card: add metadata conditioning, YaRN, likelihood, FNS note

README.md

@@ -43,6 +43,14 @@ cd llama.cpp && cmake -B build && cmake --build build -j
     -n 64 --temp 0 -no-cnv
 ```
 
+### Metadata-conditioned generation
+
+```bash
+./build/bin/llama-completion -m carbon-8b-bf16.gguf \
+    -p '<vertebrate_mammalian><protein_coding_region><dna>ATGCGCTAG' \
+    -n 64 --temp 0 -no-cnv
+```
+
 ### Speculative decoding with Carbon-500M draft (~2x speedup)
 
 The 500M shares the HybridDNA vocab, so it's a near-ideal draft. Measured ~2.1x speedup at temp=0 with 87% accept rate on DNA prompts. Grab the draft GGUF first:
@@ -61,6 +69,40 @@ Then run with `--model-draft`:
     -n 256 --temp 0
 ```
 
+### Likelihood scoring
+
+The source card's Python `score()` function computes mean log-prob per DNA token. In llama.cpp the closest tools are `llama-perplexity` for corpus-level perplexity (`perplexity = exp(-mean_logprob)`):
+
+```bash
+# one prompt per line in dna_corpus.txt, each wrapped in <dna>...</dna>
+./build/bin/llama-perplexity -m carbon-8b-bf16.gguf -f dna_corpus.txt --ppl-stride 0
+```
+
+Or `llama-server` with `logprobs` for per-token log-probabilities:
+
+```bash
+./build/bin/llama-server -m carbon-8b-bf16.gguf --port 8080 &
+curl -s http://localhost:8080/completion -d '{
+  "prompt": "<dna>GGGCTATAAAGGCCATCGATCGATCGATCGATCGATCGATCG</dna>",
+  "n_predict": 0,
+  "n_probs": 1
+}' | jq '.completion_probabilities'
+```
+
+### Long context with YaRN (65k tokens ≈ 393 kbp)
+
+Mirrors the source card's `rope_scaling = {type: yarn, factor: 4.0, original_max_position_embeddings: 32768}`:
+
+```bash
+./build/bin/llama-completion -m carbon-8b-bf16.gguf \
+    -c 65536 --rope-scaling yarn --rope-scale 4 --yarn-orig-ctx 32768 \
+    -p '<dna>...' -n 64 --temp 0 -no-cnv
+```
+
+### Base-pair-level generation (FNS branch) — not supported
+
+The `revision="fns"` example from the source card needs custom modeling code (factorized nucleotide supervision head), which only the Python transformers path can load. llama.cpp can't run that branch.
+
 ## See also
 
 - Source weights: [HuggingFaceBio/Carbon-8B](https://huggingface.co/HuggingFaceBio/Carbon-8B)