Merge pull request #982 from CitrineInformatics/feature/pne-6367-feature-effects

[PNE-6367] Add support for feature effects.

Author: anoto-moniz

src/citrine/__version__.py

@@ -1 +1 @@
-__version__ = "3.11.6"
+__version__ = "3.12.0"

src/citrine/informatics/feature_effects.py

@@ -0,0 +1,76 @@
+from typing import Dict
+from uuid import UUID
+
+from citrine._rest.resource import Resource
+from citrine._serialization import properties
+
+
+class ShapleyMaterial(Resource):
+    """The feature effect of a material."""
+
+    material_id = properties.UUID('material_id', serializable=False)
+    value = properties.Float('value', serializable=False)
+
+
+class ShapleyFeature(Resource):
+    """All feature effects for this feature by material."""
+
+    feature = properties.String('feature', serializable=False)
+    materials = properties.List(properties.Object(ShapleyMaterial), 'materials',
+                                serializable=False)
+
+    @property
+    def material_dict(self) -> Dict[UUID, float]:
+        """Presents the feature's effects as a dictionary by material."""
+        return {material.material_id: material.value for material in self.materials}
+
+
+class ShapleyOutput(Resource):
+    """All feature effects for this output by feature."""
+
+    output = properties.String('output', serializable=False)
+    features = properties.List(properties.Object(ShapleyFeature), 'features', serializable=False)
+
+    @property
+    def feature_dict(self) -> Dict[str, Dict[UUID, float]]:
+        """Presents the output's feature effects as a dictionary by feature."""
+        return {feature.feature: feature.material_dict for feature in self.features}
+
+
+class FeatureEffects(Resource):
+    """Captures information about the feature effects associated with a predictor."""
+
+    predictor_id = properties.UUID('metadata.predictor_id', serializable=False)
+    predictor_version = properties.Integer('metadata.predictor_version', serializable=False)
+    status = properties.String('metadata.status', serializable=False)
+    failure_reason = properties.Optional(properties.String(), 'metadata.failure_reason',
+                                                              serializable=False)
+
+    outputs = properties.Optional(properties.List(properties.Object(ShapleyOutput)), 'resultobj',
+                                  serializable=False)
+
+    @classmethod
+    def _pre_build(cls, data: dict) -> Dict:
+        shapley = data["result"]
+        material_ids = shapley["materials"]
+
+        outputs = []
+        for output, feature_dict in shapley["outputs"].items():
+            features = []
+            for feature, values in feature_dict.items():
+                items = zip(material_ids, values)
+                materials = [{"material_id": mid, "value": value} for mid, value in items]
+                features.append({
+                    "feature": feature,
+                    "materials": materials
+                })
+
+            outputs.append({"output": output, "features": features})
+
+        data["resultobj"] = outputs
+        return data
+
+    @property
+    def as_dict(self) -> Dict[str, Dict[str, Dict[UUID, float]]]:
+        """Presents the feature effects as a dictionary by output."""
+        return {output.output: output.feature_dict for output in self.outputs}

src/citrine/informatics/predictors/graph_predictor.py

@@ -7,9 +7,11 @@
 from citrine._session import Session
 from citrine._utils.functions import format_escaped_url
 from citrine.informatics.data_sources import DataSource
+from citrine.informatics.feature_effects import FeatureEffects
 from citrine.informatics.predictors.single_predict_request import SinglePredictRequest
 from citrine.informatics.predictors.single_prediction import SinglePrediction
 from citrine.informatics.predictors import PredictorNode, Predictor
+from citrine.informatics.reports import Report
 from citrine.resources.report import ReportResource
 
 __all__ = ['GraphPredictor']
@@ -104,7 +106,7 @@ def wrap_instance(predictor_data: dict) -> dict:
         }
 
     @property
-    def report(self):
+    def report(self) -> Report:
         """Fetch the predictor report."""
         if self.uid is None or self._session is None or self._project_id is None \
                 or getattr(self, "version", None) is None:
@@ -113,6 +115,13 @@ def report(self):
         report_resource = ReportResource(self._project_id, self._session)
         return report_resource.get(predictor_id=self.uid, predictor_version=self.version)
 
+    @property
+    def feature_effects(self) -> FeatureEffects:
+        """Retrieve the feature effects for all outputs in the predictor's training data.."""
+        path = self._path() + '/shapley/query'
+        response = self._session.post_resource(path, {}, version=self._api_version)
+        return FeatureEffects.build(response)
+
     def predict(self, predict_request: SinglePredictRequest) -> SinglePrediction:
         """Make a one-off prediction with this predictor."""
         path = self._path() + '/predict'

src/citrine/resources/table_config.py

@@ -88,6 +88,7 @@ class TableConfig(Resource["TableConfig"]):
         The query used to define the materials underpinning this table
     generation_algorithm: TableFromGemdQueryAlgorithm
         Which algorithm was used to generate the config based on the GemdQuery results
+
     """
 
     # FIXME (DML): rename this (this is dependent on the server side)

tests/informatics/test_predictors.py

@@ -1,7 +1,8 @@
 """Tests for citrine.informatics.predictors."""
-import uuid
-import pytest
 import mock
+import pytest
+import uuid
+from random import random
 
 from citrine.informatics.data_sources import GemTableDataSource
 from citrine.informatics.descriptors import RealDescriptor, IntegerDescriptor, \
@@ -12,6 +13,10 @@
 from citrine.informatics.predictors.single_prediction import SinglePrediction
 from citrine.informatics.design_candidate import DesignMaterial
 
+from tests.utils.factories import FeatureEffectsResponseFactory
+from tests.utils.session import FakeCall, FakeSession
+
+
 w = IntegerDescriptor("w", lower_bound=0, upper_bound=100)
 x = RealDescriptor("x", lower_bound=0, upper_bound=100, units="")
 y = RealDescriptor("y", lower_bound=0, upper_bound=100, units="")
@@ -485,3 +490,21 @@ def test_single_predict(graph_predictor):
     prediction_out = graph_predictor.predict(request)
     assert prediction_out.dump() == prediction_in.dump()
     assert session.post_resource.call_count == 1
+
+
+def test_feature_effects(graph_predictor):
+    feature_effects_response = FeatureEffectsResponseFactory()
+    feature_effects_as_dict = feature_effects_response.pop("_result_as_dict")
+
+    session = FakeSession()
+    session.set_response(feature_effects_response)
+    
+    graph_predictor._session = session
+    graph_predictor._project_id = uuid.uuid4()
+
+    fe = graph_predictor.feature_effects
+
+    expected_path = f"/projects/{graph_predictor._project_id}/predictors/{graph_predictor.uid}" + \
+        f"/versions/{graph_predictor.version}/shapley/query"
+    assert session.calls == [FakeCall(method='POST', path=expected_path, json={})]
+    assert fe.as_dict == feature_effects_as_dict

tests/utils/factories.py

@@ -859,3 +859,43 @@ class AnalysisWorkflowEntityDataFactory(factory.DictFactory):
     id = factory.Faker('uuid4')
     data = factory.SubFactory(AnalysisWorkflowDataDataFactory)
     metadata = factory.SubFactory(AnalysisWorkflowMetadataDataFactory)
+
+
+class FeatureEffectsResponseResultFactory(factory.DictFactory):
+    materials = factory.List([
+        factory.Faker('uuid4', cast_to=None),
+        factory.Faker('uuid4', cast_to=None),
+        factory.Faker('uuid4', cast_to=None)
+    ])
+    outputs = factory.Dict({
+        "output1": factory.Dict({
+            "feature1": factory.List([factory.Faker("pyfloat"), factory.Faker("pyfloat"), factory.Faker("pyfloat")])
+        }),
+        "output2": factory.Dict({
+            "feature1": factory.List([factory.Faker("pyfloat"), factory.Faker("pyfloat"), factory.Faker("pyfloat")]),
+            "feature2": factory.List([factory.Faker("pyfloat"), factory.Faker("pyfloat"), factory.Faker("pyfloat")])
+        })
+    })
+
+class FeatureEffectsMetadataFactory(factory.DictFactory):
+    predictor_id = factory.Faker('uuid4')
+    predictor_version = factory.Faker('random_digit_not_null')
+    created = factory.SubFactory(UserTimestampDataFactory)
+    updated = factory.SubFactory(UserTimestampDataFactory)
+    status = 'SUCCEEDED'
+
+
+class FeatureEffectsResponseFactory(factory.DictFactory):
+    query = {}  # Presently, querying from the SDK is not allowed.
+    metadata = factory.SubFactory(FeatureEffectsMetadataFactory)
+    result = factory.SubFactory(FeatureEffectsResponseResultFactory)
+    _result_as_dict = factory.LazyAttribute(lambda obj: _expand_condensed(obj.result))
+
+
+def _expand_condensed(result_obj):
+    whole_dict = {}
+    for output, feature_dict in result_obj["outputs"].items():
+        whole_dict[output] = {}
+        for feature, values in feature_dict.items():
+            whole_dict[output][feature] = dict(zip(result_obj["materials"], values))
+    return whole_dict