# Thesis reproduction snapshot (`thesis_repro/`)

This folder on the **dataset** Hub mirrors gitignored outputs so a fresh Git clone can regenerate `thesis_manu_v2_6/` tables and figures.

| Resource | URL |
| --- | --- |
| Code | https://github.com/jasperyeoh/pevo-msa-primate-genomics |
| Checkpoints | https://huggingface.co/jasperyeoh2/pevo-msa-mlm-19way |
| Full experiment map | GitHub `EXPERIMENT_MAP.md` |

## Layout

| Path | Regenerates (LaTeX) |
| --- | --- |
| `phylo_msa1_outputs/VEP_*.csv` | `tab:vep_*`, `tab:strictv2_*`, `Fig2A_*`, appendix leaderboard |
| `phylo_msa1_outputs/vep_all_base_models/*.parquet` | Ablation / per-run VEP (optional) |
| `dna_foundation_benchmark_results_final/` | `tab:feng_*`, `fig:feng_*` |
| `thesis_manu_v2_6_artifacts/` | Matched-width strict-v2 bootstrap (May 2026) |

## Restore into Git clone

```bash
hf download jasperyeoh2/pevo-msa-grch38-19way --repo-type dataset --local-dir data_hf \
  --include 'thesis_repro/**'

REPO=pevo-msa-primate-genomics
mkdir -p $REPO/phylo_msa1/outputs/vep_all_base_models
cp data_hf/thesis_repro/phylo_msa1_outputs/VEP_*.csv $REPO/phylo_msa1/outputs/
cp data_hf/thesis_repro/phylo_msa1_outputs/vep_all_base_models/*.parquet \
   $REPO/phylo_msa1/outputs/vep_all_base_models/
cp -a data_hf/thesis_repro/dna_foundation_benchmark_results_final \
      $REPO/downstream_tasks/dna_foundation_benchmark/results_final
mkdir -p $REPO/thesis_manu_v2_6/artifacts
cp data_hf/thesis_repro/thesis_manu_v2_6_artifacts/* $REPO/thesis_manu_v2_6/artifacts/
```

## Regenerate LaTeX

```bash
cd $REPO/thesis_manu_v2_6/scripts
python3 gen_strictv2_ci_artifacts.py
python3 gen_feng_combined_seq_and_l7_auroc.py
```

Many CSVs are also tracked on **GitHub** — `git clone` alone may suffice without this download.