Update llmeval.py

llmeval.py

@@ -42,16 +42,16 @@ class LLM_as_Evaluator():
         
         SYSTEM='''
 Task:
-Evaluate the biological quality of a prompt, research data, paradigm list, and the selected paradigm on a 0–1 continuous scale.
+Evaluate the biological quality of a prompt, research data, paradigm list, and response on a 0–1 continuous scale.
 
 Goal:
 Assess:
 
 Whether the Prompt is clear, biologically specific, and aligned with the Research Data and the Paradigm List.
 
-Whether the selected Paradigm is biologically relevant, mechanistically coherent, and experimentally actionable based on the Research Data.
+Whether the response is biologically relevant, mechanistically coherent, and experimentally actionable based on the Research Data.
 
-Whether the selected Paradigm is correctly chosen from the Paradigm List in light of the Research Data.
+Whether the response is correctly chosen from the Paradigm List in light of the Research Data.
 
 Scoring Guide (0–1 continuous scale):
 
@@ -59,15 +59,15 @@ Score 1.0 if:
 
 The Prompt is clear, biologically detailed, and well-aligned to the Research Data and Paradigm List.
 
-The selected Paradigm correctly reflects a biologically valid interpretation of the Research Data and is appropriately drawn from the Paradigm List.
+The response correctly reflects a biologically valid interpretation of the Research Data and is appropriately drawn from the Paradigm List.
 
 Lower scores if:
 
 The prompt is vague or misaligned with the research context.
 
-The selected paradigm is biologically irrelevant, mechanistically incoherent, or mismatched with the Research Data.
+The response is biologically irrelevant, mechanistically incoherent, or mismatched with the Research Data.
 
-The selected paradigm is not the most plausible or supported choice from the Paradigm List.
+The paradigm is not the most plausible or supported choice from the Paradigm List.
 
     
 Your output must begin with Score: and contain only two fields: Score: and Reasoning:. No extra commentary, no markdown, no explanations before or after.:
@@ -97,7 +97,7 @@ Think step by step
     def Observation_LLM_Evaluator(self,promptversion):
         SYSTEM='''
 Task:
-Evaluate the biological quality of a prompt , research data . response triplet from an Observations Generator Agent on a 0–1 continuous scale.
+Evaluate the biological quality of a prompt , research data and response  from an Observations Generator Agent on a 0–1 continuous scale.
 
 Goal:
 Assess:
@@ -122,6 +122,8 @@ The response includes irrelevant, biologically implausible, contradictory, or tr
 
 Your output must begin with Score: and contain only two fields: Score: and Reasoning: No extra commentary, no markdown, no explanations before or after.
 
+Think step by step
+
 '''
         data_to_evaluate=dbe.GetData(promptversion)
         messages =[
@@ -146,36 +148,42 @@ Your output must begin with Score: and contain only two fields: Score: and Reaso
     def  Anomaly_LLM_Evaluator(self,promptversion):
         SYSTEM='''
 Task:
-Evaluate the biological quality of a prompt–observations–response triplet from an Anomaly Detector Agent on a 0–1 continuous scale.
+Evaluate the biological quality of a prompt , observations , paradigms and response  from an Anomaly Detector Agent on a 0–1 continuous scale.
 
 Goal:
 Assess:
+
 Whether the Prompt clearly defines the biological context and intent.
 
 Whether the Observations are biologically plausible and internally consistent.
 
-Whether the Response correctly identifies biologically relevant inconsistencies between the Paradigm and Observations.  
+Whether the Paradigms are plausible biological frameworks given the context.
+
+Whether the Response correctly identifies biologically relevant inconsistencies or contradictions between the Paradigms and the Observations.
 
 Scoring Guide (0–1 continuous scale):
 
 Score 1.0 if:
 
-The prompt is clear and biologically grounded.
+The Prompt is clear, biologically grounded, and well-scoped.
 
-The response lists true, biologically meaningful anomalies based on the observations.
+The Observations are plausible and logically consistent.
 
-All major contradictions or gaps are captured.
+The Response accurately identifies true anomalies—i.e., meaningful contradictions or gaps—between the Paradigms and the Observations.
+
+All major conflicts are captured.
 
 Lower scores if:
 
-The prompt is vague.
+The Prompt is vague or misaligned with the context.
+
+Observations are biologically implausible or incoherent.
 
-The response misses key anomalies, adds irrelevant ones, or shows poor biological reasoning.
+The Response overlooks key inconsistencies, includes irrelevant anomalies, or shows poor biological reasoning.
 
 Your output must begin with Score: and contain only two fields: Score: and Reasoning: No extra commentary, no markdown, no explanations before or after.
-Output:
-Score: 0.2
-Reasoning: Your reasoning.
+
+Think step by step
 '''
 
         data_to_evaluate=dbe.GetData(promptversion)