File size: 2,880 Bytes
1fac52c | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | """Use Carbon-X as a tool for any chat model with OpenAI-style tool calling.
Serve Carbon-X first: vllm serve HuggingFaceBio/Carbon-X --trust-remote-code
Then set the agent client and model below and run: python agent_tool.py
"""
import json
from openai import OpenAI
carbon = OpenAI(base_url="http://localhost:8000/v1", api_key="EMPTY")
def ask_carbon(question: str, sequences: dict[str, str], context: str = "") -> str:
"""Ask Carbon-X a question about one or more named DNA sequences."""
parts = [context, question] if context else [question]
parts += [f"{name}: <dna>{seq}</dna>" for name, seq in sequences.items()]
response = carbon.chat.completions.create(
model="HuggingFaceBio/Carbon-X",
messages=[{"role": "user", "content": "\n\n".join(parts)}],
max_tokens=4096,
extra_body={"chat_template_kwargs": {"enable_thinking": False}},
)
return response.choices[0].message.content
sequences = {"reference.fa": "ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGG",
"variant.fa": "ATGGTGCATCTGACTCCTGTGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGG"}
carbon_tool = {
"type": "function",
"function": {
"name": "ask_carbon",
"description": (
"Ask Carbon-X, a DNA language model, a question about DNA sequences: variant effects, "
"regulatory elements, organism of origin, sequence features. Refer to sequences by name; "
"do not paste DNA. Its answers are model predictions, not verified facts."
),
"parameters": {
"type": "object",
"properties": {
"question": {"type": "string", "description": "One self-contained question."},
"sequences": {"type": "array", "items": {"type": "string", "enum": list(sequences)}},
"context": {"type": "string", "description": "Known gene, coordinates or annotations, if any."},
},
"required": ["question", "sequences"],
},
},
}
agent = OpenAI() # the agent model's provider
messages = [
{"role": "system", "content": "For questions about DNA, consult Carbon-X with the ask_carbon tool before answering."},
{"role": "user", "content": "variant.fa differs from reference.fa by one base. Is the change likely benign or pathogenic?"},
]
while True:
reply = agent.chat.completions.create(model="<agent model>", messages=messages, tools=[carbon_tool])
message = reply.choices[0].message
messages.append(message)
if not message.tool_calls:
break
for call in message.tool_calls:
args = json.loads(call.function.arguments)
answer = ask_carbon(args["question"], {name: sequences[name] for name in args["sequences"]}, args.get("context", ""))
messages.append({"role": "tool", "tool_call_id": call.id, "content": answer})
print(message.content)
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