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fix: add tiktoken to main_cascade.py #2

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fix: add tiktoken to main_cascade.py #2

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0c9a444
fix: add tiktoken to main_cascade.py
BinglanLi Aug 28, 2025
0a7fe7f
fix: error caused by invalid output path
BinglanLi Aug 28, 2025
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7 changes: 7 additions & 0 deletions main_cascade.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@

from worker import AgentPhD

import tiktoken
MAX_TOKENS = 127900
encoding = tiktoken.encoding_for_model("gpt-4o")

## baseline
system = "You are an efficient and insightful assistant to a molecular biologist."
Expand Down Expand Up @@ -120,6 +123,10 @@ def GeneAgent(ID, genes):
pattern = re.compile(r'^[a-zA-Z0-9,.;?!*()_-]+$')
## send genes to GPT-4 and generate the original template of process name and analysis
try:
# Ensure output directories exist
os.makedirs("Outputs/GPT-4", exist_ok=True)
os.makedirs("Outputs/GeneAgent/Cascade", exist_ok=True)
os.makedirs("Verification Reports/Cascade", exist_ok=True)
prompt_baseline = baseline(genes)
first_step = prompt_baseline + system
token_baseline = encoding.encode(first_step)
Expand Down