Embedding name: PROBE-PROTVec

Modality: Protein representation
Embedding source URL: https://huggingface.co/spaces/HUBioDataLab/PROBE
Original model/code URL: https://github.com/HUBioDataLab/PROBE

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: 18,873 genes × 100 dimensions
Dtype: float32

Detailed processing notes

Source and interpretation

This embedding is one PROBE human UniProt representation table standardized into the shared gene-embedding resource.

This is a ProtVec protein representation from the PROBE archive.

The source file used for this component was PROTVEC_UNIPROT_HUMAN.csv from the official PROBE human UniProt representation archive.

Provenance fields

source_name: PROBE-PROTVec
original_model_or_method: PROBE human UniProt representation archive
input_data_type: official PROBE human UniProt CSV representation table
input_source_file: PROTVEC_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: 100
training_or_finetuning: none
final_embedding_dtype: float32

Mapping and processing decisions

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.

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

For this PROBE embedding:

1. Read `PROTVEC_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

All PROBE embeddings use the same mapping logic, so differences between PROBE outputs reflect the source representation type rather than different gene-mapping rules.

Summary of final mapping:

Source identifiers / source rows or entries: 18,873 mapped source genes
Dimensions: 100
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

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`
`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

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

{
  "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": 100,
    "final_mapped_genes": 18873,
    "mapped_source_rows_before_duplicate_collapse": 18905,
    "master_rows": 20097,
    "source_dimensions": 100,
    "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_protvec_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_PROTVEC"
}