pretty_name: PhaseFlow-Peptide
license: other
tags:
- peptide
- liquid-liquid-phase-separation
- phase-diagram
- flow-matching
PhaseFlow-Peptide
The peptide/ package contains the short-peptide 4×4 PSSI phase-diagram data used
by the peptide branch of PhaseFlow. It contains the exact 280,778-row verified
PhaseFlow input table and the script needed to generate its missing-count
training views locally.
Open access
All files in this package are openly available for research, benchmarking, method development, and reproducible studies. We welcome community use and redistribution; please cite the PhaseFlow work and retain relevant source attribution.
Data Structure
peptide/
├── configs/
│ ├── dataset_contract.yaml
│ └── training.yaml # best phase-prediction training setting
├── data/
│ ├── raw/
│ │ └── phase_diagram_original_scale.csv
├── metadata/
│ ├── data_dictionary.md
│ ├── dataset_summary.json
│ ├── feature_reproduction.md
│ └── file_inventory.csv
└── scripts/
└── prepare_missing_splits.py
data/raw/phase_diagram_original_scale.csv is the direct PhaseFlow training
input. It has AminoAcidSequence plus group_11 through group_44; NaN
denotes an unobserved PSSI-grid cell. Generate the required sibling
by_missing/missing_<0-15>.csv training views locally with the supplied script.
Reproducibility
From this directory, generate the missing-count views locally:
python scripts/prepare_missing_splits.py
The final peptide PhaseFlow setting is in configs/training.yaml: Flow weight
32, language-model weight 0, batch size 2048, learning rate 0.0008, and
missing_threshold 15.
To train with the PhaseFlow peptide workflow, point --data_path at
data/raw/phase_diagram_original_scale.csv; its by_missing/ sibling will
be discovered automatically.
Provenance and limitations
The CSV is the earliest verified input available in this workspace. The upstream, pre-CSV source and the historical conversion procedure were not available, so this release does not assert a lineage beyond that table. It does fully reproduce the missing-count views from the distributed CSV. The package is for research and reproducibility, not clinical, diagnostic, or experimental annotation use. Please cite the accompanying PhaseFlow manuscript or public repository release when using or redistributing these data.