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39 changes: 39 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -130,6 +130,45 @@ or:
make training-up
```

### 4) Training data (preprocess / train)

Serving (`make up`) does **not** need these files. They are required for CLI preprocess, embedding generation, training, and holdout evaluation.

Dataset on Kaggle: [cafa-5-6-train-dataset](https://www.kaggle.com/datasets/behrouzmirabdi/cafa-5-6-train-dataset)

**Expected layout** (matches `configs/config.yaml`):

```text
data/cafa-5-cafa-6-protein-function-prediction/
└── Train/
├── train_sequences.fasta
└── train_terms.tsv
```

**Download via Kaggle CLI** (requires [`kaggle`](https://github.com/Kaggle/kaggle-cli) and `~/.kaggle/kaggle.json`):

```bash
mkdir -p data/cafa-5-cafa-6-protein-function-prediction/Train
kaggle datasets download -d behrouzmirabdi/cafa-5-6-train-dataset \
-p data/cafa-5-cafa-6-protein-function-prediction/Train --unzip
```

Alternatively, download the zip from the Kaggle page in a browser and extract so the two files end under `Train/` as shown above.

**Verify integrity** (sha256 of the files this repo was developed against):

```bash
sha256sum data/cafa-5-cafa-6-protein-function-prediction/Train/train_sequences.fasta \
data/cafa-5-cafa-6-protein-function-prediction/Train/train_terms.tsv
```

Expected digests:

| File | sha256 |
|------|--------|
| `train_sequences.fasta` | `434addef94c14eb8fb263ad2f5801a73a43fcb69d10955e5463d20c6b8aaac82` |
| `train_terms.tsv` | `c9489b802b8955d3cb14c23cc465674de86e08ad23107296260c8a8040361535` |

## Access Points

- Gateway root: `https://localhost`
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