| --- |
| license: cc-by-4.0 |
| task_categories: |
| - text-regression |
| language: |
| - en |
| tags: |
| - biology |
| - dna |
| - genomics |
| - promoter |
| - gene-expression |
| - carbon |
| --- |
| |
| # Random Promoter DREAM Challenge 2022 |
|
|
| This dataset repackages the processed Random Promoter DREAM Challenge 2022 |
| files from Zenodo record `10633252` for use with `datasets`. |
|
|
| The task is sequence-to-expression regression on synthetic yeast promoter |
| sequences. The canonical supervised config contains random promoter training |
| examples, validation examples, and labeled designed test promoters. |
|
|
| ## Configs |
|
|
| - `supervised`: `train`, `validation`, and `test` splits with promoter |
| sequences and measured activity. |
| - `challenge_test_sequences`: unlabeled test sequences for submission-style |
| prediction workflows. |
| - `test_subset_membership`: normalized IDs from `test_subset_ids.tar.gz`. |
| - `public_leaderboard_ids`: normalized IDs from `public_leaderboard_ids.tar.gz`. |
|
|
| ## Schema |
|
|
| `supervised`: |
|
|
| - `sequence`: DNA sequence. |
| - `activity`: measured promoter activity. |
| - `sequence_length`: sequence length in base pairs. |
| - `source_file`: source filename. |
| - `row_id`: zero-based row index within the source split. |
|
|
| ID metadata configs: |
|
|
| - `subset`: subset name inferred from the archive member. |
| - `item_id`: raw ID token from the source line. |
| - `row_id`: integer row ID when `item_id` is numeric; otherwise `-1`. |
| - `source_member`: archive member path. |
| - `line_number`: line number within the member. |
| - `raw_line`: unmodified stripped source line. |
|
|
| ## Usage |
|
|
| ```py |
| from datasets import load_dataset |
| |
| ds = load_dataset("HuggingFaceBio/random-promoter-dream-2022", "supervised") |
| train = ds["train"] |
| validation = ds["validation"] |
| test = ds["test"] |
| |
| subsets = load_dataset("HuggingFaceBio/random-promoter-dream-2022", "test_subset_membership", split="train") |
| ``` |
|
|
| ## Source |
|
|
| Source: Random Promoter DREAM Challenge 2022, Zenodo DOI |
| `10.5281/zenodo.10633252`. |
|
|
| The source record is licensed CC BY 4.0. Cite the original DREAM Challenge data |
| and paper when using this dataset. |
|
|
| ## Reproduction |
|
|
| This dataset repo includes `create_dataset.py`, the script used to download, |
| convert, and upload the configs. |
|
|
