Delete data/embeddings/probe_ksep

data/embeddings/probe_ksep/README.md

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-# Embedding name: PROBE-KSEP
-
-- 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: `18,801 genes × 400 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 KSEP protein representation from the PROBE archive.
-
-The source file used for this component was `KSEP_UNIPROT_HUMAN.csv` from the official PROBE human UniProt representation archive.
-
-### Provenance fields
-
-    source_name: PROBE-KSEP
-    original_model_or_method: PROBE human UniProt representation archive
-    input_data_type: official PROBE human UniProt CSV representation table
-    input_source_file: KSEP_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: 18,801 mapped source genes
-    final_mapped_genes: 18,801
-    model_or_feature_dimension: 400
-    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 `KSEP_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: 18,801 mapped source genes
-    Dimensions: 400
-    Final mapped genes: 18,801
-    Master table rows: 20,097
-    Master coverage: 93.55%
-    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
-
-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
-
-```json
-{
-  "all_zero_rows": {
-    "count": 23,
-    "documented": true,
-    "expected": true,
-    "reason": "These exact all-zero vectors were already present in the official PROBE source file KSEP_UNIPROT_HUMAN.csv. They were retained unchanged during identifier mapping and standardization to preserve the released source representation and matrix-to-gene alignment. They were not created through padding, missing-value replacement, or imputation.",
-    "source_file": "KSEP_UNIPROT_HUMAN.csv",
-    "source_provenance_column": "source_keys_examples",
-    "source_verification": "All 23 final all-zero rows were traced through source_keys_examples to official PROBE source vectors that were also exactly all-zero."
-  },
-  "counts": {
-    "ambiguous_source_rows": 183,
-    "duplicate_final_mappings_averaged": 29,
-    "final_dimensions": 400,
-    "final_mapped_genes": 18801,
-    "mapped_source_rows_before_duplicate_collapse": 18832,
-    "master_rows": 20097,
-    "source_dimensions": 400,
-    "source_rows": 20199,
-    "unmapped_source_rows": 1184
-  },
-  "coverage": {
-    "master_gene_coverage_fraction": 0.93551276309897,
-    "source_row_mapping_fraction": 0.9323233823456607
-  },
-  "former_processing_embedding_id": "probe_ksep_v1_1",
-  "mapping_method_counts": {
-    "uniprot_accession_exact_unique": 18801
-  },
-  "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_KSEP"
-}
-```
-
-<!-- END CATALOG NORMALIZATION: LEGACY METADATA -->

data/embeddings/probe_ksep/embeddings.npz

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data/embeddings/probe_ksep/metadata.json

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-{
-  "embedding_id": "probe_ksep",
-  "display_name": "ksep",
-  "modality": "protein sequence / protein representation from PROBE human UniProt archive",
-  "species": "Homo sapiens",
-  "original_identifier_type": "UniProt accession",
-  "mapping_method": "Exact UniProt accession mapping to master_gene_table_v1_1_enriched.csv using uniprot_id, hgnc_uniprot_ids, and map_uniprot_ids_all. Only unique mappings are accepted. Duplicate source rows mapping to the same final master gene are averaged.",
-  "n_genes": 18801,
-  "n_dimensions": 400,
-  "master_coverage_fraction": 0.93551276309897,
-  "original_method": "KSEP",
-  "embedding_generated_by": "PROBE authors / original PROBE human representation archive",
-  "input_data_source": "Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository"
-}