# Data Dictionary

## Training data

| File | Unit of observation | Required keys | Description |
| --- | --- | --- | --- |
| `data/proteins.parquet` | protein sequence | `protein_id`, `sequence_sha256` | Canonical training protein sequences, sequence lengths, and accession fields. |
| `data/training_units.parquet` | protein training record | `protein_id`, `sequence_sha256` | LLPS labels, weights, evidence roles, source/protocol metadata, and teacher-derived scalar covariates. |
| `data/training_plan/batch_plan_epoch_*.parquet` | planned batch placement | `dataset_index`, `plan_dataset_index`, `protein_id`, `sequence_sha256` | Fixed three-epoch 8-GPU batch protocol. |

Join `training_units.parquet` to `proteins.parquet` on both `protein_id` and `sequence_sha256`. A training-plan row must resolve by `dataset_index` and `plan_dataset_index` to the same `protein_id` and `sequence_sha256` in `training_units.parquet`; do not treat plan indices as stable external identifiers.

## Evaluation benchmark

| File | Unit of observation | Description |
| --- | --- | --- |
| `benchmark/proteins.csv` | benchmark protein | Evaluation sequences, labels, conditions, and source text. |
| `benchmark/constructs.csv` | assay construct | Experimental construct sequences, labels, conditions, and source text. The first two rows encode the original header representation; the release copy is UTF-8 after a lossless GB18030-to-UTF-8 transcode. |
| `benchmark/panel_membership.csv` | panel-protein membership | Named evaluation panels, labels, classes, dataset tokens, and descriptions. |

The entire `benchmark/` directory is evaluation-only. Do not include its records in fitting, threshold optimization, or checkpoint selection for benchmark reporting.

## Configuration and integrity metadata

`configs/dataset_contract.yaml` and `configs/training.yaml` document the public package contract and training settings. `metadata/feature_reproduction.md` defines the source-first feature policy. `metadata/file_inventory.csv` lists every package file other than itself with byte size and SHA-256 digest.