Carbon-X vs Qwen3.5-9B

Carbon-X

A DNA specialist cousin that another agent calls for variant-effect and sequence questions, with DNA kept on the machine. Hugging Face's Q4_K_M GGUF needs about 12 GB and Q8_0 about 19 GB, on llama.cpp b11742 or later. It isn't clinically validated, it isn't trained for tool calls or reasoning, and the card contradicts its own GGUF repository on llama.cpp support.

Qwen3.5-9B

A small dense vision-language cousin with trained tool calling, switchable thinking and a 262,144-token context, for local agent subtasks. Ollama's 4-bit build needs about 8 GB and the BF16 files about 24 GB, in every major runtime. The main risk is neglect, with no file changes since March, no replies from Qwen to reports and no safety results.

Carbon-X

1. Quickest start is llama-server -hf HuggingFaceBio/Carbon-X-GGUF:Q8_0 -ngl 99 -c 40960 --jinja --chat-template-kwargs '{"enable_thinking": false}' --temp 0.6 --top-p 0.95 --top-k 20 --min-p 0, on llama.cpp b11742 or later
2. With vLLM or Transformers pass trust_remote_code, and expect the tokenizer to fetch Qwen/Qwen3-4B-Base at a pinned revision on first load
3. Keep enable_thinking false and the card's sampling (temperature 0.6, top_p 0.95, top_k 20), the settings every reported result used
4. Keep DNA in files and pass sequences by name, compute positions and base changes in code and send them as context, the card says the model miscounts long sequences
5. Only A, C, G and T form 6-mers, so filter N and other IUPAC codes first or they become a single oov token
6. Strip the dna tags from answers if you need bare sequence, llama.cpp keeps them in the text
7. Cap max_tokens for next-base questions, long DNA generation is slow and degrades

Qwen3.5-9B

1. Smallest start is ollama run qwen3.5:9b (6.6 GB, q4_k_m)
2. On vLLM run vllm serve Qwen/Qwen3.5-9B --port 8000 --max-model-len 262144 --reasoning-parser qwen3 --enable-auto-tool-choice --tool-call-parser qwen3_coder, or tool calls come back as text
3. Tool calls use the XML style <tool_call><function=name><parameter=x>, not Hermes JSON, so use the qwen3_coder parser and not hermes
4. Thinking is on by default; pass chat_template_kwargs with enable_thinking false for short tasks, since /nothink isn't supported
5. There's no generation_config.json, so pass sampling yourself, temperature 1.0, top_p 0.95, top_k 20, presence_penalty 1.5 when thinking, or 0.7, 0.8, 20, 1.5 without
6. Keep at least 128K of context when thinking, and turn on YaRN only beyond 262,144 tokens
7. Validate JSON output yourself or use the runtime's guided decoding