Blame for README.md

---
language:
  - en
pretty_name: "NTv3 benchmark dataset (revised) - Genomes & functional tracks"
tags:
  - 🧬 genomics
  - 📊 bigwig / functional tracks
  - 🎯 regression
  - ⚡ fine-tuning
  - 🧪 sequence-to-signal
  - 📐 functional-genomics
  - 🔬 bioinformatics
task_categories:
  - other
size_categories:
  - n<1K
license: cc-by-nc-4.0
---

# 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

```python
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.