_clustering_multiflip_mcmc.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2006-2019 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_partition_mode_clustering.hh"
+#include "../blockmodel/graph_blockmodel_multiflip_mcmc.hh"
+#include "../loops/mcmc_loop.hh"
+
+using namespace boost;
+using namespace graph_tool;
+
+GEN_DISPATCH(block_state, ModeClusterState, BLOCK_STATE_params)
+
+template <class State>
+GEN_DISPATCH(mcmc_block_state, MCMC<State>::template MCMCBlockState,
+             MCMC_BLOCK_STATE_params(State))
+
+python::object mode_clustering_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_mode_cluster_multiflip_mcmc()
+{
+    using namespace boost::python;
+    def("mode_clustering_multiflip_mcmc_sweep",
+        &mode_clustering_multiflip_mcmc_sweep);
+}

src/graph_tool/Makefile.am

@@ -76,6 +76,7 @@ graph_tool_inference_PYTHON = \
     inference/minimize.py \
     inference/modularity.py \
     inference/partition_centroid.py \
+    inference/partition_modes.py \
     inference/latent_multigraph.py \
     inference/util.py
 graph_tool_inferencedir = $(MOD_DIR)/inference

src/graph_tool/inference/__init__.py

@@ -157,6 +157,8 @@ __all__ = ["minimize_blockmodel_dl",
            "LayeredBlockState",
            "NestedBlockState",
            "VICenterState",
+           "PartitionModeState",
+           "ModeClusterState",
            "LatentMultigraphBlockState",
            "UncertainBlockState",
            "MeasuredBlockState",
@@ -203,3 +205,4 @@ from . util import *
 from . modularity import *
 from . latent_multigraph import *
 from . partition_centroid import *
+from . partition_modes import *

src/graph_tool/inference/partition_centroid.py

@@ -53,7 +53,7 @@ class VICenterState(object):
             b = np.zeros(bs.shape[1], dtype="int32")
         self.b = np.array(b, dtype="int32")
 
-        self.g = Graph(directed=False)
+        self.g = Graph()
         self.g.add_vertex(bs.shape[1])
         self.bg = self.g
         self._abg = self.bg._get_any()

src/graph_tool/inference/partition_modes.py

+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# graph_tool -- a general graph manipulation python module
+#
+# Copyright (C) 2006-2019 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/>.
+
+from __future__ import division, absolute_import, print_function
+import sys
+if sys.version_info < (3,):
+    range = xrange
+
+from .. import _degree, _prop, Graph, GraphView, _get_rng, Vector_size_t
+from . blockmodel import DictState, get_entropy_args, _bm_test
+
+from .. dl_import import dl_import
+dl_import("from . import libgraph_tool_inference as libinference")
+
+import numpy as np
+import math
+
+class PartitionModeState(object):
+    def __init__(self, bs, relabel=True, **kwargs):
+        self.bs = {}
+
+        if len(kwargs) > 0:
+            N = kwargs["N"]
+            self._base = kwargs["base"]
+        else:
+            N = len(bs[0])
+            self._base = libinference.PartitionModeState(N)
+            for b in bs:
+                self.add_partition(b, relabel)
+
+    def add_partition(self, b, relabel=True):
+        b = np.array(b, dtype="int32")
+        i = self._base.add_partition(b, relabel)
+        self.bs[i] = b
+
+    def remove_partition(self, i):
+        self._base.remove_partition(i)
+        if self.bs.has_key(i):
+            del self.bs[i]
+
+    def replace_partitions(self):
+        return self._base.replace_partitions()
+
+    def get_partition(self, i):
+        return self._base.get_partition(i)
+
+    def get_partitions(self):
+        return self._base.get_partitions()
+
+    def relabel(self):
+        return self._base.relabel()
+
+    def entropy(self):
+        return self._base.entropy()
+
+    def posterior_entropy(self):
+        return self._base.posterior_entropy()
+
+    def get_marginal(self, g):
+        bm = g.new_vp("vector<int>")
+        self._base.get_marginal(g._Graph__graph, bm._get_any())
+        return bm
+
+class ModeClusterState(object):
+    def __init__(self, bs, b=None, B=1, relabel=True):
+        self.bs = np.asarray(bs, dtype="int32")
+
+        if b is None:
+            self.b = np.random.randint(0, B, self.bs.shape[0], dtype="int32")
+        else:
+            self.b = np.asarray(b, dtype="int32")
+
+        self.relabel_init = relabel
+        self.g = Graph()
+        self.g.add_vertex(self.b.shape[0])
+        self.bg = self.g
+        self._abg = self.bg._get_any()
+        self._state = libinference.make_mode_cluster_state(self)
+
+        self._entropy_args = dict(adjacency=True, deg_entropy=True, dl=True,
+                                  partition_dl=True, degree_dl=True,
+                                  degree_dl_kind="distributed", edges_dl=True,
+                                  dense=False, multigraph=True, exact=True,
+                                  recs=True, recs_dl=True, beta_dl=1.,
+                                  Bfield=True)
+
+    def __copy__(self):
+        return self.copy()
+
+    def __deepcopy__(self, memo):
+        b = copy.deepcopy(self.b, memo)
+        bs = copy.deepcopy(self.bs, memo)
+        return self.copy(bs=bs, b=b)
+
+    def copy(self, bs=None, b=None):
+        r"""Copies the state. The parameters override the state properties, and
+         have the same meaning as in the constructor."""