Makes sure the names can computed from benchmark object

MachineLearningLifeScience · Aug 7, 2024 · d55f0a8 · d55f0a8
1 parent 2db0107
commit d55f0a8
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Showing 5 changed files with 47 additions and 18 deletions.
diff --git a/src/poli/benchmarks/guacamol.py b/src/poli/benchmarks/guacamol.py
@@ -95,7 +95,7 @@ def __init__(
             evaluation_budget=evaluation_budget,
         )
 
-        self.problem_factory_names = [
+        self.problem_factories = [
             AlbuterolSimilarityProblemFactory(),
             AmlodipineMPOProblemFactory(),
             CelecoxibRediscoveryProblemFactory(),
@@ -122,7 +122,7 @@ def __init__(
         self.string_representation = string_representation
 
     def _initialize_problem(self, index: int) -> Problem:
-        problem_factory = self.problem_factory_names[index]
+        problem_factory = self.problem_factories[index]
 
         problem = problem_factory.create(
             string_representation=self.string_representation,

diff --git a/src/poli/benchmarks/pmo.py b/src/poli/benchmarks/pmo.py
@@ -86,7 +86,7 @@ def __init__(
             evaluation_budget=evaluation_budget,
         )
 
-        self.problem_factory_names.extend(
+        self.problem_factories.extend(
             [
                 JNK3ProblemFactory(),
                 GSK3BetaProblemFactory(),

diff --git a/src/poli/benchmarks/toy_continuous_functions_benchmark.py b/src/poli/benchmarks/toy_continuous_functions_benchmark.py
@@ -73,12 +73,12 @@ def __init__(
                 - set(SIX_DIMENSIONAL_PROBLEMS)
             )
         )
-        self.problem_factory_names = [ToyContinuousProblemFactory()] * len(
+        self.problem_factories = [ToyContinuousProblemFactory()] * len(
             self.function_names
         )
 
     def _initialize_problem(self, index: int) -> Problem:
-        problem_factory: ToyContinuousProblemFactory = self.problem_factory_names[index]
+        problem_factory: ToyContinuousProblemFactory = self.problem_factories[index]
 
         problem = problem_factory.create(
             function_name=self.function_names[index],
@@ -131,12 +131,10 @@ def __init__(
             evaluation_budget,
         )
         self.embed_in = [5, 10, 25, 50, 100]
-        self.problem_factory_names = [ToyContinuousProblemFactory()] * len(
-            self.embed_in
-        )
+        self.problem_factories = [ToyContinuousProblemFactory()] * len(self.embed_in)
 
     def _initialize_problem(self, index: int) -> Problem:
-        problem_factory: ToyContinuousProblemFactory = self.problem_factory_names[index]
+        problem_factory: ToyContinuousProblemFactory = self.problem_factories[index]
 
         problem = problem_factory.create(
             function_name="branin_2d",
@@ -186,12 +184,10 @@ def __init__(
             evaluation_budget,
         )
         self.embed_in = [None, 10, 25, 50, 100]
-        self.problem_factory_names = [ToyContinuousProblemFactory()] * len(
-            self.embed_in
-        )
+        self.problem_factories = [ToyContinuousProblemFactory()] * len(self.embed_in)
 
     def _initialize_problem(self, index: int) -> Problem:
-        problem_factory: ToyContinuousProblemFactory = self.problem_factory_names[index]
+        problem_factory: ToyContinuousProblemFactory = self.problem_factories[index]
 
         if index == 0:
             problem = problem_factory.create(

diff --git a/src/poli/core/abstract_benchmark.py b/src/poli/core/abstract_benchmark.py
@@ -7,7 +7,7 @@
 
 
 class AbstractBenchmark:
-    problem_factory_names: List[str] | List[AbstractProblemFactory]
+    problem_factories: List[AbstractProblemFactory]
     index: int = 0
 
     def __init__(
@@ -25,13 +25,13 @@ def __init__(
         self.evaluation_budget = evaluation_budget
 
     def __len__(self) -> int:
-        return len(self.problem_factory_names)
+        return len(self.problem_factories)
 
     def __getitem__(self, index: int) -> Problem:
         return self._initialize_problem(index)
 
     def __next__(self) -> Problem:
-        if self.index < len(self.problem_factory_names):
+        if self.index < len(self.problem_factories):
             self.index += 1
             return self._initialize_problem(self.index - 1)
         else:
@@ -48,6 +48,8 @@ def info(self) -> str:
     @property
     def problem_names(self) -> List[str]:
         return [
-            problem_factory.get_problem_name()
-            for problem_factory in self.problem_factory_names
+            problem_factory.__module__.replace(
+                "poli.objective_repository.", ""
+            ).replace(".register", "")
+            for problem_factory in self.problem_factories
         ]
diff --git a/src/poli/tests/benchmarks/test_benchmark_creation.py b/src/poli/tests/benchmarks/test_benchmark_creation.py
@@ -29,6 +29,37 @@ def test_creating_embedded_toy_continuous_functions_benchmark():
             f(x0)
 
 
+def test_names_from_guacamol_benchmark():
+    from poli.benchmarks import GuacaMolGoalDirectedBenchmark
+
+    assert GuacaMolGoalDirectedBenchmark(
+        string_representation="SMILES"
+    ).problem_names == [
+        "albuterol_similarity",
+        "amlodipine_mpo",
+        "celecoxib_rediscovery",
+        "deco_hop",
+        "fexofenadine_mpo",
+        "isomer_c7h8n2o2",
+        "isomer_c9h10n2o2pf2cl",
+        "median_1",
+        "median_2",
+        "mestranol_similarity",
+        "osimetrinib_mpo",
+        "perindopril_mpo",
+        "ranolazine_mpo",
+        "rdkit_logp",
+        "rdkit_qed",
+        "sa_tdc",
+        "scaffold_hop",
+        "sitagliptin_mpo",
+        "thiothixene_rediscovery",
+        "troglitazone_rediscovery",
+        "valsartan_smarts",
+        "zaleplon_mpo",
+    ]
+
+
 @pytest.mark.poli__tdc
 def test_creating_guacamol_benchmark():
     from poli.benchmarks import GuacaMolGoalDirectedBenchmark