deprecated/early_sft_checkpoint/DEPRECATION.md

# deprecated/early_sft_checkpoint/

Files in this folder were generated using the **broken SFT model.safetensors checkpoint**
that was the default in `UCL-CSSB/PlasmidGPT-SFT` until the 2026-05-02 cleanup commit
`daeaabf`. The HF repo had two safetensors files, and `AutoModelForCausalLM.from_pretrained`
defaulted to a Base-clone duplicate. The corrected checkpoint generates substantively
different outputs (see `evaluation/eight_prompt/SFT/` for the post-fix data).

Original locations on the bucket (before move):
- `evaluation/temperature_sweep/SFT_t0.95/` — T=0.95 SFT generations + qc
- `rejection_sampling_v2/direct/SFT/` — original Table 4 direct SFT cell (was reported as 7.15%)
- `rejection_sampling_v2/best_of_16/SFT/` — original Table 4 best-of-16 SFT cell (was reported as 32.4%)

The Base + GRPO cells in `rejection_sampling_v2/` are unaffected and remain in their
original locations to preserve Table 4 reproducibility for the original paper protocol.

For the camera-ready, the canonical SFT analyses live under:
- `evaluation/eight_prompt/SFT/` — main 8-prompt eval, T=1.0, pass rate 10.975%
- `mfe/SFT_real/` — MFE on corrected-checkpoint generations
- `continuation_benchmark/eval_set_656/` — held-out continuation/surprisal
- `rejection_v3/SFT/` — 8-prompt rejection sampling with corrected SFT (10.87%)