| --- |
| configs: |
| - config_name: EMP_H3 |
| data_files: |
| - split: train |
| path: EMP_H3/EMP_H3_train.csv.gz |
| - split: validation |
| path: EMP_H3/EMP_H3_val.csv.gz |
| - split: test |
| path: EMP_H3/EMP_H3_test.csv.gz |
|
|
| - config_name: EMP_H3K14ac |
| data_files: |
| - split: train |
| path: EMP_H3K14ac/EMP_H3K14ac_train.csv.gz |
| - split: validation |
| path: EMP_H3K14ac/EMP_H3K14ac_val.csv.gz |
| - split: test |
| path: EMP_H3K14ac/EMP_H3K14ac_test.csv.gz |
|
|
| - config_name: EMP_H3K36me3 |
| data_files: |
| - split: train |
| path: EMP_H3K36me3/EMP_H3K36me3_train.csv.gz |
| - split: validation |
| path: EMP_H3K36me3/EMP_H3K36me3_val.csv.gz |
| - split: test |
| path: EMP_H3K36me3/EMP_H3K36me3_test.csv.gz |
|
|
| - config_name: EMP_H3K4me1 |
| data_files: |
| - split: train |
| path: EMP_H3K4me1/EMP_H3K4me1_train.csv.gz |
| - split: validation |
| path: EMP_H3K4me1/EMP_H3K4me1_val.csv.gz |
| - split: test |
| path: EMP_H3K4me1/EMP_H3K4me1_test.csv.gz |
|
|
| - config_name: EMP_H3K4me2 |
| data_files: |
| - split: train |
| path: EMP_H3K4me2/EMP_H3K4me2_train.csv.gz |
| - split: validation |
| path: EMP_H3K4me2/EMP_H3K4me2_val.csv.gz |
| - split: test |
| path: EMP_H3K4me2/EMP_H3K4me2_test.csv.gz |
|
|
| - config_name: EMP_H3K4me3 |
| data_files: |
| - split: train |
| path: EMP_H3K4me3/EMP_H3K4me3_train.csv.gz |
| - split: validation |
| path: EMP_H3K4me3/EMP_H3K4me3_val.csv.gz |
| - split: test |
| path: EMP_H3K4me3/EMP_H3K4me3_test.csv.gz |
|
|
| - config_name: EMP_H3K79me3 |
| data_files: |
| - split: train |
| path: EMP_H3K79me3/EMP_H3K79me3_train.csv.gz |
| - split: validation |
| path: EMP_H3K79me3/EMP_H3K79me3_val.csv.gz |
| - split: test |
| path: EMP_H3K79me3/EMP_H3K79me3_test.csv.gz |
|
|
| - config_name: EMP_H3K9ac |
| data_files: |
| - split: train |
| path: EMP_H3K9ac/EMP_H3K9ac_train.csv.gz |
| - split: validation |
| path: EMP_H3K9ac/EMP_H3K9ac_val.csv.gz |
| - split: test |
| path: EMP_H3K9ac/EMP_H3K9ac_test.csv.gz |
|
|
| - config_name: EMP_H4 |
| data_files: |
| - split: train |
| path: EMP_H4/EMP_H4_train.csv.gz |
| - split: validation |
| path: EMP_H4/EMP_H4_val.csv.gz |
| - split: test |
| path: EMP_H4/EMP_H4_test.csv.gz |
|
|
| - config_name: EMP_H4ac |
| data_files: |
| - split: train |
| path: EMP_H4ac/EMP_H4ac_train.csv.gz |
| - split: validation |
| path: EMP_H4ac/EMP_H4ac_val.csv.gz |
| - split: test |
| path: EMP_H4ac/EMP_H4ac_test.csv.gz |
|
|
| - config_name: EPI_GM12878 |
| data_files: |
| - split: train |
| path: EPI_GM12878/EPI_GM12878_train.csv.gz |
| - split: validation |
| path: EPI_GM12878/EPI_GM12878_val.csv.gz |
| - split: test |
| path: EPI_GM12878/EPI_GM12878_test.csv.gz |
|
|
| - config_name: EPI_HUVEC |
| data_files: |
| - split: train |
| path: EPI_HUVEC/EPI_HUVEC_train.csv.gz |
| - split: validation |
| path: EPI_HUVEC/EPI_HUVEC_val.csv.gz |
| - split: test |
| path: EPI_HUVEC/EPI_HUVEC_test.csv.gz |
|
|
| - config_name: EPI_HeLa-S3 |
| data_files: |
| - split: train |
| path: EPI_HeLa-S3/EPI_HeLa-S3_train.csv.gz |
| - split: validation |
| path: EPI_HeLa-S3/EPI_HeLa-S3_val.csv.gz |
| - split: test |
| path: EPI_HeLa-S3/EPI_HeLa-S3_test.csv.gz |
|
|
| - config_name: EPI_IMR90 |
| data_files: |
| - split: train |
| path: EPI_IMR90/EPI_IMR90_train.csv.gz |
| - split: validation |
| path: EPI_IMR90/EPI_IMR90_val.csv.gz |
| - split: test |
| path: EPI_IMR90/EPI_IMR90_test.csv.gz |
|
|
| - config_name: EPI_K562 |
| data_files: |
| - split: train |
| path: EPI_K562/EPI_K562_train.csv.gz |
| - split: validation |
| path: EPI_K562/EPI_K562_val.csv.gz |
| - split: test |
| path: EPI_K562/EPI_K562_test.csv.gz |
|
|
| - config_name: EPI_NHEK |
| data_files: |
| - split: train |
| path: EPI_NHEK/EPI_NHEK_train.csv.gz |
| - split: validation |
| path: EPI_NHEK/EPI_NHEK_val.csv.gz |
| - split: test |
| path: EPI_NHEK/EPI_NHEK_test.csv.gz |
|
|
| - config_name: mouse_0 |
| data_files: |
| - split: train |
| path: mouse_0/mouse_0_train.csv.gz |
| - split: validation |
| path: mouse_0/mouse_0_val.csv.gz |
| - split: test |
| path: mouse_0/mouse_0_test.csv.gz |
|
|
| - config_name: mouse_1 |
| data_files: |
| - split: train |
| path: mouse_1/mouse_1_train.csv.gz |
| - split: validation |
| path: mouse_1/mouse_1_val.csv.gz |
| - split: test |
| path: mouse_1/mouse_1_test.csv.gz |
|
|
| - config_name: mouse_2 |
| data_files: |
| - split: train |
| path: mouse_2/mouse_2_train.csv.gz |
| - split: validation |
| path: mouse_2/mouse_2_val.csv.gz |
| - split: test |
| path: mouse_2/mouse_2_test.csv.gz |
|
|
| - config_name: mouse_3 |
| data_files: |
| - split: train |
| path: mouse_3/mouse_3_train.csv.gz |
| - split: validation |
| path: mouse_3/mouse_3_val.csv.gz |
| - split: test |
| path: mouse_3/mouse_3_test.csv.gz |
|
|
| - config_name: mouse_4 |
| data_files: |
| - split: train |
| path: mouse_4/mouse_4_train.csv.gz |
| - split: validation |
| path: mouse_4/mouse_4_val.csv.gz |
| - split: test |
| path: mouse_4/mouse_4_test.csv.gz |
|
|
| - config_name: prom_300_all |
| data_files: |
| - split: train |
| path: prom_300_all/prom_300_all_train.csv.gz |
| - split: validation |
| path: prom_300_all/prom_300_all_val.csv.gz |
| - split: test |
| path: prom_300_all/prom_300_all_test.csv.gz |
|
|
| - config_name: prom_300_notata |
| data_files: |
| - split: train |
| path: prom_300_notata/prom_300_notata_train.csv.gz |
| - split: validation |
| path: prom_300_notata/prom_300_notata_val.csv.gz |
| - split: test |
| path: prom_300_notata/prom_300_notata_test.csv.gz |
|
|
| - config_name: prom_300_tata |
| data_files: |
| - split: train |
| path: prom_300_tata/prom_300_tata_train.csv.gz |
| - split: validation |
| path: prom_300_tata/prom_300_tata_val.csv.gz |
| - split: test |
| path: prom_300_tata/prom_300_tata_test.csv.gz |
|
|
| - config_name: prom_core_all |
| data_files: |
| - split: train |
| path: prom_core_all/prom_core_all_train.csv.gz |
| - split: validation |
| path: prom_core_all/prom_core_all_val.csv.gz |
| - split: test |
| path: prom_core_all/prom_core_all_test.csv.gz |
|
|
| - config_name: prom_core_notata |
| data_files: |
| - split: train |
| path: prom_core_notata/prom_core_notata_train.csv.gz |
| - split: validation |
| path: prom_core_notata/prom_core_notata_val.csv.gz |
| - split: test |
| path: prom_core_notata/prom_core_notata_test.csv.gz |
|
|
| - config_name: prom_core_tata |
| data_files: |
| - split: train |
| path: prom_core_tata/prom_core_tata_train.csv.gz |
| - split: validation |
| path: prom_core_tata/prom_core_tata_val.csv.gz |
| - split: test |
| path: prom_core_tata/prom_core_tata_test.csv.gz |
|
|
| - config_name: tf_0 |
| data_files: |
| - split: train |
| path: tf_0/tf_0_train.csv.gz |
| - split: validation |
| path: tf_0/tf_0_val.csv.gz |
| - split: test |
| path: tf_0/tf_0_test.csv.gz |
|
|
| - config_name: tf_1 |
| data_files: |
| - split: train |
| path: tf_1/tf_1_train.csv.gz |
| - split: validation |
| path: tf_1/tf_1_val.csv.gz |
| - split: test |
| path: tf_1/tf_1_test.csv.gz |
|
|
| - config_name: tf_2 |
| data_files: |
| - split: train |
| path: tf_2/tf_2_train.csv.gz |
| - split: validation |
| path: tf_2/tf_2_val.csv.gz |
| - split: test |
| path: tf_2/tf_2_test.csv.gz |
|
|
| - config_name: tf_3 |
| data_files: |
| - split: train |
| path: tf_3/tf_3_train.csv.gz |
| - split: validation |
| path: tf_3/tf_3_val.csv.gz |
| - split: test |
| path: tf_3/tf_3_test.csv.gz |
|
|
| - config_name: tf_4 |
| data_files: |
| - split: train |
| path: tf_4/tf_4_train.csv.gz |
| - split: validation |
| path: tf_4/tf_4_val.csv.gz |
| - split: test |
| path: tf_4/tf_4_test.csv.gz |
| --- |
| |
| # GUE_v2 |
| |
| ## Overview |
| |
| [GUE_v2](https://arxiv.org/pdf/2306.15006) is a collection of multi-species genome classification datasets. This respository includes datasets from GUE (v2) that have been filtered by our criteria to be included in our quality-curated genomic benchmark datasets. |
| |
| ## Dataset structure |
| |
| The repository is organized as follows: |
| ``` |
| GUE_v2/ |
| ├── README.md |
| ├── EMP_H3/ |
| │ ├── EMP_H3_train.csv.gz |
| │ ├── EMP_H3_val.csv.gz |
| │ └── EMP_H3_test.csv.gz |
| ├── EMP_H3K14ac/ |
| │ ├── EMP_H3K14ac_train.csv.gz |
| │ ├── EMP_H3K14ac_val.csv.gz |
| │ └── EMP_H3K14ac_test.csv.gz |
| ├── EMP_H3K36me3/ |
| │ ├── EMP_H3K36me3_train.csv.gz |
| │ ├── EMP_H3K36me3_val.csv.gz |
| │ └── EMP_H3K36me3_test.csv.gz |
| ├── EMP_H3K4me1/ |
| │ ├── EMP_H3K4me1_train.csv.gz |
| │ ├── EMP_H3K4me1_val.csv.gz |
| │ └── EMP_H3K4me1_test.csv.gz |
| ├── EMP_H3K4me2/ |
| │ ├── EMP_H3K4me2_train.csv.gz |
| │ ├── EMP_H3K4me2_val.csv.gz |
| │ └── EMP_H3K4me2_test.csv.gz |
| ├── EMP_H3K4me3/ |
| │ ├── EMP_H3K4me3_train.csv.gz |
| │ ├── EMP_H3K4me3_val.csv.gz |
| │ └── EMP_H3K4me3_test.csv.gz |
| ├── EMP_H3K79me3/ |
| │ ├── EMP_H3K79me3_train.csv.gz |
| │ ├── EMP_H3K79me3_val.csv.gz |
| │ └── EMP_H3K79me3_test.csv.gz |
| ├── EMP_H3K9ac/ |
| │ ├── EMP_H3K9ac_train.csv.gz |
| │ ├── EMP_H3K9ac_val.csv.gz |
| │ └── EMP_H3K9ac_test.csv.gz |
| ├── EMP_H4/ |
| │ ├── EMP_H4_train.csv.gz |
| │ ├── EMP_H4_val.csv.gz |
| │ └── EMP_H4_test.csv.gz |
| ├── EMP_H4ac/ |
| │ ├── EMP_H4ac_train.csv.gz |
| │ ├── EMP_H4ac_val.csv.gz |
| │ └── EMP_H4ac_test.csv.gz |
| ├── EPI_GM12878/ |
| │ ├── EPI_GM12878_train.csv.gz |
| │ ├── EPI_GM12878_val.csv.gz |
| │ └── EPI_GM12878_test.csv.gz |
| ├── EPI_HUVEC/ |
| │ ├── EPI_HUVEC_train.csv.gz |
| │ ├── EPI_HUVEC_val.csv.gz |
| │ └── EPI_HUVEC_test.csv.gz |
| ├── EPI_HeLa-S3/ |
| │ ├── EPI_HeLa-S3_train.csv.gz |
| │ ├── EPI_HeLa-S3_val.csv.gz |
| │ └── EPI_HeLa-S3_test.csv.gz |
| ├── EPI_IMR90/ |
| │ ├── EPI_IMR90_train.csv.gz |
| │ ├── EPI_IMR90_val.csv.gz |
| │ └── EPI_IMR90_test.csv.gz |
| ├── EPI_K562/ |
| │ ├── EPI_K562_train.csv.gz |
| │ ├── EPI_K562_val.csv.gz |
| │ └── EPI_K562_test.csv.gz |
| ├── EPI_NHEK/ |
| │ ├── EPI_NHEK_train.csv.gz |
| │ ├── EPI_NHEK_val.csv.gz |
| │ └── EPI_NHEK_test.csv.gz |
| ├── mouse_0/ |
| │ ├── mouse_0_train.csv.gz |
| │ ├── mouse_0_val.csv.gz |
| │ └── mouse_0_test.csv.gz |
| ├── mouse_1/ |
| │ ├── mouse_1_train.csv.gz |
| │ ├── mouse_1_val.csv.gz |
| │ └── mouse_1_test.csv.gz |
| ├── mouse_2/ |
| │ ├── mouse_2_train.csv.gz |
| │ ├── mouse_2_val.csv.gz |
| │ └── mouse_2_test.csv.gz |
| ├── mouse_3/ |
| │ ├── mouse_3_train.csv.gz |
| │ ├── mouse_3_val.csv.gz |
| │ └── mouse_3_test.csv.gz |
| ├── mouse_4/ |
| │ ├── mouse_4_train.csv.gz |
| │ ├── mouse_4_val.csv.gz |
| │ └── mouse_4_test.csv.gz |
| ├── prom_300_all/ |
| │ ├── prom_300_all_train.csv.gz |
| │ ├── prom_300_all_val.csv.gz |
| │ └── prom_300_all_test.csv.gz |
| ├── prom_300_notata/ |
| │ ├── prom_300_notata_train.csv.gz |
| │ ├── prom_300_notata_val.csv.gz |
| │ └── prom_300_notata_test.csv.gz |
| ├── prom_300_tata/ |
| │ ├── prom_300_tata_train.csv.gz |
| │ ├── prom_300_tata_val.csv.gz |
| │ └── prom_300_tata_test.csv.gz |
| ├── prom_core_all/ |
| │ ├── prom_core_all_train.csv.gz |
| │ ├── prom_core_all_val.csv.gz |
| │ └── prom_core_all_test.csv.gz |
| ├── prom_core_notata/ |
| │ ├── prom_core_notata_train.csv.gz |
| │ ├── prom_core_notata_val.csv.gz |
| │ └── prom_core_notata_test.csv.gz |
| ├── prom_core_tata/ |
| │ ├── prom_core_tata_train.csv.gz |
| │ ├── prom_core_tata_val.csv.gz |
| │ └── prom_core_tata_test.csv.gz |
| ├── tf_0/ |
| │ ├── tf_0_train.csv.gz |
| │ ├── tf_0_val.csv.gz |
| │ └── tf_0_test.csv.gz |
| ├── tf_1/ |
| │ ├── tf_1_train.csv.gz |
| │ ├── tf_1_val.csv.gz |
| │ └── tf_1_test.csv.gz |
| ├── tf_2/ |
| │ ├── tf_2_train.csv.gz |
| │ ├── tf_2_val.csv.gz |
| │ └── tf_2_test.csv.gz |
| ├── tf_3/ |
| │ ├── tf_3_train.csv.gz |
| │ ├── tf_3_val.csv.gz |
| │ └── tf_3_test.csv.gz |
| └── tf_4/ |
| ├── tf_4_train.csv.gz |
| ├── tf_4_val.csv.gz |
| └── tf_4_test.csv.gz |
| ``` |
