| --- |
| configs: |
| - config_name: lncrna_g_max |
| data_files: |
| - split: train |
| path: lncrna_g_max/lncrna_g_max_train.csv.gz |
| - split: validation |
| path: lncrna_g_max/lncrna_g_max_test.csv.gz |
| - split: test |
| path: lncrna_g_max/lncrna_g_max_test.csv.gz |
|
|
| - config_name: lncrna_m_esculenta |
| data_files: |
| - split: train |
| path: lncrna_m_esculenta/lncrna_m_esculenta_train.csv.gz |
| - split: validation |
| path: lncrna_m_esculenta/lncrna_m_esculenta_test.csv.gz |
| - split: test |
| path: lncrna_m_esculenta/lncrna_m_esculenta_test.csv.gz |
|
|
| - config_name: lncrna_s_bicolor |
| data_files: |
| - split: train |
| path: lncrna_s_bicolor/lncrna_s_bicolor_train.csv.gz |
| - split: validation |
| path: lncrna_s_bicolor/lncrna_s_bicolor_test.csv.gz |
| - split: test |
| path: lncrna_s_bicolor/lncrna_s_bicolor_test.csv.gz |
|
|
| - config_name: lncrna_s_lycopersicum |
| data_files: |
| - split: train |
| path: lncrna_s_lycopersicum/lncrna_s_lycopersicum_train.csv.gz |
| - split: validation |
| path: lncrna_s_lycopersicum/lncrna_s_lycopersicum_test.csv.gz |
| - split: test |
| path: lncrna_s_lycopersicum/lncrna_s_lycopersicum_test.csv.gz |
|
|
| - config_name: lncrna_t_aestivum |
| data_files: |
| - split: train |
| path: lncrna_t_aestivum/lncrna_t_aestivum_train.csv.gz |
| - split: validation |
| path: lncrna_t_aestivum/lncrna_t_aestivum_test.csv.gz |
| - split: test |
| path: lncrna_t_aestivum/lncrna_t_aestivum_test.csv.gz |
|
|
| - config_name: lncrna_z_mays |
| data_files: |
| - split: train |
| path: lncrna_z_mays/lncrna_z_mays_train.csv.gz |
| - split: validation |
| path: lncrna_z_mays/lncrna_z_mays_test.csv.gz |
| - split: test |
| path: lncrna_z_mays/lncrna_z_mays_test.csv.gz |
|
|
| - config_name: poly_a_arabidopsis_thaliana |
| data_files: |
| - split: train |
| path: poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_train.csv.gz |
| - split: validation |
| path: poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_test.csv.gz |
| - split: test |
| path: poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_test.csv.gz |
|
|
| - config_name: poly_a_chlamydomonas_reinhardtii |
| data_files: |
| - split: train |
| path: poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_train.csv.gz |
| - split: validation |
| path: poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_test.csv.gz |
| - split: test |
| path: poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_test.csv.gz |
|
|
| - config_name: poly_a_medicago_truncatula |
| data_files: |
| - split: train |
| path: poly_a_medicago_truncatula/poly_a_medicago_truncatula_train.csv.gz |
| - split: validation |
| path: poly_a_medicago_truncatula/poly_a_medicago_truncatula_test.csv.gz |
| - split: test |
| path: poly_a_medicago_truncatula/poly_a_medicago_truncatula_test.csv.gz |
|
|
| - config_name: poly_a_oryza_sativa_indica_group |
| data_files: |
| - split: train |
| path: poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_train.csv.gz |
| - split: validation |
| path: poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_test.csv.gz |
| - split: test |
| path: poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_test.csv.gz |
|
|
| - config_name: poly_a_oryza_sativa_japonica_group |
| data_files: |
| - split: train |
| path: poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_train.csv.gz |
| - split: validation |
| path: poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_test.csv.gz |
| - split: test |
| path: poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_test.csv.gz |
|
|
| - config_name: poly_a_trifolium_pratense |
| data_files: |
| - split: train |
| path: poly_a_trifolium_pratense/poly_a_trifolium_pratense_train.csv.gz |
| - split: validation |
| path: poly_a_trifolium_pratense/poly_a_trifolium_pratense_test.csv.gz |
| - split: test |
| path: poly_a_trifolium_pratense/poly_a_trifolium_pratense_test.csv.gz |
|
|
| - config_name: pro_seq_m_esculenta |
| data_files: |
| - split: train |
| path: pro_seq_m_esculenta/pro_seq_m_esculenta_train.csv.gz |
| - split: validation |
| path: pro_seq_m_esculenta/pro_seq_m_esculenta_test.csv.gz |
| - split: test |
| path: pro_seq_m_esculenta/pro_seq_m_esculenta_test.csv.gz |
|
|
| - config_name: promoter_strength_leaf |
| data_files: |
| - split: train |
| path: promoter_strength_leaf/promoter_strength_leaf_train.csv.gz |
| - split: validation |
| path: promoter_strength_leaf/promoter_strength_leaf_test.csv.gz |
| - split: test |
| path: promoter_strength_leaf/promoter_strength_leaf_test.csv.gz |
|
|
| - config_name: promoter_strength_protoplast |
| data_files: |
| - split: train |
| path: promoter_strength_protoplast/promoter_strength_protoplast_train.csv.gz |
| - split: validation |
| path: promoter_strength_protoplast/promoter_strength_protoplast_test.csv.gz |
| - split: test |
| path: promoter_strength_protoplast/promoter_strength_protoplast_test.csv.gz |
|
|
| - config_name: splicing_arabidopsis_thaliana_acceptor |
| data_files: |
| - split: train |
| path: splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_train.csv.gz |
| - split: validation |
| path: splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_test.csv.gz |
| - split: test |
| path: splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_test.csv.gz |
|
|
| - config_name: splicing_arabidopsis_thaliana_donor |
| data_files: |
| - split: train |
| path: splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_train.csv.gz |
| - split: validation |
| path: splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_test.csv.gz |
| - split: test |
| path: splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_test.csv.gz |
|
|
| - config_name: te_prediction_arabidopsis |
| data_files: |
| - split: train |
| path: te_prediction_arabidopsis/te_prediction_arabidopsis_train.csv.gz |
| - split: validation |
| path: te_prediction_arabidopsis/te_prediction_arabidopsis_val.csv.gz |
| - split: test |
| path: te_prediction_arabidopsis/te_prediction_arabidopsis_test.csv.gz |
|
|
| - config_name: te_prediction_rice |
| data_files: |
| - split: train |
| path: te_prediction_rice/te_prediction_rice_train.csv.gz |
| - split: validation |
| path: te_prediction_rice/te_prediction_rice_val.csv.gz |
| - split: test |
| path: te_prediction_rice/te_prediction_rice_test.csv.gz |
|
|
| - config_name: terminator_strength_leaf |
| data_files: |
| - split: train |
| path: terminator_strength_leaf/terminator_strength_leaf_train.csv.gz |
| - split: validation |
| path: terminator_strength_leaf/terminator_strength_leaf_test.csv.gz |
| - split: test |
| path: terminator_strength_leaf/terminator_strength_leaf_test.csv.gz |
|
|
| - config_name: terminator_strength_protoplast |
| data_files: |
| - split: train |
| path: terminator_strength_protoplast/terminator_strength_protoplast_train.csv.gz |
| - split: validation |
| path: terminator_strength_protoplast/terminator_strength_protoplast_test.csv.gz |
| - split: test |
| path: terminator_strength_protoplast/terminator_strength_protoplast_test.csv.gz |
| --- |
| |
| # OmniGenBench |
|
|
| ## Overview |
|
|
| [OmniGenBench](https://arxiv.org/pdf/2505.14402) is a collection of benchmark suites. This respository includes datasets from OmniGenBench 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: |
| ``` |
| OmniGenBench/ |
| ├── README.md |
| ├── lncrna_g_max/ |
| │ ├── lncrna_g_max_train.csv.gz |
| │ └── lncrna_g_max_test.csv.gz |
| ├── lncrna_m_esculenta/ |
| │ ├── lncrna_m_esculenta_train.csv.gz |
| │ └── lncrna_m_esculenta_test.csv.gz |
| ├── lncrna_s_bicolor/ |
| │ ├── lncrna_s_bicolor_train.csv.gz |
| │ └── lncrna_s_bicolor_test.csv.gz |
| ├── lncrna_s_lycopersicum/ |
| │ ├── lncrna_s_lycopersicum_train.csv.gz |
| │ └── lncrna_s_lycopersicum_test.csv.gz |
| ├── lncrna_t_aestivum/ |
| │ ├── lncrna_t_aestivum_train.csv.gz |
| │ └── lncrna_t_aestivum_test.csv.gz |
| ├── lncrna_z_mays/ |
| │ ├── lncrna_z_mays_train.csv.gz |
| │ └── lncrna_z_mays_test.csv.gz |
| ├── poly_a_arabidopsis_thaliana/ |
| │ ├── poly_a_arabidopsis_thaliana_train.csv.gz |
| │ └── poly_a_arabidopsis_thaliana_test.csv.gz |
| ├── poly_a_chlamydomonas_reinhardtii/ |
| │ ├── poly_a_chlamydomonas_reinhardtii_train.csv.gz |
| │ └── poly_a_chlamydomonas_reinhardtii_test.csv.gz |
| ├── poly_a_medicago_truncatula/ |
| │ ├── poly_a_medicago_truncatula_train.csv.gz |
| │ └── poly_a_medicago_truncatula_test.csv.gz |
| ├── poly_a_oryza_sativa_indica_group/ |
| │ ├── poly_a_oryza_sativa_indica_group_train.csv.gz |
| │ └── poly_a_oryza_sativa_indica_group_test.csv.gz |
| ├── poly_a_oryza_sativa_japonica_group/ |
| │ ├── poly_a_oryza_sativa_japonica_group_train.csv.gz |
| │ └── poly_a_oryza_sativa_japonica_group_test.csv.gz |
| ├── poly_a_trifolium_pratense/ |
| │ ├── poly_a_trifolium_pratense_train.csv.gz |
| │ └── poly_a_trifolium_pratense_test.csv.gz |
| ├── pro_seq_m_esculenta/ |
| │ ├── pro_seq_m_esculenta_train.csv.gz |
| │ └── pro_seq_m_esculenta_test.csv.gz |
| ├── promoter_strength_leaf/ |
| │ ├── promoter_strength_leaf_train.csv.gz |
| │ └── promoter_strength_leaf_test.csv.gz |
| ├── promoter_strength_protoplast/ |
| │ ├── promoter_strength_protoplast_train.csv.gz |
| │ └── promoter_strength_protoplast_test.csv.gz |
| ├── splicing_arabidopsis_thaliana_acceptor/ |
| │ ├── splicing_arabidopsis_thaliana_acceptor_train.csv.gz |
| │ └── splicing_arabidopsis_thaliana_acceptor_test.csv.gz |
| ├── splicing_arabidopsis_thaliana_donor/ |
| │ ├── splicing_arabidopsis_thaliana_donor_train.csv.gz |
| │ └── splicing_arabidopsis_thaliana_donor_test.csv.gz |
| ├── te_prediction_arabidopsis/ |
| │ ├── te_prediction_arabidopsis_train.csv.gz |
| │ ├── te_prediction_arabidopsis_val.csv.gz |
| │ └── te_prediction_arabidopsis_test.csv.gz |
| ├── te_prediction_rice/ |
| │ ├── te_prediction_rice_train.csv.gz |
| │ ├── te_prediction_rice_val.csv.gz |
| │ └── te_prediction_rice_test.csv.gz |
| ├── terminator_strength_leaf/ |
| │ ├── terminator_strength_leaf_train.csv.gz |
| │ └── terminator_strength_leaf_test.csv.gz |
| └── terminator_strength_protoplast/ |
| ├── terminator_strength_protoplast_train.csv.gz |
| └── terminator_strength_protoplast_test.csv.gz |
| ``` |
