| """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() |
| 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) |
|
|
