How to deploy Carbon on Lambda

TL;DR: nucleotide throughput

Both Carbon-500M and Carbon-3B run on a single NVIDIA A10 GPU, served with SGLang or vLLM. Because Carbon tokenizes DNA as non-overlapping 6-mers, each token carries roughly 6 base pairs, so the token rates below correspond to roughly 6× as many base pairs per second.

Carbon-500M

1× NVIDIA A10 GPU, workload 2048 input / 6000 output tokens, 32 concurrent requests.

Carbon-3B

1× NVIDIA A10 GPU, workload 2048 input / 8192 output tokens, 12 concurrent requests.

Benchmark command

The two sizes were benchmarked at different workloads (Carbon-500M at 6000 output tokens / 32 concurrent; Carbon-3B at 8192 output tokens / 12 concurrent), reflecting the longer generations and tighter memory budget of the larger model. Re-run the Carbon-3B benchmark:

vllm bench serve \
  --model HuggingFaceBio/Carbon-3B \
  --served-model-name Carbon-3B \
  --endpoint /v1/completions \
  --random-input-len 2048 --random-output-len 8192 \
  --num-prompts 256 --max-concurrency 12

Copy ("Tokens" here are 6-mer DNA tokens. Multiply by ~6 for base pairs per second.)

Background

Carbon is a DNA language model: a Llama-style LLM whose vocabulary is a genetic sequence instead of English. It comes from HuggingFaceBio (Hugging Face, Zhongguancun Academy, and TIGEM / University of Naples "Federico II"). The family ships in three sizes, two of which are covered by this card: Carbon-500M and Carbon-3B (the flagship), with a larger Carbon-8B in the family. Because Carbon-3B ships as a stock LlamaForCausalLM, both covered sizes run in vLLM and SGLang with no custom serving code and fit on a single NVIDIA A10 GPU.

Carbon's value comes down to one tradeoff: resolution versus reach. Reading DNA one base at a time gives maximum precision but runs slow and expensive; grouping bases into chunks goes far faster but blurs the single-base detail that clinical variant tasks depend on. Carbon takes the fast path, tokenizing DNA as non-overlapping 6-mers (six bases per token). It then recovers the lost precision with a training objective called Factorized Nucleotide Supervision (FNS). FNS factorizes each 6-mer prediction into six per-position softmaxes over {A, C, G, T}, so the model generates at single-nucleotide granularity and exposes per-base likelihoods for variant scoring.

Underneath, Carbon-3B runs as a standard 30-layer Llama decoder (hidden size 3072, FFN 8448, 32 attention heads with 4 KV groups, SwiGLU, RMSNorm). Its tokenizer mixes two schemes: fixed 6-mer tokens for DNA plus the full Qwen3 BPE vocabulary for English, roughly 156k entries in all, which is why DNA must be wrapped in <dna>…</dna> and kept to uppercase ACGT. Native context runs to 32,768 tokens (≈ 197 kbp) and extends to 65,536 (≈ 393 kbp) with a YaRN factor=4. Pretraining used 1T 6-mer tokens (≈ 6T base pairs) on a staged Cross-Entropy then FNS objective, with the data mix shifted toward mRNA and prokaryotic sequences late in training.

On HuggingFaceBio's zero-shot evaluations, Carbon-3B matches the much larger Evo2-7B on sequence recovery, variant-effect prediction, and perturbation discrimination while running several times faster. The card reports >150× faster generation than the Evo2 family and >100,000 base pairs/sec on a single NVIDIA H100 GPU. Against GENERator-v2-3B, its same-size sibling, Carbon-3B wins every benchmarked task.

Model specifications

• Author: HuggingFaceBio
• Architecture: Decoder-only Llama-style Transformer (GQA, SwiGLU, RMSNorm) with Factorised Nucleotide Supervision (FNS)
• Domain: DNA / genomic foundation model (nucleotide sequence)
• Tokenization: non-overlapping 6-mer DNA (~6 bp/token); shared 155,776-entry vocabulary (4,096 DNA 6-mers + DNA/metadata tags + Qwen3 BPE)
• License: Apache 2.0

The two sizes share the same architecture, tokenizer, and DNA template, differing only in scale and native context:

Carbon-500M is useful both as a standalone genomic model on minimal hardware and as a draft model for speculative decoding on Carbon-3B / Carbon-8B (they share a tokenizer and DNA template).

Hardware requirements

Both Carbon sizes fit comfortably on a single NVIDIA A10 GPU (23 GB) in BF16

• Carbon-500M: 1× NVIDIA A10 GPU
• Carbon-3B: 1× NVIDIA A10 GPU

Deployment and benchmarking

Deploying Carbon

Both sizes can be served with SGLang or vLLM on a single NVIDIA A10 GPU. The commands below deploy the flagship Carbon-3B; to serve Carbon-500M instead, swap the model path and served name (and, for SGLang, drop --attention-backend triton and raise --mem-fraction-static to 0.9)

1. Launch an instance with 1× NVIDIA A10 GPU from the Lambda Cloud Console using the GPU Base 24.04 image.
2. Connect to your instance via SSH or the JupyterLab terminal. See Connecting to an instance for detailed instructions.
3. Start the inference server using either SGLang or vLLM:

SGLangvLLM

docker run -d --gpus all \
  --ipc=host -p 8000:8000 \
  -v ~/.cache/huggingface:/root/.cache/huggingface \
  lmsysorg/sglang:nightly-dev-cu12-20260529-a8cfae0b \
  python3 -m sglang.launch_server \
    --model-path HuggingFaceBio/Carbon-3B \
    --served-model-name Carbon-3B \
    --tp 1 \
    --host 0.0.0.0 --port 8000 \
    --trust-remote-code \
    --mem-fraction-static 0.85 \
    --attention-backend triton

docker run -d --gpus all \
  --ipc=host -p 8000:8000 \
  -v ~/.cache/huggingface:/root/.cache/huggingface \
  vllm/vllm-openai:nightly-22a58640b4563f5945aa2052e9e61d425351588d \
  --model HuggingFaceBio/Carbon-3B \
  --served-model-name Carbon-3B \
  --tensor-parallel-size 1 \
  --host 0.0.0.0 --port 8000 \
  --max-model-len auto \
  --trust-remote-code \
  --gpu-memory-utilization 0.9

Notable flags:

• --trust-remote-code is required for both sizes as Carbon's base-pair-level generation/scoring lives in a custom fns modeling branch loaded from the model repo.
• --attention-backend triton (Carbon-3B SGLang) selects the Triton attention kernel, which is the reliable path for Carbon-3B on the NVIDIA A10 GPU.
• --mem-fraction-static is set slightly lower for Carbon-3B (0.85 vs 0.9) to leave headroom for the larger weights on a single A10.

Verify the server

Either command launches an inference server with an OpenAI-compatible API on port 8000. Verify it:

curl -X GET http://localhost:8000/v1/models \
  -H "Content-Type: application/json"

You should see Carbon-3B (or Carbon-500M) listed in the response.

Benchmarking results: Carbon

The two sizes were benchmarked at different workloads. Carbon-500M: 2048 input / 6000 output tokens, 32 concurrent requests. Carbon-3B: 2048 input / 8192 output tokens, 12 concurrent requests. All on a single NVIDIA A10 GPU.

Carbon-500M

Token throughput:

Latency (Mean / P99 in ms):

Carbon-3B

Token throughput:

Latency (Mean / P99 in ms):

Next steps

Upstream

• Download Carbon-3B on Hugging Face
• Download Carbon-500M on Hugging Face

Downstream: genomics workflows

Because Carbon exposes per-base likelihoods and operates at single-nucleotide resolution via FNS, your self-hosted endpoint can drive standard genomic foundation-model tasks:

• Sequence embeddings. Encode DNA/RNA sequences (wrapped in <dna>…</dna>, uppercase ACGT) into hidden-state representations for downstream classifiers and clustering. The generation server above does not expose /v1/embeddings — start a separate instance in pooling mode (vLLM: add --runner pooling; SGLang: add --is-embedding), then call /v1/embeddings with the same <dna>…</dna> formatting.
• Variant-effect prediction (VEP). Score a variant by comparing the model's per-base likelihoods for the reference vs. alternate sequence. Carbon's 6-mer logits factorize exactly into per-position {A, T, C, G} distributions (the FNS objective), so you can recover single-base resolution straight from a standard vLLM server: launch it with --max-logprobs 4096 to cover the DNA vocabulary, request prompt_logprobs, then marginalize each 6-mer distribution to per-base client-side. The score_sequence method on the fns branch (Carbon-*-remote) is a drop-in reference for that marginalization. Carbon-3B is competitive with Evo2-7B on BRCA2, ClinVar coding/non-coding, and TraitGym Mendelian.
• DNA generation. Generate biologically plausible sequences, with optional metadata conditioning on species type and gene-region type (e.g. <vertebrate_mammalian><protein_coding_region><dna>…). Temperature, top-p, exact base counts, and per-position masking all operate at nucleotide granularity on the model's fns branch.
• Long-context retrieval. Run Genomic needle-in-a-haystack tasks out to 393 kbp by enabling the YaRN factor=4 extension.
• Speculative decoding. Pair Carbon-500M as a draft model with Carbon-3B (or Carbon-8B) for lossless generation speedups, since they share a tokenizer and DNA template.

Tokenizer caution: Always wrap DNA in <dna>…</dna> — without the tag the input is silently routed through the English BPE vocabulary and performance collapses. Non-ACGT characters map to <oov>, and sequence lengths that are not a multiple of 6 are right-padded with A.

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