Embedding name: Node2Vec-consensus-PPI

Modality: Protein-protein interaction network / direct PPI graph embedding
Algorithm: Node2Vec-style random walks with Word2Vec skip-gram training
Embedding source URL: https://github.com/ylaboratory/gene-embedding-benchmarks
Original model/code URL: Embedding was locally generated from a recovered PPI edge list using node2vec-style random walks and Word2Vec

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: 18356 genes × 128 dimensions
Dtype: float32

Detailed processing notes

Source and interpretation

This embedding is a gene-level direct PPI network representation generated locally from the recovered consensus.dat PPI graph input used in the Zhong gene-embedding benchmark preprocessing repository.

The source graph is a two-column Entrez-ID PPI edge list. The final embedding was generated by running node2vec-style random walks over the recovered graph and training a Word2Vec skip-gram model on the walks. Each graph node is therefore represented by its position in the direct PPI network.

This embedding should be interpreted as a direct PPI graph embedding. It is complementary to PrimeKG and Hetionet, which were deliberately processed as non-PPI heterogeneous biomedical context embeddings.

Provenance fields

source_name: Node2Vec consensus PPI
original_model_or_method: node2vec-style random walks with Word2Vec skip-gram
input_data_type: recovered consensus PPI edge list
input_source_file: consensus.dat
source_download_or_code_page: https://github.com/ylaboratory/gene-embedding-benchmarks
source_identifier_type: Entrez Gene ID graph node
mapping_identifier_type: Entrez Gene ID matched to master_gene_table.csv
source_graph_nodes: 20,349
raw_edge_rows: 822,311
undirected_non_self_edges: 816,726
skipped_self_or_bad_edges: 5,585
dimensions: 128
walk_length: 80
num_walks: 10
p: 1
q: 1
window: 10
epochs: 5
min_count: 1
sg: 1
seed: 42
workers: 8
final_embedding_dtype: float32

Mapping and graph-processing decisions

Source graph nodes were treated as Entrez Gene IDs. They were mapped through entrez_id, hgnc_entrez_id, and map_entrez_ids_all in master_gene_table.csv.

Only source Entrez IDs that mapped uniquely to one master-table gene were accepted. Source nodes that were unmapped or ambiguous across master rows were excluded.

Duplicate source rows were averaged only when they safely mapped to the same final master gene. This keeps the final output aligned to master_gene_table.csv while avoiding ambiguous Entrez-to-gene assignments.

Processing workflow

For the Node2Vec consensus PPI embedding:

1. Read the recovered consensus.dat PPI graph.
2. Parse graph nodes as Entrez Gene IDs.
3. Remove self or malformed edges.
4. Build the undirected PPI graph.
5. Run node2vec-style random walks with walk_length=80, num_walks=10, p=1, and q=1.
6. Train Word2Vec skip-gram on the generated walks with window=10, epochs=5, min_count=1, and seed=42.
7. Map source Entrez graph nodes to master_gene_table.csv.
8. Exclude unmapped or ambiguous source nodes.
9. Average duplicate source rows only when they map to the same final master gene.
10. Save the final matrix as float32.

Important implementation decisions

The exact graph input was recovered, but the exact Zhong NODE2VEC hyperparameters were not found in the inspected preprocessing notebook. Therefore this output should not be described as byte-identical to Zhong's archived NODE2VEC matrix.

This output is the dedicated direct PPI embedding in the resource. Broader KG embeddings such as PrimeKG and Hetionet should be compared against it to test whether heterogeneous biomedical context adds information beyond direct PPI graph structure.

Summary of final mapping:

Source identifiers / PPI graph nodes: 20,349
Raw edge rows: 822,311
Undirected non-self edges: 816,726
Skipped self/bad edges: 5,585
Mapped source nodes before duplicate collapse: 18,404
Unmapped source nodes: 1,792
Ambiguous source nodes: 153
Dimensions: 128
Rows generated before duplicate collapse: 18,404
Final mapped genes: 18,356
Master table rows: 20,097
Master coverage: 91.34%
Duplicate final mappings averaged: 44

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_nodes": 153,
    "duplicate_final_mappings_averaged": 44,
    "final_dimensions": 128,
    "final_mapped_genes": 18356,
    "mapped_source_nodes_before_duplicate_collapse": 18404,
    "master_rows": 20097,
    "raw_edge_rows": 822311,
    "skipped_self_or_bad_edges": 5585,
    "source_dimensions": 128,
    "source_nodes": 20349,
    "undirected_nonself_edges": 816726,
    "unmapped_source_nodes": 1792
  },
  "coverage": {
    "master_gene_coverage_fraction": 0.9133701547494651,
    "source_node_mapping_fraction": 0.9044179075138827
  },
  "exact_zhong_reproduction": false,
  "exact_zhong_reproduction_note": "The graph input was recovered, but exact NODE2VEC hyperparameters were not found in the inspected Zhong preprocessing notebook. This is therefore a local reproducible node2vec-on-consensus-PPI embedding, not guaranteed byte-identical to Zhong's archived NODE2VEC.",
  "former_processing_embedding_id": "node2vec_consensus_ppi_v1_1",
  "input_graph": "Consensus human PPI edge list used by Zhong preprocessing; two-column Entrez-ID interaction file",
  "node2vec_parameters": {
    "dimensions": 128,
    "epochs": 5,
    "min_count": 1,
    "num_walks": 10,
    "p": 1,
    "q": 1,
    "seed": 42,
    "sg": 1,
    "walk_length": 80,
    "window": 10,
    "workers": 8
  },
  "public_file_structure": {
    "embeddings": "embeddings.npz",
    "genes": "genes.tsv",
    "metadata": "metadata.json",
    "readme": "README.md"
  },
  "source_embedding": "Node2Vec-consensus-PPI-v1.1"
}