Hugging Face's logo

Datasets:
genomic-benchmarks
/
OmniGenBench

Modalities:
Text
Formats:
csv
Size:
100K - 1M
ArXiv:
Libraries:
Datasets
pandas
Polars
Dataset card Data Studio Files
xet
 Community
stephaniesamm commited on
Commit
cd77c2e
·
verified ·
1 Parent(s): 2ec1971

Upload folder using huggingface_hub

Browse files
Files changed (47) hide show
  1. OmniGenBench_metadata.json +2246 -0
  2. README.md +271 -0
  3. lncrna_g_max/lncrna_g_max_test.csv.gz +3 -0
  4. lncrna_g_max/lncrna_g_max_train.csv.gz +3 -0
  5. lncrna_m_esculenta/lncrna_m_esculenta_test.csv.gz +3 -0
  6. lncrna_m_esculenta/lncrna_m_esculenta_train.csv.gz +3 -0
  7. lncrna_s_bicolor/lncrna_s_bicolor_test.csv.gz +3 -0
  8. lncrna_s_bicolor/lncrna_s_bicolor_train.csv.gz +3 -0
  9. lncrna_s_lycopersicum/lncrna_s_lycopersicum_test.csv.gz +3 -0
  10. lncrna_s_lycopersicum/lncrna_s_lycopersicum_train.csv.gz +3 -0
  11. lncrna_t_aestivum/lncrna_t_aestivum_test.csv.gz +3 -0
  12. lncrna_t_aestivum/lncrna_t_aestivum_train.csv.gz +3 -0
  13. lncrna_z_mays/lncrna_z_mays_test.csv.gz +3 -0
  14. lncrna_z_mays/lncrna_z_mays_train.csv.gz +3 -0
  15. poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_test.csv.gz +3 -0
  16. poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_train.csv.gz +3 -0
  17. poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_test.csv.gz +3 -0
  18. poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_train.csv.gz +3 -0
  19. poly_a_medicago_truncatula/poly_a_medicago_truncatula_test.csv.gz +3 -0
  20. poly_a_medicago_truncatula/poly_a_medicago_truncatula_train.csv.gz +3 -0
  21. poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_test.csv.gz +3 -0
  22. poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_train.csv.gz +3 -0
  23. poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_test.csv.gz +3 -0
  24. poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_train.csv.gz +3 -0
  25. poly_a_trifolium_pratense/poly_a_trifolium_pratense_test.csv.gz +3 -0
  26. poly_a_trifolium_pratense/poly_a_trifolium_pratense_train.csv.gz +3 -0
  27. pro_seq_m_esculenta/pro_seq_m_esculenta_test.csv.gz +3 -0
  28. pro_seq_m_esculenta/pro_seq_m_esculenta_train.csv.gz +3 -0
  29. promoter_strength_leaf/promoter_strength_leaf_test.csv.gz +3 -0
  30. promoter_strength_leaf/promoter_strength_leaf_train.csv.gz +3 -0
  31. promoter_strength_protoplast/promoter_strength_protoplast_test.csv.gz +3 -0
  32. promoter_strength_protoplast/promoter_strength_protoplast_train.csv.gz +3 -0
  33. splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_test.csv.gz +3 -0
  34. splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_train.csv.gz +3 -0
  35. splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_test.csv.gz +3 -0
  36. splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_train.csv.gz +3 -0
  37. te_prediction_arabidopsis/te_prediction_arabidopsis_test.csv.gz +3 -0
  38. te_prediction_arabidopsis/te_prediction_arabidopsis_train.csv.gz +3 -0
  39. te_prediction_arabidopsis/te_prediction_arabidopsis_val.csv.gz +3 -0
  40. te_prediction_rice/te_prediction_rice_test.csv.gz +3 -0
  41. te_prediction_rice/te_prediction_rice_train.csv.gz +3 -0
  42. te_prediction_rice/te_prediction_rice_val.csv.gz +3 -0
  43. te_prediction_rice/te_prediction_rice_valid.csv.gz +3 -0
  44. terminator_strength_leaf/terminator_strength_leaf_test.csv.gz +3 -0
  45. terminator_strength_leaf/terminator_strength_leaf_train.csv.gz +3 -0
  46. terminator_strength_protoplast/terminator_strength_protoplast_test.csv.gz +3 -0
  47. terminator_strength_protoplast/terminator_strength_protoplast_train.csv.gz +3 -0
OmniGenBench_metadata.json ADDED
@@ -0,0 +1,2246 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "collection": "OmniGenBench",
3
+ "collection_doi": "https://doi.org/10.48550/arXiv.2505.14402",
4
+ "datasets": [
5
+ {
6
+ "dataset_name": "mRNA",
7
+ "task_description": "mRNA Degradation Rate Prediction: measures in-line hydrolysis of 102-130 nt constructs under different conditions",
8
+ "dataset_doi": "https://doi.org/10.1038/s42256-024-00946-z",
9
+ "species": null,
10
+ "task_type": "Token Regression",
11
+ "seq_col": [
12
+ "sequence"
13
+ ],
14
+ "label_col": [
15
+ "deg_Mg_pH10",
16
+ "deg_pH10",
17
+ "deg_Mg_50C",
18
+ "deg_50C"
19
+ ],
20
+ "label_categories": null,
21
+ "splits": null,
22
+ "excluded": "Token regression data format is not supported by our framework.",
23
+ "task_category": "RNA Stability Prediction",
24
+ "molecular_level": "RNA"
25
+ },
26
+ {
27
+ "dataset_name": "snmd",
28
+ "task_description": "Single Nucleotide Mutation Detection: flags mutated positions in synthetic plant RNAs (up to ten random SNVs per sequence)",
29
+ "dataset_doi": "collection_doi",
30
+ "species": "Plant",
31
+ "task_type": "Token Classification",
32
+ "seq_col": [
33
+ "seq",
34
+ "mut"
35
+ ],
36
+ "label_col": "ratio",
37
+ "label_categories": null,
38
+ "splits": null,
39
+ "excluded": "Token classification data format is not supported by our framework.",
40
+ "task_category": "Variant Effect Prediction",
41
+ "molecular_level": "RNA"
42
+ },
43
+ {
44
+ "dataset_name": "snmr",
45
+ "task_description": "Single Nucleotide Mutation Repair: proposes the corrected base at each mutated position",
46
+ "dataset_doi": "collection_doi",
47
+ "species": null,
48
+ "task_type": "Token Classification",
49
+ "seq_col": [
50
+ "seq",
51
+ "mut"
52
+ ],
53
+ "label_col": "ratio",
54
+ "label_categories": null,
55
+ "splits": null,
56
+ "excluded": "Token classification data format is not supported by our framework.",
57
+ "task_category": "Variant Effect Prediction",
58
+ "molecular_level": "RNA"
59
+ },
60
+ {
61
+ "dataset_name": "ssp_archive2",
62
+ "task_description": "RNA Secondary Structure Prediction",
63
+ "dataset_doi": "collection_doi",
64
+ "species": null,
65
+ "task_type": "Multi-label Classification",
66
+ "seq_col": [
67
+ "seq"
68
+ ],
69
+ "label_col": "label",
70
+ "label_categories": null,
71
+ "splits": null,
72
+ "excluded": "Multi-label classification data format is not supported by our framework.",
73
+ "task_category": "RNA Structure Prediction",
74
+ "molecular_level": "RNA"
75
+ },
76
+ {
77
+ "dataset_name": "ssp_bprna",
78
+ "task_description": "RNA Secondary Structure Prediction",
79
+ "dataset_doi": "collection_doi",
80
+ "species": null,
81
+ "task_type": "Multi-label Classification",
82
+ "seq_col": [
83
+ "seq"
84
+ ],
85
+ "label_col": "label",
86
+ "label_categories": null,
87
+ "splits": null,
88
+ "excluded": "Multi-label classification data format is not supported by our framework.",
89
+ "task_category": "RNA Structure Prediction",
90
+ "molecular_level": "RNA"
91
+ },
92
+ {
93
+ "dataset_name": "ssp_rnastralign",
94
+ "task_description": "RNA Secondary Structure Prediction",
95
+ "dataset_doi": "collection_doi",
96
+ "species": null,
97
+ "task_type": "Multi-label Classification",
98
+ "seq_col": [
99
+ "seq"
100
+ ],
101
+ "label_col": "label",
102
+ "label_categories": null,
103
+ "splits": null,
104
+ "excluded": "Multi-label classification data format is not supported by our framework.",
105
+ "task_category": "RNA Structure Prediction",
106
+ "molecular_level": "RNA"
107
+ },
108
+ {
109
+ "dataset_name": "ssp_strand2",
110
+ "task_description": "RNA Secondary Structure Prediction",
111
+ "dataset_doi": "collection_doi",
112
+ "species": null,
113
+ "task_type": "Multi-label Classification",
114
+ "seq_col": [
115
+ "seq"
116
+ ],
117
+ "label_col": "label",
118
+ "label_categories": null,
119
+ "splits": null,
120
+ "excluded": "Multi-label classification data format is not supported by our framework.",
121
+ "task_category": "RNA Structure Prediction",
122
+ "molecular_level": "RNA"
123
+ },
124
+ {
125
+ "dataset_name": "region_classification_arabidopsis",
126
+ "task_description": "Token-level 3-way classification of 5'UTR, CDS, and 3'UTR regions in Arabidopsis transcripts.",
127
+ "dataset_doi": "https://doi.org/10.1038/s42256-024-00946-z",
128
+ "species": "Arabidopsis thaliana",
129
+ "task_type": "Token Classification",
130
+ "seq_col": [
131
+ "5utr",
132
+ "cds",
133
+ "3utr"
134
+ ],
135
+ "label_col": null,
136
+ "label_categories": null,
137
+ "splits": null,
138
+ "excluded": "Token classification data format is not supported by our framework.",
139
+ "task_category": "Sequence Annotation",
140
+ "molecular_level": "RNA"
141
+ },
142
+ {
143
+ "dataset_name": "region_classification_rice",
144
+ "task_description": "Token-level 3-way classification of 5'UTR, CDS, and 3'UTR regions in Rice transcripts.",
145
+ "dataset_doi": "https://doi.org/10.1038/s42256-024-00946-z",
146
+ "species": "Oryza sativa L. ssp. japonica",
147
+ "task_type": "Token Classification",
148
+ "seq_col": [
149
+ "5utr",
150
+ "cds",
151
+ "3utr"
152
+ ],
153
+ "label_col": null,
154
+ "label_categories": null,
155
+ "splits": null,
156
+ "excluded": "Token classification data format is not supported by our framework.",
157
+ "task_category": "Sequence Annotation",
158
+ "molecular_level": "RNA"
159
+ },
160
+ {
161
+ "dataset_name": "te_prediction_arabidopsis",
162
+ "task_description": "Prediction of high vs low translational efficiency on 5' UTRs in Arabidopsis",
163
+ "dataset_doi": "https://doi.org/10.1038/s42256-024-00946-z",
164
+ "species": "Arabidopsis thaliana",
165
+ "task_type": "Binary Classification",
166
+ "seq_col": [
167
+ "seq"
168
+ ],
169
+ "label_col": "label",
170
+ "label_categories": {
171
+ "0": "low",
172
+ "1": "high"
173
+ },
174
+ "splits": [
175
+ "train",
176
+ "val",
177
+ "test"
178
+ ],
179
+ "excluded": null,
180
+ "split_metadata": {
181
+ "train": {
182
+ "seq_length": {
183
+ "seq": {
184
+ "min": 27,
185
+ "max": 500,
186
+ "median": 500
187
+ }
188
+ },
189
+ "seq_alphabet": {
190
+ "seq": [
191
+ "A",
192
+ "C",
193
+ "G",
194
+ "T"
195
+ ]
196
+ },
197
+ "labels": [
198
+ 0,
199
+ 1
200
+ ],
201
+ "dataset_size": 3399,
202
+ "class_ratio": {
203
+ "0": 0.45,
204
+ "1": 0.55
205
+ },
206
+ "all_columns": [
207
+ "seq",
208
+ "label"
209
+ ],
210
+ "dataset_path": "./OmniGenBench/te_prediction_arabidopsis_train.csv.gz"
211
+ },
212
+ "val": {
213
+ "seq_length": {
214
+ "seq": {
215
+ "min": 500,
216
+ "max": 500,
217
+ "median": 500
218
+ }
219
+ },
220
+ "seq_alphabet": {
221
+ "seq": [
222
+ "A",
223
+ "C",
224
+ "G",
225
+ "T"
226
+ ]
227
+ },
228
+ "labels": [
229
+ 0,
230
+ 1
231
+ ],
232
+ "dataset_size": 424,
233
+ "class_ratio": {
234
+ "0": 0.47,
235
+ "1": 0.53
236
+ },
237
+ "all_columns": [
238
+ "seq",
239
+ "label"
240
+ ],
241
+ "dataset_path": "./OmniGenBench/te_prediction_arabidopsis_val.csv.gz"
242
+ },
243
+ "test": {
244
+ "seq_length": {
245
+ "seq": {
246
+ "min": 500,
247
+ "max": 500,
248
+ "median": 500
249
+ }
250
+ },
251
+ "seq_alphabet": {
252
+ "seq": [
253
+ "A",
254
+ "C",
255
+ "G",
256
+ "T"
257
+ ]
258
+ },
259
+ "labels": [
260
+ 0,
261
+ 1
262
+ ],
263
+ "dataset_size": 426,
264
+ "class_ratio": {
265
+ "0": 0.49,
266
+ "1": 0.51
267
+ },
268
+ "all_columns": [
269
+ "seq",
270
+ "label"
271
+ ],
272
+ "dataset_path": "./OmniGenBench/te_prediction_arabidopsis_test.csv.gz"
273
+ }
274
+ },
275
+ "task_category": "Translation Efficiency Prediction",
276
+ "molecular_level": "RNA"
277
+ },
278
+ {
279
+ "dataset_name": "te_prediction_rice",
280
+ "task_description": "Prediction of high vs low translational efficiency on 5' UTRs in Rice",
281
+ "dataset_doi": "https://doi.org/10.1038/s42256-024-00946-z",
282
+ "species": "Oryza sativa L. ssp. japonica",
283
+ "task_type": "Binary Classification",
284
+ "seq_col": [
285
+ "seq"
286
+ ],
287
+ "label_col": "label",
288
+ "label_categories": {
289
+ "0": "low",
290
+ "1": "high"
291
+ },
292
+ "splits": [
293
+ "train",
294
+ "val",
295
+ "test"
296
+ ],
297
+ "excluded": null,
298
+ "split_metadata": {
299
+ "train": {
300
+ "seq_length": {
301
+ "seq": {
302
+ "min": 500,
303
+ "max": 500,
304
+ "median": 500
305
+ }
306
+ },
307
+ "seq_alphabet": {
308
+ "seq": [
309
+ "A",
310
+ "C",
311
+ "G",
312
+ "N",
313
+ "T"
314
+ ]
315
+ },
316
+ "labels": [
317
+ 0,
318
+ 1
319
+ ],
320
+ "dataset_size": 4697,
321
+ "class_ratio": {
322
+ "0": 0.47,
323
+ "1": 0.53
324
+ },
325
+ "all_columns": [
326
+ "seq",
327
+ "label"
328
+ ],
329
+ "dataset_path": "./OmniGenBench/te_prediction_rice_train.csv.gz"
330
+ },
331
+ "val": {
332
+ "seq_length": {
333
+ "seq": {
334
+ "min": 500,
335
+ "max": 500,
336
+ "median": 500
337
+ }
338
+ },
339
+ "seq_alphabet": {
340
+ "seq": [
341
+ "A",
342
+ "C",
343
+ "G",
344
+ "N",
345
+ "T"
346
+ ]
347
+ },
348
+ "labels": [
349
+ 0,
350
+ 1
351
+ ],
352
+ "dataset_size": 587,
353
+ "class_ratio": {
354
+ "0": 0.44,
355
+ "1": 0.56
356
+ },
357
+ "all_columns": [
358
+ "seq",
359
+ "label"
360
+ ],
361
+ "dataset_path": "./OmniGenBench/te_prediction_rice_val.csv.gz"
362
+ },
363
+ "test": {
364
+ "seq_length": {
365
+ "seq": {
366
+ "min": 500,
367
+ "max": 500,
368
+ "median": 500
369
+ }
370
+ },
371
+ "seq_alphabet": {
372
+ "seq": [
373
+ "A",
374
+ "C",
375
+ "G",
376
+ "T"
377
+ ]
378
+ },
379
+ "labels": [
380
+ 0,
381
+ 1
382
+ ],
383
+ "dataset_size": 588,
384
+ "class_ratio": {
385
+ "0": 0.44,
386
+ "1": 0.56
387
+ },
388
+ "all_columns": [
389
+ "seq",
390
+ "label"
391
+ ],
392
+ "dataset_path": "./OmniGenBench/te_prediction_rice_test.csv.gz"
393
+ }
394
+ },
395
+ "task_category": "Translation Efficiency Prediction",
396
+ "molecular_level": "RNA"
397
+ },
398
+ {
399
+ "dataset_name": "chromatin_access_arabidopis_thaliana",
400
+ "task_description": "Prediction of chromatin accessibility in Arabidopsis thaliana (plant)",
401
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
402
+ "species": "Arabidopsis thaliana",
403
+ "task_type": "Multi-label Classification",
404
+ "seq_col": [
405
+ "sequence"
406
+ ],
407
+ "label_col": "labels",
408
+ "label_categories": null,
409
+ "splits": null,
410
+ "excluded": "Multi-label classification data format is not supported by our framework.",
411
+ "task_category": "Sequence Annotation",
412
+ "molecular_level": "DNA"
413
+ },
414
+ {
415
+ "dataset_name": "chromatin_access_oryza_sativa_MH63_RS2",
416
+ "task_description": "Prediction of chromatin accessibility in Oryza sativa MH63 RS2 (plant)",
417
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
418
+ "species": "Oryza sativa",
419
+ "task_type": "Multi-label Classification",
420
+ "seq_col": [
421
+ "sequence"
422
+ ],
423
+ "label_col": "labels",
424
+ "label_categories": null,
425
+ "splits": null,
426
+ "excluded": "Multi-label classification data format is not supported by our framework.",
427
+ "task_category": "Sequence Annotation",
428
+ "molecular_level": "DNA"
429
+ },
430
+ {
431
+ "dataset_name": "chromatin_access_setaria_italica",
432
+ "task_description": "Prediction of chromatin accessibility in Setaria italica (plant)",
433
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
434
+ "species": "Setaria italica",
435
+ "task_type": "Multi-label Classification",
436
+ "seq_col": [
437
+ "sequence"
438
+ ],
439
+ "label_col": "labels",
440
+ "label_categories": null,
441
+ "splits": null,
442
+ "excluded": "Multi-label classification data format is not supported by our framework.",
443
+ "task_category": "Sequence Annotation",
444
+ "molecular_level": "DNA"
445
+ },
446
+ {
447
+ "dataset_name": "chromatin_access_oryza_sativa_ZS97_RS2",
448
+ "task_description": "Prediction of chromatin accessibility in Oryza sativa ZS97 RS2 (plant)",
449
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
450
+ "species": "Oryza sativa",
451
+ "task_type": "Multi-label Classification",
452
+ "seq_col": [
453
+ "sequence"
454
+ ],
455
+ "label_col": "labels",
456
+ "label_categories": null,
457
+ "splits": null,
458
+ "excluded": "Multi-label classification data format is not supported by our framework.",
459
+ "task_category": "Sequence Annotation",
460
+ "molecular_level": "DNA"
461
+ },
462
+ {
463
+ "dataset_name": "chromatin_access_brachypodium_distachyon",
464
+ "task_description": "Prediction of chromatin accessibility in Brachypodium distachyon (plant)",
465
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
466
+ "species": "Brachypodium distachyon",
467
+ "task_type": "Multi-label Classification",
468
+ "seq_col": [
469
+ "sequence"
470
+ ],
471
+ "label_col": "labels",
472
+ "label_categories": null,
473
+ "splits": null,
474
+ "excluded": "Multi-label classification data format is not supported by our framework.",
475
+ "task_category": "Sequence Annotation",
476
+ "molecular_level": "DNA"
477
+ },
478
+ {
479
+ "dataset_name": "chromatin_access_sorghum_bicolor",
480
+ "task_description": "Prediction of chromatin accessibility in Sorghum bicolor (plant)",
481
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
482
+ "species": "Sorghum bicolor",
483
+ "task_type": "Multi-label Classification",
484
+ "seq_col": [
485
+ "sequence"
486
+ ],
487
+ "label_col": "labels",
488
+ "label_categories": null,
489
+ "splits": null,
490
+ "excluded": "Multi-label classification data format is not supported by our framework.",
491
+ "task_category": "Sequence Annotation",
492
+ "molecular_level": "DNA"
493
+ },
494
+ {
495
+ "dataset_name": "chromatin_access_zea_mays",
496
+ "task_description": "Prediction of chromatin accessibility in Zea mays (plant)",
497
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
498
+ "species": "Zea mays",
499
+ "task_type": "Multi-label Classification",
500
+ "seq_col": [
501
+ "sequence"
502
+ ],
503
+ "label_col": "labels",
504
+ "label_categories": null,
505
+ "splits": null,
506
+ "excluded": "Multi-label classification data format is not supported by our framework.",
507
+ "task_category": "Sequence Annotation",
508
+ "molecular_level": "DNA"
509
+ },
510
+ {
511
+ "dataset_name": "gene_exp_glycine_max",
512
+ "task_description": "Prediction of tissue-specific gene expression in Glycine max (plant)",
513
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
514
+ "species": "Glycine max",
515
+ "task_type": "Multi-variable Regression",
516
+ "seq_col": [
517
+ "sequence"
518
+ ],
519
+ "label_col": "labels",
520
+ "label_categories": null,
521
+ "splits": null,
522
+ "excluded": "Multi-variable regression data format is not supported by our framework.",
523
+ "task_category": "Gene Expression Prediction",
524
+ "molecular_level": "RNA"
525
+ },
526
+ {
527
+ "dataset_name": "gene_exp_oryza_sativa",
528
+ "task_description": "Prediction of tissue-specific gene expression in Oryza sativa (plant)",
529
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
530
+ "species": "Oryza sativa",
531
+ "task_type": "Multi-variable Regression",
532
+ "seq_col": [
533
+ "sequence"
534
+ ],
535
+ "label_col": "labels",
536
+ "label_categories": null,
537
+ "splits": null,
538
+ "excluded": "Multi-variable regression data format is not supported by our framework.",
539
+ "task_category": "Gene Expression Prediction",
540
+ "molecular_level": "RNA"
541
+ },
542
+ {
543
+ "dataset_name": "gene_exp_solanum_lycopersicum",
544
+ "task_description": "Prediction of tissue-specific gene expression in Solanum lycopersicum (plant)",
545
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
546
+ "species": "Solanum lycopersicum",
547
+ "task_type": "Multi-variable Regression",
548
+ "seq_col": [
549
+ "sequence"
550
+ ],
551
+ "label_col": "labels",
552
+ "label_categories": null,
553
+ "splits": null,
554
+ "excluded": "Multi-variable regression data format is not supported by our framework.",
555
+ "task_category": "Gene Expression Prediction",
556
+ "molecular_level": "RNA"
557
+ },
558
+ {
559
+ "dataset_name": "gene_exp_zea_mays",
560
+ "task_description": "Prediction of tissue-specific gene expression in Zea mays (plant)",
561
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
562
+ "species": "Zea mays",
563
+ "task_type": "Multi-variable Regression",
564
+ "seq_col": [
565
+ "sequence"
566
+ ],
567
+ "label_col": "labels",
568
+ "label_categories": null,
569
+ "splits": null,
570
+ "excluded": "Multi-variable regression data format is not supported by our framework.",
571
+ "task_category": "Gene Expression Prediction",
572
+ "molecular_level": "RNA"
573
+ },
574
+ {
575
+ "dataset_name": "gene_exp_arabidopsis_thaliana",
576
+ "task_description": "Prediction of tissue-specific gene expression in Arabidopsis thaliana (plant)",
577
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
578
+ "species": "Arabidopsis thaliana",
579
+ "task_type": "Multi-variable Regression",
580
+ "seq_col": [
581
+ "sequence"
582
+ ],
583
+ "label_col": "labels",
584
+ "label_categories": null,
585
+ "splits": null,
586
+ "excluded": "Multi-variable regression data format is not supported by our framework.",
587
+ "task_category": "Gene Expression Prediction",
588
+ "molecular_level": "RNA"
589
+ },
590
+ {
591
+ "dataset_name": "lncrna_m_esculenta",
592
+ "task_description": "Prediction of long non-coding RNA in Manihot esculenta (plant)",
593
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
594
+ "species": "Manihot esculenta",
595
+ "task_type": "Binary Classification",
596
+ "seq_col": [
597
+ "sequence"
598
+ ],
599
+ "label_col": "label",
600
+ "label_categories": {
601
+ "0": "negative",
602
+ "1": "positive"
603
+ },
604
+ "splits": [
605
+ "train",
606
+ "test"
607
+ ],
608
+ "excluded": null,
609
+ "split_metadata": {
610
+ "train": {
611
+ "seq_length": {
612
+ "sequence": {
613
+ "min": 108,
614
+ "max": 2534,
615
+ "median": 592
616
+ }
617
+ },
618
+ "seq_alphabet": {
619
+ "sequence": [
620
+ "A",
621
+ "C",
622
+ "G",
623
+ "T"
624
+ ]
625
+ },
626
+ "labels": [
627
+ 0,
628
+ 1
629
+ ],
630
+ "dataset_size": 4934,
631
+ "class_ratio": {
632
+ "0": 0.5,
633
+ "1": 0.5
634
+ },
635
+ "all_columns": [
636
+ "sequence",
637
+ "name",
638
+ "label"
639
+ ],
640
+ "dataset_path": "./OmniGenBench/lncrna_m_esculenta_train.csv.gz"
641
+ },
642
+ "test": {
643
+ "seq_length": {
644
+ "sequence": {
645
+ "min": 138,
646
+ "max": 1719,
647
+ "median": 580
648
+ }
649
+ },
650
+ "seq_alphabet": {
651
+ "sequence": [
652
+ "A",
653
+ "C",
654
+ "G",
655
+ "T"
656
+ ]
657
+ },
658
+ "labels": [
659
+ 0,
660
+ 1
661
+ ],
662
+ "dataset_size": 360,
663
+ "class_ratio": {
664
+ "0": 0.52,
665
+ "1": 0.48
666
+ },
667
+ "all_columns": [
668
+ "sequence",
669
+ "name",
670
+ "label"
671
+ ],
672
+ "dataset_path": "./OmniGenBench/lncrna_m_esculenta_test.csv.gz"
673
+ }
674
+ },
675
+ "task_category": "RNA / Transcript Classification",
676
+ "molecular_level": "RNA"
677
+ },
678
+ {
679
+ "dataset_name": "lncrna_z_mays",
680
+ "task_description": "Prediction of long non-coding RNA in Zea mays (plant)",
681
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
682
+ "species": "Zea mays",
683
+ "task_type": "Binary Classification",
684
+ "seq_col": [
685
+ "sequence"
686
+ ],
687
+ "label_col": "label",
688
+ "label_categories": {
689
+ "0": "negative",
690
+ "1": "positive"
691
+ },
692
+ "splits": [
693
+ "train",
694
+ "test"
695
+ ],
696
+ "excluded": null,
697
+ "split_metadata": {
698
+ "train": {
699
+ "seq_length": {
700
+ "sequence": {
701
+ "min": 201,
702
+ "max": 2600,
703
+ "median": 496
704
+ }
705
+ },
706
+ "seq_alphabet": {
707
+ "sequence": [
708
+ "A",
709
+ "C",
710
+ "G",
711
+ "T"
712
+ ]
713
+ },
714
+ "labels": [
715
+ 0,
716
+ 1
717
+ ],
718
+ "dataset_size": 8000,
719
+ "class_ratio": {
720
+ "0": 0.51,
721
+ "1": 0.49
722
+ },
723
+ "all_columns": [
724
+ "sequence",
725
+ "name",
726
+ "label"
727
+ ],
728
+ "dataset_path": "./OmniGenBench/lncrna_z_mays_train.csv.gz"
729
+ },
730
+ "test": {
731
+ "seq_length": {
732
+ "sequence": {
733
+ "min": 201,
734
+ "max": 2467,
735
+ "median": 453
736
+ }
737
+ },
738
+ "seq_alphabet": {
739
+ "sequence": [
740
+ "A",
741
+ "C",
742
+ "G",
743
+ "T"
744
+ ]
745
+ },
746
+ "labels": [
747
+ 0,
748
+ 1
749
+ ],
750
+ "dataset_size": 1000,
751
+ "class_ratio": {
752
+ "0": 0.44,
753
+ "1": 0.56
754
+ },
755
+ "all_columns": [
756
+ "sequence",
757
+ "name",
758
+ "label"
759
+ ],
760
+ "dataset_path": "./OmniGenBench/lncrna_z_mays_test.csv.gz"
761
+ }
762
+ },
763
+ "task_category": "RNA / Transcript Classification",
764
+ "molecular_level": "RNA"
765
+ },
766
+ {
767
+ "dataset_name": "lncrna_g_max",
768
+ "task_description": "Prediction of long non-coding RNA in Glycine max (plant)",
769
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
770
+ "species": "Glycine max",
771
+ "task_type": "Binary Classification",
772
+ "seq_col": [
773
+ "sequence"
774
+ ],
775
+ "label_col": "label",
776
+ "label_categories": {
777
+ "0": "negative",
778
+ "1": "positive"
779
+ },
780
+ "splits": [
781
+ "train",
782
+ "test"
783
+ ],
784
+ "excluded": null,
785
+ "split_metadata": {
786
+ "train": {
787
+ "seq_length": {
788
+ "sequence": {
789
+ "min": 102,
790
+ "max": 1740,
791
+ "median": 621
792
+ }
793
+ },
794
+ "seq_alphabet": {
795
+ "sequence": [
796
+ "A",
797
+ "C",
798
+ "G",
799
+ "T"
800
+ ]
801
+ },
802
+ "labels": [
803
+ 0,
804
+ 1
805
+ ],
806
+ "dataset_size": 8000,
807
+ "class_ratio": {
808
+ "0": 0.5,
809
+ "1": 0.5
810
+ },
811
+ "all_columns": [
812
+ "sequence",
813
+ "name",
814
+ "label"
815
+ ],
816
+ "dataset_path": "./OmniGenBench/lncrna_g_max_train.csv.gz"
817
+ },
818
+ "test": {
819
+ "seq_length": {
820
+ "sequence": {
821
+ "min": 120,
822
+ "max": 1644,
823
+ "median": 600
824
+ }
825
+ },
826
+ "seq_alphabet": {
827
+ "sequence": [
828
+ "A",
829
+ "C",
830
+ "G",
831
+ "T"
832
+ ]
833
+ },
834
+ "labels": [
835
+ 0,
836
+ 1
837
+ ],
838
+ "dataset_size": 490,
839
+ "class_ratio": {
840
+ "0": 0.5,
841
+ "1": 0.5
842
+ },
843
+ "all_columns": [
844
+ "sequence",
845
+ "name",
846
+ "label"
847
+ ],
848
+ "dataset_path": "./OmniGenBench/lncrna_g_max_test.csv.gz"
849
+ }
850
+ },
851
+ "task_category": "RNA / Transcript Classification",
852
+ "molecular_level": "RNA"
853
+ },
854
+ {
855
+ "dataset_name": "lncrna_s_lycopersicum",
856
+ "task_description": "Prediction of long non-coding RNA in Solanum lycopersicum (plant)",
857
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
858
+ "species": "Solanum lycopersicum",
859
+ "task_type": "Binary Classification",
860
+ "seq_col": [
861
+ "sequence"
862
+ ],
863
+ "label_col": "label",
864
+ "label_categories": {
865
+ "0": "negative",
866
+ "1": "positive"
867
+ },
868
+ "splits": [
869
+ "train",
870
+ "test"
871
+ ],
872
+ "excluded": null,
873
+ "split_metadata": {
874
+ "train": {
875
+ "seq_length": {
876
+ "sequence": {
877
+ "min": 105,
878
+ "max": 5964,
879
+ "median": 331
880
+ }
881
+ },
882
+ "seq_alphabet": {
883
+ "sequence": [
884
+ "A",
885
+ "C",
886
+ "G",
887
+ "N",
888
+ "T"
889
+ ]
890
+ },
891
+ "labels": [
892
+ 0,
893
+ 1
894
+ ],
895
+ "dataset_size": 7274,
896
+ "class_ratio": {
897
+ "0": 0.5,
898
+ "1": 0.5
899
+ },
900
+ "all_columns": [
901
+ "sequence",
902
+ "name",
903
+ "label"
904
+ ],
905
+ "dataset_path": "./OmniGenBench/lncrna_s_lycopersicum_train.csv.gz"
906
+ },
907
+ "test": {
908
+ "seq_length": {
909
+ "sequence": {
910
+ "min": 111,
911
+ "max": 6000,
912
+ "median": 339
913
+ }
914
+ },
915
+ "seq_alphabet": {
916
+ "sequence": [
917
+ "A",
918
+ "C",
919
+ "G",
920
+ "T"
921
+ ]
922
+ },
923
+ "labels": [
924
+ 0,
925
+ 1
926
+ ],
927
+ "dataset_size": 1000,
928
+ "class_ratio": {
929
+ "0": 0.47,
930
+ "1": 0.53
931
+ },
932
+ "all_columns": [
933
+ "sequence",
934
+ "name",
935
+ "label"
936
+ ],
937
+ "dataset_path": "./OmniGenBench/lncrna_s_lycopersicum_test.csv.gz"
938
+ }
939
+ },
940
+ "task_category": "RNA / Transcript Classification",
941
+ "molecular_level": "RNA"
942
+ },
943
+ {
944
+ "dataset_name": "lncrna_t_aestivum",
945
+ "task_description": "Prediction of long non-coding RNA in Triticum aestivum (plant)",
946
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
947
+ "species": "Triticum aestivum",
948
+ "task_type": "Binary Classification",
949
+ "seq_col": [
950
+ "sequence"
951
+ ],
952
+ "label_col": "label",
953
+ "label_categories": {
954
+ "0": "negative",
955
+ "1": "positive"
956
+ },
957
+ "splits": [
958
+ "train",
959
+ "test"
960
+ ],
961
+ "excluded": null,
962
+ "split_metadata": {
963
+ "train": {
964
+ "seq_length": {
965
+ "sequence": {
966
+ "min": 108,
967
+ "max": 4880,
968
+ "median": 330
969
+ }
970
+ },
971
+ "seq_alphabet": {
972
+ "sequence": [
973
+ "A",
974
+ "C",
975
+ "G",
976
+ "N",
977
+ "T"
978
+ ]
979
+ },
980
+ "labels": [
981
+ 0,
982
+ 1
983
+ ],
984
+ "dataset_size": 8000,
985
+ "class_ratio": {
986
+ "0": 0.5,
987
+ "1": 0.5
988
+ },
989
+ "all_columns": [
990
+ "sequence",
991
+ "name",
992
+ "label"
993
+ ],
994
+ "dataset_path": "./OmniGenBench/lncrna_t_aestivum_train.csv.gz"
995
+ },
996
+ "test": {
997
+ "seq_length": {
998
+ "sequence": {
999
+ "min": 111,
1000
+ "max": 4073,
1001
+ "median": 321
1002
+ }
1003
+ },
1004
+ "seq_alphabet": {
1005
+ "sequence": [
1006
+ "A",
1007
+ "C",
1008
+ "G",
1009
+ "N",
1010
+ "T"
1011
+ ]
1012
+ },
1013
+ "labels": [
1014
+ 0,
1015
+ 1
1016
+ ],
1017
+ "dataset_size": 1000,
1018
+ "class_ratio": {
1019
+ "0": 0.49,
1020
+ "1": 0.51
1021
+ },
1022
+ "all_columns": [
1023
+ "sequence",
1024
+ "name",
1025
+ "label"
1026
+ ],
1027
+ "dataset_path": "./OmniGenBench/lncrna_t_aestivum_test.csv.gz"
1028
+ }
1029
+ },
1030
+ "task_category": "RNA / Transcript Classification",
1031
+ "molecular_level": "RNA"
1032
+ },
1033
+ {
1034
+ "dataset_name": "lncrna_s_bicolor",
1035
+ "task_description": "Prediction of long non-coding RNA in Sorghum bicolor (plant)",
1036
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1037
+ "species": "Sorghum bicolor",
1038
+ "task_type": "Binary Classification",
1039
+ "seq_col": [
1040
+ "sequence"
1041
+ ],
1042
+ "label_col": "label",
1043
+ "label_categories": {
1044
+ "0": "negative",
1045
+ "1": "positive"
1046
+ },
1047
+ "splits": [
1048
+ "train",
1049
+ "test"
1050
+ ],
1051
+ "excluded": null,
1052
+ "split_metadata": {
1053
+ "train": {
1054
+ "seq_length": {
1055
+ "sequence": {
1056
+ "min": 117,
1057
+ "max": 5971,
1058
+ "median": 802
1059
+ }
1060
+ },
1061
+ "seq_alphabet": {
1062
+ "sequence": [
1063
+ "A",
1064
+ "C",
1065
+ "G",
1066
+ "T"
1067
+ ]
1068
+ },
1069
+ "labels": [
1070
+ 0,
1071
+ 1
1072
+ ],
1073
+ "dataset_size": 8000,
1074
+ "class_ratio": {
1075
+ "0": 0.5,
1076
+ "1": 0.5
1077
+ },
1078
+ "all_columns": [
1079
+ "sequence",
1080
+ "name",
1081
+ "label"
1082
+ ],
1083
+ "dataset_path": "./OmniGenBench/lncrna_s_bicolor_train.csv.gz"
1084
+ },
1085
+ "test": {
1086
+ "seq_length": {
1087
+ "sequence": {
1088
+ "min": 171,
1089
+ "max": 5473,
1090
+ "median": 908
1091
+ }
1092
+ },
1093
+ "seq_alphabet": {
1094
+ "sequence": [
1095
+ "A",
1096
+ "C",
1097
+ "G",
1098
+ "T"
1099
+ ]
1100
+ },
1101
+ "labels": [
1102
+ 0,
1103
+ 1
1104
+ ],
1105
+ "dataset_size": 734,
1106
+ "class_ratio": {
1107
+ "0": 0.53,
1108
+ "1": 0.47
1109
+ },
1110
+ "all_columns": [
1111
+ "sequence",
1112
+ "name",
1113
+ "label"
1114
+ ],
1115
+ "dataset_path": "./OmniGenBench/lncrna_s_bicolor_test.csv.gz"
1116
+ }
1117
+ },
1118
+ "task_category": "RNA / Transcript Classification",
1119
+ "molecular_level": "RNA"
1120
+ },
1121
+ {
1122
+ "dataset_name": "poly_a_arabidopsis_thaliana",
1123
+ "task_description": "Prediction of polyadenylation sites in Arabidopsis thaliana (plant)",
1124
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1125
+ "species": "Arabidopsis thaliana",
1126
+ "task_type": "Binary Classification",
1127
+ "seq_col": [
1128
+ "sequence"
1129
+ ],
1130
+ "label_col": "label",
1131
+ "label_categories": {
1132
+ "0": "negative",
1133
+ "1": "positive"
1134
+ },
1135
+ "splits": [
1136
+ "train",
1137
+ "test"
1138
+ ],
1139
+ "excluded": null,
1140
+ "split_metadata": {
1141
+ "train": {
1142
+ "seq_length": {
1143
+ "sequence": {
1144
+ "min": 400,
1145
+ "max": 400,
1146
+ "median": 400
1147
+ }
1148
+ },
1149
+ "seq_alphabet": {
1150
+ "sequence": [
1151
+ "A",
1152
+ "C",
1153
+ "G",
1154
+ "T"
1155
+ ]
1156
+ },
1157
+ "labels": [
1158
+ 0,
1159
+ 1
1160
+ ],
1161
+ "dataset_size": 8000,
1162
+ "class_ratio": {
1163
+ "0": 0.66,
1164
+ "1": 0.34
1165
+ },
1166
+ "all_columns": [
1167
+ "sequence",
1168
+ "name",
1169
+ "label"
1170
+ ],
1171
+ "dataset_path": "./OmniGenBench/poly_a_arabidopsis_thaliana_train.csv.gz"
1172
+ },
1173
+ "test": {
1174
+ "seq_length": {
1175
+ "sequence": {
1176
+ "min": 400,
1177
+ "max": 400,
1178
+ "median": 400
1179
+ }
1180
+ },
1181
+ "seq_alphabet": {
1182
+ "sequence": [
1183
+ "A",
1184
+ "C",
1185
+ "G",
1186
+ "T"
1187
+ ]
1188
+ },
1189
+ "labels": [
1190
+ 0,
1191
+ 1
1192
+ ],
1193
+ "dataset_size": 1000,
1194
+ "class_ratio": {
1195
+ "0": 0.64,
1196
+ "1": 0.36
1197
+ },
1198
+ "all_columns": [
1199
+ "sequence",
1200
+ "name",
1201
+ "label"
1202
+ ],
1203
+ "dataset_path": "./OmniGenBench/poly_a_arabidopsis_thaliana_test.csv.gz"
1204
+ }
1205
+ },
1206
+ "task_category": "RNA Processing Prediction",
1207
+ "molecular_level": "RNA"
1208
+ },
1209
+ {
1210
+ "dataset_name": "poly_a_oryza_sativa_indica_group",
1211
+ "task_description": "Prediction of polyadenylation sites in Oryza sativa indica (plant)",
1212
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1213
+ "species": "Oryza sativa indica",
1214
+ "task_type": "Binary Classification",
1215
+ "seq_col": [
1216
+ "sequence"
1217
+ ],
1218
+ "label_col": "label",
1219
+ "label_categories": {
1220
+ "0": "negative",
1221
+ "1": "positive"
1222
+ },
1223
+ "splits": [
1224
+ "train",
1225
+ "test"
1226
+ ],
1227
+ "excluded": null,
1228
+ "split_metadata": {
1229
+ "train": {
1230
+ "seq_length": {
1231
+ "sequence": {
1232
+ "min": 400,
1233
+ "max": 400,
1234
+ "median": 400
1235
+ }
1236
+ },
1237
+ "seq_alphabet": {
1238
+ "sequence": [
1239
+ "A",
1240
+ "C",
1241
+ "G",
1242
+ "N",
1243
+ "T"
1244
+ ]
1245
+ },
1246
+ "labels": [
1247
+ 0,
1248
+ 1
1249
+ ],
1250
+ "dataset_size": 8000,
1251
+ "class_ratio": {
1252
+ "0": 0.66,
1253
+ "1": 0.34
1254
+ },
1255
+ "all_columns": [
1256
+ "sequence",
1257
+ "name",
1258
+ "label"
1259
+ ],
1260
+ "dataset_path": "./OmniGenBench/poly_a_oryza_sativa_indica_group_train.csv.gz"
1261
+ },
1262
+ "test": {
1263
+ "seq_length": {
1264
+ "sequence": {
1265
+ "min": 400,
1266
+ "max": 400,
1267
+ "median": 400
1268
+ }
1269
+ },
1270
+ "seq_alphabet": {
1271
+ "sequence": [
1272
+ "A",
1273
+ "C",
1274
+ "G",
1275
+ "N",
1276
+ "T"
1277
+ ]
1278
+ },
1279
+ "labels": [
1280
+ 0,
1281
+ 1
1282
+ ],
1283
+ "dataset_size": 1000,
1284
+ "class_ratio": {
1285
+ "0": 0.66,
1286
+ "1": 0.34
1287
+ },
1288
+ "all_columns": [
1289
+ "sequence",
1290
+ "name",
1291
+ "label"
1292
+ ],
1293
+ "dataset_path": "./OmniGenBench/poly_a_oryza_sativa_indica_group_test.csv.gz"
1294
+ }
1295
+ },
1296
+ "task_category": "RNA Processing Prediction",
1297
+ "molecular_level": "RNA"
1298
+ },
1299
+ {
1300
+ "dataset_name": "poly_a_trifolium_pratense",
1301
+ "task_description": "Prediction of polyadenylation sites in Trifolium pratense (plant)",
1302
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1303
+ "species": "Trifolium pratense",
1304
+ "task_type": "Binary Classification",
1305
+ "seq_col": [
1306
+ "sequence"
1307
+ ],
1308
+ "label_col": "label",
1309
+ "label_categories": {
1310
+ "0": "negative",
1311
+ "1": "positive"
1312
+ },
1313
+ "splits": [
1314
+ "train",
1315
+ "test"
1316
+ ],
1317
+ "excluded": null,
1318
+ "split_metadata": {
1319
+ "train": {
1320
+ "seq_length": {
1321
+ "sequence": {
1322
+ "min": 400,
1323
+ "max": 400,
1324
+ "median": 400
1325
+ }
1326
+ },
1327
+ "seq_alphabet": {
1328
+ "sequence": [
1329
+ "A",
1330
+ "C",
1331
+ "G",
1332
+ "N",
1333
+ "T"
1334
+ ]
1335
+ },
1336
+ "labels": [
1337
+ 0,
1338
+ 1
1339
+ ],
1340
+ "dataset_size": 8000,
1341
+ "class_ratio": {
1342
+ "0": 0.67,
1343
+ "1": 0.33
1344
+ },
1345
+ "all_columns": [
1346
+ "sequence",
1347
+ "name",
1348
+ "label"
1349
+ ],
1350
+ "dataset_path": "./OmniGenBench/poly_a_trifolium_pratense_train.csv.gz"
1351
+ },
1352
+ "test": {
1353
+ "seq_length": {
1354
+ "sequence": {
1355
+ "min": 400,
1356
+ "max": 400,
1357
+ "median": 400
1358
+ }
1359
+ },
1360
+ "seq_alphabet": {
1361
+ "sequence": [
1362
+ "A",
1363
+ "C",
1364
+ "G",
1365
+ "N",
1366
+ "T"
1367
+ ]
1368
+ },
1369
+ "labels": [
1370
+ 0,
1371
+ 1
1372
+ ],
1373
+ "dataset_size": 1000,
1374
+ "class_ratio": {
1375
+ "0": 0.65,
1376
+ "1": 0.35
1377
+ },
1378
+ "all_columns": [
1379
+ "sequence",
1380
+ "name",
1381
+ "label"
1382
+ ],
1383
+ "dataset_path": "./OmniGenBench/poly_a_trifolium_pratense_test.csv.gz"
1384
+ }
1385
+ },
1386
+ "task_category": "RNA Processing Prediction",
1387
+ "molecular_level": "RNA"
1388
+ },
1389
+ {
1390
+ "dataset_name": "poly_a_medicago_truncatula",
1391
+ "task_description": "Prediction of polyadenylation sites in Medicago truncatula (plant)",
1392
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1393
+ "species": "Medicago truncatula",
1394
+ "task_type": "Binary Classification",
1395
+ "seq_col": [
1396
+ "sequence"
1397
+ ],
1398
+ "label_col": "label",
1399
+ "label_categories": {
1400
+ "0": "negative",
1401
+ "1": "positive"
1402
+ },
1403
+ "splits": [
1404
+ "train",
1405
+ "test"
1406
+ ],
1407
+ "excluded": null,
1408
+ "split_metadata": {
1409
+ "train": {
1410
+ "seq_length": {
1411
+ "sequence": {
1412
+ "min": 400,
1413
+ "max": 400,
1414
+ "median": 400
1415
+ }
1416
+ },
1417
+ "seq_alphabet": {
1418
+ "sequence": [
1419
+ "A",
1420
+ "C",
1421
+ "G",
1422
+ "N",
1423
+ "T"
1424
+ ]
1425
+ },
1426
+ "labels": [
1427
+ 0,
1428
+ 1
1429
+ ],
1430
+ "dataset_size": 8000,
1431
+ "class_ratio": {
1432
+ "0": 0.67,
1433
+ "1": 0.33
1434
+ },
1435
+ "all_columns": [
1436
+ "sequence",
1437
+ "name",
1438
+ "label"
1439
+ ],
1440
+ "dataset_path": "./OmniGenBench/poly_a_medicago_truncatula_train.csv.gz"
1441
+ },
1442
+ "test": {
1443
+ "seq_length": {
1444
+ "sequence": {
1445
+ "min": 400,
1446
+ "max": 400,
1447
+ "median": 400
1448
+ }
1449
+ },
1450
+ "seq_alphabet": {
1451
+ "sequence": [
1452
+ "A",
1453
+ "C",
1454
+ "G",
1455
+ "N",
1456
+ "T"
1457
+ ]
1458
+ },
1459
+ "labels": [
1460
+ 0,
1461
+ 1
1462
+ ],
1463
+ "dataset_size": 1000,
1464
+ "class_ratio": {
1465
+ "0": 0.66,
1466
+ "1": 0.34
1467
+ },
1468
+ "all_columns": [
1469
+ "sequence",
1470
+ "name",
1471
+ "label"
1472
+ ],
1473
+ "dataset_path": "./OmniGenBench/poly_a_medicago_truncatula_test.csv.gz"
1474
+ }
1475
+ },
1476
+ "task_category": "RNA Processing Prediction",
1477
+ "molecular_level": "RNA"
1478
+ },
1479
+ {
1480
+ "dataset_name": "poly_a_chlamydomonas_reinhardtii",
1481
+ "task_description": "Prediction of polyadenylation sites in Chlamydomonas reinhardtii (plant)",
1482
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1483
+ "species": "Chlamydomonas reinhardtii",
1484
+ "task_type": "Binary Classification",
1485
+ "seq_col": [
1486
+ "sequence"
1487
+ ],
1488
+ "label_col": "label",
1489
+ "label_categories": {
1490
+ "0": "negative",
1491
+ "1": "positive"
1492
+ },
1493
+ "splits": [
1494
+ "train",
1495
+ "test"
1496
+ ],
1497
+ "excluded": null,
1498
+ "split_metadata": {
1499
+ "train": {
1500
+ "seq_length": {
1501
+ "sequence": {
1502
+ "min": 400,
1503
+ "max": 400,
1504
+ "median": 400
1505
+ }
1506
+ },
1507
+ "seq_alphabet": {
1508
+ "sequence": [
1509
+ "A",
1510
+ "C",
1511
+ "G",
1512
+ "N",
1513
+ "T"
1514
+ ]
1515
+ },
1516
+ "labels": [
1517
+ 0,
1518
+ 1
1519
+ ],
1520
+ "dataset_size": 8000,
1521
+ "class_ratio": {
1522
+ "0": 0.67,
1523
+ "1": 0.33
1524
+ },
1525
+ "all_columns": [
1526
+ "sequence",
1527
+ "name",
1528
+ "label"
1529
+ ],
1530
+ "dataset_path": "./OmniGenBench/poly_a_chlamydomonas_reinhardtii_train.csv.gz"
1531
+ },
1532
+ "test": {
1533
+ "seq_length": {
1534
+ "sequence": {
1535
+ "min": 400,
1536
+ "max": 400,
1537
+ "median": 400
1538
+ }
1539
+ },
1540
+ "seq_alphabet": {
1541
+ "sequence": [
1542
+ "A",
1543
+ "C",
1544
+ "G",
1545
+ "N",
1546
+ "T"
1547
+ ]
1548
+ },
1549
+ "labels": [
1550
+ 0,
1551
+ 1
1552
+ ],
1553
+ "dataset_size": 1000,
1554
+ "class_ratio": {
1555
+ "0": 0.65,
1556
+ "1": 0.35
1557
+ },
1558
+ "all_columns": [
1559
+ "sequence",
1560
+ "name",
1561
+ "label"
1562
+ ],
1563
+ "dataset_path": "./OmniGenBench/poly_a_chlamydomonas_reinhardtii_test.csv.gz"
1564
+ }
1565
+ },
1566
+ "task_category": "RNA Processing Prediction",
1567
+ "molecular_level": "RNA"
1568
+ },
1569
+ {
1570
+ "dataset_name": "poly_a_oryza_sativa_japonica_group",
1571
+ "task_description": "Prediction of polyadenylation sites in Oryza sativa japonica (plant)",
1572
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1573
+ "species": "Oryza sativa japonica",
1574
+ "task_type": "Binary Classification",
1575
+ "seq_col": [
1576
+ "sequence"
1577
+ ],
1578
+ "label_col": "label",
1579
+ "label_categories": {
1580
+ "0": "negative",
1581
+ "1": "positive"
1582
+ },
1583
+ "splits": [
1584
+ "train",
1585
+ "test"
1586
+ ],
1587
+ "excluded": null,
1588
+ "split_metadata": {
1589
+ "train": {
1590
+ "seq_length": {
1591
+ "sequence": {
1592
+ "min": 400,
1593
+ "max": 400,
1594
+ "median": 400
1595
+ }
1596
+ },
1597
+ "seq_alphabet": {
1598
+ "sequence": [
1599
+ "A",
1600
+ "C",
1601
+ "G",
1602
+ "T"
1603
+ ]
1604
+ },
1605
+ "labels": [
1606
+ 0,
1607
+ 1
1608
+ ],
1609
+ "dataset_size": 8000,
1610
+ "class_ratio": {
1611
+ "0": 0.67,
1612
+ "1": 0.33
1613
+ },
1614
+ "all_columns": [
1615
+ "sequence",
1616
+ "name",
1617
+ "label"
1618
+ ],
1619
+ "dataset_path": "./OmniGenBench/poly_a_oryza_sativa_japonica_group_train.csv.gz"
1620
+ },
1621
+ "test": {
1622
+ "seq_length": {
1623
+ "sequence": {
1624
+ "min": 400,
1625
+ "max": 400,
1626
+ "median": 400
1627
+ }
1628
+ },
1629
+ "seq_alphabet": {
1630
+ "sequence": [
1631
+ "A",
1632
+ "C",
1633
+ "G",
1634
+ "T"
1635
+ ]
1636
+ },
1637
+ "labels": [
1638
+ 0,
1639
+ 1
1640
+ ],
1641
+ "dataset_size": 1000,
1642
+ "class_ratio": {
1643
+ "0": 0.69,
1644
+ "1": 0.32
1645
+ },
1646
+ "all_columns": [
1647
+ "sequence",
1648
+ "name",
1649
+ "label"
1650
+ ],
1651
+ "dataset_path": "./OmniGenBench/poly_a_oryza_sativa_japonica_group_test.csv.gz"
1652
+ }
1653
+ },
1654
+ "task_category": "RNA Processing Prediction",
1655
+ "molecular_level": "RNA"
1656
+ },
1657
+ {
1658
+ "dataset_name": "pro_seq_m_esculenta",
1659
+ "task_description": "Prediction of enhancer elements in Manihot esculenta seedlings (plant)",
1660
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1661
+ "species": "Manihot esculenta",
1662
+ "task_type": "Binary Classification",
1663
+ "seq_col": [
1664
+ "sequence"
1665
+ ],
1666
+ "label_col": "label",
1667
+ "label_categories": {
1668
+ "0": "negative",
1669
+ "1": "positive"
1670
+ },
1671
+ "splits": [
1672
+ "train",
1673
+ "test"
1674
+ ],
1675
+ "excluded": null,
1676
+ "split_metadata": {
1677
+ "train": {
1678
+ "seq_length": {
1679
+ "sequence": {
1680
+ "min": 1000,
1681
+ "max": 1000,
1682
+ "median": 1000
1683
+ }
1684
+ },
1685
+ "seq_alphabet": {
1686
+ "sequence": [
1687
+ "A",
1688
+ "C",
1689
+ "G",
1690
+ "T"
1691
+ ]
1692
+ },
1693
+ "labels": [
1694
+ 0,
1695
+ 1
1696
+ ],
1697
+ "dataset_size": 8000,
1698
+ "class_ratio": {
1699
+ "0": 0.51,
1700
+ "1": 0.49
1701
+ },
1702
+ "all_columns": [
1703
+ "sequence",
1704
+ "name",
1705
+ "label"
1706
+ ],
1707
+ "dataset_path": "./OmniGenBench/pro_seq_m_esculenta_train.csv.gz"
1708
+ },
1709
+ "test": {
1710
+ "seq_length": {
1711
+ "sequence": {
1712
+ "min": 1000,
1713
+ "max": 1000,
1714
+ "median": 1000
1715
+ }
1716
+ },
1717
+ "seq_alphabet": {
1718
+ "sequence": [
1719
+ "A",
1720
+ "C",
1721
+ "G",
1722
+ "T"
1723
+ ]
1724
+ },
1725
+ "labels": [
1726
+ 0,
1727
+ 1
1728
+ ],
1729
+ "dataset_size": 812,
1730
+ "class_ratio": {
1731
+ "0": 0.51,
1732
+ "1": 0.49
1733
+ },
1734
+ "all_columns": [
1735
+ "sequence",
1736
+ "name",
1737
+ "label"
1738
+ ],
1739
+ "dataset_path": "./OmniGenBench/pro_seq_m_esculenta_test.csv.gz"
1740
+ }
1741
+ },
1742
+ "task_category": "Sequence Annotation",
1743
+ "molecular_level": "DNA"
1744
+ },
1745
+ {
1746
+ "dataset_name": "promoter_strength_leaf",
1747
+ "task_description": "Prediction of promoter strength in leaf tissue (plant)",
1748
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1749
+ "species": "Tobacco",
1750
+ "task_type": "Regression",
1751
+ "seq_col": [
1752
+ "sequence"
1753
+ ],
1754
+ "label_col": "label",
1755
+ "label_categories": null,
1756
+ "splits": [
1757
+ "train",
1758
+ "test"
1759
+ ],
1760
+ "excluded": null,
1761
+ "split_metadata": {
1762
+ "train": {
1763
+ "seq_length": {
1764
+ "sequence": {
1765
+ "min": 170,
1766
+ "max": 170,
1767
+ "median": 170
1768
+ }
1769
+ },
1770
+ "seq_alphabet": {
1771
+ "sequence": [
1772
+ "A",
1773
+ "C",
1774
+ "G",
1775
+ "T"
1776
+ ]
1777
+ },
1778
+ "labels": {
1779
+ "min": -4.3744649887,
1780
+ "max": 5.1592421532,
1781
+ "median": 0.9741330147
1782
+ },
1783
+ "dataset_size": 8000,
1784
+ "class_ratio": null,
1785
+ "all_columns": [
1786
+ "sequence",
1787
+ "name",
1788
+ "label"
1789
+ ],
1790
+ "dataset_path": "./OmniGenBench/promoter_strength_leaf_train.csv.gz"
1791
+ },
1792
+ "test": {
1793
+ "seq_length": {
1794
+ "sequence": {
1795
+ "min": 170,
1796
+ "max": 170,
1797
+ "median": 170
1798
+ }
1799
+ },
1800
+ "seq_alphabet": {
1801
+ "sequence": [
1802
+ "A",
1803
+ "C",
1804
+ "G",
1805
+ "T"
1806
+ ]
1807
+ },
1808
+ "labels": {
1809
+ "min": -3.8293364048000003,
1810
+ "max": 5.3175988197,
1811
+ "median": 0.8837240636
1812
+ },
1813
+ "dataset_size": 1000,
1814
+ "class_ratio": null,
1815
+ "all_columns": [
1816
+ "sequence",
1817
+ "name",
1818
+ "label"
1819
+ ],
1820
+ "dataset_path": "./OmniGenBench/promoter_strength_leaf_test.csv.gz"
1821
+ }
1822
+ },
1823
+ "task_category": "Sequence Annotation",
1824
+ "molecular_level": "DNA"
1825
+ },
1826
+ {
1827
+ "dataset_name": "promoter_strength_protoplast",
1828
+ "task_description": "Prediction of promoter strength in protoplasts (plant)",
1829
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1830
+ "species": "Zea mays",
1831
+ "task_type": "Regression",
1832
+ "seq_col": [
1833
+ "sequence"
1834
+ ],
1835
+ "label_col": "label",
1836
+ "label_categories": null,
1837
+ "splits": [
1838
+ "train",
1839
+ "test"
1840
+ ],
1841
+ "excluded": null,
1842
+ "split_metadata": {
1843
+ "train": {
1844
+ "seq_length": {
1845
+ "sequence": {
1846
+ "min": 170,
1847
+ "max": 170,
1848
+ "median": 170
1849
+ }
1850
+ },
1851
+ "seq_alphabet": {
1852
+ "sequence": [
1853
+ "A",
1854
+ "C",
1855
+ "G",
1856
+ "T"
1857
+ ]
1858
+ },
1859
+ "labels": {
1860
+ "min": -4.5865321159,
1861
+ "max": 4.4492254257,
1862
+ "median": -0.2792313695
1863
+ },
1864
+ "dataset_size": 8000,
1865
+ "class_ratio": null,
1866
+ "all_columns": [
1867
+ "sequence",
1868
+ "name",
1869
+ "label"
1870
+ ],
1871
+ "dataset_path": "./OmniGenBench/promoter_strength_protoplast_train.csv.gz"
1872
+ },
1873
+ "test": {
1874
+ "seq_length": {
1875
+ "sequence": {
1876
+ "min": 170,
1877
+ "max": 170,
1878
+ "median": 170
1879
+ }
1880
+ },
1881
+ "seq_alphabet": {
1882
+ "sequence": [
1883
+ "A",
1884
+ "C",
1885
+ "G",
1886
+ "T"
1887
+ ]
1888
+ },
1889
+ "labels": {
1890
+ "min": -4.7575125694,
1891
+ "max": 3.7787706852,
1892
+ "median": -0.18113671985000002
1893
+ },
1894
+ "dataset_size": 1000,
1895
+ "class_ratio": null,
1896
+ "all_columns": [
1897
+ "sequence",
1898
+ "name",
1899
+ "label"
1900
+ ],
1901
+ "dataset_path": "./OmniGenBench/promoter_strength_protoplast_test.csv.gz"
1902
+ }
1903
+ },
1904
+ "task_category": "Sequence Annotation",
1905
+ "molecular_level": "DNA"
1906
+ },
1907
+ {
1908
+ "dataset_name": "splicing_arabidopsis_thaliana_donor",
1909
+ "task_description": "Prediction of splice donor sites in Arabidopsis thaliana (plant)",
1910
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1911
+ "species": "Arabidopsis thaliana",
1912
+ "task_type": "Binary Classification",
1913
+ "seq_col": [
1914
+ "sequence"
1915
+ ],
1916
+ "label_col": "label",
1917
+ "label_categories": {
1918
+ "0": "negative",
1919
+ "1": "positive"
1920
+ },
1921
+ "splits": [
1922
+ "train",
1923
+ "test"
1924
+ ],
1925
+ "excluded": null,
1926
+ "split_metadata": {
1927
+ "train": {
1928
+ "seq_length": {
1929
+ "sequence": {
1930
+ "min": 398,
1931
+ "max": 398,
1932
+ "median": 398
1933
+ }
1934
+ },
1935
+ "seq_alphabet": {
1936
+ "sequence": [
1937
+ "A",
1938
+ "C",
1939
+ "G",
1940
+ "T"
1941
+ ]
1942
+ },
1943
+ "labels": [
1944
+ 0,
1945
+ 1
1946
+ ],
1947
+ "dataset_size": 8000,
1948
+ "class_ratio": {
1949
+ "0": 0.5,
1950
+ "1": 0.5
1951
+ },
1952
+ "all_columns": [
1953
+ "sequence",
1954
+ "name",
1955
+ "label"
1956
+ ],
1957
+ "dataset_path": "./OmniGenBench/splicing_arabidopsis_thaliana_donor_train.csv.gz"
1958
+ },
1959
+ "test": {
1960
+ "seq_length": {
1961
+ "sequence": {
1962
+ "min": 398,
1963
+ "max": 398,
1964
+ "median": 398
1965
+ }
1966
+ },
1967
+ "seq_alphabet": {
1968
+ "sequence": [
1969
+ "A",
1970
+ "C",
1971
+ "G",
1972
+ "T"
1973
+ ]
1974
+ },
1975
+ "labels": [
1976
+ 0,
1977
+ 1
1978
+ ],
1979
+ "dataset_size": 1000,
1980
+ "class_ratio": {
1981
+ "0": 0.5,
1982
+ "1": 0.5
1983
+ },
1984
+ "all_columns": [
1985
+ "sequence",
1986
+ "name",
1987
+ "label"
1988
+ ],
1989
+ "dataset_path": "./OmniGenBench/splicing_arabidopsis_thaliana_donor_test.csv.gz"
1990
+ }
1991
+ },
1992
+ "task_category": "RNA Processing Prediction",
1993
+ "molecular_level": "RNA"
1994
+ },
1995
+ {
1996
+ "dataset_name": "splicing_arabidopsis_thaliana_acceptor",
1997
+ "task_description": "Prediction of splice acceptor sites in Arabidopsis thaliana (plant)",
1998
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
1999
+ "species": "Arabidopsis thaliana",
2000
+ "task_type": "Binary Classification",
2001
+ "seq_col": [
2002
+ "sequence"
2003
+ ],
2004
+ "label_col": "label",
2005
+ "label_categories": {
2006
+ "0": "negative",
2007
+ "1": "positive"
2008
+ },
2009
+ "splits": [
2010
+ "train",
2011
+ "test"
2012
+ ],
2013
+ "excluded": null,
2014
+ "split_metadata": {
2015
+ "train": {
2016
+ "seq_length": {
2017
+ "sequence": {
2018
+ "min": 398,
2019
+ "max": 398,
2020
+ "median": 398
2021
+ }
2022
+ },
2023
+ "seq_alphabet": {
2024
+ "sequence": [
2025
+ "A",
2026
+ "C",
2027
+ "G",
2028
+ "T"
2029
+ ]
2030
+ },
2031
+ "labels": [
2032
+ 0,
2033
+ 1
2034
+ ],
2035
+ "dataset_size": 8000,
2036
+ "class_ratio": {
2037
+ "0": 0.5,
2038
+ "1": 0.5
2039
+ },
2040
+ "all_columns": [
2041
+ "sequence",
2042
+ "name",
2043
+ "label"
2044
+ ],
2045
+ "dataset_path": "./OmniGenBench/splicing_arabidopsis_thaliana_acceptor_train.csv.gz"
2046
+ },
2047
+ "test": {
2048
+ "seq_length": {
2049
+ "sequence": {
2050
+ "min": 398,
2051
+ "max": 398,
2052
+ "median": 398
2053
+ }
2054
+ },
2055
+ "seq_alphabet": {
2056
+ "sequence": [
2057
+ "A",
2058
+ "C",
2059
+ "G",
2060
+ "T"
2061
+ ]
2062
+ },
2063
+ "labels": [
2064
+ 0,
2065
+ 1
2066
+ ],
2067
+ "dataset_size": 1000,
2068
+ "class_ratio": {
2069
+ "0": 0.5,
2070
+ "1": 0.5
2071
+ },
2072
+ "all_columns": [
2073
+ "sequence",
2074
+ "name",
2075
+ "label"
2076
+ ],
2077
+ "dataset_path": "./OmniGenBench/splicing_arabidopsis_thaliana_acceptor_test.csv.gz"
2078
+ }
2079
+ },
2080
+ "task_category": "RNA Processing Prediction",
2081
+ "molecular_level": "RNA"
2082
+ },
2083
+ {
2084
+ "dataset_name": "terminator_strength_leaf",
2085
+ "task_description": "Prediction of terminator strength in leaf tissue (plant)",
2086
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
2087
+ "species": "Tobacco",
2088
+ "task_type": "Regression",
2089
+ "seq_col": [
2090
+ "sequence"
2091
+ ],
2092
+ "label_col": "label",
2093
+ "label_categories": null,
2094
+ "splits": [
2095
+ "train",
2096
+ "test"
2097
+ ],
2098
+ "excluded": null,
2099
+ "split_metadata": {
2100
+ "train": {
2101
+ "seq_length": {
2102
+ "sequence": {
2103
+ "min": 170,
2104
+ "max": 170,
2105
+ "median": 170
2106
+ }
2107
+ },
2108
+ "seq_alphabet": {
2109
+ "sequence": [
2110
+ "A",
2111
+ "C",
2112
+ "G",
2113
+ "T"
2114
+ ]
2115
+ },
2116
+ "labels": {
2117
+ "min": -6.1418619156,
2118
+ "max": 0.0800649896,
2119
+ "median": -3.4766187667999997
2120
+ },
2121
+ "dataset_size": 8000,
2122
+ "class_ratio": null,
2123
+ "all_columns": [
2124
+ "sequence",
2125
+ "name",
2126
+ "label"
2127
+ ],
2128
+ "dataset_path": "./OmniGenBench/terminator_strength_leaf_train.csv.gz"
2129
+ },
2130
+ "test": {
2131
+ "seq_length": {
2132
+ "sequence": {
2133
+ "min": 170,
2134
+ "max": 170,
2135
+ "median": 170
2136
+ }
2137
+ },
2138
+ "seq_alphabet": {
2139
+ "sequence": [
2140
+ "A",
2141
+ "C",
2142
+ "G",
2143
+ "T"
2144
+ ]
2145
+ },
2146
+ "labels": {
2147
+ "min": -5.2695832253,
2148
+ "max": -0.3980841637,
2149
+ "median": -3.4671332836
2150
+ },
2151
+ "dataset_size": 1000,
2152
+ "class_ratio": null,
2153
+ "all_columns": [
2154
+ "sequence",
2155
+ "name",
2156
+ "label"
2157
+ ],
2158
+ "dataset_path": "./OmniGenBench/terminator_strength_leaf_test.csv.gz"
2159
+ }
2160
+ },
2161
+ "task_category": "Sequence Annotation",
2162
+ "molecular_level": "DNA"
2163
+ },
2164
+ {
2165
+ "dataset_name": "terminator_strength_protoplast",
2166
+ "task_description": "Prediction of terminator strength in protoplasts (plant)",
2167
+ "dataset_doi": "https://doi.org/10.1126/science.ado9336",
2168
+ "species": "Zea mays",
2169
+ "task_type": "Regression",
2170
+ "seq_col": [
2171
+ "sequence"
2172
+ ],
2173
+ "label_col": "label",
2174
+ "label_categories": null,
2175
+ "splits": [
2176
+ "train",
2177
+ "test"
2178
+ ],
2179
+ "excluded": null,
2180
+ "split_metadata": {
2181
+ "train": {
2182
+ "seq_length": {
2183
+ "sequence": {
2184
+ "min": 170,
2185
+ "max": 170,
2186
+ "median": 170
2187
+ }
2188
+ },
2189
+ "seq_alphabet": {
2190
+ "sequence": [
2191
+ "A",
2192
+ "C",
2193
+ "G",
2194
+ "T"
2195
+ ]
2196
+ },
2197
+ "labels": {
2198
+ "min": -3.5004365444000003,
2199
+ "max": -0.039726451,
2200
+ "median": -1.99826437235
2201
+ },
2202
+ "dataset_size": 8000,
2203
+ "class_ratio": null,
2204
+ "all_columns": [
2205
+ "sequence",
2206
+ "name",
2207
+ "label"
2208
+ ],
2209
+ "dataset_path": "./OmniGenBench/terminator_strength_protoplast_train.csv.gz"
2210
+ },
2211
+ "test": {
2212
+ "seq_length": {
2213
+ "sequence": {
2214
+ "min": 170,
2215
+ "max": 170,
2216
+ "median": 170
2217
+ }
2218
+ },
2219
+ "seq_alphabet": {
2220
+ "sequence": [
2221
+ "A",
2222
+ "C",
2223
+ "G",
2224
+ "T"
2225
+ ]
2226
+ },
2227
+ "labels": {
2228
+ "min": -3.5410215855000002,
2229
+ "max": 0.0205871966,
2230
+ "median": -1.9980075955499998
2231
+ },
2232
+ "dataset_size": 1000,
2233
+ "class_ratio": null,
2234
+ "all_columns": [
2235
+ "sequence",
2236
+ "name",
2237
+ "label"
2238
+ ],
2239
+ "dataset_path": "./OmniGenBench/terminator_strength_protoplast_test.csv.gz"
2240
+ }
2241
+ },
2242
+ "task_category": "Sequence Annotation",
2243
+ "molecular_level": "DNA"
2244
+ }
2245
+ ]
2246
+ }
README.md ADDED
@@ -0,0 +1,271 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
2
+ configs:
3
+ - config_name: lncrna_g_max
4
+ data_files:
5
+ - split: train
6
+ path: lncrna_g_max/lncrna_g_max_train.csv.gz
7
+ - split: validation
8
+ path: lncrna_g_max/lncrna_g_max_test.csv.gz
9
+ - split: test
10
+ path: lncrna_g_max/lncrna_g_max_test.csv.gz
11
+
12
+ - config_name: lncrna_m_esculenta
13
+ data_files:
14
+ - split: train
15
+ path: lncrna_m_esculenta/lncrna_m_esculenta_train.csv.gz
16
+ - split: validation
17
+ path: lncrna_m_esculenta/lncrna_m_esculenta_test.csv.gz
18
+ - split: test
19
+ path: lncrna_m_esculenta/lncrna_m_esculenta_test.csv.gz
20
+
21
+ - config_name: lncrna_s_bicolor
22
+ data_files:
23
+ - split: train
24
+ path: lncrna_s_bicolor/lncrna_s_bicolor_train.csv.gz
25
+ - split: validation
26
+ path: lncrna_s_bicolor/lncrna_s_bicolor_test.csv.gz
27
+ - split: test
28
+ path: lncrna_s_bicolor/lncrna_s_bicolor_test.csv.gz
29
+
30
+ - config_name: lncrna_s_lycopersicum
31
+ data_files:
32
+ - split: train
33
+ path: lncrna_s_lycopersicum/lncrna_s_lycopersicum_train.csv.gz
34
+ - split: validation
35
+ path: lncrna_s_lycopersicum/lncrna_s_lycopersicum_test.csv.gz
36
+ - split: test
37
+ path: lncrna_s_lycopersicum/lncrna_s_lycopersicum_test.csv.gz
38
+
39
+ - config_name: lncrna_t_aestivum
40
+ data_files:
41
+ - split: train
42
+ path: lncrna_t_aestivum/lncrna_t_aestivum_train.csv.gz
43
+ - split: validation
44
+ path: lncrna_t_aestivum/lncrna_t_aestivum_test.csv.gz
45
+ - split: test
46
+ path: lncrna_t_aestivum/lncrna_t_aestivum_test.csv.gz
47
+
48
+ - config_name: lncrna_z_mays
49
+ data_files:
50
+ - split: train
51
+ path: lncrna_z_mays/lncrna_z_mays_train.csv.gz
52
+ - split: validation
53
+ path: lncrna_z_mays/lncrna_z_mays_test.csv.gz
54
+ - split: test
55
+ path: lncrna_z_mays/lncrna_z_mays_test.csv.gz
56
+
57
+ - config_name: poly_a_arabidopsis_thaliana
58
+ data_files:
59
+ - split: train
60
+ path: poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_train.csv.gz
61
+ - split: validation
62
+ path: poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_test.csv.gz
63
+ - split: test
64
+ path: poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_test.csv.gz
65
+
66
+ - config_name: poly_a_chlamydomonas_reinhardtii
67
+ data_files:
68
+ - split: train
69
+ path: poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_train.csv.gz
70
+ - split: validation
71
+ path: poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_test.csv.gz
72
+ - split: test
73
+ path: poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_test.csv.gz
74
+
75
+ - config_name: poly_a_medicago_truncatula
76
+ data_files:
77
+ - split: train
78
+ path: poly_a_medicago_truncatula/poly_a_medicago_truncatula_train.csv.gz
79
+ - split: validation
80
+ path: poly_a_medicago_truncatula/poly_a_medicago_truncatula_test.csv.gz
81
+ - split: test
82
+ path: poly_a_medicago_truncatula/poly_a_medicago_truncatula_test.csv.gz
83
+
84
+ - config_name: poly_a_oryza_sativa_indica_group
85
+ data_files:
86
+ - split: train
87
+ path: poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_train.csv.gz
88
+ - split: validation
89
+ path: poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_test.csv.gz
90
+ - split: test
91
+ path: poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_test.csv.gz
92
+
93
+ - config_name: poly_a_oryza_sativa_japonica_group
94
+ data_files:
95
+ - split: train
96
+ path: poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_train.csv.gz
97
+ - split: validation
98
+ path: poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_test.csv.gz
99
+ - split: test
100
+ path: poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_test.csv.gz
101
+
102
+ - config_name: poly_a_trifolium_pratense
103
+ data_files:
104
+ - split: train
105
+ path: poly_a_trifolium_pratense/poly_a_trifolium_pratense_train.csv.gz
106
+ - split: validation
107
+ path: poly_a_trifolium_pratense/poly_a_trifolium_pratense_test.csv.gz
108
+ - split: test
109
+ path: poly_a_trifolium_pratense/poly_a_trifolium_pratense_test.csv.gz
110
+
111
+ - config_name: pro_seq_m_esculenta
112
+ data_files:
113
+ - split: train
114
+ path: pro_seq_m_esculenta/pro_seq_m_esculenta_train.csv.gz
115
+ - split: validation
116
+ path: pro_seq_m_esculenta/pro_seq_m_esculenta_test.csv.gz
117
+ - split: test
118
+ path: pro_seq_m_esculenta/pro_seq_m_esculenta_test.csv.gz
119
+
120
+ - config_name: promoter_strength_leaf
121
+ data_files:
122
+ - split: train
123
+ path: promoter_strength_leaf/promoter_strength_leaf_train.csv.gz
124
+ - split: validation
125
+ path: promoter_strength_leaf/promoter_strength_leaf_test.csv.gz
126
+ - split: test
127
+ path: promoter_strength_leaf/promoter_strength_leaf_test.csv.gz
128
+
129
+ - config_name: promoter_strength_protoplast
130
+ data_files:
131
+ - split: train
132
+ path: promoter_strength_protoplast/promoter_strength_protoplast_train.csv.gz
133
+ - split: validation
134
+ path: promoter_strength_protoplast/promoter_strength_protoplast_test.csv.gz
135
+ - split: test
136
+ path: promoter_strength_protoplast/promoter_strength_protoplast_test.csv.gz
137
+
138
+ - config_name: splicing_arabidopsis_thaliana_acceptor
139
+ data_files:
140
+ - split: train
141
+ path: splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_train.csv.gz
142
+ - split: validation
143
+ path: splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_test.csv.gz
144
+ - split: test
145
+ path: splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_test.csv.gz
146
+
147
+ - config_name: splicing_arabidopsis_thaliana_donor
148
+ data_files:
149
+ - split: train
150
+ path: splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_train.csv.gz
151
+ - split: validation
152
+ path: splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_test.csv.gz
153
+ - split: test
154
+ path: splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_test.csv.gz
155
+
156
+ - config_name: te_prediction_arabidopsis
157
+ data_files:
158
+ - split: train
159
+ path: te_prediction_arabidopsis/te_prediction_arabidopsis_train.csv.gz
160
+ - split: validation
161
+ path: te_prediction_arabidopsis/te_prediction_arabidopsis_val.csv.gz
162
+ - split: test
163
+ path: te_prediction_arabidopsis/te_prediction_arabidopsis_test.csv.gz
164
+
165
+ - config_name: te_prediction_rice
166
+ data_files:
167
+ - split: train
168
+ path: te_prediction_rice/te_prediction_rice_train.csv.gz
169
+ - split: validation
170
+ path: te_prediction_rice/te_prediction_rice_val.csv.gz
171
+ - split: test
172
+ path: te_prediction_rice/te_prediction_rice_test.csv.gz
173
+
174
+ - config_name: terminator_strength_leaf
175
+ data_files:
176
+ - split: train
177
+ path: terminator_strength_leaf/terminator_strength_leaf_train.csv.gz
178
+ - split: validation
179
+ path: terminator_strength_leaf/terminator_strength_leaf_test.csv.gz
180
+ - split: test
181
+ path: terminator_strength_leaf/terminator_strength_leaf_test.csv.gz
182
+
183
+ - config_name: terminator_strength_protoplast
184
+ data_files:
185
+ - split: train
186
+ path: terminator_strength_protoplast/terminator_strength_protoplast_train.csv.gz
187
+ - split: validation
188
+ path: terminator_strength_protoplast/terminator_strength_protoplast_test.csv.gz
189
+ - split: test
190
+ path: terminator_strength_protoplast/terminator_strength_protoplast_test.csv.gz
191
+ ---
192
+
193
+ # OmniGenBench
194
+
195
+ ## Overview
196
+
197
+ OmniGenBench is a collection ...
198
+
199
+ ## Dataset structure
200
+
201
+ The repository is organized as follows:
202
+ ```
203
+ OmniGenBench/
204
+ ├── OmniGenBench_metadata.json
205
+ ├── README.md
206
+ ├── lncrna_g_max/
207
+ │ ├── lncrna_g_max_train.csv.gz
208
+ │ └── lncrna_g_max_test.csv.gz
209
+ ├── lncrna_m_esculenta/
210
+ │ ├── lncrna_m_esculenta_train.csv.gz
211
+ │ └── lncrna_m_esculenta_test.csv.gz
212
+ ├── lncrna_s_bicolor/
213
+ │ ├── lncrna_s_bicolor_train.csv.gz
214
+ │ └── lncrna_s_bicolor_test.csv.gz
215
+ ├── lncrna_s_lycopersicum/
216
+ │ ├── lncrna_s_lycopersicum_train.csv.gz
217
+ │ └── lncrna_s_lycopersicum_test.csv.gz
218
+ ├── lncrna_t_aestivum/
219
+ │ ├── lncrna_t_aestivum_train.csv.gz
220
+ │ └── lncrna_t_aestivum_test.csv.gz
221
+ ├── lncrna_z_mays/
222
+ │ ├── lncrna_z_mays_train.csv.gz
223
+ │ └── lncrna_z_mays_test.csv.gz
224
+ ├── poly_a_arabidopsis_thaliana/
225
+ │ ├── poly_a_arabidopsis_thaliana_train.csv.gz
226
+ │ └── poly_a_arabidopsis_thaliana_test.csv.gz
227
+ ├── poly_a_chlamydomonas_reinhardtii/
228
+ │ ├── poly_a_chlamydomonas_reinhardtii_train.csv.gz
229
+ │ └── poly_a_chlamydomonas_reinhardtii_test.csv.gz
230
+ ├── poly_a_medicago_truncatula/
231
+ │ ├── poly_a_medicago_truncatula_train.csv.gz
232
+ │ └── poly_a_medicago_truncatula_test.csv.gz
233
+ ├── poly_a_oryza_sativa_indica_group/
234
+ │ ├── poly_a_oryza_sativa_indica_group_train.csv.gz
235
+ │ └── poly_a_oryza_sativa_indica_group_test.csv.gz
236
+ ├── poly_a_oryza_sativa_japonica_group/
237
+ │ ├── poly_a_oryza_sativa_japonica_group_train.csv.gz
238
+ │ └── poly_a_oryza_sativa_japonica_group_test.csv.gz
239
+ ├── poly_a_trifolium_pratense/
240
+ │ ├── poly_a_trifolium_pratense_train.csv.gz
241
+ │ └── poly_a_trifolium_pratense_test.csv.gz
242
+ ├── pro_seq_m_esculenta/
243
+ │ ├── pro_seq_m_esculenta_train.csv.gz
244
+ │ └── pro_seq_m_esculenta_test.csv.gz
245
+ ├── promoter_strength_leaf/
246
+ │ ├── promoter_strength_leaf_train.csv.gz
247
+ │ └── promoter_strength_leaf_test.csv.gz
248
+ ├── promoter_strength_protoplast/
249
+ │ ├── promoter_strength_protoplast_train.csv.gz
250
+ │ └── promoter_strength_protoplast_test.csv.gz
251
+ ├── splicing_arabidopsis_thaliana_acceptor/
252
+ │ ├── splicing_arabidopsis_thaliana_acceptor_train.csv.gz
253
+ │ └── splicing_arabidopsis_thaliana_acceptor_test.csv.gz
254
+ ├── splicing_arabidopsis_thaliana_donor/
255
+ │ ├── splicing_arabidopsis_thaliana_donor_train.csv.gz
256
+ │ └── splicing_arabidopsis_thaliana_donor_test.csv.gz
257
+ ├── te_prediction_arabidopsis/
258
+ │ ├── te_prediction_arabidopsis_train.csv.gz
259
+ │ ├── te_prediction_arabidopsis_val.csv.gz
260
+ │ └── te_prediction_arabidopsis_test.csv.gz
261
+ ├── te_prediction_rice/
262
+ │ ├── te_prediction_rice_train.csv.gz
263
+ │ ├── te_prediction_rice_val.csv.gz
264
+ │ └── te_prediction_rice_test.csv.gz
265
+ ├── terminator_strength_leaf/
266
+ │ ├── terminator_strength_leaf_train.csv.gz
267
+ │ └── terminator_strength_leaf_test.csv.gz
268
+ └── terminator_strength_protoplast/
269
+ ├── terminator_strength_protoplast_train.csv.gz
270
+ └── terminator_strength_protoplast_test.csv.gz
271
+ ```
lncrna_g_max/lncrna_g_max_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d338a7181d21d98bd1e60d817b7e7f67391a50a153dba51ac4fd65162bfc1502
3
+ size 86291
lncrna_g_max/lncrna_g_max_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:590ec7240c6aec8a8f154ba63ad36790addc44d14dfbcdfef679c72ee1bc1fe9
3
+ size 1505985
lncrna_m_esculenta/lncrna_m_esculenta_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:67ca5f8cf720475568bb2c2a02fac15f86f39c4fe65b9ed10c93f72f57cb86ae
3
+ size 65586
lncrna_m_esculenta/lncrna_m_esculenta_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3dd9d6c2c8ba29e6592059f90242a67c880bc7e0174e11f0b0248b5005b4b231
3
+ size 939915
lncrna_s_bicolor/lncrna_s_bicolor_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:cf9390b022fe5f8ec1a9b2a7d97f9fe0bd4decc71a0b132216eabdb93170cde8
3
+ size 232432
lncrna_s_bicolor/lncrna_s_bicolor_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:7e12f10a35de1186ab0d5eec1b36191c0630d5accb76db4095b4cdc4207726c0
3
+ size 2259814
lncrna_s_lycopersicum/lncrna_s_lycopersicum_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a616d1159d2c838ad185aaf27dcc980b2f89f82d5d15dde6e5a74119e33946b0
3
+ size 162442
lncrna_s_lycopersicum/lncrna_s_lycopersicum_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:83a4871923ce34e152a03a819674246bd5676e5fd3c0636cf98da634349071dc
3
+ size 1146958
lncrna_t_aestivum/lncrna_t_aestivum_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ebb274ed7e383df336c76f1cdc8c84a2d847050153d6144e818f456519c253a9
3
+ size 120014
lncrna_t_aestivum/lncrna_t_aestivum_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:9325b0419bad1f3c7b807b39518874eaae2054aed5120a428b767404ade48fa5
3
+ size 1013870
lncrna_z_mays/lncrna_z_mays_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:6136b99850decbe5412ca4283d4b2cdd1f591f1854352d83387a8a661ec9d8f1
3
+ size 156200
lncrna_z_mays/lncrna_z_mays_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5f9b9f20d9a328565f423828a0d2cb26e6adcadaa93c76602a4aed48423aaef9
3
+ size 1312081
poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:574434c5d5741dc6bf06324cb977e030aa9143bbcfa96c80e8104d293a7a1364
3
+ size 122486
poly_a_arabidopsis_thaliana/poly_a_arabidopsis_thaliana_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3d36c2dc73da6ae6edc55f8dac48541ce95baaf895d718178a0cec8e2fd28c4a
3
+ size 985471
poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d2cc3d870591cb59bf78235cbc81941360e55b2de3a18e8b6d54ce5113539cec
3
+ size 120416
poly_a_chlamydomonas_reinhardtii/poly_a_chlamydomonas_reinhardtii_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:4fda507e4759d4ead4fdd8497437dbd7fa383a057857f951b3ee2decccc42743
3
+ size 995361
poly_a_medicago_truncatula/poly_a_medicago_truncatula_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:97f45cc19cf46e3e4f2db51e41b36193b9b33c2e88ad3606866b77e5a1afa085
3
+ size 120924
poly_a_medicago_truncatula/poly_a_medicago_truncatula_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f4030a9c92207341ca5207ede7f90de32234b77abc8549fd3f4f794b52b62da1
3
+ size 979829
poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:bea5df5ae90352edcd6e540dec688ed662b1d34760fd76ab61ebc6f8a5f9d89c
3
+ size 123958
poly_a_oryza_sativa_indica_group/poly_a_oryza_sativa_indica_group_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:9ecb1bb2064d5cda7bff7200fe5563f56c12ca32946c0153ccf2469401c418f1
3
+ size 999107
poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:88c8ad4f74d47fa14d65692f7f87ae9e2d7e4b09d8cbdcf58c59bdb0ff528072
3
+ size 123348
poly_a_oryza_sativa_japonica_group/poly_a_oryza_sativa_japonica_group_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e9d897ddde9bf2d268ce21494c63c37c5f659af120006bd69b2f737835d21105
3
+ size 998677
poly_a_trifolium_pratense/poly_a_trifolium_pratense_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5687afbe13b7ffca021ddfbc50768afea5214c9792521315d08e01b751f4c298
3
+ size 119305
poly_a_trifolium_pratense/poly_a_trifolium_pratense_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:7503f00a2190a091c29fdb883029fa0f3b6048a27594c7cd2e250d7a90efe736
3
+ size 979351
pro_seq_m_esculenta/pro_seq_m_esculenta_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:73a7dc7a31c22d297caf3709b3fafe874c658183d8d18e07a07fac9aafed0fbb
3
+ size 236616
pro_seq_m_esculenta/pro_seq_m_esculenta_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2d92a25924a60450c1b026833c2e94618897bc52ef1cd83f6351f84aae06358d
3
+ size 2334294
promoter_strength_leaf/promoter_strength_leaf_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0f74e4682673b6043ba80950d2160f01429d7831348fa82daf8b1e0fab9dafbe
3
+ size 66810
promoter_strength_leaf/promoter_strength_leaf_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:4d59a82265681a602d6f4f3c79e734aef860b545513c5dc13d376819415d73bd
3
+ size 526257
promoter_strength_protoplast/promoter_strength_protoplast_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d47eff33566d1b61052640057e4a9a1739678f2c4c7b058cb32a843d057f0f27
3
+ size 66539
promoter_strength_protoplast/promoter_strength_protoplast_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f8d6db528381fee92f1a46a6b6017b679b30dae463413f50c1e4f22a9e726161
3
+ size 525579
splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:8b44a591af2e848253651083df375d149be001313a02f466867d27cb86559076
3
+ size 59146
splicing_arabidopsis_thaliana_acceptor/splicing_arabidopsis_thaliana_acceptor_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:03ec184728dbd88b87693ad3a77105b614f6fd2fc5b5121c88ea35bbdbdfac3d
3
+ size 471629
splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:8e2080be10af2e2f9f09ab326aa7a71ba98ae8f29232ef5d6024e09a05162c8b
3
+ size 59137
splicing_arabidopsis_thaliana_donor/splicing_arabidopsis_thaliana_donor_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:1e8b1a5446cbdb9bf7c5249e036678da4916280976641f2be1daac3041727031
3
+ size 467813
te_prediction_arabidopsis/te_prediction_arabidopsis_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:8decf5cbbdbd1723a28ade8ae72eea9664667b8ff1de949effbb821e7de6ed85
3
+ size 60652
te_prediction_arabidopsis/te_prediction_arabidopsis_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3fba1dab8ee68d7bf1441f93dad290b77194c14fcae798bd2a030ce3d54d3ef1
3
+ size 477413
te_prediction_arabidopsis/te_prediction_arabidopsis_val.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:484ad090d339c1925a829546dfded27f9e62c1b746f9d3e818250fbc335c38a5
3
+ size 60537
te_prediction_rice/te_prediction_rice_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:58124bc7dac0f465a73ec3be52305fb7c6e9a51203b805cc261f364eeca47554
3
+ size 84338
te_prediction_rice/te_prediction_rice_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:4d293efcdcb17cc081462f896dd1e64c44716fa97bb200aa01bc195e31c4e67f
3
+ size 666376
te_prediction_rice/te_prediction_rice_val.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:32657f7378c4607ea22f902ba3ee690afda5a4e86c0f8e5026f85cf945d71d77
3
+ size 84375
te_prediction_rice/te_prediction_rice_valid.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ca3f6db80ee96b3e809a9170a888f200bbea9b4bc838b06fe02b29a8d67ffae5
3
+ size 84377
terminator_strength_leaf/terminator_strength_leaf_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:c22ebc86fd52d47dbc18db60443108d8324a53c476fe8fea2ac3842b3e207694
3
+ size 67016
terminator_strength_leaf/terminator_strength_leaf_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a278fc59a419fc5ab28baecd25caa813376b618480824da647d5a6b853c6bcd6
3
+ size 528406
terminator_strength_protoplast/terminator_strength_protoplast_test.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:beec6c773155dc76eae92e7dee8d11e61f5b98a3f87206d30385b670c82379bc
3
+ size 66796
terminator_strength_protoplast/terminator_strength_protoplast_train.csv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:257f2644a813f4b180ec943f1da946f93a91dd836ba6ff5941084dd138dd0697
3
+ size 527501