def test_run(self, graph, schema):
df = sem_generator(
graph=graph,
schema=schema,
default_type="continuous",
noise_std=1.0,
n_samples=1000,
intercept=False,
seed=12,
)
# test binary:
assert df[0].nunique() == 2
assert df[0].nunique() == 2
# test categorical:
for col in ["1_{}".format(i) for i in range(3)]:
assert df[col].nunique() == 2
assert len([x for x in df.columns
if isinstance(x, str) and "1_" in x]) == 3
for col in ["5_{}".format(i) for i in range(5)]:
assert df[col].nunique() == 2
assert len([x for x in df.columns
if isinstance(x, str) and "5_" in x]) == 5
# test continuous
assert df[3].nunique() == 1000
assert df[4].nunique() == 1000
def generate_categorical_dataframe(
sm: nx.DiGraph,
n_samples: int,
distribution: str = "logit",
n_categories: int = 3,
noise_scale: float = 1.0,
intercept: bool = False,
seed: int = None,
kernel: Optional[Kernel] = None,
) -> pd.DataFrame:
"""
Generates a dataframe with samples from SEM with specified type of noise.
Args:
sm: A DAG in form of a networkx or StructureModel. Does not require weights.
n_samples: The number of rows/observations to sample.
kernel: A kernel from sklearn.gaussian_process.kernels like RBF(1) or
Matern(1) or any combinations thereof. The kernels are used to
create the latent variable for the binary / categorical variables
and are directly used for continuous variables.
distribution: The type of distribution to use for the noise
of a variable. Options: 'probit'/'normal' (alias),
"logit"/"gumbel" (alias). Logit is default.
n_categories: Number of categories per variable/node.
noise_scale: The standard deviation of the noise. The categorical features
are created using a latent variable approach. The noise standard
deviation determines how much weight the "mean" estimate has on
the feature value.
intercept: Whether to use an intercept for the latent variable of each feature.
seed: Random state
Returns:
x_mat: [n_samples, d_nodes] sample matrix
Raises:
ValueError: if distribution is not 'probit', 'normal', 'logit', 'gumbel'
"""
if kernel is None:
return sem_generator(
graph=sm,
default_type=f"categorical:{n_categories}",
n_samples=n_samples,
distributions={"categorical": distribution},
noise_std=noise_scale,
intercept=intercept,
seed=seed,
)
return nonlinear_sem_generator(
graph=sm,
kernel=kernel,
default_type=f"categorical:{n_categories}",
n_samples=n_samples,
distributions={"categorical": distribution},
noise_std=noise_scale,
seed=seed,
)
def generate_binary_data(
sm: nx.DiGraph,
n_samples: int,
distribution: str = "logit",
noise_scale: float = 1.0,
intercept: bool = False,
seed: int = None,
kernel: Optional[Kernel] = None,
) -> np.ndarray:
"""
Simulate samples from SEM with specified type of noise.
The order of the columns on the returned array is the one provided by `sm.nodes`
Args:
sm: A DAG in form of a networkx or StructureModel. Does not require weights.
n_samples: The number of rows/observations to sample.
kernel: A kernel from sklearn.gaussian_process.kernels like RBF(1) or
Matern(1) or any combinations thereof. The kernels are used to
create the latent variable for the binary / categorical variables
and are directly used for continuous variables.
distribution: The type of distribution to use for the noise
of a variable. Options: 'probit'/'normal' (alias),
'logit' (default).
noise_scale: The standard deviation of the noise. The binary and
categorical features are created using a latent variable approach.
The noise standard deviation determines how much weight the "mean"
estimate has on the feature value.
intercept: Whether to use an intercept for the latent variable of each feature.
seed: Random state
Returns:
x_mat: [n_samples,d_nodes] sample matrix
Raises:
ValueError: if distribution isn't 'probit', 'normal', 'logit'
"""
if kernel is None:
df = sem_generator(
graph=sm,
default_type="binary",
n_samples=n_samples,
distributions={"binary": distribution},
noise_std=noise_scale,
intercept=intercept,
seed=seed,
)
else:
df = nonlinear_sem_generator(
graph=sm,
kernel=kernel,
default_type="binary",
n_samples=n_samples,
distributions={"binary": distribution},
noise_std=noise_scale,
seed=seed,
)
return df[list(sm.nodes())].values
def test_missing_default_type(self, graph):
with pytest.raises(ValueError, match="Unknown default data type"):
_ = sem_generator(
graph=graph,
schema=schema,
default_type="unknown",
noise_std=1.0,
n_samples=1000,
intercept=False,
seed=12,
)
def test_incorrect_intercept_dist(self, graph):
with pytest.raises(ValueError, match="Unknown intercept distribution"):
_ = sem_generator(
graph=graph,
schema=None,
default_type="continuous",
distributions={"intercept": "unknown"},
noise_std=2.0,
n_samples=10,
intercept=True,
seed=10,
)
def generate_continuous_dataframe(
sm: nx.DiGraph,
n_samples: int,
distribution: str = "gaussian",
noise_scale: float = 1.0,
intercept: bool = False,
seed: int = None,
kernel: Optional[Kernel] = None,
) -> pd.DataFrame:
"""
Generates a dataframe with samples from SEM with specified type of noise.
Args:
sm: A DAG in form of a networkx or StructureModel. Does not require weights.
n_samples: The number of rows/observations to sample.
kernel: A kernel from sklearn.gaussian_process.kernels like RBF(1) or
Matern(1) or any combinations thereof. The kernels are used to
create the latent variable for the binary / categorical variables
and are directly used for continuous variables.
distribution: The type of distribution to use for the noise
of a variable. Options: 'gaussian'/'normal' (alias), 'student-t',
'exponential', 'gumbel'.
noise_scale: The standard deviation of the noise.
intercept: Whether to use an intercept for each feature.
seed: Random state
Returns:
Dataframe with the node names as column names
Raises:
ValueError: if distribution is not 'gaussian', 'normal', 'student-t',
'exponential', 'gumbel'
"""
if kernel is None:
return sem_generator(
graph=sm,
default_type="continuous",
n_samples=n_samples,
distributions={"continuous": distribution},
noise_std=noise_scale,
intercept=intercept,
seed=seed,
)
return nonlinear_sem_generator(
graph=sm,
kernel=kernel,
default_type="continuous",
n_samples=n_samples,
distributions={"continuous": distribution},
noise_std=noise_scale,
seed=seed,
)
def test_not_permissible_type(self, graph):
schema = {
0: "unknown data type",
}
with pytest.raises(ValueError, match="Unknown data type"):
_ = sem_generator(
graph=graph,
schema=schema,
default_type="continuous",
noise_std=1.0,
n_samples=1000,
intercept=False,
seed=12,
)
def generate_count_dataframe(
sm: nx.DiGraph,
n_samples: int,
zero_inflation_factor: float = 0.1,
intercept: bool = False,
seed: int = None,
kernel: Optional[Kernel] = None,
) -> pd.DataFrame:
"""
Generates a dataframe with samples from SEM with specified type of noise.
Args:
sm: A DAG in form of a networkx or StructureModel. Does not require weights.
n_samples: The number of rows/observations to sample.
kernel: A kernel from sklearn.gaussian_process.kernels like RBF(1) or
Matern(1) or any combinations thereof. The kernels are used to
create the latent variable for the binary / categorical variables
and are directly used for continuous variables.
zero_inflation_factor: The probability of zero inflation for count data.
intercept: Whether to use an intercept for the latent variable of each feature.
seed: Random state
Returns:
x_mat: [n_samples, d_nodes] sample matrix
Raises:
ValueError: if ``zero_inflation_factor`` is not a float in [0, 1].
"""
if kernel is None:
return sem_generator(
graph=sm,
default_type="count",
n_samples=n_samples,
distributions={"count": zero_inflation_factor},
noise_std=1, # not used for poisson
intercept=intercept,
seed=seed,
)
return nonlinear_sem_generator(
graph=sm,
kernel=kernel,
default_type="count",
n_samples=n_samples,
distributions={"count": zero_inflation_factor},
noise_std=1, # not used for poisson
seed=seed,
)
def test_missing_cardinality(self, graph):
schema = {
0: "categorical",
1: "categorical:3",
5: "categorical:5",
}
with pytest.raises(ValueError,
match="Missing cardinality for categorical"):
_ = sem_generator(
graph=graph,
schema=schema,
default_type="continuous",
noise_std=1.0,
n_samples=1000,
intercept=False,
seed=12,
)
def test_incorrect_weight_dist(self):
sm = StructureModel()
nodes = list(str(x) for x in range(6))
np.random.shuffle(nodes)
sm.add_nodes_from(nodes)
sm.add_weighted_edges_from([("0", "1", None), ("2", "4", None)])
with pytest.raises(ValueError, match="Unknown weight distribution"):
_ = sem_generator(
graph=sm,
schema=None,
default_type="continuous",
distributions={"weight": "unknown"},
noise_std=2.0,
n_samples=1000,
intercept=False,
seed=10,
)
def test_mixed_type_independence(self, seed, n_categories,
weight_distribution,
intercept_distribution):
"""
Test whether the relation is accurate, implicitly tests sequence of
nodes.
"""
np.random.seed(seed)
sm = StructureModel()
nodes = list(str(x) for x in range(6))
np.random.shuffle(nodes)
sm.add_nodes_from(nodes)
# binary -> categorical
sm.add_weighted_edges_from([("0", "1", 10)])
# binary -> continuous
sm.add_weighted_edges_from([("2", "4", None)])
schema = {
"0": "binary",
"1": "categorical:{}".format(n_categories),
"2": "binary",
"4": "continuous",
"5": "categorical:{}".format(n_categories),
}
df = sem_generator(
graph=sm,
schema=schema,
default_type="continuous",
distributions={
"weight": weight_distribution,
"intercept": intercept_distribution,
},
noise_std=2,
n_samples=100000,
intercept=True,
seed=seed,
)
atol = 0.05 # 5% difference bewteen joint & factored!
# 1. dependent links
# 0 -> 1 (we look at the class with the highest deviation from uniform
# to avoid small values)
c, _ = max(
[(c, np.abs(df["1_{}".format(c)].mean() - 1 / n_categories))
for c in range(n_categories)],
key=operator.itemgetter(1),
)
joint_proba, factored_proba = calculate_proba(df, "0",
"1_{}".format(c))
assert not np.isclose(joint_proba, factored_proba, rtol=0, atol=atol)
# 2 -> 4
assert not np.isclose(
df["4"].mean(), df["4"][df["2"] == 1].mean(), rtol=0, atol=atol)
tol = 0.15 # relative tolerance of +- 15% of the
# 2. independent links
# categorical
c, _ = max(
[(c, np.abs(df["1_{}".format(c)].mean() - 1 / n_categories))
for c in range(n_categories)],
key=operator.itemgetter(1),
)
joint_proba, factored_proba = calculate_proba(df, "0",
"5_{}".format(c))
assert np.isclose(joint_proba, factored_proba, rtol=tol, atol=0)
# binary
joint_proba, factored_proba = calculate_proba(df, "0", "2")
assert np.isclose(joint_proba, factored_proba, rtol=tol, atol=0)
# categorical
c, _ = max(
[(c, np.abs(df["1_{}".format(c)].mean() - 1 / n_categories))
for c in range(n_categories)],
key=operator.itemgetter(1),
)
d, _ = max(
[(d, np.abs(df["5_{}".format(d)].mean() - 1 / n_categories))
for d in range(n_categories)],
key=operator.itemgetter(1),
)
joint_proba, factored_proba = calculate_proba(df, "1_{}".format(d),
"5_{}".format(c))
assert np.isclose(joint_proba, factored_proba, rtol=tol, atol=0)
# continuous
# for gaussian distributions, zero variance is equivalent to independence
assert np.isclose(df[["3", "4"]].corr().values[0, 1], 0, atol=tol)
def test_graph_not_a_dag(self):
graph = StructureModel()
graph.add_edges_from([(0, 1), (1, 2), (2, 0)])
with pytest.raises(ValueError, match="Provided graph is not a DAG"):
_ = sem_generator(graph=graph)