PhasePro DPR Benchmark
This directory is an exact copy of the PhasePro-derived DPR evaluation payload used by the local PhaseFlow workflow. It is an evaluation resource, not part of the PhaseFlow-DPR training data. The six payload files are kept byte-for-byte identical to data/benchmarks/dpr_benchmark_phasepro/; this README is release documentation only.
Files
| File | Records | Purpose |
|---|---|---|
proteins.csv |
121 proteins | Benchmark sequence records, identifiers, source membership, and split metadata |
regions.csv |
140 regions | Tabular DPR annotations with both zero-based and one-based coordinates |
region_master.jsonl |
139 regions | Canonical region records with evaluation metadata and tensor-coordinate fields |
region_spans.jsonl |
119 proteins | Per-protein DPR and negative-span representation for evaluators |
source_records.csv |
1,337 records | Source-level evidence and label provenance records |
source_map.csv |
1,327 records | Mapping from source identifiers to benchmark protein identifiers |
Record counts exclude CSV headers. The apparent difference between regions.csv, region_master.jsonl, and region_spans.jsonl is expected because each file represents a different level of the annotation graph.
Keys and coordinates
protein_id is the primary key across all files. uniprot_id and sequence_hash are useful secondary identifiers but should not replace protein_id in benchmark joins. region_id is the key for region-level records.
regions.csv carries both conventions: start/end are zero-based half-open coordinates ([start, end)), while start_1based/end_1based describe the same interval in one-based inclusive form. region_master.jsonl explicitly marks coordinate_system as 1-based inclusive; its tensor_start is zero-based and tensor_end is the matching exclusive endpoint. Preserve these conventions when evaluating predicted residue scores.
Evaluation boundary
Keep all files in this directory outside the training sampler, hyperparameter search, threshold selection, and checkpoint choice. Training data are under ../data/; their protein_id values are disjoint from proteins.csv. If a downstream workflow requires a different split or a transformed representation, retain the original files unchanged and write derived artifacts elsewhere.
Provenance and attribution
The source fields retain the provenance assembled by the local benchmark workflow. Please cite the original PhaSePro/PhasePro resource when using or discussing these benchmark-derived annotations.