| --- |
| license: cc-by-4.0 |
| pretty_name: CodonTranslator Data |
| task_categories: |
| - text-generation |
| tags: |
| - biology |
| - dna |
| - codon-optimization |
| - protein-conditioned-generation |
| size_categories: |
| - 10M<n<100M |
| --- |
| |
| # CodonTranslator Data |
|
|
| This repository contains the final public training-data release used for CodonTranslator. |
|
|
| ## Contents |
|
|
| - `train/`: representative-only training shards |
| - `val/`: representative-only validation shards |
| - `test/`: representative-only held-out test shards |
| - `embeddings_v2/`: precomputed species conditioning embeddings used in training |
| - `_work/final_representative_counts.json`: final released split sizes |
| - `_work/split_report.json`: split audit report |
| - `_work/mmseqs_manifest.json`: MMseqs version and clustering parameters |
| - `_work/cluster_split.parquet`: cluster-level split assignments |
| - `_work/seq_cluster.parquet`: MMseqs cluster assignments |
| - `_work/seq_split.parquet`: split assignments before representative selection |
|
|
| ## Split definition |
|
|
| The public `data_v3` split was rebuilt from `data_v2` with the following rules: |
|
|
| - MMseqs clustering in **protein space** |
| - test holdout by **binomial species** |
| - validation split from **seen species but unseen clusters** |
| - representative-only parquet outputs, one retained row per released representative sequence |
|
|
| Mixed seen/held-out protein clusters and exact-protein leakage cases are removed on the seen side before final release. |
|
|
| ## Final released split sizes |
|
|
| - `train = 36,888,301` |
| - `val = 373,637` |
| - `test = 331,455` |
|
|
| All three released splits satisfy: |
|
|
| - exact protein overlap `train/val = 0` |
| - exact protein overlap `train/test = 0` |
| - test species not seen in train/val |
| - representatives-only rows, so `rows == unique_seq_id` |
|
|
| ## Parquet schema |
|
|
| Each released parquet shard contains these columns: |
|
|
| - `RefseqID` |
| - `protein_refseq_id` |
| - `protein_seq` |
| - `cds_DNA` |
| - `taxon` |
| - `shard` |
|
|
| ## Embeddings |
|
|
| `embeddings_v2/` is the exact species embedding store used in training. It contains: |
|
|
| - `species_vocab.json` |
| - `species_index.json` |
| - `species_tok_emb.bin` |
| - `metadata.json` |
| - `taxonomy_database.json` |
|
|
| The released `data_v3` taxa are fully covered by this embedding store. |
|
|
| ## Model and code |
|
|
| The corresponding public model and code release is: |
|
|
| - `alegendaryfish/CodonTranslator` |
|
|
| ## Attribution |
|
|
| This release redistributes processed training data and derived embeddings for reproducibility of the CodonTranslator experiments. See the audit files in `_work/` for construction details and final verification outputs. |
|
|
| The raw MMseqs working database is not included because it is large, machine-specific intermediate state. The released `_work/` files are the reproducibility artifacts needed to audit and reconstruct the clustering and split decisions. |
|
|
