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--- |
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license: apache-2.0 |
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language: |
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- en |
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tags: |
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- chemistry |
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pretty_name: medea_db |
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--- |
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# MEDEA-DB |
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This database contains curated databases and pre-trained model weights across multiple domains of tools leveraged by Medea, including: |
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- PPI networks & Multi-scale gene/protein embeddings (PINNACLE, TranscriptFormer, etc.) |
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- Gene correlation and dependency statistics (Chronos gene-effect profiles from DepMap 24Q2 CRISPR) |
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- Immunotherapy response prediction model checkpoints (COMPASS pretrain checkpoint) |
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--- |
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## Available Data & Resources |
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### 1. Gene/Protein Embeddings |
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#### **PINNACLE Embeddings** (`pinnacle_embeds/`) |
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- **Model**: PINNACLE |
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- **Files**: |
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- `pinnacle_protein_embed.pth`: Protein-level embeddings with cell type specificity |
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- `pinnacle_mg_embed.pth`: Meta-graph level embeddings on cellular interactions and tissue hierarchy |
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- `ppi_embed_dict.pth`: PPI-based embeddings |
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- `pinnacle_labels_dict.txt`: Gene/protein labels |
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- **Config Names**: `pinnacle_protein_embed`, `labels_dict` |
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- **Format**: PyTorch tensors |
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#### **Transcriptformer Embeddings** (`transcriptformer_embedding/`) |
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- **Model**: Transcriptformer (Transcriptomics transformer) |
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- **Structure**: |
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- `embedding_generation/`: Scripts for generating embeddings |
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- `embedding_store/`: Pre-computed embeddings (138 `.npy` files) |
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- **Format**: NumPy arrays, compressed archives |
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--- |
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### 2. Gene Dependency & Correlation Data |
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#### **DepMap 24Q2** (`depmap_24q2/`) |
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- **Release**: DepMap Public 24Q2 |
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- **Files**: |
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- `corr_matrix.npy`: Gene correlation matrix |
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- `p_val_matrix.npy`: Statistical significance values |
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- `p_adj_matrix.npy`: Adjusted p-values (multiple testing correction) |
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- `gene_correlations.h5`: HDF5 format correlations |
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- `gene_idx_array.npy`: Gene index mappings |
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- `gene_names.txt`: Gene identifiers |
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--- |
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### 3. Immunotherapy Response Prediction Models |
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#### **COMPASS Checkpoints** (`compass/checkpoint/`) |
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- **Model**: COMPASS |
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- **Checkpoints**: |
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- `pretrainer.pt`: Pre-trained base model |
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- `pft_leave_IMVigor210.pt`: Leave-one-cohort-out (IMVigor210) fintuned model |
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--- |
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## Data Sources & Citations |
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Please cite the original sources when using specific datasets or models. |
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--- |
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## License |
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This dataset is released under the [CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/) license. |
