# 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` ## 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. 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. 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 For each gene in the mature RNA transcript table: 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 ## 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" } ```