InstaDeepAI/NTv3_benchmark_dataset_revised

NTv3 Benchmark Dataset (revised)

Genomes, train/val/test splits and functional tracks (BigWig) of the revised NTv3 benchmark: 155 tracks over 11 species. The benchmark fine-tunes a model to predict every track of a species from its DNA sequence, and reports the mean Pearson correlation over the tracks of the test regions.

Dataset organization

InstaDeepAI/NTv3_benchmark_dataset_revised/
├── benchmark_metadata.tsv          # one row per track
└── <species>/
    ├── genome.fasta                # one record per chromosome
    ├── splits.bed                  # train / val / test regions
    └── functional_tracks/
        └── <file_id>.bigwig

Species

Directory	Species	Scientific name	Assembly	Tracks	Assays
arabidopsis	Arabidopsis	Arabidopsis thaliana	TAIR10	4	ribo-seq (4)
human	Human	Homo sapiens	hg38	34	PRO-cap (10), eCLIP (10), ATAC-seq (5), Histone ChIP-seq (4), total RNA-seq (3), polyA plus RNA-seq (2)
maize	Maize	Zea mays	Zm-B73-REFERENCE-NAM-5.0	8	ribo-seq (8)
rice	Rice	Oryza sativa	IRGSP-1.0	14	ribo-seq (14)
tomato	Tomato	Solanum lycopersicum	SL3	20	RNA-seq (13), ATAC-seq (7)
cattle	Cattle	Bos taurus	ARS-UCD1.2	30	Histone ChIP-seq (12), ATAC-seq (7), TF ChIP-seq (6), RNA-seq (5)
fission_yeast	Fission yeast	Schizosaccharomyces pombe	ASM294v2	7	ATAC-seq (5), RNA-seq (2)
malaria_parasite	Malaria parasite	Plasmodium falciparum	GCA000002765v3	7	ATAC-seq (4), RNA-seq (3)
rat	Rat	Rattus norvegicus	mRatBN7	12	RNA-seq (9), ATAC-seq (3)
soil_amoeba	Soil amoeba	Dictyostelium discoideum	dicty_2.7	7	RNA-seq (7)
yeast	Yeast	Saccharomyces cerevisiae	R64	12	RNA-seq (7), ATAC-seq (5)

Files

• genome.fasta: the reference genome. Record names match the chromosome names of splits.bed and of the BigWig files.
• splits.bed: tab-separated, no header, columns chrom, start, end, split (train, val or test), 0-based half-open. The regions do not overlap, and each one belongs to a single split.
• functional_tracks/<file_id>.bigwig: per-base signal, read with pyBigWig.
• benchmark_metadata.tsv: one row per track, with columns
  • file_id: name of the BigWig file,
  • species_common_name: the species directory,
  • species_name, file_assembly,
  • mean, std: genome-wide statistics of the track,
  • assay: experiment type,
  • description: biosample and assay of the track.

Target scaling used in the benchmark

Targets are divided by the track's genome-wide mean, tracks whose assay contains RNA-seq are raised to the power 0.75, and values above 10 are soft-clipped. Input sequences are upper-cased and any character outside ACGTN is replaced by N.

Download

from huggingface_hub import hf_hub_download, snapshot_download

# One file
bigwig_path = hf_hub_download(
    repo_id="InstaDeepAI/NTv3_benchmark_dataset_revised",
    filename="cattle/functional_tracks/ERR1464183.bigwig",
    repo_type="dataset",
)

# One species
local_dir = snapshot_download(
    repo_id="InstaDeepAI/NTv3_benchmark_dataset_revised",
    repo_type="dataset",
    allow_patterns=["benchmark_metadata.tsv", "yeast/*"],
)

Tracks

Arabidopsis (arabidopsis, TAIR10)

file_id	assay	description
SRR13808079	ribo-seq	flower_mature_riboseq
SRR13808080	ribo-seq	flower_mature_riboseq_2
SRR13808081	ribo-seq	fruit_mature_riboseq
SRR13808084	ribo-seq	root_mature_riboseq

Human (human, hg38)

file_id	assay	description
ENCSR628PLS	ATAC-seq	GM18861_chromatin_accessibility
ENCSR487QSB	ATAC-seq	GM18907_chromatin_accessibility
ENCSR410DWV	ATAC-seq	motor_neuron_chromatin_accessibility
ENCSR325NFE	ATAC-seq	bile_duct_chromatin_accessibility
ENCSR814RGG	ATAC-seq	ureter_chromatin_accessibility
ENCSR863PSM	Histone ChIP-seq	BLaER1_H3K4me1
ENCSR682BFG	Histone ChIP-seq	motor_neuron_H3K4me1
ENCSR754DRC	Histone ChIP-seq	motor_neuron_H3K27ac
ENCSR962OTG	Histone ChIP-seq	motor_neuron_H3K4me3
ENCSR046BCI_M	PRO-cap	A673_PROcap_minus
ENCSR046BCI_P	PRO-cap	A673_PROcap_plus
ENCSR100LIJ_M	PRO-cap	Caco-2_PROcap_minus
ENCSR100LIJ_P	PRO-cap	Caco-2_PROcap_plus
ENCSR935RNW_M	PRO-cap	Calu3_PROcap_minus
ENCSR935RNW_P	PRO-cap	Calu3_PROcap_plus
ENCSR114HGS_M	PRO-cap	K562_PROcap_minus
ENCSR114HGS_P	PRO-cap	K562_PROcap_plus
ENCSR799DGV_M	PRO-cap	MCF10A_PROcap_minus
ENCSR799DGV_P	PRO-cap	MCF10A_PROcap_plus
ENCSR154HRN_M	eCLIP	K562_HNRNPA1_eCLIP_minus
ENCSR154HRN_P	eCLIP	K562_HNRNPA1_eCLIP_plus
ENCSR249ROI_M	eCLIP	K562_HNRNPC_eCLIP_minus
ENCSR249ROI_P	eCLIP	K562_HNRNPC_eCLIP_plus
ENCSR321PWZ_M	eCLIP	K562_SRSF1_eCLIP_minus
ENCSR321PWZ_P	eCLIP	K562_SRSF1_eCLIP_plus
ENCSR484LTQ_M	eCLIP	K562_NCBP2_eCLIP_minus
ENCSR484LTQ_P	eCLIP	K562_NCBP2_eCLIP_plus
ENCSR862QCH_M	eCLIP	K562_U2AF1_eCLIP_minus
ENCSR862QCH_P	eCLIP	K562_U2AF1_eCLIP_plus
ENCSR527JGN_M	polyA plus RNA-seq	BLaER1_gene_expression_minus
ENCSR527JGN_P	polyA plus RNA-seq	BLaER1_gene_expression_plus
ENCSR701YIC	total RNA-seq	motor_neuron_gene_expression
ENCSR619DQO_M	total RNA-seq	ureter_gene_expression_minus
ENCSR619DQO_P	total RNA-seq	ureter_gene_expression_plus

Maize (maize, Zm-B73-REFERENCE-NAM-5.0)

file_id	assay	description
SRR13808051	ribo-seq	ear_V12_stage_riboseq
SRR13808052	ribo-seq	ear_V12_stage_riboseq_2
SRR13808056	ribo-seq	root_14days_riboseq
SRR13808058	ribo-seq	seedling_14days_riboseq
SRR13808059	ribo-seq	stem_14days_riboseq
SRR13808061	ribo-seq	stem_14days_riboseq_2
SRR13808062	ribo-seq	tassel_V12_stage_riboseq
SRR13808063	ribo-seq	tassel_V12_stage_riboseq_2

Rice (rice, IRGSP-1.0)

file_id	assay	description
SRR13808067	ribo-seq	leaf_booting_stage_riboseq
SRR13808068	ribo-seq	root_V2_stage_riboseq
SRR13808069	ribo-seq	seedling_V2_stage_riboseq
SRR13808070	ribo-seq	sheath_V2_stage_riboseq
SRR13808072	ribo-seq	sheath_V2_stage_riboseq_2
SRR13808073	ribo-seq	sheath_booting_stage_riboseq
SRR13808074	ribo-seq	sheath_booting_stage_riboseq_2
SRR13808075	ribo-seq	spikelet_booting_stage_riboseq
SRR13808076	ribo-seq	spikelet_booting_stage_riboseq_2
SRR13808077	ribo-seq	stem_booting_stage_riboseq
SRR13808078	ribo-seq	stem_booting_stage_riboseq_2
SRR13808064	ribo-seq	leaf_V2_stage_riboseq
SRR13808065	ribo-seq	leaf_V2_stage_riboseq_2
SRR13808066	ribo-seq	leaf_booting_stage_riboseq_2

Tomato (tomato, SL3)

file_id	assay	description
SRX27799703	ATAC-seq	fruit_0DPA_chromatin_accessibility
SRX27799731	ATAC-seq	fruit_10DPA_chromatin_accessibility
SRX27799719	ATAC-seq	fruit_3DPA_chromatin_accessibility
SRX27799727	ATAC-seq	fruit_5DPA_chromatin_accessibility
SRX27799722	ATAC-seq	fruit_3DBA_chromatin_accessibility
SRX27799718	ATAC-seq	fruit_7DPA_chromatin_accessibility
SRX27799733	ATAC-seq	leaf_chromatin_accessibility
SRX29291448	RNA-seq	fruit_10DPA_MicroTom_gene_expression
SRX29291447	RNA-seq	fruit_10DPA_MicroTom_gene_expression_2
SRX29291446	RNA-seq	fruit_10DPA_MicroTom_gene_expression_3
SRX29291445	RNA-seq	fruit_15DPA_Wild_LA1781_gene_expression
SRX29291444	RNA-seq	fruit_5DPA_MicroTom_gene_expression
SRX29291443	RNA-seq	fruit_5DPA_MicroTom_gene_expression_2
SRX29291442	RNA-seq	fruit_15DPA_Wild_LA1781_gene_expression_2
SRX29291441	RNA-seq	fruit_5DPA_MicroTom_gene_expression_3
SRX29291440	RNA-seq	fruit_0DPA_MicroTom_gene_expression
SRX29291439	RNA-seq	fruit_0DPA_MicroTom_gene_expression_2
SRX29291438	RNA-seq	fruit_0DPA_MicroTom_gene_expression_3
SRX29291431	RNA-seq	fruit_15DPA_MicroTom_gene_expression
SRX29291430	RNA-seq	fruit_15DPA_MicroTom_gene_expression_2

Cattle (cattle, ARS-UCD1.2)

file_id	assay	description
ERR1464183	RNA-seq	spleen_gene_expression
ERR1464180	RNA-seq	left_lung_lobe_gene_expression
ERR1464175	RNA-seq	hypothalamus_gene_expression
ERR2664213	RNA-seq	CD8_gene_expression
ERR1464174	RNA-seq	frontal_cortex_gene_expression
SRX9176795	ATAC-seq	lung_chromatin_accessibility
ERX2628478	ATAC-seq	cd4_chromatin_accessibility
ERX2628481	ATAC-seq	cd8_chromatin_accessibility
SRX5649072	ATAC-seq	rumen_epithelial_cells_chromatin_accessibility
SRX9176799	ATAC-seq	skeletal_muscle_chromatin_accessibility
SRX9176803	ATAC-seq	spleen_chromatin_accessibility
SRX7703304	ATAC-seq	embryo_day_14_elongating_chromatin_accessibility
ERX5798621	Histone ChIP-seq	hypothalamus_H3K4Me3
ERX5798616	Histone ChIP-seq	frontal_cortex_H3K4Me3
ERX5798633	Histone ChIP-seq	semimembranosus_muscle_H3K4Me3
ERX4795023	Histone ChIP-seq	liver_H3K27Me3
ERX5798749	Histone ChIP-seq	semimembranosus_muscle_H3K4Me1
ERX4794967	Histone ChIP-seq	renal_medulla_H3K4Me1
ERX4795038	Histone ChIP-seq	mammary_gland_H3K27Ac
ERX5798687	Histone ChIP-seq	semimembranosus_muscle_H3K27Ac
ERX4794981	Histone ChIP-seq	lung_H3K27Ac
ERX4795026	Histone ChIP-seq	liver_H3K4Me1
ERX4794986	Histone ChIP-seq	mammary_gland_H3K27Me3
ERX5798711	Histone ChIP-seq	semimembranosus_muscle_H3K27Me3
ERX4795019	TF ChIP-seq	renal_medulla_CTCF
ERX4795059	TF ChIP-seq	kidney_CTCF
ERX4794984	TF ChIP-seq	lung_CTCF
ERX4795088	TF ChIP-seq	spleen_CTCF
ERX3800751	TF ChIP-seq	cerebellum_CTCF
ERX4795054	TF ChIP-seq	heart_CTCF

Fission yeast (fission_yeast, ASM294v2)

file_id	assay	description
SRX893731	ATAC-seq	1m_5min_chromatin_accessibility
SRX893735	ATAC-seq	20m_20min_chromatin_accessibility
SRX893733	ATAC-seq	20m_5min_chromatin_accessibility
SRX893734	ATAC-seq	5m_20min_chromatin_accessibility
SRX893732	ATAC-seq	5m_5min_chromatin_accessibility
ERR1162944	RNA-seq	grown_with_nitrogen_gene_expression
ERR1162946	RNA-seq	grown_without_nitrogen_gene_expression

Malaria parasite (malaria_parasite, GCA000002765v3)

file_id	assay	description
SRR16019126	RNA-seq	ring_10-15_hpi_gene_expression
SRR16019133	RNA-seq	schizont_40-45_hpi_gene_expression
SRR16019130	RNA-seq	trophozoite_25-30_hpi_gene_expression
SRX5494567	ATAC-seq	stage_10hpi_chromatin_accessibility
SRX5494566	ATAC-seq	stage_20hpi_chromatin_accessibility
SRX5494565	ATAC-seq	stage_30hpi_chromatin_accessibility
SRX5494564	ATAC-seq	stage_40hpi_chromatin_accessibility

Rat (rat, mRatBN7)

file_id	assay	description
SRR594428	RNA-seq	brain_gene_expression
SRR594429	RNA-seq	colon_gene_expression
SRR594430	RNA-seq	heart_gene_expression
SRR594431	RNA-seq	kidney_gene_expression
SRR594432	RNA-seq	liver_gene_expression
SRR594433	RNA-seq	lung_gene_expression
SRR594434	RNA-seq	skeletal_muscle_gene_expression
SRR594435	RNA-seq	spleen_gene_expression
SRR594436	RNA-seq	testes_gene_expression
SRX9339411	ATAC-seq	liver_chromatin_accessibility
SRX9339415	ATAC-seq	primary_motor_cortex_m1_chromatin_accessibility
SRX9339416	ATAC-seq	striatum_chromatin_accessibility

Soil amoeba (soil_amoeba, dicty_2.7)

file_id	assay	description
SRR12055126	RNA-seq	dev_stage_hr00_gene_expression
SRR12055127	RNA-seq	dev_stage_hr04_gene_expression
SRR12055128	RNA-seq	dev_stage_hr08_gene_expression
SRR12055129	RNA-seq	dev_stage_hr12_gene_expression
SRR12055130	RNA-seq	dev_stage_hr16_gene_expression
SRR12055131	RNA-seq	dev_stage_hr20_gene_expression
SRR12055132	RNA-seq	dev_stage_hr24_gene_expression

Yeast (yeast, R64)

file_id	assay	description
SRX893741	ATAC-seq	0.6_m_nacl_15_minutes_chromatin_accessibility
SRX893743	ATAC-seq	0.6_m_nacl_30_minutes_chromatin_accessibility
SRX893745	ATAC-seq	0.6_m_nacl_45_minutes_chromatin_accessibility
SRX893747	ATAC-seq	0.6_m_nacl_60_minutes_chromatin_accessibility
SRX893737	ATAC-seq	chromatin_accessibility
ERR3772438	RNA-seq	ethanol_cycle_102min_gene_expression
ERR3772439	RNA-seq	ethanol_cycle_132min_gene_expression
ERR3772440	RNA-seq	ethanol_cycle_142min_gene_expression
ERR3772434	RNA-seq	ethanol_cycle_14min_gene_expression
ERR3772428	RNA-seq	ethanol_cycle_162min_gene_expression
ERR3772436	RNA-seq	ethanol_cycle_20min_gene_expression
ERR3772430	RNA-seq	ethanol_cycle_92min_gene_expression

Changes from InstaDeepAI/NTv3_benchmark_dataset

• Genome annotation BED files (exon, intron, splice acceptor, start codon) are removed: the benchmark only covers functional tracks.
• Chicken is removed.
• Cattle now uses the ARS-UCD1.2 assembly (the previous genome.fasta was ARS-UCD2.0) with its benchmark splits, and gains its 30 functional tracks.
• New species: fission yeast, malaria parasite, rat, soil amoeba and yeast.
• benchmark_metadata.tsv gains a description column.