ProtCompass release (anonymous submission)

Co-authored-by: anonymous researcher <anonymous researcher@users.noreply.huggingface.co>

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README.md

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+---
+license: mit
+---
+
+# ProtCompass Embeddings
+
+Pre-computed protein embeddings from 70+ encoders across 15 downstream tasks, plus probing results and evaluation outputs.
+
+## Dataset Structure
+
+```
+embeddings/                          # Compressed embeddings (~150GB)
+├── contact_prediction/              # Per-encoder compressed (300GB → ~60GB)
+│   ├── esm2.tar.gz
+│   ├── gearnet.tar.gz
+│   └── ... (36 encoders)
+├── secondary_structure/             # Per-encoder compressed (129GB → ~30GB)
+├── ppi_site/                        # Per-encoder compressed (80GB → ~20GB)
+├── metal_binding/                   # Per-encoder compressed (41GB → ~10GB)
+├── mutation_effect.tar.gz           # Per-task compressed (27GB → ~7GB)
+├── go_bp.tar.gz                     # Per-task compressed (7.9GB → ~2GB)
+├── stability.tar.gz                 # Per-task compressed (4.1GB → ~1GB)
+├── solubility.tar.gz                # Per-task compressed (3.6GB → ~900MB)
+├── go_mf.tar.gz                     # Per-task compressed (3.1GB → ~800MB)
+├── fluorescence.tar.gz              # Per-task compressed (3.0GB → ~800MB)
+├── ec_classification.tar.gz         # Per-task compressed (1.9GB → ~500MB)
+├── subcellular_localization.tar.gz  # Per-task compressed (1.4GB → ~400MB)
+├── membrane_soluble.tar.gz          # Per-task compressed (1.4GB → ~400MB)
+├── remote_homology.tar.gz           # Per-task compressed (805MB → ~200MB)
+└── ppi_affinity.tar.gz              # Per-task compressed (169MB → ~50MB)
+
+probing_IF/                          # Probing results (2.8GB)
+├── probing_embeddings/              # Invariant family embeddings (12 encoders)
+└── probing_results_architecture_full/  # Full probing results (195 files)
+
+results/                             # Evaluation results (6.9MB)
+└── {encoder}/{task}/                # Per-encoder, per-task results
+
+outputs/                             # Analysis outputs (12MB)
+├── alignment_analysis/              # Alignment analysis figures
+├── paper_figures_v12/               # Final paper figures
+└── uncertainty_appendix/            # Uncertainty analysis
+```
+
+## Decompression Instructions
+
+All embeddings are compressed with gzip. Decompress before use:
+
+### Large Tasks (per-encoder compression)
+For `contact_prediction`, `secondary_structure`, `ppi_site`, `metal_binding`:
+
+```bash
+# Decompress all encoders in a task
+cd embeddings/contact_prediction/
+for f in *.tar.gz; do tar -xzf "$f"; done
+
+# Or decompress specific encoder
+tar -xzf esm2.tar.gz
+```
+
+### Medium/Small Tasks (per-task compression)
+For all other tasks:
+
+```bash
+# Decompress entire task
+cd embeddings/
+tar -xzf mutation_effect.tar.gz
+tar -xzf secondary_structure.tar.gz
+# etc.
+
+# Or decompress all tasks at once
+for f in *.tar.gz; do tar -xzf "$f"; done
+```
+
+## File Format
+
+After decompression, each encoder directory contains:
+- `train_embeddings.npy`: Training set embeddings (N × D)
+- `test_embeddings.npy`: Test set embeddings (M × D)
+- `train_labels.npy`: Training labels
+- `test_labels.npy`: Test labels
+- `train_ids.txt`: Protein IDs for training set
+- `test_ids.txt`: Protein IDs for test set
+- `meta.json`: Metadata (encoder name, dimensions, dataset info)
+
+## Usage
+
+```python
+import numpy as np
+from huggingface_hub import hf_hub_download
+import tarfile
+
+# Download and decompress embeddings
+tar_path = hf_hub_download(
+    repo_id="Anonymoususer2223/ProtCompass_Embeddings",
+    filename="embeddings/mutation_effect.tar.gz",
+    repo_type="dataset"
+)
+
+# Extract
+with tarfile.open(tar_path, 'r:gz') as tar:
+    tar.extractall(path="./embeddings/")
+
+# Load embeddings
+train_emb = np.load("embeddings/mutation_effect/esm2/train_embeddings.npy")
+test_emb = np.load("embeddings/mutation_effect/esm2/test_embeddings.npy")
+train_labels = np.load("embeddings/mutation_effect/esm2/train_labels.npy")
+test_labels = np.load("embeddings/mutation_effect/esm2/test_labels.npy")
+
+# Use for downstream tasks
+from sklearn.linear_model import Ridge
+model = Ridge()
+model.fit(train_emb, train_labels)
+score = model.score(test_emb, test_labels)
+print(f"Test R²: {score:.3f}")
+```
+
+## Encoders Included
+
+### Sequence Encoders (8)
+ESM2 (650M, 150M, 35M), ESM1b, ESM3, ProtTrans, ProstT5, ProteinBERT-BFD, Ankh
+
+### Structure Encoders (50+)
+GearNet, GCPNet, EGNN, GVP, IPA, TFN, SchNet, DimeNet, MACE, CDConv, ProteinMPNN, PottsMPNN, dMaSIF, and more
+
+### Multimodal Encoders (5)
+SaProt, ESM-IF, FoldVision
+
+### Baselines (5)
+Random, Length, Torsion, One-hot, BLOSUM
+
+## Dataset Statistics
+
+- **Compressed size**: ~150GB
+- **Uncompressed size**: ~600GB
+- **Total encoders**: 70+
+- **Total tasks**: 15
+- **Total proteins**: ~500K across all tasks
+- **Compression ratio**: ~4x (gzip)
+
+## Compression Details
+
+- **Large tasks** (>30GB): Per-encoder compression for flexibility
+  - Users can download only specific encoders
+  - Enables parallel decompression
+  
+- **Medium/Small tasks** (<30GB): Per-task compression
+  - Single archive per task
+  - Faster download for complete task data
+
+## Citation
+
+If you use these embeddings, please cite:
+
+```bibtex
+@article{protcompass2026,
+  title={ProtCompass: Interpretable Benchmarking and Task-Aware Evaluation of Protein Encoders},
+  author={Your Name et al.},
+  journal={NeurIPS},
+  year={2026}
+}
+```
+
+## Related Resources
+
+- **Code Repository**: [GitHub](https://github.com/yourusername/protcompass)
+- **Raw Datasets**: [ProtEnv on HuggingFace](https://huggingface.co/datasets/Anonymoususer2223/ProtEnv)
+- **Paper**: [arXiv](https://arxiv.org/abs/xxxx.xxxxx)
+
+## License
+
+MIT License
+
+## Contact
+
+For questions or issues, please open an issue on the [GitHub repository](https://github.com/yourusername/protcompass).