| --- |
| configs: |
| - config_name: eukaryote_generator |
| data_files: |
| - split: train |
| path: eukaryote_generator/**/*.parquet |
| - config_name: mrna_evo2 |
| data_files: |
| - split: train |
| path: mrna_evo2/*.parquet |
| - config_name: mrna_splice_evo2 |
| data_files: |
| - split: train |
| path: mrna_splice_evo2/*.parquet |
| - config_name: prokaryote_evo2 |
| data_files: |
| - split: train |
| path: prokaryote_evo2/*.parquet |
| --- |
| |
| # Carbon pretraining corpus |
|
|
| Private aggregation of the four sources used for Carbon pure-DNA pretraining, |
| all stored as parquet for direct `load_dataset` access. |
|
|
| ## Subsets |
|
|
| | Subset | Source | Description | |
| |---|---|---| |
| | `eukaryote_generator` | [GenerTeam/pretrain_data_eukaryote](https://huggingface.co/datasets/GenerTeam/pretrain_data_eukaryote) | Eukaryote DNA, sharded by species (`fungi/`, `plants/`, `protozoa/`, `vertebrate_mammalian/`, ...) | |
| | `mrna_evo2` | [arcinstitute/opengenome2 / mrna](https://huggingface.co/datasets/arcinstitute/opengenome2/tree/main/json/pretraining_or_both_phases/mrna) | mRNA sequences, train chunks only | |
| | `mrna_splice_evo2` | [arcinstitute/opengenome2 / mrna_splice_promoter](https://huggingface.co/datasets/arcinstitute/opengenome2/tree/main/json/pretraining_or_both_phases/mrna_splice_promoter) | mRNA + splice + promoter, train chunks only | |
| | `prokaryote_evo2` | [arcinstitute/opengenome2 / gtdb_v220_imgpr](https://huggingface.co/datasets/arcinstitute/opengenome2/tree/main/json/pretraining_or_both_phases/gtdb_v220_imgpr) | Prokaryote (GTDB v220 + IMG/PR), train chunks only | |
|
|
| Test splits from opengenome2 are not included (this is a pretraining corpus). |
|
|
| ## Usage |
|
|
| ```python |
| from datasets import load_dataset |
| |
| # pick any subset |
| ds = load_dataset("hf-carbon/carbon-pretraining-corpus", "mrna_evo2", split="train", streaming=True) |
| print(next(iter(ds))) |
| ``` |
|
|
| ## License |
|
|
| Defer to upstream sources: |
| - GenerTeam/pretrain_data_eukaryote — see upstream repo. |
| - arcinstitute/opengenome2 — see upstream repo. |
|
|
