def validate_data_interface(ds: smlb.Data) -> bool:
"""Tests for compliance with Data interface.
Runs tests that every Data-compliant class should satisfy.
Returns:
True
Raises:
AssertionError for failed tests
"""
# actual or "virtual" abc inheritance
assert isinstance(ds, smlb.Data)
if ds.num_samples == float("inf"):
# infinite data tests
pass
else:
# finite data test
# integer-representable non-negative size
assert int(ds.num_samples) == ds.num_samples
assert ds.num_samples >= 0
# all samples are returned
assert len(ds.samples()) == ds.num_samples
# subsets
assert ds.subset([]).num_samples == 0
assert ds.subset().num_samples <= ds.num_samples
assert ds.subset(duplicates=True).num_samples == ds.num_samples
# intersection with self
assert smlb.intersection(ds, ds).num_samples <= ds.num_samples
# assert smlb.intersection(ds, ds, duplicates=True).num_samples == ds.num_samples # todo: support this as well
# complement with self
assert smlb.complement(ds, ds).num_samples == 0
# assert smlb.complement(ds, ds, duplicates=True).num_samples == 0 # todo: support this as well
if ds.is_labeled:
# all labels are returned
assert len(ds.labels()) == ds.num_samples
# subsets
assert ds.subset([]).is_labeled
assert ds.subset().is_labeled
# intersection
assert smlb.intersection(ds, ds).is_labeled
# assert smlb.intersection(ds, ds, duplicates=True).is_labeled # todo: support this as well
# complement
assert smlb.complement(ds, ds).is_labeled
# assert smlb.complement(ds, ds, duplicates=True).is_labeled # todo: support this as well
return True
def apply(self, data: Data) -> TabularData:
"""Compute matminer composition-based materials features.
Parameters:
data: material compositions, given as sum formula strings
Can be labeled, and labels will be retained
Returns:
TabularData or TabularLabeledData with matminer composition-based
materials features as samples
"""
data = params.instance(data, Data)
inputs_ = tuple(self._composition(self.samplef(s)) for s in data.samples())
features = self._mmfeatures.featurize_many(inputs_, pbar=False)
features = np.asfarray(features)
result = TabularData(data=features, labels=data.labels() if data.is_labeled else None)
return result
def fit(self, data: Data) -> "RandomForestRegressionSklearn":
"""Fits the model using training data.
Parameters:
data: tabular labeled data to train on
Returns:
self (allows chaining)
"""
data = params.instance(
data,
Data) # todo: params.data(..., is_finite=True, is_labeled=True)
n = data.num_samples
xtrain = params.real_matrix(data.samples(), nrows=n)
ytrain = params.real_vector(data.labels(), dimensions=n)
self._model.fit(xtrain, ytrain)
return self
def fit(self, data: Data) -> "ExtremelyRandomizedTreesRegressionSklearn":
"""Fits the model using training data.
Parameters:
data: tabular labeled data to train on
Returns:
self (allows chaining)
"""
data = params.instance(data, Data)
if not data.is_labeled:
raise InvalidParameterError("labeled data", "unlabeled data")
n = data.num_samples
xtrain = params.real_matrix(data.samples(), nrows=n)
ytrain = params.real_vector(data.labels(), dimensions=n)
self._model.fit(xtrain, ytrain)
return self
def fit(self, data: Data) -> "GaussianProcessRegressionSklearn":
"""Fits the model using training data.
Parameters:
data: labeled data to train on;
must derive from IndexedData and LabeledData
Returns:
self (allows chaining)
"""
data = params.instance(
data,
Data) # todo: params.data(..., is_finite=True, is_labeled=True)
n = data.num_samples
xtrain = params.real_matrix(data.samples(), nrows=n)
ytrain = params.real_vector(data.labels(), dimensions=n)
self._model.fit(xtrain, ytrain)
return self
def fit(self, data: Data) -> "RandomForestRegressionLolo":
"""Fits the model using training data.
Parameters:
data: labeled tabular data to train on
Returns:
self (allows chaining)
"""
data = params.instance(
data, Data
) # todo: params.data(..., is_labeled=True, is_finite=True)
n = data.num_samples
xtrain = params.real_matrix(data.samples(), nrows=n)
ytrain = params.real_vector(data.labels(), dimensions=n)
try:
self._model.fit(xtrain, ytrain)
except Py4JJavaError as e:
raise BenchmarkError("training lolo model failed") from e
return self
def apply(self, data: Data) -> TabularData:
"""Compute selected molecular features.
Parameters:
data: molecular structures given as SMILES strings.
Can be labeled, and labels will be retained
Returns:
TabularData with CDK molecular features as samples
"""
data = params.instance(data, Data) # todo: params.data(data, is_finite=True)
failmode = DataTransformationFailureMode(self._failmode, data.num_samples)
# set up molecule SMILES
builder = self._java_gateway.jvm.org.openscience.cdk.DefaultChemObjectBuilder.getInstance()
parser = self._java_gateway.jvm.org.openscience.cdk.smiles.SmilesParser(builder)
def parse_smiles(s: str, i: int):
"""Return parsed SMILES string or None on failure."""
try:
return parser.parseSmiles(self._samplef(s))
except py4j.protocol.Py4JJavaError:
# expected to be raised from org.openscience.cdk.exception.InvalidSmilesException
failmode.handle_failure(i)
return None # internal sentinel value
smiles = tuple(parse_smiles(s, i) for i, s in enumerate(data.samples()))
# compute descriptors
# todo: the dtype of the columns could be set in advance by querying the descriptors
# currently, all values are stored as floating point numbers
features = np.empty((data.num_samples, np.sum(self._arities)))
index = 0
def java_is_instance_of(object_, class_):
return py4j.java_gateway.is_instance_of(
self._java_gateway, object_, "org.openscience.cdk.qsar.result." + class_
)
def check_arity(expected, actual):
if expected != actual:
raise BenchmarkError(
f"Invalid descriptor result arity (expected {expected}, was {actual})"
)
for descriptor, arity in zip(self._descriptors, self._arities):
for i, smile in enumerate(smiles):
if smiles is None:
features[i, index : index + arity] = float("nan")
continue
try:
value = descriptor.calculate(smile).getValue()
except py4j.protocol.Py4JJavaError:
failmode.handle_failure(i)
features[i, index : index + arity] = float("nan")
continue
if java_is_instance_of(value, "IntegerResult"):
check_arity(arity, 1)
features[i, index] = int(value.intValue())
elif java_is_instance_of(value, "DoubleResult"):
check_arity(arity, 1)
features[i, index] = float(value.doubleValue())
elif java_is_instance_of(value, "BooleanResult"):
check_arity(arity, 1)
features[i, index] = bool(value.booleanValue())
elif java_is_instance_of(value, "IntegerArrayResult"):
check_arity(arity, value.length())
features[i, index : index + arity] = tuple(
int(value.get(j)) for j in range(value.length())
)
elif java_is_instance_of(value, "DoubleArrayResult"):
check_arity(arity, value.length())
features[i, index : index + arity] = tuple(
float(value.get(j)) for j in range(value.length())
)
# there seems to be no BooleanArrayResult in CDK
else:
name = value.getClass().getSimpleName()
raise BenchmarkError(f"Unsupported CDK result type '{name}'")
index += arity
result = (
TabularData(data=features, labels=data.labels())
if data.is_labeled
else TabularData(data=features)
)
result = failmode.finalize(result)
return result