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darlednik/geneb-tasks

Dataset

GENEB — Genomic Embedding Benchmark (task data)

4

15 commits

2 linked in READMEs

updated Jun 9, 2026

See the code

README

GENEB — Genomic Embedding Benchmark (task data)

Task-level sequence classification data for GENEB, a multi-task benchmark for DNA sequence encoders introduced in the paper: GENEB: Why Genomic Models Are Hard to Compare.

GENEB evaluates frozen representations from 40 genomic foundation models across 100 tasks in 13 functional categories using a unified probing-based protocol. This repository release contains train and test partitions only.

Sample Usage

To sync the GENEB task data locally using the reference tools:

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

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):

ItemSpecification
Tasks100
Functional categories13
Reporting regimesfull, 10shot, 1shot
MetricsMCC, Acc, F1 (primary: MCC)
Probelogistic_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

CategoryTasks
Histone Mod.30
Promoters22
Enhancers8
DNA Methyl.8
Splice Sites7
lncRNA6
Mouse Enh.5
TF Binding5
Species Clf.3
Regulatory2
Virus/Phage2
Coding/NC1
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.

Task index

Subset (config_name)Short labelTask identifierCategory
NT_H3NT H3InstaDeepAI_nucleotide_transformer_downstream_tasks_H3Histone Mod.
NT_H3K14acNT H3K14acInstaDeepAI_nucleotide_transformer_downstream_tasks_H3K14acHistone Mod.
NT_H3K36me3NT H3K36me3InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K36me3Histone Mod.
NT_H3K4me1NT H3K4me1InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K4me1Histone Mod.
NT_H3K4me2NT H3K4me2InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K4me2Histone Mod.
NT_H3K4me3NT H3K4me3InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K4me3Histone Mod.
NT_H3K79me3NT H3K79me3InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K79me3Histone Mod.
NT_H3K9acNT H3K9acInstaDeepAI_nucleotide_transformer_downstream_tasks_H3K9acHistone Mod.
NT_H4NT H4InstaDeepAI_nucleotide_transformer_downstream_tasks_H4Histone Mod.
NT_H4acNT H4acInstaDeepAI_nucleotide_transformer_downstream_tasks_H4acHistone Mod.
NT-rev_H2AFZNT-rev H2AFZInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H2AFZHistone Mod.
NT-rev_H3K27acNT-rev H3K27acInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K27acHistone Mod.
NT-rev_H3K27me3NT-rev H3K27me3InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K27me3Histone Mod.
NT-rev_H3K36me3NT-rev H3K36me3InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K36me3Histone Mod.
NT-rev_H3K4me1NT-rev H3K4me1InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K4me1Histone Mod.
NT-rev_H3K4me2NT-rev H3K4me2InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K4me2Histone Mod.
NT-rev_H3K4me3NT-rev H3K4me3InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K4me3Histone Mod.
NT-rev_H3K9acNT-rev H3K9acInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K9acHistone Mod.
NT-rev_H3K9me3NT-rev H3K9me3InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K9me3Histone Mod.
NT-rev_H4K20me1NT-rev H4K20me1InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H4K20me1Histone Mod.
GUE-emp_H3GUE-emp H3leannmlindsey_GUE_emp_H3Histone Mod.
GUE-emp_H3K14acGUE-emp H3K14acleannmlindsey_GUE_emp_H3K14acHistone Mod.
GUE-emp_H3K36me3GUE-emp H3K36me3leannmlindsey_GUE_emp_H3K36me3Histone Mod.
GUE-emp_H3K4me1GUE-emp H3K4me1leannmlindsey_GUE_emp_H3K4me1Histone Mod.
GUE-emp_H3K4me2GUE-emp H3K4me2leannmlindsey_GUE_emp_H3K4me2Histone Mod.
GUE-emp_H3K4me3GUE-emp H3K4me3leannmlindsey_GUE_emp_H3K4me3Histone Mod.
GUE-emp_H3K79me3GUE-emp H3K79me3leannmlindsey_GUE_emp_H3K79me3Histone Mod.
GUE-emp_H3K9acGUE-emp H3K9acleannmlindsey_GUE_emp_H3K9acHistone Mod.
GUE-emp_H4GUE-emp H4leannmlindsey_GUE_emp_H4Histone Mod.
GUE-emp_H4acGUE-emp H4acleannmlindsey_GUE_emp_H4acHistone Mod.
NT_promoter_allNT promoter allInstaDeepAI_nucleotide_transformer_downstream_tasks_promoter_allPromoters
NT_promoter_no_tataNT promoter no tataInstaDeepAI_nucleotide_transformer_downstream_tasks_promoter_no_tataPromoters
NT_promoter_tataNT promoter tataInstaDeepAI_nucleotide_transformer_downstream_tasks_promoter_tataPromoters
NT-rev_promoter_allNT-rev promoter allInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_promoter_allPromoters
NT-rev_promoter_no_tataNT-rev promoter no tataInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_promoter_no_tataPromoters
NT-rev_promoter_tataNT-rev promoter tataInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_promoter_tataPromoters
PGB_pro_seq.m_esculentaPGB pro seq.m esculentaInstaDeepAI_plant-genomic-benchmark_pro_seq.m_esculentaPromoters
iPro_Arabidopsis_NonTATAiPro Arabidopsis NonTATAiPro-WAEL_Promoter_Arabidopsis_NonTATAPromoters
iPro_Arabidopsis_TATAiPro Arabidopsis TATAiPro-WAEL_Promoter_Arabidopsis_TATAPromoters
iPro_B_amyloliquefaciensiPro B amyloliquefaciensiPro-WAEL_Promoter_B_amyloliquefaciensPromoters
iPro_GM12878iPro GM12878iPro-WAEL_Promoter_GM12878Promoters
iPro_HUVECiPro HUVECiPro-WAEL_Promoter_HUVECPromoters
iPro_Hela-S3iPro Hela-S3iPro-WAEL_Promoter_Hela-S3Promoters
iPro_NHEKiPro NHEKiPro-WAEL_Promoter_NHEKPromoters
iPro_R_capsulatusiPro R capsulatusiPro-WAEL_Promoter_R_capsulatusPromoters
GB_human_nontata_promotersGB human nontata promoterskatarinagresova_Genomic_Benchmarks_human_nontata_promotersPromoters
GUE_prom_300_allGUE prom 300 allleannmlindsey_GUE_prom_300_allPromoters
GUE_prom_300_notataGUE prom 300 notataleannmlindsey_GUE_prom_300_notataPromoters
GUE_prom_300_tataGUE prom 300 tataleannmlindsey_GUE_prom_300_tataPromoters
GUE_prom_core_allGUE prom core allleannmlindsey_GUE_prom_core_allPromoters
GUE_prom_core_notataGUE prom core notataleannmlindsey_GUE_prom_core_notataPromoters
GUE_prom_core_tataGUE prom core tataleannmlindsey_GUE_prom_core_tataPromoters
NT_enhancersNT enhancersInstaDeepAI_nucleotide_transformer_downstream_tasks_enhancersEnhancers
NT_enhancers_typesNT enhancers typesInstaDeepAI_nucleotide_transformer_downstream_tasks_enhancers_typesEnhancers
NT-rev_enhancersNT-rev enhancersInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_enhancersEnhancers
NT-rev_enhancers_typesNT-rev enhancers typesInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_enhancers_typesEnhancers
GB_drosophila_enhancers_starkGB drosophila enhancers starkkatarinagresova_Genomic_Benchmarks_drosophila_enhancers_starkEnhancers
GB_dummy_mouse_enhancers_ensemblGB dummy mouse enhancers ensemblkatarinagresova_Genomic_Benchmarks_dummy_mouse_enhancers_ensemblEnhancers
GB_human_enhancers_cohnGB human enhancers cohnkatarinagresova_Genomic_Benchmarks_human_enhancers_cohnEnhancers
GB_human_enhancers_ensemblGB human enhancers ensemblkatarinagresova_Genomic_Benchmarks_human_enhancers_ensemblEnhancers
4mC_A.thaliana_4mC4mC A.thaliana 4mCdeep4mc_A.thaliana_4mCDNA Methyl.
4mC_C.elegans_4mC4mC C.elegans 4mCdeep4mc_C.elegans_4mCDNA Methyl.
4mC_D.melanogaster_4mC4mC D.melanogaster 4mCdeep4mc_D.melanogaster_4mCDNA Methyl.
4mC_E.coli_4mC4mC E.coli 4mCdeep4mc_E.coli_4mCDNA Methyl.
4mC_G.pickeringii_4mC4mC G.pickeringii 4mCdeep4mc_G.pickeringii_4mCDNA Methyl.
4mC_G.subterraneus_4mC4mC G.subterraneus 4mCdeep4mc_G.subterraneus_4mCDNA Methyl.
iDNA_5mCiDNA 5mCiDNA_ABF_5mCDNA Methyl.
iDNA_6mAiDNA 6mAiDNA_ABF_6mADNA Methyl.
NT-rev_splice_sites_acceptorsNT-rev splice sites acceptorsInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_splice_sites_acceptorsSplice Sites
NT-rev_splice_sites_allNT-rev splice sites allInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_splice_sites_allSplice Sites
NT-rev_splice_sites_donorsNT-rev splice sites donorsInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_splice_sites_donorsSplice Sites
NT_splice_sites_acceptorsNT splice sites acceptorsInstaDeepAI_nucleotide_transformer_downstream_tasks_splice_sites_acceptorsSplice Sites
NT_splice_sites_allNT splice sites allInstaDeepAI_nucleotide_transformer_downstream_tasks_splice_sites_allSplice Sites
NT_splice_sites_donorsNT splice sites donorsInstaDeepAI_nucleotide_transformer_downstream_tasks_splice_sites_donorsSplice Sites
GUE_splice_reconstructedGUE splice reconstructedleannmlindsey_GUE_splice_reconstructedSplice Sites
PGB_lncrna.g_maxPGB lncrna.g maxInstaDeepAI_plant-genomic-benchmark_lncrna.g_maxlncRNA
PGB_lncrna.m_esculentaPGB lncrna.m esculentaInstaDeepAI_plant-genomic-benchmark_lncrna.m_esculentalncRNA
PGB_lncrna.s_bicolorPGB lncrna.s bicolorInstaDeepAI_plant-genomic-benchmark_lncrna.s_bicolorlncRNA
PGB_lncrna.s_lycopersicumPGB lncrna.s lycopersicumInstaDeepAI_plant-genomic-benchmark_lncrna.s_lycopersicumlncRNA
PGB_lncrna.t_aestivumPGB lncrna.t aestivumInstaDeepAI_plant-genomic-benchmark_lncrna.t_aestivumlncRNA
PGB_lncrna.z_maysPGB lncrna.z maysInstaDeepAI_plant-genomic-benchmark_lncrna.z_mayslncRNA
GUE_mouse_0GUE mouse 0leannmlindsey_GUE_mouse_0Mouse Enh.
GUE_mouse_1GUE mouse 1leannmlindsey_GUE_mouse_1Mouse Enh.
GUE_mouse_2GUE mouse 2leannmlindsey_GUE_mouse_2Mouse Enh.
GUE_mouse_3GUE mouse 3leannmlindsey_GUE_mouse_3Mouse Enh.
GUE_mouse_4GUE mouse 4leannmlindsey_GUE_mouse_4Mouse Enh.
GUE_human_tf_0GUE human tf 0leannmlindsey_GUE_human_tf_0TF Binding
GUE_human_tf_1GUE human tf 1leannmlindsey_GUE_human_tf_1TF Binding
GUE_human_tf_2GUE human tf 2leannmlindsey_GUE_human_tf_2TF Binding
GUE_human_tf_3GUE human tf 3leannmlindsey_GUE_human_tf_3TF Binding
GUE_human_tf_4GUE human tf 4leannmlindsey_GUE_human_tf_4TF Binding
GB_demo_human_or_wormGB demo human or wormkatarinagresova_Genomic_Benchmarks_demo_human_or_wormSpecies Clf.
GUE_fungi_species_20GUE fungi species 20leannmlindsey_GUE_fungi_species_20Species Clf.
GUE_virus_species_40GUE virus species 40leannmlindsey_GUE_virus_species_40Species Clf.
GB_human_ensembl_regulatoryGB human ensembl regulatorykatarinagresova_Genomic_Benchmarks_human_ensembl_regulatoryRegulatory
GB_human_ocr_ensemblGB human ocr ensemblkatarinagresova_Genomic_Benchmarks_human_ocr_ensemblRegulatory
GUE_phage_fragmentsGUE phage fragmentsleannmlindsey_GUE_phage_fragmentsVirus/Phage
GUE_virus_covidGUE virus covidleannmlindsey_GUE_virus_covidVirus/Phage
GB_demo_coding_vs_intergenomic_seqsGB demo coding vs intergenomic seqskatarinagresova_Genomic_Benchmarks_demo_coding_vs_intergenomic_seqsCoding/NC
iDHS_DNase_IiDHS DNase IiDHS-EL_DNase_IChromatin Acc.

Citation

@misc{ledneva2026genebgenomicmodelshard,
  title         = {GENEB: Why Genomic Models Are Hard to Compare},
  author        = {Daria Ledneva and Mikhail Nuridinov and Denis Kuznetsov},
  year          = {2026},
  eprint        = {2606.04525},
  archivePrefix = {arXiv},
  primaryClass  = {cs.CL},
  url           = {https://arxiv.org/abs/2606.04525}
}

Contact

GENEB is led and maintained by Daria Ledneva.
For questions, suggestions, or model submissions, please contact
a.ledn2026@gmail.com.

benchmark
biology
dna-language-model
genomics

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darlednik/geneb-tasks

Dataset

GENEB — Genomic Embedding Benchmark (task data)

4

15 commits

2 linked in READMEs

updated Jun 9, 2026

See the code

README

GENEB — Genomic Embedding Benchmark (task data)

Task-level sequence classification data for GENEB, a multi-task benchmark for DNA sequence encoders introduced in the paper: GENEB: Why Genomic Models Are Hard to Compare.

GENEB evaluates frozen representations from 40 genomic foundation models across 100 tasks in 13 functional categories using a unified probing-based protocol. This repository release contains train and test partitions only.

Sample Usage

To sync the GENEB task data locally using the reference tools:

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

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):

ItemSpecification
Tasks100
Functional categories13
Reporting regimesfull, 10shot, 1shot
MetricsMCC, Acc, F1 (primary: MCC)
Probelogistic_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

CategoryTasks
Histone Mod.30
Promoters22
Enhancers8
DNA Methyl.8
Splice Sites7
lncRNA6
Mouse Enh.5
TF Binding5
Species Clf.3
Regulatory2
Virus/Phage2
Coding/NC1
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.

Task index

Subset (config_name)Short labelTask identifierCategory
NT_H3NT H3InstaDeepAI_nucleotide_transformer_downstream_tasks_H3Histone Mod.
NT_H3K14acNT H3K14acInstaDeepAI_nucleotide_transformer_downstream_tasks_H3K14acHistone Mod.
NT_H3K36me3NT H3K36me3InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K36me3Histone Mod.
NT_H3K4me1NT H3K4me1InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K4me1Histone Mod.
NT_H3K4me2NT H3K4me2InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K4me2Histone Mod.
NT_H3K4me3NT H3K4me3InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K4me3Histone Mod.
NT_H3K79me3NT H3K79me3InstaDeepAI_nucleotide_transformer_downstream_tasks_H3K79me3Histone Mod.
NT_H3K9acNT H3K9acInstaDeepAI_nucleotide_transformer_downstream_tasks_H3K9acHistone Mod.
NT_H4NT H4InstaDeepAI_nucleotide_transformer_downstream_tasks_H4Histone Mod.
NT_H4acNT H4acInstaDeepAI_nucleotide_transformer_downstream_tasks_H4acHistone Mod.
NT-rev_H2AFZNT-rev H2AFZInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H2AFZHistone Mod.
NT-rev_H3K27acNT-rev H3K27acInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K27acHistone Mod.
NT-rev_H3K27me3NT-rev H3K27me3InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K27me3Histone Mod.
NT-rev_H3K36me3NT-rev H3K36me3InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K36me3Histone Mod.
NT-rev_H3K4me1NT-rev H3K4me1InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K4me1Histone Mod.
NT-rev_H3K4me2NT-rev H3K4me2InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K4me2Histone Mod.
NT-rev_H3K4me3NT-rev H3K4me3InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K4me3Histone Mod.
NT-rev_H3K9acNT-rev H3K9acInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K9acHistone Mod.
NT-rev_H3K9me3NT-rev H3K9me3InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H3K9me3Histone Mod.
NT-rev_H4K20me1NT-rev H4K20me1InstaDeepAI_nucleotide_transformer_downstream_tasks_revised_H4K20me1Histone Mod.
GUE-emp_H3GUE-emp H3leannmlindsey_GUE_emp_H3Histone Mod.
GUE-emp_H3K14acGUE-emp H3K14acleannmlindsey_GUE_emp_H3K14acHistone Mod.
GUE-emp_H3K36me3GUE-emp H3K36me3leannmlindsey_GUE_emp_H3K36me3Histone Mod.
GUE-emp_H3K4me1GUE-emp H3K4me1leannmlindsey_GUE_emp_H3K4me1Histone Mod.
GUE-emp_H3K4me2GUE-emp H3K4me2leannmlindsey_GUE_emp_H3K4me2Histone Mod.
GUE-emp_H3K4me3GUE-emp H3K4me3leannmlindsey_GUE_emp_H3K4me3Histone Mod.
GUE-emp_H3K79me3GUE-emp H3K79me3leannmlindsey_GUE_emp_H3K79me3Histone Mod.
GUE-emp_H3K9acGUE-emp H3K9acleannmlindsey_GUE_emp_H3K9acHistone Mod.
GUE-emp_H4GUE-emp H4leannmlindsey_GUE_emp_H4Histone Mod.
GUE-emp_H4acGUE-emp H4acleannmlindsey_GUE_emp_H4acHistone Mod.
NT_promoter_allNT promoter allInstaDeepAI_nucleotide_transformer_downstream_tasks_promoter_allPromoters
NT_promoter_no_tataNT promoter no tataInstaDeepAI_nucleotide_transformer_downstream_tasks_promoter_no_tataPromoters
NT_promoter_tataNT promoter tataInstaDeepAI_nucleotide_transformer_downstream_tasks_promoter_tataPromoters
NT-rev_promoter_allNT-rev promoter allInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_promoter_allPromoters
NT-rev_promoter_no_tataNT-rev promoter no tataInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_promoter_no_tataPromoters
NT-rev_promoter_tataNT-rev promoter tataInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_promoter_tataPromoters
PGB_pro_seq.m_esculentaPGB pro seq.m esculentaInstaDeepAI_plant-genomic-benchmark_pro_seq.m_esculentaPromoters
iPro_Arabidopsis_NonTATAiPro Arabidopsis NonTATAiPro-WAEL_Promoter_Arabidopsis_NonTATAPromoters
iPro_Arabidopsis_TATAiPro Arabidopsis TATAiPro-WAEL_Promoter_Arabidopsis_TATAPromoters
iPro_B_amyloliquefaciensiPro B amyloliquefaciensiPro-WAEL_Promoter_B_amyloliquefaciensPromoters
iPro_GM12878iPro GM12878iPro-WAEL_Promoter_GM12878Promoters
iPro_HUVECiPro HUVECiPro-WAEL_Promoter_HUVECPromoters
iPro_Hela-S3iPro Hela-S3iPro-WAEL_Promoter_Hela-S3Promoters
iPro_NHEKiPro NHEKiPro-WAEL_Promoter_NHEKPromoters
iPro_R_capsulatusiPro R capsulatusiPro-WAEL_Promoter_R_capsulatusPromoters
GB_human_nontata_promotersGB human nontata promoterskatarinagresova_Genomic_Benchmarks_human_nontata_promotersPromoters
GUE_prom_300_allGUE prom 300 allleannmlindsey_GUE_prom_300_allPromoters
GUE_prom_300_notataGUE prom 300 notataleannmlindsey_GUE_prom_300_notataPromoters
GUE_prom_300_tataGUE prom 300 tataleannmlindsey_GUE_prom_300_tataPromoters
GUE_prom_core_allGUE prom core allleannmlindsey_GUE_prom_core_allPromoters
GUE_prom_core_notataGUE prom core notataleannmlindsey_GUE_prom_core_notataPromoters
GUE_prom_core_tataGUE prom core tataleannmlindsey_GUE_prom_core_tataPromoters
NT_enhancersNT enhancersInstaDeepAI_nucleotide_transformer_downstream_tasks_enhancersEnhancers
NT_enhancers_typesNT enhancers typesInstaDeepAI_nucleotide_transformer_downstream_tasks_enhancers_typesEnhancers
NT-rev_enhancersNT-rev enhancersInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_enhancersEnhancers
NT-rev_enhancers_typesNT-rev enhancers typesInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_enhancers_typesEnhancers
GB_drosophila_enhancers_starkGB drosophila enhancers starkkatarinagresova_Genomic_Benchmarks_drosophila_enhancers_starkEnhancers
GB_dummy_mouse_enhancers_ensemblGB dummy mouse enhancers ensemblkatarinagresova_Genomic_Benchmarks_dummy_mouse_enhancers_ensemblEnhancers
GB_human_enhancers_cohnGB human enhancers cohnkatarinagresova_Genomic_Benchmarks_human_enhancers_cohnEnhancers
GB_human_enhancers_ensemblGB human enhancers ensemblkatarinagresova_Genomic_Benchmarks_human_enhancers_ensemblEnhancers
4mC_A.thaliana_4mC4mC A.thaliana 4mCdeep4mc_A.thaliana_4mCDNA Methyl.
4mC_C.elegans_4mC4mC C.elegans 4mCdeep4mc_C.elegans_4mCDNA Methyl.
4mC_D.melanogaster_4mC4mC D.melanogaster 4mCdeep4mc_D.melanogaster_4mCDNA Methyl.
4mC_E.coli_4mC4mC E.coli 4mCdeep4mc_E.coli_4mCDNA Methyl.
4mC_G.pickeringii_4mC4mC G.pickeringii 4mCdeep4mc_G.pickeringii_4mCDNA Methyl.
4mC_G.subterraneus_4mC4mC G.subterraneus 4mCdeep4mc_G.subterraneus_4mCDNA Methyl.
iDNA_5mCiDNA 5mCiDNA_ABF_5mCDNA Methyl.
iDNA_6mAiDNA 6mAiDNA_ABF_6mADNA Methyl.
NT-rev_splice_sites_acceptorsNT-rev splice sites acceptorsInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_splice_sites_acceptorsSplice Sites
NT-rev_splice_sites_allNT-rev splice sites allInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_splice_sites_allSplice Sites
NT-rev_splice_sites_donorsNT-rev splice sites donorsInstaDeepAI_nucleotide_transformer_downstream_tasks_revised_splice_sites_donorsSplice Sites
NT_splice_sites_acceptorsNT splice sites acceptorsInstaDeepAI_nucleotide_transformer_downstream_tasks_splice_sites_acceptorsSplice Sites
NT_splice_sites_allNT splice sites allInstaDeepAI_nucleotide_transformer_downstream_tasks_splice_sites_allSplice Sites
NT_splice_sites_donorsNT splice sites donorsInstaDeepAI_nucleotide_transformer_downstream_tasks_splice_sites_donorsSplice Sites
GUE_splice_reconstructedGUE splice reconstructedleannmlindsey_GUE_splice_reconstructedSplice Sites
PGB_lncrna.g_maxPGB lncrna.g maxInstaDeepAI_plant-genomic-benchmark_lncrna.g_maxlncRNA
PGB_lncrna.m_esculentaPGB lncrna.m esculentaInstaDeepAI_plant-genomic-benchmark_lncrna.m_esculentalncRNA
PGB_lncrna.s_bicolorPGB lncrna.s bicolorInstaDeepAI_plant-genomic-benchmark_lncrna.s_bicolorlncRNA
PGB_lncrna.s_lycopersicumPGB lncrna.s lycopersicumInstaDeepAI_plant-genomic-benchmark_lncrna.s_lycopersicumlncRNA
PGB_lncrna.t_aestivumPGB lncrna.t aestivumInstaDeepAI_plant-genomic-benchmark_lncrna.t_aestivumlncRNA
PGB_lncrna.z_maysPGB lncrna.z maysInstaDeepAI_plant-genomic-benchmark_lncrna.z_mayslncRNA
GUE_mouse_0GUE mouse 0leannmlindsey_GUE_mouse_0Mouse Enh.
GUE_mouse_1GUE mouse 1leannmlindsey_GUE_mouse_1Mouse Enh.
GUE_mouse_2GUE mouse 2leannmlindsey_GUE_mouse_2Mouse Enh.
GUE_mouse_3GUE mouse 3leannmlindsey_GUE_mouse_3Mouse Enh.
GUE_mouse_4GUE mouse 4leannmlindsey_GUE_mouse_4Mouse Enh.
GUE_human_tf_0GUE human tf 0leannmlindsey_GUE_human_tf_0TF Binding
GUE_human_tf_1GUE human tf 1leannmlindsey_GUE_human_tf_1TF Binding
GUE_human_tf_2GUE human tf 2leannmlindsey_GUE_human_tf_2TF Binding
GUE_human_tf_3GUE human tf 3leannmlindsey_GUE_human_tf_3TF Binding
GUE_human_tf_4GUE human tf 4leannmlindsey_GUE_human_tf_4TF Binding
GB_demo_human_or_wormGB demo human or wormkatarinagresova_Genomic_Benchmarks_demo_human_or_wormSpecies Clf.
GUE_fungi_species_20GUE fungi species 20leannmlindsey_GUE_fungi_species_20Species Clf.
GUE_virus_species_40GUE virus species 40leannmlindsey_GUE_virus_species_40Species Clf.
GB_human_ensembl_regulatoryGB human ensembl regulatorykatarinagresova_Genomic_Benchmarks_human_ensembl_regulatoryRegulatory
GB_human_ocr_ensemblGB human ocr ensemblkatarinagresova_Genomic_Benchmarks_human_ocr_ensemblRegulatory
GUE_phage_fragmentsGUE phage fragmentsleannmlindsey_GUE_phage_fragmentsVirus/Phage
GUE_virus_covidGUE virus covidleannmlindsey_GUE_virus_covidVirus/Phage
GB_demo_coding_vs_intergenomic_seqsGB demo coding vs intergenomic seqskatarinagresova_Genomic_Benchmarks_demo_coding_vs_intergenomic_seqsCoding/NC
iDHS_DNase_IiDHS DNase IiDHS-EL_DNase_IChromatin Acc.

Citation

@misc{ledneva2026genebgenomicmodelshard,
  title         = {GENEB: Why Genomic Models Are Hard to Compare},
  author        = {Daria Ledneva and Mikhail Nuridinov and Denis Kuznetsov},
  year          = {2026},
  eprint        = {2606.04525},
  archivePrefix = {arXiv},
  primaryClass  = {cs.CL},
  url           = {https://arxiv.org/abs/2606.04525}
}

Contact

GENEB is led and maintained by Daria Ledneva.
For questions, suggestions, or model submissions, please contact
a.ledn2026@gmail.com.

benchmark
biology
dna-language-model
genomics

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