# DOTAD 2.0 Derived Benchmark Package v1.1

This benchmark package is a derived export generated from the harmonized DOTAD 2.0 source-layer workbooks. It is not the internal database storage schema.

Raw replicate-level experimental data are not used as primary benchmark labels.

The top-level task folders keep a v1.0-compatible DOTAD_ID-level train/validation/test split. Identical DOTAD_ID entries are kept in the same partition.

Additional split-scheme folders are provided under `splits/`:

- `splits/id_random/`: DOTAD_ID-level random split, matching the top-level task folders.
- `splits/vhvl_exact/`: exact paired VH/VL sequence split. Entries sharing the same paired variable-chain amino-acid sequences are kept in one partition. This is a leakage-aware exact-sequence split, not a 90% sequence-identity clustering split.

Some benchmark entries may lack therapeutic metadata such as format, target, species, or clinical stage. Missing metadata fields are marked as Unknown, and Metadata_Available indicates whether major metadata are available.

Optional metadata fields such as production_host and tag are retained when available and otherwise set to Unknown.

Each benchmark CSV includes endpoint percentiles, risk direction, tier cutpoints, label confidence, sequence-cluster metadata, and source-linked provenance fields. `excluded_labels_manifest.csv` records source-level labels that were not exported as benchmark labels because they were non-comparable, not aggregation-eligible, or outside the benchmark task definitions.

## Coverage notes

- `endpoint_coverage.csv` is the authoritative endpoint coverage table for this benchmark package and for Fig. 6 Panel C.
- `split_summary.csv` is the authoritative split summary table for this benchmark package and for Fig. 6 Panel D.
- `split_summary_by_scheme.csv` reports split counts for every exported split scheme.
- `Matrix_Label_Count` records the corresponding non-null count in the current harmonized antibody-level matrix.
- Differences between package coverage and harmonized matrix coverage are explained in `Coverage_Filter_Reason`.

## Current coverage interpretation

- AC_SINS: package labels=388, harmonized matrix labels=401; only source-traceable labels included; only benchmark-compatible endpoint labels included
- HIC: package labels=384, harmonized matrix labels=497; only source-traceable labels included; only benchmark-compatible endpoint labels included
- SMAC: package labels=341, harmonized matrix labels=345; only source-traceable labels included; only benchmark-compatible endpoint labels included
- PR_score: package labels=277, harmonized matrix labels=325; only source-traceable labels included; only benchmark-compatible endpoint labels included
- PSR: package labels=180, harmonized matrix labels=228; only source-traceable labels included; only benchmark-compatible endpoint labels included
