# 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 - `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` ## Detailed processing notes ### Source and interpretation This embedding represents genes using the pretrained Mashup human STRING network vectors. 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 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 The source was treated as an already-computed network embedding. Therefore, the local processing did not rebuild STRING networks and did not retrain Mashup. ### Mapping and duplicate-handling decisions 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. 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. ### Processing workflow For this embedding: 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 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. For Mashup, the original biological representation was preserved from the downloaded pretrained Mashup/STRING vectors. ### Summary of final mapping: 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 ## Processing and provenance metadata 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. Source catalog commit: `ab37742040d20b523aebd188d3079871a0c2b534`. ### Canonicalized field names | 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 - `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" } } ```