| # Embedding name: RNA-FM-full-transcript |
|
|
| - Modality: RNA/mRNA sequence / full mature transcript language-model embedding |
| - Algorithm: Transformer RNA language model |
| - Embedding source URL: Local generation from Ensembl release 114 GRCh38 mature RNA transcript sequences and master_gene_table.csv |
| - Original model/code URL: https://github.com/ml4bio/RNA-FM |
|
|
| ## 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: `19976 genes × 640 dimensions` |
| - Dtype: `float32` |
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|
|
| ## Detailed processing notes |
|
|
| ### Source and interpretation |
|
|
| This embedding is a gene-level mature RNA transcript representation derived from RNA-FM. It was generated locally from the mature transcript sequence universe prepared from Ensembl release 114 GRCh38 cDNA sequences and the canonical transcript IDs in master_gene_table.csv. |
|
|
| The model used was RNA-FM / `rna_fm_t12` with the official pretrained checkpoint `RNA-FM_pretrained.pth`. For each matched gene, the mature transcript sequence was represented as raw RNA sequence. No Helix-specific `E` codon-start markers were inserted. RNA-FM final layer 12 token representations were extracted, BOS/EOS tokens were excluded, token embeddings were mean-pooled within each chunk, and long transcripts were combined by sequence-length weighted mean pooling across chunks. |
|
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| This embedding should therefore be interpreted as a full mature transcript RNA language-model representation. It differs from Helix-mRNA because it uses raw RNA sequence without CDS-aware `E` markers, and it differs from CDS-only DNA embeddings because it includes UTR sequence from the mature transcript. |
|
|
| ### Provenance fields |
|
|
| source_name: RNA-FM full mature transcript |
| original_model_or_method: RNA-FM / rna_fm_t12 RNA language model |
| input_sequence_type: mature RNA full transcript |
| input_sequence_source: Ensembl release 114 GRCh38 cDNA-derived mature RNA sequences and master_gene_table.csv canonical transcript IDs |
| genome_build: GRCh38 |
| sequence_reference: Ensembl release 114 |
| model_checkpoint: RNA-FM_pretrained.pth |
| model_checkpoint_sha256: 5b5d7d87b37c291ef42c140ef9edf7aea29f255fa2a4fd435f776c52e93d5e99 |
| model_code_url: https://github.com/ml4bio/RNA-FM |
| model_interface: fm.pretrained.rna_fm_t12() |
| model_output_dimension: 640 |
| final_layer_used: 12 |
| chunk_len: 900 |
| min_chunk_len: 0 |
| batch_size: 1 |
| pooling_strategy: mean pooling over final layer 12 token embeddings, excluding BOS/EOS tokens, with sequence-length weighted mean across chunks |
| training_or_finetuning: none |
| |
| ### Sequence and transcript decisions |
|
|
| The source gene set came from master_gene_table.csv. Canonical transcript IDs from the master table were used to select one mature transcript sequence per gene from the Ensembl release 114 GRCh38 cDNA FASTA. |
|
|
| RNA-FM reused the raw mature RNA sequence universe prepared during the Helix-mRNA workflow. However, it used the raw RNA FASTA without Helix `E` codon-start markers. This decision prevents Helix-specific input formatting from contaminating the RNA-FM representation. |
|
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| Genes without a matched mature transcript sequence, without a matched CDS sequence from the shared preparation workflow, or where sequence preparation failed were excluded from this embedding. |
|
|
| ### Processing workflow |
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|
| For each gene in the mature RNA transcript table: |
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|
| 1. Read the canonical transcript ID from master_gene_table.csv. |
| 2. Reuse the mature transcript sequence table prepared from Ensembl release 114 GRCh38 cDNA. |
| 3. Convert mature cDNA-derived sequence to raw RNA sequence. |
| 4. Use the raw RNA sequence without Helix E markers. |
| 5. Load RNA-FM / rna_fm_t12 from the local checkpoint cache. |
| 6. Split long transcript sequences into 900 nt chunks. |
| 7. Run RNA-FM with batch_size=1. |
| 8. Extract final layer 12 token representations. |
| 9. Exclude BOS/EOS tokens from pooling. |
| 10. Mean-pool token embeddings within each chunk. |
| 11. Combine chunk vectors with sequence-length weighted mean pooling. |
| 12. Save the final matrix as float32. |
| |
| ### Important implementation decisions |
| |
| The standard RNA-FM loader attempted to use an external CUHK checkpoint URL that could return 403. The final workflow copied the HuggingFace snapshot checkpoint into the torch hub checkpoint cache so `fm.pretrained.rna_fm_t12()` could load the official checkpoint locally and reproducibly. |
| |
| No model training or fine-tuning was performed. The final matrix was generated only by local inference from the official pretrained checkpoint. |
| |
| ### Summary of final mapping: |
| |
| Source identifiers / mature transcript sequences: 19,976 |
| Dimensions: 640 |
| Rows generated before duplicate collapse: 19,976 |
| Missing/failed sequence genes: 121 |
| Unmapped source rows: 0 |
| Ambiguous source rows: 0 |
| Final mapped genes: 19,976 |
| Master table rows: 20,097 |
| Master coverage: 99.398% |
| Duplicate final mappings averaged: 0 |
| |
| <!-- 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` | |
| | `num_genes` | `n_genes` | |
| | `embedding_dimension` | `n_dimensions` | |
| | `matrix_shape[0]` | `n_genes` | |
| | `matrix_shape[1]` | `n_dimensions` | |
| |
| ### 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": 0, |
| "documented": true, |
| "expected": false, |
| "reason": "No exact all-zero rows were detected in embeddings.npz.", |
| "report_file": null |
| }, |
| "batch_size": 1, |
| "chunk_len": 900, |
| "created_at": "2026-07-08T10:59:52", |
| "former_processing_embedding_id": "rnafm_full_transcript_v1_1", |
| "input_sequence_source": "Derived from Helix mature mRNA preparation based on Ensembl release 114 GRCh38 cDNA/canonical transcript mapping", |
| "input_sequence_type": "mature mRNA full transcript", |
| "min_chunk_len": 0, |
| "model": "RNA-FM / rna_fm_t12", |
| "model_checkpoint_sha256": "5b5d7d87b37c291ef42c140ef9edf7aea29f255fa2a4fd435f776c52e93d5e99", |
| "public_file_structure": { |
| "embeddings": "embeddings.npz", |
| "genes": "genes.tsv", |
| "metadata": "metadata.json", |
| "readme": "README.md" |
| }, |
| "runtime_seconds": 3351.46, |
| "sequence_processing": "Helix E codon-start markers removed; T converted to U; sequences restricted to A/C/G/U/N", |
| "software": { |
| "python": "3.10", |
| "torch": "2.2.2+cu118" |
| }, |
| "status": "processed_qc_passed" |
| } |
| ``` |
|
|
| <!-- END CATALOG NORMALIZATION: LEGACY METADATA --> |
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|
