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Tiago Peixoto
graph-tool
Commits
0f5c6894
Commit
0f5c6894
authored
May 03, 2016
by
Tiago Peixoto
Browse files
inference.blockmodel: implement "waiting times"
parent
20b48710
Changes
2
Hide whitespace changes
Inline
Side-by-side
src/graph/inference/graph_blockmodel.hh
View file @
0f5c6894
...
...
@@ -56,6 +56,9 @@ typedef mpl::vector2<simple_degs_t, degs_map_t> degs_tr;
((pclabel,, vmap_t, 0)) \
((merge_map,, vmap_t, 0)) \
((deg_corr,, bool, 0)) \
((use_waiting,, bool, 0)) \
((vtfield,, vprop_map_t<double>::type, 0)) \
((btfield,, vprop_map_t<double>::type, 0)) \
((ignore_degrees,, typename vprop_map_t<uint8_t>::type, 0))
GEN_STATE_BASE
(
BlockStateBase
,
BLOCK_STATE_params
)
...
...
@@ -795,6 +798,22 @@ public:
dS
+=
ps
.
get_delta_edges_dl
(
v
,
r
,
nr
,
_vweight
,
_g
);
}
if
(
_use_waiting
&&
(
r
!=
nr
)
&&
_ignore_degrees
[
v
]
>
0
)
{
double
dt
=
_vtfield
[
v
];
int
k
=
out_degreeS
()(
v
,
_g
,
_eweight
);
if
(
_mrp
[
r
]
>
0
)
dS
-=
_mrp
[
r
]
*
log
(
_btfield
[
r
])
-
lgamma_fast
(
_mrp
[
r
]);
if
(
_mrp
[
nr
]
>
0
)
dS
-=
_mrp
[
nr
]
*
log
(
_btfield
[
nr
])
-
lgamma_fast
(
_mrp
[
nr
]);
if
(
_mrp
[
r
]
>
k
)
dS
+=
(
_mrp
[
r
]
-
k
)
*
log
(
_btfield
[
r
]
-
dt
)
-
lgamma_fast
(
_mrp
[
r
]
-
k
);
if
(
_mrp
[
nr
]
+
k
>
0
)
dS
+=
(
_mrp
[
nr
]
+
k
)
*
log
(
_btfield
[
nr
]
+
dt
)
-
lgamma_fast
(
_mrp
[
nr
]
+
k
);
}
return
dS
;
}
...
...
@@ -1053,10 +1072,19 @@ public:
double
entropy
(
bool
dense
,
bool
multigraph
,
bool
deg_entropy
)
{
double
S
=
0
;
if
(
dense
)
return
dense_entropy
(
multigraph
);
S
=
dense_entropy
(
multigraph
);
else
return
sparse_entropy
(
multigraph
,
deg_entropy
);
S
=
sparse_entropy
(
multigraph
,
deg_entropy
);
if
(
_use_waiting
)
{
for
(
auto
r
:
vertices_range
(
_bg
))
if
(
_btfield
[
r
]
>
0
)
S
+=
_mrp
[
r
]
*
log
(
_btfield
[
r
])
-
lgamma_fast
(
_mrp
[
r
]);
}
return
S
;
}
double
get_partition_dl
()
...
...
src/graph_tool/inference/blockmodel.py
View file @
0f5c6894
...
...
@@ -49,17 +49,25 @@ def _bm_test():
global
__test__
return
__test__
def
get_block_graph
(
g
,
B
,
b
,
vcount
=
None
,
ecount
=
None
):
def
get_block_graph
(
g
,
B
,
b
,
vcount
=
None
,
ecount
=
None
,
edt
=
None
):
if
isinstance
(
ecount
,
libinference
.
unity_eprop_t
):
ecount
=
None
if
isinstance
(
vcount
,
libinference
.
unity_vprop_t
):
vcount
=
None
cg
,
br
,
vcount
,
ecount
=
condensation_graph
(
g
,
b
,
vweight
=
vcount
,
eweight
=
ecount
,
self_loops
=
True
)[:
4
]
cg
.
vp
[
"count"
]
=
vcount
cg
.
ep
[
"count"
]
=
ecount
aeprops
=
[]
if
edt
is
not
None
:
aeprops
.
append
(
edt
)
cg
,
br
,
vcount
,
ecount
,
av
,
ae
=
condensation_graph
(
g
,
b
,
vweight
=
vcount
,
eweight
=
ecount
,
aeprops
=
aeprops
,
self_loops
=
True
)
cg
.
vp
.
count
=
vcount
cg
.
ep
.
count
=
ecount
if
edt
is
not
None
:
cg
.
ep
.
dt
=
ae
[
0
]
del
ae
[
0
]
cg
=
Graph
(
cg
,
vorder
=
br
)
cg
.
add_vertex
(
B
-
cg
.
num_vertices
())
...
...
@@ -137,7 +145,7 @@ class BlockState(object):
if
b
is
None
:
# create a random partition into B blocks.
if
B
is
None
:
B
=
get_max_B
(
self
.
N
,
self
.
E
,
directed
=
g
.
is_directed
()
)
raise
ValueError
(
"either 'b' or 'B' must be specified"
)
B
=
min
(
B
,
self
.
g
.
num_vertices
())
ba
=
random
.
randint
(
0
,
B
,
self
.
g
.
num_vertices
())
ba
[:
B
]
=
arange
(
B
)
# avoid empty blocks
...
...
@@ -161,7 +169,8 @@ class BlockState(object):
(
self
.
b
.
fa
.
max
(),
B
))
# Construct block-graph
self
.
bg
=
get_block_graph
(
g
,
B
,
self
.
b
,
self
.
vweight
,
self
.
eweight
)
self
.
bg
=
get_block_graph
(
g
,
B
,
self
.
b
,
self
.
vweight
,
self
.
eweight
,
edt
=
kwargs
.
get
(
"edt"
,
None
))
self
.
bg
.
set_fast_edge_removal
()
self
.
mrs
=
self
.
bg
.
ep
[
"count"
]
...
...
@@ -223,6 +232,19 @@ class BlockState(object):
self
.
block_list
=
Vector_size_t
()
self
.
block_list
.
extend
(
arange
(
self
.
B
,
dtype
=
"int"
))
self
.
edt
=
extract_arg
(
kwargs
,
"edt"
,
None
)
self
.
use_waiting
=
self
.
edt
is
not
None
if
self
.
use_waiting
:
self
.
vtfield
=
self
.
g
.
degree_property_map
(
"out"
,
self
.
edt
)
self
.
btfield
=
self
.
bg
.
degree_property_map
(
"out"
,
self
.
bg
.
ep
.
dt
)
tokens
=
self
.
ignore_degrees
.
fa
==
0
token_groups
=
bincount
(
self
.
b
.
fa
[
tokens
])
>
0
token_groups
=
token_groups
.
resize
(
self
.
bg
.
num_vertices
())
self
.
btfield
.
a
[
token_groups
]
=
0
else
:
self
.
vtfield
=
self
.
g
.
new_vp
(
"double"
)
self
.
btfield
=
self
.
bg
.
new_vp
(
"double"
)
self
.
_abg
=
self
.
bg
.
_get_any
()
self
.
_state
=
libinference
.
make_block_state
(
self
,
_get_rng
())
...
...
@@ -262,6 +284,7 @@ class BlockState(object):
ignore_degrees
=
kwargs
.
pop
(
"ignore_degrees"
,
self
.
ignore_degrees
),
degs
=
self
.
degs
.
copy
(),
merge_map
=
kwargs
.
get
(
"merge_map"
,
self
.
merge_map
.
copy
()),
edt
=
self
.
edt
,
**
dmask
(
kwargs
,
[
"ignore_degrees"
,
"merge_map"
]))
else
:
state
=
OverlapBlockState
(
self
.
g
if
g
is
None
else
g
,
...
...
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