| # Embedding name: PROBE-SeqVec |
|
|
| - Modality: Protein representation |
| - Embedding source URL: https://huggingface.co/spaces/HUBioDataLab/PROBE |
| - Original model/code URL: https://github.com/HUBioDataLab/PROBE |
|
|
| ## 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: `18,873 genes × 1,024 dimensions` |
| - Dtype: `float32` |
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|
|
| ## Detailed processing notes |
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|
| ### Source and interpretation |
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| This embedding is one PROBE human UniProt representation table standardized into the shared gene-embedding resource. |
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| This is a SeqVec protein representation from the PROBE archive. |
|
|
| The source file used for this component was `SEQVEC_UNIPROT_HUMAN.csv` from the official PROBE human UniProt representation archive. |
|
|
| ### Provenance fields |
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|
| source_name: PROBE-SeqVec |
| original_model_or_method: PROBE human UniProt representation archive |
| input_data_type: official PROBE human UniProt CSV representation table |
| input_source_file: SEQVEC_UNIPROT_HUMAN.csv |
| source_download_or_app_page: https://huggingface.co/spaces/HUBioDataLab/PROBE |
| source_code_page: https://github.com/HUBioDataLab/PROBE |
| raw_source_folder: ~/data/raw_embeddings/probe_official/human_representation_vectors/revision-1/ |
| source_identifier_type: UniProt Entry accession |
| mapping_identifier_type: UniProt accession matched to enriched master_gene_table.csv UniProt fields |
| source_rows_or_entries: 18,873 mapped source genes |
| final_mapped_genes: 18,873 |
| model_or_feature_dimension: 1,024 |
| training_or_finetuning: none |
| final_embedding_dtype: float32 |
| |
| ### Mapping and processing decisions |
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|
| Each PROBE CSV uses a UniProt accession in the `Entry` column. Source entries were cleaned to their canonical accession base by removing isoform suffixes when present. |
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| Cleaned UniProt accessions were mapped to master_gene_table.csv using `uniprot_id`, `hgnc_uniprot_ids`, and `map_uniprot_ids_all`. Only unique UniProt-to-master mappings were accepted. Ambiguous UniProt accessions were excluded. Duplicate source proteins mapping to the same final master-table gene were averaged within that gene. |
|
|
| ### Processing workflow |
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| For this PROBE embedding: |
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| 1. Read `SEQVEC_UNIPROT_HUMAN.csv` from the PROBE human representation archive. |
| 2. Use the `Entry` column as the source UniProt accession. |
| 3. Remove isoform suffixes where present to obtain the canonical UniProt accession base. |
| 4. Map source UniProt accessions to master_gene_table.csv through enriched UniProt fields. |
| 5. Exclude unmapped and ambiguous UniProt accessions. |
| 6. Average duplicate source rows only when they map to the same final master-table gene. |
| 7. Save the final matrix as float32. |
|
|
| ### Important implementation decisions |
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| The PROBE vectors were taken directly from the official archive rather than recomputed. This keeps the PROBE batch aligned with the released human UniProt representation files. |
|
|
| ### Summary of final mapping: |
|
|
| Source identifiers / source rows or entries: 18,873 mapped source genes |
| Dimensions: 1,024 |
| Final mapped genes: 18,873 |
| Master table rows: 20,097 |
| Master coverage: 93.91% |
| Mapping strategy: UniProt Entry accession mapping through enriched master table |
| Ambiguous UniProt accessions: excluded |
| Duplicate final mappings averaged: yes |
| |
| <!-- BEGIN CATALOG NORMALIZATION: LEGACY METADATA --> |
|
|
| ## 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`. |
|
|
| ### Canonicalized field names |
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|
| | Previous field | Compact metadata field | |
| | --- | --- | |
| | `embedding_name` | `display_name` | |
| | `source_identifier_type` | `original_identifier_type` | |
| | `mapping_strategy` | `mapping_method` | |
| | `num_genes` | `n_genes` | |
| | `embedding_dimension` | `n_dimensions` | |
| | `matrix_shape[0]` | `n_genes` | |
| | `matrix_shape[1]` | `n_dimensions` | |
| | `original_model_or_method` | `original_method` | |
| | `download_source` | `input_data_source` | |
|
|
| ### 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 |
| }, |
| "counts": { |
| "ambiguous_source_rows": 186, |
| "duplicate_final_mappings_averaged": 30, |
| "final_dimensions": 1024, |
| "final_mapped_genes": 18873, |
| "mapped_source_rows_before_duplicate_collapse": 18905, |
| "master_rows": 20097, |
| "source_dimensions": 1024, |
| "source_rows": 20421, |
| "unmapped_source_rows": 1330 |
| }, |
| "coverage": { |
| "master_gene_coverage_fraction": 0.9390953873712494, |
| "source_row_mapping_fraction": 0.9257626952646785 |
| }, |
| "former_processing_embedding_id": "probe_seqvec_v1_1", |
| "mapping_method_counts": { |
| "uniprot_accession_exact_unique": 18873 |
| }, |
| "public_file_structure": { |
| "embeddings": "embeddings.npz", |
| "genes": "genes.tsv", |
| "metadata": "metadata.json", |
| "readme": "README.md" |
| }, |
| "sequence_and_reference_provenance": { |
| "input_sequence_source": "PROBE human UniProt representation archive", |
| "input_sequence_type": "protein sequence-derived representation", |
| "sequence_reference_status": "PROBE archive provenance recorded; exact UniProt release to verify from original PROBE documentation if needed", |
| "source_identifier": "UniProt accession in Entry column", |
| "species": "human" |
| }, |
| "source_embedding": "PROBE_SEQVEC" |
| } |
| ``` |
|
|
| <!-- END CATALOG NORMALIZATION: LEGACY METADATA --> |
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|
