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Commit d25f8d92 authored by Tiago Peixoto's avatar Tiago Peixoto
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inference: Implement code for uncertain networks

parent 2d5051a9
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src/graph/inference/Makefile.am
View file @ d25f8d92
......@@ -54,6 +54,10 @@ libgraph_tool_inference_la_SOURCES = \
layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc \
layers/graph_blockmodel_layers_overlap_multiflip_mcmc.cc \
layers/graph_blockmodel_layers_overlap_vacate.cc \
uncertain/graph_blockmodel_measured.cc \
uncertain/graph_blockmodel_measured_mcmc.cc \
uncertain/graph_blockmodel_uncertain.cc \
uncertain/graph_blockmodel_uncertain_mcmc.cc \
support/cache.cc \
support/int_part.cc \
support/spence.cc \
......@@ -76,22 +80,25 @@ libgraph_tool_inference_la_include_HEADERS = \
blockmodel/graph_blockmodel_partition.hh \
blockmodel/graph_blockmodel_util.hh \
blockmodel/graph_blockmodel_weights.hh \
graph_modularity.hh \
overlap/graph_blockmodel_overlap.hh \
overlap/graph_blockmodel_overlap_mcmc_bundled.hh \
overlap/graph_blockmodel_overlap_util.hh \
overlap/graph_blockmodel_overlap_vacate.hh \
overlap/graph_blockmodel_overlap_partition.hh \
layers/graph_blockmodel_layers.hh \
layers/graph_blockmodel_layers_util.hh \
uncertain/graph_blockmodel_measured.hh \
uncertain/graph_blockmodel_uncertain.hh \
uncertain/graph_blockmodel_uncertain_mcmc.hh \
loops/bundled_vacate_loop.hh \
loops/exhaustive_loop.hh \
loops/gibbs_loop.hh \
loops/mcmc_loop.hh \
loops/merge_loop.hh \
overlap/graph_blockmodel_overlap.hh \
overlap/graph_blockmodel_overlap_mcmc_bundled.hh \
overlap/graph_blockmodel_overlap_util.hh \
overlap/graph_blockmodel_overlap_vacate.hh \
overlap/graph_blockmodel_overlap_partition.hh \
support/cache.hh \
support/graph_neighbor_sampler.hh \
support/graph_state.hh \
support/int_part.hh \
support/parallel_rng.hh \
support/util.hh
support/util.hh \
graph_modularity.hh
src/graph/inference/blockmodel/graph_blockmodel.hh
View file @ d25f8d92
......@@ -729,7 +729,7 @@ public:
void remove_vertex(size_t v, size_t r)
{
remove_vertex(v, r, [](auto&) { return false; });
remove_vertex(v, r, [](auto&) { return false; });
}
void remove_vertex(size_t v)
......@@ -896,6 +896,164 @@ public:
add_vertices(vs, rs);
}
template <bool Add, bool Deplete=true>
void modify_edge(size_t u, size_t v, GraphInterface::edge_t& e,
const std::vector<double>& rec)
{
size_t r = _b[u];
size_t s = _b[v];
if (is_partition_stats_enabled())
{
get_partition_stats(u).remove_vertex(u, r, _deg_corr, _g,
_vweight, _eweight,
_degs);
if (u != v)
get_partition_stats(v).remove_vertex(v, s, _deg_corr, _g,
_vweight, _eweight,
_degs);
}
auto me = _emat.get_me(r, s);
if (Add)
{
if (me == _emat.get_null_edge())
{
me = boost::add_edge(r, s, _bg).first;
_emat.put_me(r, s, me);
_c_mrs[me] = 0;
for (size_t i = 0; i < _rec_types.size(); ++i)
{
_c_brec[i][me] = 0;
_c_bdrec[i][me] = 0;
}
}
if (_coupled_state == nullptr)
_mrs[me]++;
_mrp[r]++;
_mrm[s]++;
}
else
{
assert(me != _emat.get_null_edge());
if (_coupled_state == nullptr)
_mrs[me]--;
_mrp[r]--;
_mrm[s]--;
}
// constexpr auto one = (Add) ? 1 : -1;
// for (size_t i = 0; i < _rec_types.size(); ++i)
// {
// switch (_rec_types[i])
// {
// case weight_type::REAL_NORMAL: // signed weights
// _bdrec[i][me] += one * std::pow(rec[i], 2);
// throw GraphException("Lrecdx, etc...");
// [[gnu::fallthrough]];
// default:
// _brec[i][me] += one * rec[i];
// }
// }
modify_edge<Add, Deplete>(u, v, e, _is_weighted);
if (is_partition_stats_enabled())
{
get_partition_stats(u).add_vertex(u, r, _deg_corr, _g,
_vweight, _eweight,
_degs);
if (u != v)
get_partition_stats(v).add_vertex(v, s, _deg_corr, _g,
_vweight, _eweight,
_degs);
get_partition_stats(u).change_E(Add ? 1 : -1); // FIXME: wrong for multiple partition stats
}
if (_coupled_state != nullptr)
{
if (Add)
_coupled_state->add_edge(r, s, me, rec);
else
_coupled_state->remove_edge(r, s, me, rec);
}
}
template <bool Add, bool Deplete>
void modify_edge(size_t u, size_t v, GraphInterface::edge_t& e,
std::false_type)
{
if (Add)
{
e = boost::add_edge(u, v, _g).first;
}
else
{
if (Deplete)
{
boost::remove_edge(e, _g);
e = GraphInterface::edge_t();
}
}
}
template <bool Add, bool Deplete>
void modify_edge(size_t u, size_t v, GraphInterface::edge_t& e,
std::true_type)
{
if (Add)
{
if (e == GraphInterface::edge_t())
{
e = boost::add_edge(u, v, _g).first;
auto c_eweight = _eweight.get_checked();
c_eweight[e] = 1;
}
else
{
_eweight[e]++;
}
if (_deg_corr)
{
get<1>(_degs[u].front())++;
if (graph_tool::is_directed(_g))
get<0>(_degs[v].front())++;
else
get<1>(_degs[v].front())++;
}
}
else
{
_eweight[e]--;
if (_eweight[e] == 0 && Deplete)
{
boost::remove_edge(e, _g);
e = GraphInterface::edge_t();
}
if (_deg_corr)
{
get<1>(_degs[u].front())--;
if (graph_tool::is_directed(_g))
get<0>(_degs[v].front())--;
else
get<1>(_degs[v].front())--;
}
}
}
void add_edge(size_t u, size_t v, GraphInterface::edge_t& e,
const std::vector<double>& rec)
{
modify_edge<true, false>(u, v, e, rec);
}
void remove_edge(size_t u, size_t v, GraphInterface::edge_t& e,
const std::vector<double>& rec)
{
modify_edge<false, false>(u, v, e, rec);
}
bool allow_move(size_t r, size_t nr, bool allow_empty = true)
{
if (allow_empty)
......@@ -1073,7 +1231,7 @@ public:
if (t == u)
{
t = v;
if (!is_directed_::apply<g_t>::type::value)
if (!graph_tool::is_directed(_g))
{
assert(w % 2 == 0);
w /= 2;
......@@ -1112,7 +1270,7 @@ public:
}
}
if (is_directed_::apply<g_t>::type::value)
if (graph_tool::is_directed(_g))
{
ns_u.clear();
ns_v.clear();
......@@ -1274,7 +1432,7 @@ public:
size_t kout = out_degreeS()(v, _g, _eweight);
size_t kin = kout;
if (is_directed_::apply<g_t>::type::value)
if (graph_tool::is_directed(_g))
kin = in_degreeS()(v, _g, _eweight);
int dwr = _vweight[v];
......@@ -1340,7 +1498,7 @@ public:
else
deltap[s] += _eweight[e];
}
if (!is_directed_::apply<g_t>::type::value)
if (!graph_tool::is_directed(_g))
deltal /= 2;
vector<int> deltam(num_vertices(_bg), 0);
......@@ -1376,7 +1534,7 @@ public:
int ers = (r != null_group) ? get_beprop(r, s, _mrs, _emat) : 0;
int enrs = (nr != null_group) ? get_beprop(nr, s, _mrs, _emat) : 0;
if (!is_directed_::apply<g_t>::type::value)
if (!graph_tool::is_directed(_g))
{
if (s != nr && s != r)
{
......@@ -1807,7 +1965,6 @@ public:
dS_dl += _coupled_state->recs_dS(r, nr, recs_entries, _dBdx, dL);
}
}
return dS + ea.beta_dl * dS_dl;
}
......@@ -2034,7 +2191,7 @@ public:
if (c > 0)
{
size_t B = _candidate_blocks.size() - 1;
if (is_directed_::apply<g_t>::type::value)
if (graph_tool::is_directed(_g))
p_rand = c * B / double(_mrp[t] + _mrm[t] + c * B);
else
p_rand = c * B / double(_mrp[t] + c * B);
......@@ -2446,16 +2603,16 @@ public:
return S;
}
double get_parallel_entropy()
double get_parallel_entropy(auto&& vs, auto&& skip)
{
double S = 0;
for (auto v : vertices_range(_g))
for (auto v : vs)
{
gt_hash_map<decltype(v), size_t> us;
for (auto e : out_edges_range(v, _g))
{
auto u = target(e, _g);
if (u < v && !is_directed_::apply<g_t>::type::value)
if (skip(v, u))
continue;
us[u] += _eweight[e];
}
......@@ -2466,7 +2623,7 @@ public:
auto& m = uc.second;
if (m > 1)
{
if (u == v && !is_directed_::apply<g_t>::type::value)
if (u == v && !graph_tool::is_directed(_g))
{
assert(m % 2 == 0);
S += lgamma_fast(m/2 + 1) + m * log(2) / 2;
......@@ -2481,6 +2638,219 @@ public:
return S;
}
double get_parallel_entropy()
{
return get_parallel_entropy(vertices_range(_g),
[](auto u, auto v)
{ return (u < v &&
!is_directed_::apply<g_t>::type::value);
});
}
template <bool Add>
double edge_entropy_term(size_t u, size_t v, entropy_args_t ea)
{
double S = 0, S_dl = 0;
size_t r = _b[u];
size_t s = _b[v];
if (is_partition_stats_enabled() && ea.degree_dl && _deg_corr)
{
if (r != s || u == v)
{
std::array<std::pair<size_t, size_t>, 2> degs;
degs_op(u, _vweight, _eweight, _degs, _g,
[&] (size_t kin, size_t kout, auto)
{
degs[0] = {kin, kout};
if (u != v)
{
if (Add)
degs[1] = {kin, kout + 1};
else
degs[1] = {kin, kout - 1};
}
else
{
if (!graph_tool::is_directed(this->_g))
{
if (Add)
degs[1] = {kin, kout + 2};
else
degs[1] = {kin, kout - 2};
}
else
{
if (Add)
degs[1] = {kin + 1, kout + 1};
else
degs[1] = {kin - 1, kout - 1};
}
}
});
S_dl += get_partition_stats(u).get_deg_dl(ea.degree_dl_kind,
std::array<size_t,1>({r}),
degs);
if (u != v) // r != s
{
std::array<std::pair<size_t, size_t>, 2> degs;
degs_op(v, _vweight, _eweight, _degs, _g,
[&] (size_t kin, size_t kout, auto)
{
degs[0] = {kin, kout};
if (!graph_tool::is_directed(this->_g))
{
if (Add)
degs[1] = {kin, kout + 1};
else
degs[1] = {kin, kout - 1};
}
else
{
if (Add)
degs[1] = {kin + 1, kout};
else
degs[1] = {kin - 1, kout};
}
});
S_dl += get_partition_stats(v).get_deg_dl(ea.degree_dl_kind,
std::array<size_t,1>({s}),
degs);
}
}
else // r == s && u != v
{
std::array<std::pair<size_t, size_t>, 4> degs;
degs_op(u, _vweight, _eweight, _degs, _g,
[&] (size_t kin, size_t kout, auto)
{
degs[0] = {kin, kout};
if (Add)
degs[1] = {kin, kout + 1};
else
degs[1] = {kin, kout - 1};
});
degs_op(v, _vweight, _eweight, _degs, _g,
[&] (size_t kin, size_t kout, auto)
{
degs[2] = {kin, kout};
if (!graph_tool::is_directed(this->_g))
{
if (Add)
degs[3] = {kin, kout + 1};
else
degs[3] = {kin, kout - 1};
}
else
{
if (Add)
degs[3] = {kin + 1, kout};
else
degs[3] = {kin - 1, kout};
}
for (size_t i = 0; i < 2; ++i)
{
if (degs[2] == degs[i])
degs[2] = {0, numeric_limits<size_t>::max()};
if (degs[3] == degs[i])
degs[3] = {0, numeric_limits<size_t>::max()};
}
});
S_dl += get_partition_stats(u).get_deg_dl(ea.degree_dl_kind,
std::array<size_t,1>({r}),
degs);
}
}
auto& me = _emat.get_me(r, s);
size_t mrs = 0;
if (me != _emat.get_null_edge())
mrs = _mrs[me];
if (ea.adjacency)
{
if (ea.dense)
{
S += eterm_dense(r, s, mrs, _wr[r], _wr[s], ea.multigraph, _bg);
}
else
{
if (ea.exact)
{
S += eterm_exact(r, s, mrs, _bg);
S += vterm_exact(_mrp[r], _mrm[r], _wr[r], _deg_corr, _bg);
if (s != r)
S += vterm_exact(_mrp[s], _mrm[s], _wr[s], _deg_corr, _bg);
}
else
{
S += eterm(r, s, mrs, _bg);
S += vterm(_mrp[r], _mrm[r], _wr[r], _deg_corr, _bg);
if (s != r)
S += vterm(_mrp[s], _mrm[s], _wr[s], _deg_corr, _bg);
}
if (ea.multigraph)
{
S += get_parallel_entropy(std::array<size_t, 1>({u}),
[&](auto, auto w){ return w != v; });
}
if (_deg_corr)
{
S += get_deg_entropy(u, _degs);
if (u != v)
S += get_deg_entropy(v, _degs);
}
}
}
if (_coupled_state != nullptr)
{
S_dl += _coupled_state->edge_entropy_term(r, s, _coupled_entropy_args);
}
else
{
if (ea.edges_dl && is_partition_stats_enabled())
{
size_t actual_B = 0;
for (auto& psi : _partition_stats)
actual_B += psi.get_actual_B();
auto& ps = get_partition_stats(u);
S_dl += ps.get_edges_dl(actual_B, _g);
}
}
return S + S_dl * ea.beta_dl;
}
double edge_entropy_term(size_t u, size_t v, entropy_args_t ea)
{
return edge_entropy_term<true>(u, v, ea);
}
template <bool Add>
double modify_edge_dS(size_t u, size_t v, GraphInterface::edge_t& e,
const std::vector<double>& recs, entropy_args_t ea)
{
double dS = 0;
dS -= edge_entropy_term<Add>(u, v, ea);
modify_edge<Add>(u, v, e, recs);
dS += edge_entropy_term<!Add>(u, v, ea);
modify_edge<!Add>(u, v, e, recs);
return dS;
}
void enable_partition_stats()
{
if (_partition_stats.empty())
......
src/graph/inference/blockmodel/graph_blockmodel_elist.hh
View file @ d25f8d92
......@@ -54,15 +54,15 @@ class EGroups
{
public:
template <class Vprop, class Eprop, class BGraph>
void init(Vprop b, Eprop eweight, Graph& g, BGraph& bg)
void init(Vprop b, Eprop& eweight, Graph& g, BGraph& bg)
{
_egroups.clear();
_egroups.resize(num_vertices(bg));
for (auto e : edges_range(g))
{
_epos[e] = make_pair(numeric_limits<size_t>::max(),
numeric_limits<size_t>::max());
_epos[e] = {numeric_limits<size_t>::max(),
numeric_limits<size_t>::max()};
insert_edge(e, eweight[e], b, g);
}
}
......@@ -77,12 +77,31 @@ public:
return _egroups.empty();
}
template <class Vprop>
bool check(Vprop b, Graph& g)
template <class Vprop, class Eprop>
bool check(Vprop b, Eprop& eweight, Graph& g) const
{
for (auto e : edges_range(g))
{
if (eweight[e] == 0)
continue;
auto r = b[get_source(e, g)];
auto s = b[get_target(e, g)];
const auto& pos = _epos[e];
if (!(pos.first < _egroups[r].size() &&
is_valid(pos.first, _egroups[r]) &&
get<0>(_egroups[r][pos.first]) == e &&
pos.second < _egroups[s].size() &&
is_valid(pos.second, _egroups[s]) &&
get<0>(_egroups[s][pos.second]) == e))
{
assert(false);
return false;
}
}
for (size_t r = 0; r < _egroups.size(); ++r)
{
auto& edges = _egroups[r];
const auto& edges = _egroups[r];
for (size_t i = 0; i < edges.size(); ++i)
{
const auto& e = edges[i];
......@@ -100,13 +119,13 @@ public:
}
template <class Edge>