Embedding name: Gene2Vec

Modality: Co-expression / expression
Embedding source URL: https://github.com/jingcheng-du/Gene2vec

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: 17,916 genes × 200 dimensions
Dtype: float32

Detailed processing notes

Source and interpretation

This embedding represents genes using the original Gene2Vec co-expression-derived 200-dimensional vectors.

Provenance fields

source_name: Gene2Vec
original_model_or_method: Gene2Vec
input_data_type: original Gene2Vec text vector file
raw_source: ~/data/raw_embeddings/gene2vec/gene2vec_dim_200_iter_9.txt
source_download_page: https://github.com/jingcheng-du/Gene2vec
source_code_page: https://github.com/jingcheng-du/Gene2vec
source_identifier_type: gene symbol
mapping_identifier_type: priority symbol mapping to master_gene_table.csv
source_rows_or_entries: 24,447 raw rows
final_mapped_genes: 17,916
model_or_feature_dimension: 200
training_or_finetuning: none
final_embedding_dtype: float32

Mapping and processing decisions

Source gene symbols were mapped to master_gene_table.csv using the project priority order: current gene_symbol / HGNC approved symbol first, then HGNC previous symbols, then HGNC aliases. Only unique mappings were accepted. Ambiguous identifiers were excluded. Duplicate source rows mapping to the same final gene were averaged when safe.

Processing workflow

For this embedding:

1. Read the original Gene2Vec text vector file.
2. Parse the source identifiers.
3. Map source identifiers to master_gene_table.csv using the project mapping rule for this identifier type.
4. Exclude unmapped and ambiguous source identifiers.
5. Average duplicate source rows only when they map to the same final master-table gene.
6. Save the final matrix as float32.

Summary of final mapping:

Source identifiers / source rows or entries: 24,447 raw rows
Dimensions: 200
Final mapped genes: 17,916
Master table rows: 20,097
Master coverage: 89.15%
Mapping strategy: priority symbol 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

{
  "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": 0.8914763397522019,
  "duplicate_source_rows": "averaged when multiple source rows mapped to the same master gene",
  "embedding_dim": 200,
  "former_processing_embedding_id": "gene2vec_v1_1",
  "mapping_method_counts": {
    "direct_current_gene_symbol": 16796,
    "hgnc_alias_symbol": 39,
    "hgnc_previous_symbol": 1130
  },
  "n_ambiguous_source_rows_excluded": 32,
  "n_bad_rows_skipped": 0,
  "n_genes_added_vs_gene2vec_strict_v1": 1126,
  "n_mapped_genes": 17916,
  "n_mapped_source_rows": 17965,
  "n_master_rows": 20097,
  "n_nonfinite_source_rows_skipped": 0,
  "n_source_rows_raw": 24447,
  "n_unmapped_source_rows": 6450,
  "n_zero_vectors": 0,
  "public_file_structure": {
    "embeddings": "embeddings.npz",
    "genes": "genes.tsv",
    "metadata": "metadata.json",
    "readme": "README.md"
  }
}