DeepPavlov/geneb-tasks

GENEB — Genomic Embedding Benchmark (task data)

Task-level sequence classification data for GENEB: a multi-task benchmark for DNA sequence encoders evaluated with precomputed representations and logistic regression (no encoder fine-tuning on task labels) across 100 tasks in 13 functional categories.

This repository release contains train and test partitions only. Model scores, evaluation code, and submission artifacts are maintained in the benchmark repository and summarized on the leaderboard.

Record schema

Each example is a single row with:

• text — nucleotide sequence (DNA over {A,C,G,T}; length and windowing are defined by the source task).
• label — discrete class label for the assay or prediction target.

Train and test examples are provided in separate files per task (train.csv, test.csv). Auxiliary splits present in some upstream releases (e.g. dev, validation) are excluded from this distribution and are not used in the GENEB evaluation protocol.

Evaluation protocol (summary)

GENEB scores models on these tasks under a shared protocol (full specification in the benchmark repository):

Item	Specification
Tasks	100
Functional categories	13
Reporting regimes	full, 10shot, 1shot
Metrics	MCC, Acc, F1 (primary: MCC)
Probe	logistic_regression (max_iter=1000)
Random seeds (mean over runs)	13, 17, 42, 123, 997

Participants should use the released train/test assignments as-is; relabeling, resplitting, or training on the test partition is outside the protocol.

Task categories

Category	Tasks
Histone Mod.	30
Promoters	22
Enhancers	8
DNA Methyl.	8
Splice Sites	7
lncRNA	6
Mouse Enh.	5
TF Binding	5
Species Clf.	3
Regulatory	2
Virus/Phage	2
Coding/NC	1
Chromatin Acc.	1

Repository layout and Dataset Viewer

Data are organized as tasks/<task_id>/train.csv and tasks/<task_id>/test.csv with columns text and label.

On the Hub Dataset Viewer, select:

1. Subset (config_name) — one benchmark task (short slug, e.g. NT_H3; see index below).
2. Split — train or test.

Local download (harness)

To reproduce runs with the reference harness (uses the dataset revision pinned in that spec):

python3 -m pip install "huggingface_hub>=0.24"
python3 tools/sync_geneb_dataset.py download --local_dir ./GENEB_data

This materializes GENEB_data/<task_id>.csv with columns text, label, and split for use with harness/run_GENEB.py.

Task index

Subset (config_name)	Short label	Task identifier	Category
NT_H3	NT H3	InstaDeepAI_nucleotide_transformer_downstream_tasks_H3	Histone Mod.
NT_H3K14ac	NT H3K14ac	InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K14ac	Histone Mod.
NT_H3K36me3	NT H3K36me3	InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K36me3	Histone Mod.
NT_H3K4me1	NT H3K4me1	InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K4me1	Histone Mod.
NT_H3K4me2	NT H3K4me2	InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K4me2	Histone Mod.
NT_H3K4me3	NT H3K4me3	InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K4me3	Histone Mod.
NT_H3K79me3	NT H3K79me3	InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K79me3	Histone Mod.
NT_H3K9ac	NT H3K9ac	InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K9ac	Histone Mod.
NT_H4	NT H4	InstaDeepAI_nucleotide_transformer_downstream_tasks_H4	Histone Mod.
NT_H4ac	NT H4ac	InstaDeepAI_nucleotide_transformer_downstream_tasks_H4ac	Histone Mod.
NT-rev_H2AFZ	NT-rev H2AFZ	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H2AFZ	Histone Mod.
NT-rev_H3K27ac	NT-rev H3K27ac	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K27ac	Histone Mod.
NT-rev_H3K27me3	NT-rev H3K27me3	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K27me3	Histone Mod.
NT-rev_H3K36me3	NT-rev H3K36me3	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K36me3	Histone Mod.
NT-rev_H3K4me1	NT-rev H3K4me1	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K4me1	Histone Mod.
NT-rev_H3K4me2	NT-rev H3K4me2	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K4me2	Histone Mod.
NT-rev_H3K4me3	NT-rev H3K4me3	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K4me3	Histone Mod.
NT-rev_H3K9ac	NT-rev H3K9ac	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K9ac	Histone Mod.
NT-rev_H3K9me3	NT-rev H3K9me3	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K9me3	Histone Mod.
NT-rev_H4K20me1	NT-rev H4K20me1	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H4K20me1	Histone Mod.
GUE-emp_H3	GUE-emp H3	leannmlindsey_GUE_emp_H3	Histone Mod.
GUE-emp_H3K14ac	GUE-emp H3K14ac	leannmlindsey_GUE_emp_H3K14ac	Histone Mod.
GUE-emp_H3K36me3	GUE-emp H3K36me3	leannmlindsey_GUE_emp_H3K36me3	Histone Mod.
GUE-emp_H3K4me1	GUE-emp H3K4me1	leannmlindsey_GUE_emp_H3K4me1	Histone Mod.
GUE-emp_H3K4me2	GUE-emp H3K4me2	leannmlindsey_GUE_emp_H3K4me2	Histone Mod.
GUE-emp_H3K4me3	GUE-emp H3K4me3	leannmlindsey_GUE_emp_H3K4me3	Histone Mod.
GUE-emp_H3K79me3	GUE-emp H3K79me3	leannmlindsey_GUE_emp_H3K79me3	Histone Mod.
GUE-emp_H3K9ac	GUE-emp H3K9ac	leannmlindsey_GUE_emp_H3K9ac	Histone Mod.
GUE-emp_H4	GUE-emp H4	leannmlindsey_GUE_emp_H4	Histone Mod.
GUE-emp_H4ac	GUE-emp H4ac	leannmlindsey_GUE_emp_H4ac	Histone Mod.
NT_promoter_all	NT promoter all	InstaDeepAI_nucleotide_transformer_downstream_tasks_promoter_all	Promoters
NT_promoter_no_tata	NT promoter no tata	InstaDeepAI_nucleotide_transformer_downstream_tasks_promoter_no_tata	Promoters
NT_promoter_tata	NT promoter tata	InstaDeepAI_nucleotide_transformer_downstream_tasks_promoter_tata	Promoters
NT-rev_promoter_all	NT-rev promoter all	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_promoter_all	Promoters
NT-rev_promoter_no_tata	NT-rev promoter no tata	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_promoter_no_tata	Promoters
NT-rev_promoter_tata	NT-rev promoter tata	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_promoter_tata	Promoters
PGB_pro_seq.m_esculenta	PGB pro seq.m esculenta	InstaDeepAI_plant-genomic-benchmark_pro_seq.m_esculenta	Promoters
iPro_Arabidopsis_NonTATA	iPro Arabidopsis NonTATA	iPro-WAEL_Promoter_Arabidopsis_NonTATA	Promoters
iPro_Arabidopsis_TATA	iPro Arabidopsis TATA	iPro-WAEL_Promoter_Arabidopsis_TATA	Promoters
iPro_B_amyloliquefaciens	iPro B amyloliquefaciens	iPro-WAEL_Promoter_B_amyloliquefaciens	Promoters
iPro_GM12878	iPro GM12878	iPro-WAEL_Promoter_GM12878	Promoters
iPro_HUVEC	iPro HUVEC	iPro-WAEL_Promoter_HUVEC	Promoters
iPro_Hela-S3	iPro Hela-S3	iPro-WAEL_Promoter_Hela-S3	Promoters
iPro_NHEK	iPro NHEK	iPro-WAEL_Promoter_NHEK	Promoters
iPro_R_capsulatus	iPro R capsulatus	iPro-WAEL_Promoter_R_capsulatus	Promoters
GB_human_nontata_promoters	GB human nontata promoters	katarinagresova_Genomic_Benchmarks_human_nontata_promoters	Promoters
GUE_prom_300_all	GUE prom 300 all	leannmlindsey_GUE_prom_300_all	Promoters
GUE_prom_300_notata	GUE prom 300 notata	leannmlindsey_GUE_prom_300_notata	Promoters
GUE_prom_300_tata	GUE prom 300 tata	leannmlindsey_GUE_prom_300_tata	Promoters
GUE_prom_core_all	GUE prom core all	leannmlindsey_GUE_prom_core_all	Promoters
GUE_prom_core_notata	GUE prom core notata	leannmlindsey_GUE_prom_core_notata	Promoters
GUE_prom_core_tata	GUE prom core tata	leannmlindsey_GUE_prom_core_tata	Promoters
NT_enhancers	NT enhancers	InstaDeepAI_nucleotide_transformer_downstream_tasks_enhancers	Enhancers
NT_enhancers_types	NT enhancers types	InstaDeepAI_nucleotide_transformer_downstream_tasks_enhancers_types	Enhancers
NT-rev_enhancers	NT-rev enhancers	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_enhancers	Enhancers
NT-rev_enhancers_types	NT-rev enhancers types	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_enhancers_types	Enhancers
GB_drosophila_enhancers_stark	GB drosophila enhancers stark	katarinagresova_Genomic_Benchmarks_drosophila_enhancers_stark	Enhancers
GB_dummy_mouse_enhancers_ensembl	GB dummy mouse enhancers ensembl	katarinagresova_Genomic_Benchmarks_dummy_mouse_enhancers_ensembl	Enhancers
GB_human_enhancers_cohn	GB human enhancers cohn	katarinagresova_Genomic_Benchmarks_human_enhancers_cohn	Enhancers
GB_human_enhancers_ensembl	GB human enhancers ensembl	katarinagresova_Genomic_Benchmarks_human_enhancers_ensembl	Enhancers
4mC_A.thaliana_4mC	4mC A.thaliana 4mC	deep4mc_A.thaliana_4mC	DNA Methyl.
4mC_C.elegans_4mC	4mC C.elegans 4mC	deep4mc_C.elegans_4mC	DNA Methyl.
4mC_D.melanogaster_4mC	4mC D.melanogaster 4mC	deep4mc_D.melanogaster_4mC	DNA Methyl.
4mC_E.coli_4mC	4mC E.coli 4mC	deep4mc_E.coli_4mC	DNA Methyl.
4mC_G.pickeringii_4mC	4mC G.pickeringii 4mC	deep4mc_G.pickeringii_4mC	DNA Methyl.
4mC_G.subterraneus_4mC	4mC G.subterraneus 4mC	deep4mc_G.subterraneus_4mC	DNA Methyl.
iDNA_5mC	iDNA 5mC	iDNA_ABF_5mC	DNA Methyl.
iDNA_6mA	iDNA 6mA	iDNA_ABF_6mA	DNA Methyl.
NT-rev_splice_sites_acceptors	NT-rev splice sites acceptors	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_splice_sites_acceptors	Splice Sites
NT-rev_splice_sites_all	NT-rev splice sites all	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_splice_sites_all	Splice Sites
NT-rev_splice_sites_donors	NT-rev splice sites donors	InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_splice_sites_donors	Splice Sites
NT_splice_sites_acceptors	NT splice sites acceptors	InstaDeepAI_nucleotide_transformer_downstream_tasks_splice_sites_acceptors	Splice Sites
NT_splice_sites_all	NT splice sites all	InstaDeepAI_nucleotide_transformer_downstream_tasks_splice_sites_all	Splice Sites
NT_splice_sites_donors	NT splice sites donors	InstaDeepAI_nucleotide_transformer_downstream_tasks_splice_sites_donors	Splice Sites
GUE_splice_reconstructed	GUE splice reconstructed	leannmlindsey_GUE_splice_reconstructed	Splice Sites
PGB_lncrna.g_max	PGB lncrna.g max	InstaDeepAI_plant-genomic-benchmark_lncrna.g_max	lncRNA
PGB_lncrna.m_esculenta	PGB lncrna.m esculenta	InstaDeepAI_plant-genomic-benchmark_lncrna.m_esculenta	lncRNA
PGB_lncrna.s_bicolor	PGB lncrna.s bicolor	InstaDeepAI_plant-genomic-benchmark_lncrna.s_bicolor	lncRNA
PGB_lncrna.s_lycopersicum	PGB lncrna.s lycopersicum	InstaDeepAI_plant-genomic-benchmark_lncrna.s_lycopersicum	lncRNA
PGB_lncrna.t_aestivum	PGB lncrna.t aestivum	InstaDeepAI_plant-genomic-benchmark_lncrna.t_aestivum	lncRNA
PGB_lncrna.z_mays	PGB lncrna.z mays	InstaDeepAI_plant-genomic-benchmark_lncrna.z_mays	lncRNA
GUE_mouse_0	GUE mouse 0	leannmlindsey_GUE_mouse_0	Mouse Enh.
GUE_mouse_1	GUE mouse 1	leannmlindsey_GUE_mouse_1	Mouse Enh.
GUE_mouse_2	GUE mouse 2	leannmlindsey_GUE_mouse_2	Mouse Enh.
GUE_mouse_3	GUE mouse 3	leannmlindsey_GUE_mouse_3	Mouse Enh.
GUE_mouse_4	GUE mouse 4	leannmlindsey_GUE_mouse_4	Mouse Enh.
GUE_human_tf_0	GUE human tf 0	leannmlindsey_GUE_human_tf_0	TF Binding
GUE_human_tf_1	GUE human tf 1	leannmlindsey_GUE_human_tf_1	TF Binding
GUE_human_tf_2	GUE human tf 2	leannmlindsey_GUE_human_tf_2	TF Binding
GUE_human_tf_3	GUE human tf 3	leannmlindsey_GUE_human_tf_3	TF Binding
GUE_human_tf_4	GUE human tf 4	leannmlindsey_GUE_human_tf_4	TF Binding
GB_demo_human_or_worm	GB demo human or worm	katarinagresova_Genomic_Benchmarks_demo_human_or_worm	Species Clf.
GUE_fungi_species_20	GUE fungi species 20	leannmlindsey_GUE_fungi_species_20	Species Clf.
GUE_virus_species_40	GUE virus species 40	leannmlindsey_GUE_virus_species_40	Species Clf.
GB_human_ensembl_regulatory	GB human ensembl regulatory	katarinagresova_Genomic_Benchmarks_human_ensembl_regulatory	Regulatory
GB_human_ocr_ensembl	GB human ocr ensembl	katarinagresova_Genomic_Benchmarks_human_ocr_ensembl	Regulatory
GUE_phage_fragments	GUE phage fragments	leannmlindsey_GUE_phage_fragments	Virus/Phage
GUE_virus_covid	GUE virus covid	leannmlindsey_GUE_virus_covid	Virus/Phage
GB_demo_coding_vs_intergenomic_seqs	GB demo coding vs intergenomic seqs	katarinagresova_Genomic_Benchmarks_demo_coding_vs_intergenomic_seqs	Coding/NC
iDHS_DNase_I	iDHS DNase I	iDHS-EL_DNase_I	Chromatin Acc.