Merge pull request #19 from fadynakhla/wian/fixing

some fixes

dr_claude/datamodels.py

@@ -33,14 +33,17 @@ def __hash__(self: HasUMLSClass) -> int:
         return hash(self.umls_code)
 
     def __eq__(self: HasUMLSClass, other: object) -> bool:
-        return isinstance(other, HasUMLS) and self.umls_code == other.umls_code
+        return (
+            isinstance(other, HasUMLS)
+            and self.umls_code == other.umls_code
+            and self.name
+        )
 
     cls.__hash__ = __hash__
     cls.__eq__ = __eq__
     return cls
 
 
-@set_umls_methods
 class Symptom(pydantic.BaseModel):
     """
     Symptom
@@ -53,6 +56,9 @@ class Symptom(pydantic.BaseModel):
     class Config:
         frozen = True
 
+    def __eq__(self, other):
+        return self.name == other.name and self.umls_code == other.umls_code
+
 
 @set_umls_methods
 class Condition(pydantic.BaseModel):
@@ -70,7 +76,6 @@ class Config:
         frozen = True
 
 
-@set_umls_methods
 class WeightedSymptom(Symptom):
     """
     Weight
@@ -81,6 +86,9 @@ class WeightedSymptom(Symptom):
     class Config:
         frozen = True
 
+    def __eq__(self, other):
+        return self.name == other.name and self.umls_code == other.umls_code
+
 
 class DiseaseSymptomKnowledgeBase(pydantic.BaseModel):
     condition_symptoms: Dict[Condition, List[WeightedSymptom]]
@@ -151,6 +159,8 @@ def to_numpy(kb: DiseaseSymptomKnowledgeBase) -> ProbabilityMatrix:
 
         ## the antagonist
         probas = np.zeros((len(symptom_idx), len(disease_idx)))
+        symptom_idx = dict(symptom_idx)
+        disease_idx = dict(disease_idx)
 
         ## fill noise vals
         for symptom, index in symptom_idx.items():
@@ -159,7 +169,10 @@ def to_numpy(kb: DiseaseSymptomKnowledgeBase) -> ProbabilityMatrix:
         ## fill known probas
         for condition, symptoms in kb.condition_symptoms.items():
             for symptom in symptoms:
-                probas[symptom_idx[symptom], disease_idx[condition]] = symptom.weight
+                probas[
+                    symptom_idx[SymptomTransformer.to_symptom(symptom)],
+                    disease_idx[condition],
+                ] = symptom.weight
 
         return ProbabilityMatrix(
             matrix=probas,

tests/test_mcts.py

@@ -1,8 +1,9 @@
 import copy
 import random
-from typing import Callable, Collection, Self
+from typing import Callable, Collection
 
 import loguru
+from loguru import logger
 
 from dr_claude import datamodels
 from dr_claude.mcts import action_states
@@ -58,10 +59,10 @@ def log_wrapper(state: ConvergenceTestState) -> float:
 
 def test_convergence():
     ## load the knowledge base
-    reader = kb_reading.NYPHKnowldegeBaseReader("data/NYPHKnowldegeBase.html")
+    # reader = kb_reading.NYPHKnowldegeBaseReader("data/NYPHKnowldegeBase.html")
+    reader = kb_reading.CSVKnowledgeBaseReader("data/ClaudeKnowledgeBase.csv")
     kb = reader.load_knowledge_base()
     matrix = datamodels.DiseaseSymptomKnowledgeBaseTransformer.to_numpy(kb)
-
     ## create the initial state
     conditions = list(matrix.columns.keys())
     the_condition = conditions[0]  # TODO chose condiiton here
@@ -71,23 +72,28 @@ def test_convergence():
         if matrix[symptom, the_condition] > symptom.noise_rate
     ]
     state = ConvergenceTestState(matrix, discount_rate=1e-9)
+    # state = action_states.SimulationNextActionState(matrix, discount_rate=1e-9)
+
     state.set_condition(the_condition, the_symptoms)
-    state.pertinent_pos.update(random.choices(the_symptoms, k=2))
+    state.pertinent_pos.update(random.choices(the_symptoms, k=1))
 
     ## Rollout policy
-    rollout_policy = action_states.RandomRollOutPolicy()
+    rollout_policy = action_states.ArgMaxDiagnosisRolloutPolicy()
     rollout_policy = logtrueconditionhook(rollout_policy)
 
     ## create the initial state
     searcher = mcts.mcts(timeLimit=3000, rolloutPolicy=rollout_policy)
 
     action = None
     while not isinstance(action, datamodels.Condition):
+        if action is not None:
+            assert isinstance(action, datamodels.Symptom)
         action = searcher.search(initialState=state)
-        assert isinstance(action, datamodels.Symptom)
         if action in the_symptoms:
+            logger.info("got a pertinent positive: {}", action)
             state.pertinent_pos.add(action)
         else:
+            logger.info("got a pertinent negative: {}", action)
             state.pertinent_neg.add(action)
         loguru.logger.info(f"action={action}")
     diagnosis = action