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docs: attempt log for main merge sync and attention readout branch.

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demian3b
2026-04-17 10:44:05 +09:00
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@@ -104,3 +104,5 @@ This repository is intentionally pinned to CUDA 12.6 PyTorch wheels and matching
- 2026-04-16: bond_pair subgraph **full-graph trunk fuse**: subgraph GCN first-layer input is `concat(local_coords, full-graph node h)` (same-step trunk embedding, state-dependent—not static chemistry). Full run (`epochs=320`, same stab hyperparams as prior) yielded `mean_rmsd_100=2.620511` vs `2.606118` without fuse—slightly worse, so next axis is likely rotation/geodesic coupling or subgraph depth, not more static atom features.
- 2026-04-16: **Post-fuse strategy sweep (automation)**: implemented `--torsion-sub-gcn-layers` (subgraph depth ≤ trunk) and dedicated `sub_gcn_skip` for the subgraph stack; added `scripts/run_bond_pair_strategy_sweep.sh` to run six queued experiments in order—(E1) `rotation-loss=hybrid` α=0.5, (E2) `rotation-loss=mse`, (E3) `--torsion-sub-gcn-layers 4`, (E4) `--subgraph-lr-scale 0.4`, (E5) `--subgraph-lr-scale 0.15`, (E6) main `--lr 4.5e-4`—all with `bond_pair`, `gcn-residual`, `omega_max_norm=5`, stab clip `6`, default `subgraph_lr_scale=0.25` except E4/E5/E6 as noted. Run locally: `bash scripts/run_bond_pair_strategy_sweep.sh /path/to/sample.sdf` → `reports/bond_pair_strategy_sweep.tsv`; append each `mean_rmsd_100` line to this log after the run (this agent session could not complete long GPU sweeps end-to-end).
- 2026-04-17: GPU via project `.venv`: A/B on residual-geodesic (`gcn` hidden=512 layers=8, epochs=280, batch=24, lr=7e-4, weighted displacement, seed=1, eval-runs=100). Run A with `--ema-decay 0.999` reached `mean_rmsd_100=2.554015` (late epochs showed `train_mse=1000` fallback). Run B without EMA reached `mean_rmsd_100=2.350750`; `reports/latest_eval.json` and `artifacts/latest_eval_best_model.pt` left from Run B. On this pair, EMA best-train checkpoint hurt final RMSD vs online weights; no claim vs historical branch best `2.388103` (different wall-clock / step budget semantics).
- 2026-04-17: Fast-forward merged `attempt/post-main-doc-sync` into `main`; committed `BEST_PRACTICE.json` + `artifacts/best_model.pt` sync to anchor `mean_rmsd_100=2.350750` (command matches no-EMA residual-geodesic run).
- 2026-04-17: Branch `attempt/graph-readout-geodesic` (off updated `main`): identical budget vs anchor but `--graph-readout attention` reached `mean_rmsd_100=2.716856` with early `train_mse=1000` wall; worse than anchor `2.350750`; branch not for merging to `main`.