| # Embedding name: Mashup-STRING |
|
|
| - Modality: PPI / network |
| - Algorithm: Pretrained Mashup STRING human network vectors standardized by enriched symbol/protein-ID mapping |
| - Embedding source URL: https://mashup.csail.mit.edu/ |
|
|
| ## Public files |
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| - `embeddings.npz`: compressed NumPy archive containing the embedding matrix under key `embeddings`. |
| - `genes.tsv`: row metadata table. Row order matches the embedding matrix. |
| - `metadata.json`: machine-readable provenance and processing metadata. |
|
|
| ## Matrix |
|
|
| - Shape: `16,331 genes × 800 dimensions` |
| - Dtype: `float32` |
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|
|
| ## Detailed processing notes |
|
|
| ### Source and interpretation |
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| This embedding represents genes using the pretrained Mashup human STRING network vectors. |
|
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| Mashup is a network-integration method. In this resource, the retained matrix is not a newly trained Mashup model. It is the standardized gene-level version of pretrained Mashup/STRING human vectors, mapped into the shared master_gene_table.csv universe. |
|
|
| ### Provenance fields |
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|
| source_name: Mashup-STRING |
| original_model_or_method: Mashup-STRING |
| input_data_type: pretrained Mashup STRING human vectors and matching gene list |
| raw_source: ~/data/raw_embeddings/mashup/ |
| source_download_page: https://mashup.csail.mit.edu/ |
| source_code_page: https://mashup.csail.mit.edu/ |
| source_identifier_type: Mashup gene name / gene symbol, with some source records requiring protein-ID rescue |
| mapping_identifier_type: priority symbol mapping plus enriched protein-ID mapping to master_gene_table.csv |
| source_rows_or_entries: 18,362 raw source rows |
| final_mapped_genes: 16,331 |
| model_or_feature_dimension: 800 |
| training_or_finetuning: none; source vectors were not retrained locally |
| final_embedding_dtype: float32 |
| |
| ### Source-processing decisions |
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| The source was treated as an already-computed network embedding. Therefore, the local processing did not rebuild STRING networks and did not retrain Mashup. |
|
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| ### Mapping and duplicate-handling decisions |
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| Mashup source identifiers were mapped mainly through gene-symbol matching. The mapping priority was current master-table gene symbol / HGNC-approved symbol first, then HGNC previous symbols, then HGNC aliases. Source protein-like identifiers were also mapped through enriched protein-ID columns when available. |
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| Only unique mappings were accepted. Source identifiers that could map to more than one master-table gene were excluded. When multiple accepted source rows mapped to the same final master-table gene, their vectors were averaged to keep one final vector per gene. |
|
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| ### Processing workflow |
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| For this embedding: |
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| 1. Read the pretrained Mashup human STRING vector table and its matching source gene list. |
| 2. Align each source row with its source identifier. |
| 3. Normalize source identifiers for symbol/protein-ID mapping. |
| 4. Map source identifiers to master_gene_table.csv using the enriched symbol and protein-ID fields. |
| 5. Exclude unmapped and ambiguous source identifiers. |
| 6. Average duplicate source rows only when they map to the same final master-table gene. |
| 7. Save the final gene-aligned matrix as float32. |
|
|
| ### Important implementation decisions |
|
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| The central requirement was that every retained row must align to one gene in master_gene_table.csv and that the matrix row order must match genes.tsv exactly. |
|
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| For Mashup, the original biological representation was preserved from the downloaded pretrained Mashup/STRING vectors. |
|
|
| ### Summary of final mapping: |
|
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| Source identifiers / source rows or entries: 18,362 raw source rows |
| Dimensions: 800 |
| Final mapped genes: 16,331 |
| Master table rows: 20,097 |
| Master coverage: 81.26% |
| Mapping strategy: priority symbol mapping plus enriched protein-ID mapping to master_gene_table.csv |
| Ambiguous identifiers: excluded |
| Duplicate final mappings averaged: yes |
| |
| <!-- BEGIN CATALOG NORMALIZATION: LEGACY METADATA --> |
|
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| ## Processing and provenance metadata |
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| This section preserves information moved out of `metadata.json` during catalog normalization. The loading-facing metadata is intentionally compact; detailed source, mapping, processing, quality-control, and reproducibility records remain here. |
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| Source catalog commit: `ab37742040d20b523aebd188d3079871a0c2b534`. |
|
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| ### Canonicalized field names |
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|
| | Previous field | Compact metadata field | |
| | --- | --- | |
| | `embedding_name` | `display_name` | |
| | `mapping_strategy` | `mapping_method` | |
| | `num_genes` | `n_genes` | |
| | `embedding_dimension` | `n_dimensions` | |
| | `matrix_shape[0]` | `n_genes` | |
| | `matrix_shape[1]` | `n_dimensions` | |
| | `dtype_saved` | `dtype` | |
|
|
| ### Derived standardized fields |
|
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| - `species` was set to `Homo sapiens` from the validated human Ensembl `ENSG` identifier namespace. |
| - `master_coverage_fraction` was computed as `n_genes / 20097`. |
|
|
| ### Legacy processing and provenance record |
|
|
| ```json |
| { |
| "all_zero_rows": { |
| "count": 0, |
| "documented": true, |
| "expected": false, |
| "reason": "No exact all-zero rows were detected in embeddings.npz.", |
| "report_file": null |
| }, |
| "ambiguous_source_rows": "excluded and reported", |
| "coverage_of_master_rows": 0.8126088470916057, |
| "duplicate_source_rows": "averaged when multiple source rows mapped to the same master gene", |
| "embedding_dim": 800, |
| "former_processing_embedding_id": "mashup_string_v1_1", |
| "mapping_method_counts": { |
| "direct_canonical_protein_id": 17, |
| "direct_current_gene_symbol": 15037, |
| "ensembl_grch37_gtf_protein_id": 487, |
| "ensembl_grch38_current_gtf_protein_id": 6, |
| "hgnc_alias_symbol": 1, |
| "hgnc_previous_symbol": 811 |
| }, |
| "n_ambiguous_source_rows_excluded": 23, |
| "n_mapped_genes": 16331, |
| "n_mapped_source_rows": 16359, |
| "n_master_rows": 20097, |
| "n_nonfinite_source_rows_skipped": 0, |
| "n_source_ensp_like_rows": 2352, |
| "n_source_rows_raw": 18362, |
| "n_source_symbol_like_rows": 16010, |
| "n_unmapped_source_rows": 1980, |
| "n_zero_vectors": 0, |
| "public_file_structure": { |
| "embeddings": "embeddings.npz", |
| "genes": "genes.tsv", |
| "metadata": "metadata.json", |
| "readme": "README.md" |
| } |
| } |
| ``` |
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| <!-- END CATALOG NORMALIZATION: LEGACY METADATA --> |
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|
