# RRoG-GNN

This is the working repo for RRoG/TRM-on-GNN experiments. It contains the
current experiment runner, diagnostic prototypes, paper references, scripts, and
tracked JSON/log/summary outputs.

Core rule:

```text
view/graph aggregation happens once; recursive compute is edge-free hidden-state refinement.
```

The main reported table is:

```text
Task x Backbone -> classic baseline
Task x Backbone x fixed-RRoG -> delta against the matching classic row
```

`classic` is the non-RRoG baseline for every backbone: `T=0`, `n_sup=1`.

## One-command Run On 2x A6000

On a clean machine with two visible GPUs:

```bash
git clone git@github.com:YurenHao0426/rrog.git
cd rrog
./scripts/setup_and_run_two_a6000.sh
```

Defaults:

- GPU0: `zinc-cycle56` over 17 backbones, `classic + fixed-rrog`
- GPU1: `ogbg-molhiv` over 17 backbones, `classic + fixed-rrog`
- Results: `runs/*.json`
- Logs: `logs/*.log`
- Summaries: `summaries/*.md`

If the environment already has compatible `torch`, `torch_geometric`, and `ogb`:

```bash
SKIP_SETUP=1 ./scripts/setup_and_run_two_a6000.sh
```

To override CUDA wheel index during setup:

```bash
TORCH_INDEX_URL=https://download.pytorch.org/whl/cu121 ./scripts/setup_env.sh
```

## Common Commands

Smoke test:

```bash
./scripts/setup_env.sh
DEVICE=cuda:0 ./scripts/run_smoke.sh
```

Run the paired ZINC matrix only:

```bash
DEVICE=cuda:0 EPOCHS=200 ./scripts/run_zinc_cycle56_full.sh
```

Run one OGB molecular task:

```bash
TASK=ogbg-molhiv DEVICE=cuda:1 EPOCHS=100 ./scripts/run_ogb_mol_task_full.sh
```

Run the same OGB task with the lighter fixed recursion used by the ZINC sweep:

```bash
TASK=ogbg-molhiv DEVICE=cuda:1 EPOCHS=100 FIXED_T=1 FIXED_NS=3 ./scripts/run_ogb_mol_task_full.sh
```

Run all selected OGB molecular tasks serially on one GPU:

```bash
DEVICE=cuda:1 ./scripts/run_ogb_mol_all_tasks.sh
```

Run the corrected stream-ACT sweep on two GPUs:

```bash
EPOCHS=100 SEEDS=0 ./scripts/run_ogb_act_two_gpu.sh
```

Defaults:

- GPU0: `ogbg-molhiv ogbg-molbbbp ogbg-molsider ogbg-molbace`
- GPU1: `ogbg-molesol ogbg-mollipo ogbg-moltox21 ogbg-molclintox`
- Every task runs all 17 backbones.
- ACT config: `T=1`, `n_sup=3`, `halt_max=8`, `halt_min=2`, `halt_target=loss`, `loss_threshold=0.2`, `halt_exploration=0.1`, `lam_q=0.1`, `q_warmup=0`, `act_train_mode=stream`.

Optional ACT variants:

```bash
# Add FreeSolv as a separate regression stress test.
TASKS_GPU0="ogbg-molfreesolv" TASKS_GPU1="" ./scripts/run_ogb_act_two_gpu.sh

# Classification-only exact-halt target.
TASKS_GPU0="ogbg-molhiv ogbg-molbbbp ogbg-molsider" \
TASKS_GPU1="ogbg-molbace ogbg-moltox21 ogbg-molclintox" \
HALT_TARGET=exact ./scripts/run_ogb_act_two_gpu.sh

# More robust but longer seed sweep.
SEEDS="0 1 2" ./scripts/run_ogb_act_two_gpu.sh
```

Collect summaries:

```bash
./scripts/collect_results.sh
```

Audit existing results without GPU:

```bash
python3 scripts/audit_results.py --min-epochs 10
```

This writes `analysis/result_audit.md`, `analysis/result_cells.csv`,
`analysis/paired_deltas.csv`, `analysis/delta_summary.csv`, and
`analysis/coverage.csv`.

Render a delta table PNG:

```bash
python3 scripts/render_delta_table.py \
  --title "Fixed RRoG Test Delta vs Classic" \
  --out analysis/fixed_rrog_delta_matrix.png
```

Negative raw deltas are rendered as `-`: the deployable system can fall back to
the matching classic one-step GNN, so those cells mean no confirmed RRoG gain.

Render the ZINC-only row:

```bash
python3 scripts/render_delta_table.py \
  --compute-label fixed-rrog-T1-ns3+trace \
  --label-overrides "" \
  --datasets zinc-cycle56 \
  --out analysis/zinc_delta_table.png
```

## Backbones

The implemented 2D view/backbone list is shared across ZINC and OGB:

```text
gin, gine, gcn, graphsage, gatv2, graphconv, transformer, pna,
gen, film, resgated, tag, sgc, cheb, arma, mf, appnp
```

For ZINC `gine`, there are no bond features, so GINE uses a learned constant edge token.
For OGB molecular tasks, GINE and edge-aware backbones use OGB bond encodings.

## Notes

- Runs are resumable at the cell level: scripts skip existing expected JSON files.
- ZINC cycle-count cache is generated under `data/cycle_cache`.
- OGB datasets are downloaded under `data/ogb`.
- Override data/runs locations with `RROG_DATA_DIR` and `RROG_RUNS_DIR`.
- Large artifacts are intentionally not versioned in Git: `data/`, checkpoints,
  `*.pt`, and `*.pth` are ignored. Use external storage or Git LFS if those need
  to be shared.

## Upload Results

After a remote machine finishes:

```bash
git pull
git add -f runs/*.json logs/*.log summaries/*.md
git commit -m "Add stream ACT OGB results"
git push
```