mixes/README.md

# Training mixes

Each mix is a weighted, shuffled, materialized set of token shards (`.bin`/`.idx`/`.desc` +
`manifest.json`, per `molvae.data.format`), built from `../raw/` by [`mix_dataset.py`](mix_dataset.py).
The shards live on **S3** (`s3://mechanophore/molvae/tokens/<name>/`) and are mirrored under each
mix's `data/`. The `*.config.json` here is the exact, re-runnable spec.

## Builder
`mix_dataset.py` is torch-free (numpy + pyarrow + boto3 + huggingface_hub). Disk-backed & bounded-RAM:
**Phase A** streams each source once and fraction-samples it to disk (vectorized per parquet batch —
~7M rows/s; parquets are downloaded, not fsspec-streamed); **Phase B** external scatter-shuffles the
per-source temp shards into `--out-shards` output buckets. Per-source knobs: `weight`, `min_len`/`max_len`
(length filter, e.g. long-molecule streams — keep-prob is calibrated to the post-filter pool), and for
`bin` sources a size-`stratified` shard selection with `per_shard_cap` (or default largest-first).
Every build **dedups against the held-out mechanophore test set** (`--dedup-holdout`).

```bash
# rebuild a mix (on the CPU node; source S3 creds first)
python mix_dataset.py --config mix-v2-1B.config.json \
    --dedup-holdout mechano_test.jsonl --out /tmp/mix \
    --s3 s3://mechanophore/molvae/tokens/mix-v2-1B --out-shards 512 --shard-size 100000
```

## Design principle
Sample by **weights, not raw counts** — the mechanophore target is a *strained core at ~27 heavy
atoms with esters/nitriles*, which no single source spans. GDB gives strained ring grammar (but
small); mcule/eMolecules give the long molecules (but drug-like); ZINC gives a medium size anchor.
The mix's job is to span the composition. (Long+strained *together* still needs Phase-2 sources —
COCONUT / SAVI — not yet added.)

## `mix-v2-1B` — the strained-rich pretrain mix (current)
~60% GDB (strain) · ~40% size/length · ~9–13% of mols ≥55 tokens (long-decode).

| weight | source | role |
|------:|--------|------|
| 35% | gdb13 | strain-volume workhorse (≤13 HA rings) |
| 8% | GDB4c3D | curated strained |
| 8% | GDB-13s | ring diversity |
| 4% | gdb11 | small exhaustive |
| 5% | GDBMedChem | drug-like ring |
| 12% | ZINC (largest-first) | medium size anchor |
| 10% | mcule | long-ish (median 46) |
| 5% | mcule-long (`min_len 55`) | long-decode leg (all ≥55, to 154 tok) |
| 13% | eMolecules ordersc | long + diverse (to 168 tok) |

`mix-v2-40M` is the same composition at 40M (pilot). `mix-phase1-40M` is the earlier v1
(ZINC 40% / GDB4c3D 35% / GDBMedChem 15% / ChEMBL 10%). See each `*.config.json` for exact specs.

## Loading (training side, needs torch)
```python
from molvae.data import MolvaeDataset, make_loader
ds = MolvaeDataset("<local>/mix-v2-1B", "train")      # mmap token shards
loader = make_loader(ds, pad_id=3, token_budget=12288)
```