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updated to include provenance information

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This commit is contained in:
Karthik Soman
2024-03-13 01:31:29 -07:00
parent 0af80b5cbd
commit c53d325fce
2 changed files with 9 additions and 8 deletions
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6
kg_rag/rag_based_generation/GPT/drug_repurposing_v2.py
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@@ -35,14 +35,14 @@ print('')
question = input("Question : ")
question_template = f'''
To the question asked at the end, answer by referring the context. Explain with reasons and give Provenance for the reasons which you can find from the context provided. See example below
To the question asked at the end, answer by referring the context. Explain with reasons. See example below
Example 1:
Question:
What drugs can be repurposed to treat disease X?
Context:
Compound Alizapride DOWNREGULATES Gene APOE. Gene APOE ASSOCIATES Disease X. Gene TTR encodes Protein Transthyretin (ATTR). Compound Acetylcysteine treats Disease X.
Compound Alizapride DOWNREGULATES Gene APOE and Provenance of this association is XX. Gene APOE ASSOCIATES Disease X and Provenance of this association is YY. Gene TTR encodes Protein Transthyretin (ATTR) and Provenance of this association is ZZ. Compound Acetylcysteine treats Disease X and Provenance of this association is PP.
Answer:
Since Alizapride downregulates gene APOE and APOE is associated with Disease X, Alizapride can be repurposed to treat Disease X.
Since Alizapride downregulates gene APOE (Provenance XX) and APOE is associated with Disease X (Provenance YY), Alizapride can be repurposed to treat Disease X.
Question:
{question}
'''

11
system_prompts.yaml
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@@ -93,13 +93,14 @@ DRUG_REPURPOSING_V2: |
Gene ASSOCIATES Disease
Then stitch these associations to give your final answer to the question.
More importantly, DO NOT consider 'Compound TREATS Disease' as the repurposing candidate.
Do not forget to give Provenance information which you can find from the context provided.
For example:
Question:
What drugs can be repurposed to treat disease X?
Context:
Compound X DOWNREGULATES Gene Y.
Gene Y ASSOCIATES Disease X.
Compound Y UPREGULATES Gene Z.
Gene Z ASSOCIATES Disease X.
Compound X DOWNREGULATES Gene Y and Provenance for this information is XX.
Gene Y ASSOCIATES Disease X and Provenance for this information is YY.
Compound Y UPREGULATES Gene Z and Provenance for this information is ZZ.
Gene Z ASSOCIATES Disease X and Provenance for this information is PP.
Answer:
Since Compound X downregulates Gene Y and Gene Y is associated with Disease X, Compound X can be repurposed to treat Disease X. Since Compound Y upregulates Gene Z and Gene Z is associated with Disease X, Compound Y can be repurposed to treat Disease X.
Since Compound X downregulates Gene Y (provenance is XX) and Gene Y is associated with Disease X (provenance YY), Compound X can be repurposed to treat Disease X. Since Compound Y upregulates Gene Z (Provenance ZZ) and Gene Z is associated with Disease X (Provenance PP), Compound Y can be repurposed to treat Disease X.