Missing method implementations in RefinementAgent #1

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1. Carringbrinks commented on Aug 28, 2025

   

   Carringbrinks

   on Aug 28, 2025

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   @ASIWU Hi, how did you solve this problem? I also encountered the same problem as you.
2. mhSepehri commented on Sep 2, 2025

   

   mhSepehri

   on Sep 2, 2025

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   Hi, I encountered the same problem during Task Analysis. Did you find any manual fix to this problem?
3. ASIWU commented on Sep 4, 2025

   

   ASIWU

   on Sep 4, 2025

   Author

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   @Carringbrinks @mhSepehri Sorry, I haven't found a solution yet.
4. Amazingren commented on Sep 5, 2025

   

   Amazingren

   on Sep 5, 2025

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   Dear all @Carringbrinks @ASIWU @mhSepehri @Jiahao-Gao @tangxiangru ,

   I also encountered the same problem during reproduction. Are there any solutions you guys have already found or suggested?

   Best regards and many thx,
5. mhSepehri commented on Sep 5, 2025

   

   mhSepehri

   on Sep 5, 2025

   Last edited by mhSepehri

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   @Amazingren @ASIWU @Carringbrinks

   You can add blocks of code like these inside RefinementAgent class of cellforge/Task_Analysis/refinement_agent.py and temporarily fix the AttributeError.

    def _format_dataset_refinement_prompt(self, dataset_info: dict, context: dict) -> str:
           """
           Format a prompt for refining dataset descriptions.
           """
           return (
               "You are an expert bioinformatics assistant. Refine the following dataset "
               "description so that it is concise, standardized, and ready for analysis. "
               "Preserve important details such as organism, tissue, assay, technology, "
               "and sample size.\n\n"
               f"DATASET INFO:\n{dataset_info}\n\n"
               f"CONTEXT:\n{context}\n\n"
               "REFINED DESCRIPTION:"
           )
   

       def _format_problem_refinement_prompt(self, problem_statement: str, context: dict) -> str:
           """
           Format a prompt for refining problem statements.
           """
           return (
               "You are an expert research planner. Refine the following research problem "
               "statement to be clear, precise, and suitable for inclusion in a research "
               "plan. Keep the scientific intent intact.\n\n"
               f"PROBLEM STATEMENT:\n{problem_statement}\n\n"
               f"CONTEXT:\n{context}\n\n"
               "REFINED PROBLEM:"
           )
   

       def _format_baseline_refinement_prompt(self, baseline_info: str, context: dict) -> str:
           """
           Format a prompt for refining baseline assessments.
           """
           return (
               "You are an expert reviewer. Refine the following baseline assessment so that "
               "it is clear, concise, and captures the key findings. Ensure terminology is "
               "consistent with standard biomedical reporting.\n\n"
               f"BASELINE INFO:\n{baseline_info}\n\n"
               f"CONTEXT:\n{context}\n\n"
               "REFINED BASELINE ASSESSMENT:"
           )
   
6. Amazingren commented on Sep 5, 2025

   

   Amazingren

   on Sep 5, 2025

   More actions

   @Amazingren @ASIWU @Carringbrinks

   You can add a blocks of code like this inside RefinementAgent class of cellforge/Task_Analysis/refinement_agent.py and temporarily fix the AttributeError.

    def _format_dataset_refinement_prompt(self, dataset_info: dict, context: dict) -> str:
           """
           Format a prompt for refining dataset descriptions.
           """
           return (
               "You are an expert bioinformatics assistant. Refine the following dataset "
               "description so that it is concise, standardized, and ready for analysis. "
               "Preserve important details such as organism, tissue, assay, technology, "
               "and sample size.\n\n"
               f"DATASET INFO:\n{dataset_info}\n\n"
               f"CONTEXT:\n{context}\n\n"
               "REFINED DESCRIPTION:"
           )
   

       def _format_problem_refinement_prompt(self, problem_statement: str, context: dict) -> str:
           """
           Format a prompt for refining problem statements.
           """
           return (
               "You are an expert research planner. Refine the following research problem "
               "statement to be clear, precise, and suitable for inclusion in a research "
               "plan. Keep the scientific intent intact.\n\n"
               f"PROBLEM STATEMENT:\n{problem_statement}\n\n"
               f"CONTEXT:\n{context}\n\n"
               "REFINED PROBLEM:"
           )
   

       def _format_baseline_refinement_prompt(self, baseline_info: str, context: dict) -> str:
           """
           Format a prompt for refining baseline assessments.
           """
           return (
               "You are an expert reviewer. Refine the following baseline assessment so that "
               "it is clear, concise, and captures the key findings. Ensure terminology is "
               "consistent with standard biomedical reporting.\n\n"
               f"BASELINE INFO:\n{baseline_info}\n\n"
               f"CONTEXT:\n{context}\n\n"
               "REFINED BASELINE ASSESSMENT:"
           )
   

   Great! Thx for sharing this experience!

   Bests,