Multi-sample CARNIVAL#
import numpy as np
import pandas as pd
import corneto as cn
cn.info()
|
|
Toy example#
from corneto.graph import Graph
# A toy PKN signalling network
G = Graph.from_tuples(
[
("rec1", 1, "a"),
("rec1", -1, "b"),
("rec1", 1, "f"),
("rec1", -1, "c"),
("rec2", 1, "b"),
("rec2", 1, "tf2"),
("b", 1, "g"),
("g", -1, "d"),
("rec2", -1, "d"),
("a", 1, "c"),
("a", -1, "d"),
("c", 1, "d"),
("c", -1, "e"),
("c", 1, "tf3"),
("e", 1, "a"),
("d", -1, "c"),
("e", 1, "tf1"),
("a", -1, "tf1"),
("d", 1, "tf2"),
("c", -1, "tf2"),
("tf1", 1, "tf2"),
("tf1", -1, "rec2"),
("tf2", 1, "rec1"),
("tf1", 1, "f"),
]
)
G.plot()
from corneto.methods.future.carnival import CarnivalFlow
samples = {
"c1": {
"rec2": {"value": 1, "mapping": "vertex", "role": "input"},
"tf1": {"value": -2, "mapping": "vertex", "role": "output"},
"tf2": {"value": 1, "mapping": "vertex", "role": "output"},
},
"c2": {
"rec1": {"value": 1, "mapping": "vertex", "role": "input"},
"rec2": {"value": -1, "mapping": "vertex", "role": "input"},
"tf1": {"value": 1, "mapping": "vertex", "role": "output"},
"tf2": {"value": -1, "mapping": "vertex", "role": "output"},
"tf3": {"value": 3, "mapping": "vertex", "role": "output"},
},
}
data = cn.Data.from_cdict(samples)
data
Data(n_samples=2, n_feats=[3 5])
Multi-sample CARNIVAL#
c = CarnivalFlow(lambda_reg=1e-3)
P = c.build(G, data)
# Solve the problem using the HIGHs solver included in Scipy
P.solve(verbosity=0, solver="scipy");
Unreachable vertices for sample: 1
Unreachable vertices for sample: 0
# The preprocessed G graph (flow graph)
c.processed_graph.plot()
# Show the sub-graph where the signal propagates for all samples (union graph)
c.processed_graph.edge_subgraph(np.flatnonzero(P.expr.flow.value)).plot()
# Extract the values from the problem
pd.DataFrame(
P.expr.edge_value.value,
index=c.processed_graph.E,
columns=["condition_1", "condition_2"],
).astype(int)
| condition_1 | condition_2 | ||
|---|---|---|---|
| (rec1) | (a) | 1 | 1 |
| (b) | 0 | 0 | |
| (c) | 0 | 0 | |
| (rec2) | (b) | 0 | 0 |
| (tf2) | 1 | -1 | |
| (b) | (g) | 0 | 0 |
| (g) | (d) | 0 | 0 |
| (rec2) | (d) | 0 | 0 |
| (a) | (c) | 0 | 1 |
| (d) | 0 | 0 | |
| (c) | (d) | 0 | 0 |
| (e) | 0 | 0 | |
| (tf3) | 0 | 1 | |
| (e) | (a) | 0 | 0 |
| (d) | (c) | 0 | 0 |
| (e) | (tf1) | 0 | 0 |
| (a) | (tf1) | -1 | 0 |
| (d) | (tf2) | 0 | 0 |
| (c) | (tf2) | 0 | 0 |
| (tf1) | (tf2) | 0 | 0 |
| (rec2) | 0 | 0 | |
| (tf2) | (rec1) | 1 | 0 |
| () | 0 | 0 | |
| (tf3) | () | 0 | 0 |
| (tf1) | () | 0 | 0 |
| () | (rec2) | 1 | -1 |
| (rec1) | 0 | 1 |
# Solution for sample 1
c.processed_graph.edge_subgraph(np.flatnonzero(P.expr.edge_has_signal.value[:, 0] > 0.5)).plot()
# Solution for sample 2
c.processed_graph.edge_subgraph(np.flatnonzero(P.expr.edge_has_signal.value[:, 1] > 0.5)).plot()
for o in P.objectives:
print(o.value)
0.0
1.0
8.0
Plotting solutions on top of the PKN#
c.processed_graph.plot_values(
vertex_values=P.expr.vertex_value.value[:, 0],
edge_values=P.expr.edge_value.value[:, 0],
)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:76, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
75 kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
---> 76 proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
77 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:96, in _run_input_lines(cmd, input_lines, kwargs)
95 def _run_input_lines(cmd, input_lines, *, kwargs):
---> 96 popen = subprocess.Popen(cmd, stdin=subprocess.PIPE, **kwargs)
98 stdin_write = popen.stdin.write
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1039, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1036 self.stderr = io.TextIOWrapper(self.stderr,
1037 encoding=encoding, errors=errors)
-> 1039 self._execute_child(args, executable, preexec_fn, close_fds,
1040 pass_fds, cwd, env,
1041 startupinfo, creationflags, shell,
1042 p2cread, p2cwrite,
1043 c2pread, c2pwrite,
1044 errread, errwrite,
1045 restore_signals,
1046 gid, gids, uid, umask,
1047 start_new_session, process_group)
1048 except:
1049 # Cleanup if the child failed starting.
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1991, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1990 if err_filename is not None:
-> 1991 raise child_exception_type(errno_num, err_msg, err_filename)
1992 else:
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('dot')
The above exception was the direct cause of the following exception:
ExecutableNotFound Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/IPython/core/formatters.py:1036, in MimeBundleFormatter.__call__(self, obj, include, exclude)
1033 method = get_real_method(obj, self.print_method)
1035 if method is not None:
-> 1036 return method(include=include, exclude=exclude)
1037 return None
1038 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:98, in JupyterIntegration._repr_mimebundle_(self, include, exclude, **_)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:112, in JupyterIntegration._repr_image_svg_xml(self)
110 def _repr_image_svg_xml(self) -> str:
111 """Return the rendered graph as SVG string."""
--> 112 return self.pipe(format='svg', encoding=SVG_ENCODING)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:104, in Pipe.pipe(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
55 def pipe(self,
56 format: typing.Optional[str] = None,
57 renderer: typing.Optional[str] = None,
(...)
61 engine: typing.Optional[str] = None,
62 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
63 """Return the source piped through the Graphviz layout command.
64
65 Args:
(...)
102 '<?xml version='
103 """
--> 104 return self._pipe_legacy(format,
105 renderer=renderer,
106 formatter=formatter,
107 neato_no_op=neato_no_op,
108 quiet=quiet,
109 engine=engine,
110 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/_tools.py:171, in deprecate_positional_args.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
162 wanted = ', '.join(f'{name}={value!r}'
163 for name, value in deprecated.items())
164 warnings.warn(f'The signature of {func.__name__} will be reduced'
165 f' to {supported_number} positional args'
166 f' {list(supported)}: pass {wanted}'
167 ' as keyword arg(s)',
168 stacklevel=stacklevel,
169 category=category)
--> 171 return func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:121, in Pipe._pipe_legacy(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
112 @_tools.deprecate_positional_args(supported_number=2)
113 def _pipe_legacy(self,
114 format: typing.Optional[str] = None,
(...)
119 engine: typing.Optional[str] = None,
120 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
--> 121 return self._pipe_future(format,
122 renderer=renderer,
123 formatter=formatter,
124 neato_no_op=neato_no_op,
125 quiet=quiet,
126 engine=engine,
127 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:149, in Pipe._pipe_future(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
146 if encoding is not None:
147 if codecs.lookup(encoding) is codecs.lookup(self.encoding):
148 # common case: both stdin and stdout need the same encoding
--> 149 return self._pipe_lines_string(*args, encoding=encoding, **kwargs)
150 try:
151 raw = self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/piping.py:212, in pipe_lines_string(engine, format, input_lines, encoding, renderer, formatter, neato_no_op, quiet)
206 cmd = dot_command.command(engine, format,
207 renderer=renderer,
208 formatter=formatter,
209 neato_no_op=neato_no_op)
210 kwargs = {'input_lines': input_lines, 'encoding': encoding}
--> 212 proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
213 return proc.stdout
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:81, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
79 except OSError as e:
80 if e.errno == errno.ENOENT:
---> 81 raise ExecutableNotFound(cmd) from e
82 raise
84 if not quiet and proc.stderr:
ExecutableNotFound: failed to execute PosixPath('dot'), make sure the Graphviz executables are on your systems' PATH
<graphviz.graphs.Digraph at 0x13d7c1950>
c.processed_graph.plot_values(
vertex_values=P.expr.vertex_value.value[:, 1],
edge_values=P.expr.edge_value.value[:, 1],
)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:76, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
75 kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
---> 76 proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
77 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:96, in _run_input_lines(cmd, input_lines, kwargs)
95 def _run_input_lines(cmd, input_lines, *, kwargs):
---> 96 popen = subprocess.Popen(cmd, stdin=subprocess.PIPE, **kwargs)
98 stdin_write = popen.stdin.write
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1039, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1036 self.stderr = io.TextIOWrapper(self.stderr,
1037 encoding=encoding, errors=errors)
-> 1039 self._execute_child(args, executable, preexec_fn, close_fds,
1040 pass_fds, cwd, env,
1041 startupinfo, creationflags, shell,
1042 p2cread, p2cwrite,
1043 c2pread, c2pwrite,
1044 errread, errwrite,
1045 restore_signals,
1046 gid, gids, uid, umask,
1047 start_new_session, process_group)
1048 except:
1049 # Cleanup if the child failed starting.
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1991, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1990 if err_filename is not None:
-> 1991 raise child_exception_type(errno_num, err_msg, err_filename)
1992 else:
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('dot')
The above exception was the direct cause of the following exception:
ExecutableNotFound Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/IPython/core/formatters.py:1036, in MimeBundleFormatter.__call__(self, obj, include, exclude)
1033 method = get_real_method(obj, self.print_method)
1035 if method is not None:
-> 1036 return method(include=include, exclude=exclude)
1037 return None
1038 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:98, in JupyterIntegration._repr_mimebundle_(self, include, exclude, **_)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:112, in JupyterIntegration._repr_image_svg_xml(self)
110 def _repr_image_svg_xml(self) -> str:
111 """Return the rendered graph as SVG string."""
--> 112 return self.pipe(format='svg', encoding=SVG_ENCODING)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:104, in Pipe.pipe(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
55 def pipe(self,
56 format: typing.Optional[str] = None,
57 renderer: typing.Optional[str] = None,
(...)
61 engine: typing.Optional[str] = None,
62 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
63 """Return the source piped through the Graphviz layout command.
64
65 Args:
(...)
102 '<?xml version='
103 """
--> 104 return self._pipe_legacy(format,
105 renderer=renderer,
106 formatter=formatter,
107 neato_no_op=neato_no_op,
108 quiet=quiet,
109 engine=engine,
110 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/_tools.py:171, in deprecate_positional_args.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
162 wanted = ', '.join(f'{name}={value!r}'
163 for name, value in deprecated.items())
164 warnings.warn(f'The signature of {func.__name__} will be reduced'
165 f' to {supported_number} positional args'
166 f' {list(supported)}: pass {wanted}'
167 ' as keyword arg(s)',
168 stacklevel=stacklevel,
169 category=category)
--> 171 return func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:121, in Pipe._pipe_legacy(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
112 @_tools.deprecate_positional_args(supported_number=2)
113 def _pipe_legacy(self,
114 format: typing.Optional[str] = None,
(...)
119 engine: typing.Optional[str] = None,
120 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
--> 121 return self._pipe_future(format,
122 renderer=renderer,
123 formatter=formatter,
124 neato_no_op=neato_no_op,
125 quiet=quiet,
126 engine=engine,
127 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:149, in Pipe._pipe_future(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
146 if encoding is not None:
147 if codecs.lookup(encoding) is codecs.lookup(self.encoding):
148 # common case: both stdin and stdout need the same encoding
--> 149 return self._pipe_lines_string(*args, encoding=encoding, **kwargs)
150 try:
151 raw = self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/piping.py:212, in pipe_lines_string(engine, format, input_lines, encoding, renderer, formatter, neato_no_op, quiet)
206 cmd = dot_command.command(engine, format,
207 renderer=renderer,
208 formatter=formatter,
209 neato_no_op=neato_no_op)
210 kwargs = {'input_lines': input_lines, 'encoding': encoding}
--> 212 proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
213 return proc.stdout
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:81, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
79 except OSError as e:
80 if e.errno == errno.ENOENT:
---> 81 raise ExecutableNotFound(cmd) from e
82 raise
84 if not quiet and proc.stderr:
ExecutableNotFound: failed to execute PosixPath('dot'), make sure the Graphviz executables are on your systems' PATH
<graphviz.graphs.Digraph at 0x13dcbbd90>
Penalizing indirect signaling rules#
The original version of CARNIVAL treats indirect rules (A -> B, A inhibited => B inhibited, and A -| B, A inhibited => B activated) similarly that more direct rules (…). The reverse or inactive-state implications rely, in general, on additional assumptions, such as A being the sole regulator of B or the existence of efficient off-switch mechanisms, and these might be in general less reliable. To control for this, we added a tunable parameter called indirect_rule_penalty that penalizes the number of indirect rules selected in each sample
c = CarnivalFlow(lambda_reg=1e-3, indirect_rule_penalty=1)
P = c.build(G, data)
P.solve(verbosity=0, solver="scipy")
for o in P.objectives:
print(o.name, o.value)
Unreachable vertices for sample: 1
Unreachable vertices for sample: 0
error_c1_0 0.0
penalty_indirect_rules_0 [0.]
error_c2_1 1.0
penalty_indirect_rules_1 [1.]
regularization_edge_has_signal_OR 9.0
c.processed_graph.plot_values(
vertex_values=P.expr.vertex_value.value[:, 0],
edge_values=P.expr.edge_value.value[:, 0],
)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:76, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
75 kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
---> 76 proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
77 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:96, in _run_input_lines(cmd, input_lines, kwargs)
95 def _run_input_lines(cmd, input_lines, *, kwargs):
---> 96 popen = subprocess.Popen(cmd, stdin=subprocess.PIPE, **kwargs)
98 stdin_write = popen.stdin.write
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1039, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1036 self.stderr = io.TextIOWrapper(self.stderr,
1037 encoding=encoding, errors=errors)
-> 1039 self._execute_child(args, executable, preexec_fn, close_fds,
1040 pass_fds, cwd, env,
1041 startupinfo, creationflags, shell,
1042 p2cread, p2cwrite,
1043 c2pread, c2pwrite,
1044 errread, errwrite,
1045 restore_signals,
1046 gid, gids, uid, umask,
1047 start_new_session, process_group)
1048 except:
1049 # Cleanup if the child failed starting.
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1991, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1990 if err_filename is not None:
-> 1991 raise child_exception_type(errno_num, err_msg, err_filename)
1992 else:
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('dot')
The above exception was the direct cause of the following exception:
ExecutableNotFound Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/IPython/core/formatters.py:1036, in MimeBundleFormatter.__call__(self, obj, include, exclude)
1033 method = get_real_method(obj, self.print_method)
1035 if method is not None:
-> 1036 return method(include=include, exclude=exclude)
1037 return None
1038 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:98, in JupyterIntegration._repr_mimebundle_(self, include, exclude, **_)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:112, in JupyterIntegration._repr_image_svg_xml(self)
110 def _repr_image_svg_xml(self) -> str:
111 """Return the rendered graph as SVG string."""
--> 112 return self.pipe(format='svg', encoding=SVG_ENCODING)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:104, in Pipe.pipe(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
55 def pipe(self,
56 format: typing.Optional[str] = None,
57 renderer: typing.Optional[str] = None,
(...)
61 engine: typing.Optional[str] = None,
62 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
63 """Return the source piped through the Graphviz layout command.
64
65 Args:
(...)
102 '<?xml version='
103 """
--> 104 return self._pipe_legacy(format,
105 renderer=renderer,
106 formatter=formatter,
107 neato_no_op=neato_no_op,
108 quiet=quiet,
109 engine=engine,
110 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/_tools.py:171, in deprecate_positional_args.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
162 wanted = ', '.join(f'{name}={value!r}'
163 for name, value in deprecated.items())
164 warnings.warn(f'The signature of {func.__name__} will be reduced'
165 f' to {supported_number} positional args'
166 f' {list(supported)}: pass {wanted}'
167 ' as keyword arg(s)',
168 stacklevel=stacklevel,
169 category=category)
--> 171 return func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:121, in Pipe._pipe_legacy(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
112 @_tools.deprecate_positional_args(supported_number=2)
113 def _pipe_legacy(self,
114 format: typing.Optional[str] = None,
(...)
119 engine: typing.Optional[str] = None,
120 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
--> 121 return self._pipe_future(format,
122 renderer=renderer,
123 formatter=formatter,
124 neato_no_op=neato_no_op,
125 quiet=quiet,
126 engine=engine,
127 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:149, in Pipe._pipe_future(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
146 if encoding is not None:
147 if codecs.lookup(encoding) is codecs.lookup(self.encoding):
148 # common case: both stdin and stdout need the same encoding
--> 149 return self._pipe_lines_string(*args, encoding=encoding, **kwargs)
150 try:
151 raw = self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/piping.py:212, in pipe_lines_string(engine, format, input_lines, encoding, renderer, formatter, neato_no_op, quiet)
206 cmd = dot_command.command(engine, format,
207 renderer=renderer,
208 formatter=formatter,
209 neato_no_op=neato_no_op)
210 kwargs = {'input_lines': input_lines, 'encoding': encoding}
--> 212 proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
213 return proc.stdout
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:81, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
79 except OSError as e:
80 if e.errno == errno.ENOENT:
---> 81 raise ExecutableNotFound(cmd) from e
82 raise
84 if not quiet and proc.stderr:
ExecutableNotFound: failed to execute PosixPath('dot'), make sure the Graphviz executables are on your systems' PATH
<graphviz.graphs.Digraph at 0x13d69f390>
c.processed_graph.plot_values(
vertex_values=P.expr.vertex_value.value[:, 1],
edge_values=P.expr.edge_value.value[:, 1],
)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:76, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
75 kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
---> 76 proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
77 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:96, in _run_input_lines(cmd, input_lines, kwargs)
95 def _run_input_lines(cmd, input_lines, *, kwargs):
---> 96 popen = subprocess.Popen(cmd, stdin=subprocess.PIPE, **kwargs)
98 stdin_write = popen.stdin.write
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1039, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1036 self.stderr = io.TextIOWrapper(self.stderr,
1037 encoding=encoding, errors=errors)
-> 1039 self._execute_child(args, executable, preexec_fn, close_fds,
1040 pass_fds, cwd, env,
1041 startupinfo, creationflags, shell,
1042 p2cread, p2cwrite,
1043 c2pread, c2pwrite,
1044 errread, errwrite,
1045 restore_signals,
1046 gid, gids, uid, umask,
1047 start_new_session, process_group)
1048 except:
1049 # Cleanup if the child failed starting.
File /opt/homebrew/Cellar/python@3.13/3.13.11_2/Frameworks/Python.framework/Versions/3.13/lib/python3.13/subprocess.py:1991, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session, process_group)
1990 if err_filename is not None:
-> 1991 raise child_exception_type(errno_num, err_msg, err_filename)
1992 else:
FileNotFoundError: [Errno 2] No such file or directory: PosixPath('dot')
The above exception was the direct cause of the following exception:
ExecutableNotFound Traceback (most recent call last)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/IPython/core/formatters.py:1036, in MimeBundleFormatter.__call__(self, obj, include, exclude)
1033 method = get_real_method(obj, self.print_method)
1035 if method is not None:
-> 1036 return method(include=include, exclude=exclude)
1037 return None
1038 else:
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:98, in JupyterIntegration._repr_mimebundle_(self, include, exclude, **_)
96 include = set(include) if include is not None else {self._jupyter_mimetype}
97 include -= set(exclude or [])
---> 98 return {mimetype: getattr(self, method_name)()
99 for mimetype, method_name in MIME_TYPES.items()
100 if mimetype in include}
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/corneto/_plotting.py:27, in suppress_repr_warnings.<locals>.make_wrapper.<locals>.wrapper(*args, **kwargs)
25 def wrapper(*args, **kwargs):
26 with contextlib.redirect_stderr(io.StringIO()):
---> 27 return orig_func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/jupyter_integration.py:112, in JupyterIntegration._repr_image_svg_xml(self)
110 def _repr_image_svg_xml(self) -> str:
111 """Return the rendered graph as SVG string."""
--> 112 return self.pipe(format='svg', encoding=SVG_ENCODING)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:104, in Pipe.pipe(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
55 def pipe(self,
56 format: typing.Optional[str] = None,
57 renderer: typing.Optional[str] = None,
(...)
61 engine: typing.Optional[str] = None,
62 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
63 """Return the source piped through the Graphviz layout command.
64
65 Args:
(...)
102 '<?xml version='
103 """
--> 104 return self._pipe_legacy(format,
105 renderer=renderer,
106 formatter=formatter,
107 neato_no_op=neato_no_op,
108 quiet=quiet,
109 engine=engine,
110 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/_tools.py:171, in deprecate_positional_args.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
162 wanted = ', '.join(f'{name}={value!r}'
163 for name, value in deprecated.items())
164 warnings.warn(f'The signature of {func.__name__} will be reduced'
165 f' to {supported_number} positional args'
166 f' {list(supported)}: pass {wanted}'
167 ' as keyword arg(s)',
168 stacklevel=stacklevel,
169 category=category)
--> 171 return func(*args, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:121, in Pipe._pipe_legacy(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
112 @_tools.deprecate_positional_args(supported_number=2)
113 def _pipe_legacy(self,
114 format: typing.Optional[str] = None,
(...)
119 engine: typing.Optional[str] = None,
120 encoding: typing.Optional[str] = None) -> typing.Union[bytes, str]:
--> 121 return self._pipe_future(format,
122 renderer=renderer,
123 formatter=formatter,
124 neato_no_op=neato_no_op,
125 quiet=quiet,
126 engine=engine,
127 encoding=encoding)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/piping.py:149, in Pipe._pipe_future(self, format, renderer, formatter, neato_no_op, quiet, engine, encoding)
146 if encoding is not None:
147 if codecs.lookup(encoding) is codecs.lookup(self.encoding):
148 # common case: both stdin and stdout need the same encoding
--> 149 return self._pipe_lines_string(*args, encoding=encoding, **kwargs)
150 try:
151 raw = self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/piping.py:212, in pipe_lines_string(engine, format, input_lines, encoding, renderer, formatter, neato_no_op, quiet)
206 cmd = dot_command.command(engine, format,
207 renderer=renderer,
208 formatter=formatter,
209 neato_no_op=neato_no_op)
210 kwargs = {'input_lines': input_lines, 'encoding': encoding}
--> 212 proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
213 return proc.stdout
File /private/var/folders/b4/gwkwsdb93sv11rtztqbm3l040000gn/T/tmp.Dst0hQI0PJ/wt-v1.0.0-beta.2/.venv/lib/python3.13/site-packages/graphviz/backend/execute.py:81, in run_check(cmd, input_lines, encoding, quiet, **kwargs)
79 except OSError as e:
80 if e.errno == errno.ENOENT:
---> 81 raise ExecutableNotFound(cmd) from e
82 raise
84 if not quiet and proc.stderr:
ExecutableNotFound: failed to execute PosixPath('dot'), make sure the Graphviz executables are on your systems' PATH
<graphviz.graphs.Digraph at 0x13d69ed50>
Single sample using the same multi-sample method#
# Only c1
subset = cn.Data.from_cdict({"c1": samples["c1"]})
c = CarnivalFlow(lambda_reg=1e-3)
P = c.build(G, subset)
P.solve(verbosity=0, solver="scipy")
for o in P.objectives:
print(o.value)
c.processed_graph.edge_subgraph(np.flatnonzero(P.expr.edge_has_signal.value)).plot()
Unreachable vertices for sample: 0
0.0
5.0
# Only c2
subset = cn.Data.from_cdict({"c2": samples["c2"]})
c = CarnivalFlow(lambda_reg=1e-3)
P = c.build(G, subset)
P.solve(verbosity=0, solver="scipy")
for o in P.objectives:
print(o.value)
c.processed_graph.edge_subgraph(np.flatnonzero(P.expr.edge_has_signal.value)).plot()
Unreachable vertices for sample: 0
1.0
6.0