README.md

metadata

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.