| # Feature Reconstruction | |
| This source-first release excludes all precomputed embeddings, graph tensors, structural features, and packed feature caches. Reconstruct derived features from `data/proteins.parquet` using the published PhaseFlow preprocessing workflow and its documented pretrained components. Store all generated artifacts outside this dataset directory so the distributed inventory remains stable. | |
| Use `protein_id` and `sequence_sha256` together to bind reconstructed features to source records. Confirm sequence lengths and hashes before reusing any cache. `data/base_training_schedule.parquet` and `data/region_supervision.parquet` are protocol/supervision tables, not feature caches. | |
| The files under `benchmark/` are evaluation inputs. Feature generation for benchmark sequences may be necessary for inference, but the benchmark must remain outside training, hyperparameter selection, and checkpoint selection. | |