tags:
- DNA
- Genomics
- Plants
pretty_name: Plant Genomic Benchmark
license: cc-by-nc-sa-4.0
Dataset Overview
This dataset features the 8 evaluation tasks presented in the AgroNT (A Foundational Large Language Model for Edible Plant Genomes) paper. The tasks cover single output regression, multi output regression, binary classification, and multi-label classification which aim to provide a comprehensive plant genomics benchmark. Additionally, we provide results from in silico saturation mutagenesis analysis of sequences from the cassava genome, assessing the impact of >10 million mutations on gene expression levels and enhancer elements. See the ISM section below for details regarding the data from this analysis.
| Name | # of Datasets(Species) | Task Type | Sequence Length (base pair) |
|---|---|---|---|
| Polyadenylation | 6 | Binary Classification | 400 |
| Splice Site | 2 | Binary Classification | 398 |
| LncRNA | 6 | Binary Classification | 101-6000 |
| Promoter Strength | 2 | Single Variable Regression | 170 |
| Terminator Strength | 2 | Single Variable Regression | 170 |
| Chromatin Accessibility | 7 | Multi-label Classification | 1000 |
| Gene Expression | 6 | Multi-Variable Regression | 6000 |
| Enhancer Region | 1 | Binary Classification | 1000 |
Dataset Sizes
| Task Name | # Train Samples | # Validation Samples | # Test Samples |
|---|---|---|---|
| poly_a.arabidopsis_thaliana | 170835 | --- | 30384 |
| poly_a.oryza_sativa_indica_group | 98139 | --- | 16776 |
| poly_a.trifolium_pratense | 111138 | --- | 13746 |
| poly_a.medicago_truncatula | 47277 | --- | 8850 |
| poly_a.chlamydomonas_reinhardtii | 90378 | --- | 10542 |
| poly_a.oryza_sativa_japonica_group | 120621 | --- | 20232 |
| splicing.arabidopsis_thaliana_donor | 2588034 | --- | 377873 |
| splicing.arabidopsis_thaliana_acceptor | 1704844 | --- | 250084 |
| lncrna.m_esculenta | 4934 | --- | 360 |
| lncrna.z_mays | 8423 | --- | 1629 |
| lncrna.g_max | 11430 | --- | 490 |
| lncrna.s_lycopersicum | 7274 | --- | 1072 |
| lncrna.t_aestivum | 11252 | --- | 1810 |
| lncrna.s_bicolor | 8654 | --- | 734 |
| promoter_strength.leaf | 58179 | 6825 | 7154 |
| promoter_strength.protoplast | 61051 | 7162 | 7595 |
| terminator_strength.leaf | 43294 | 5309 | 4806 |
| terminator_strength.protoplast | 43289 | 5309 | 4811 |
| gene_exp.glycine_max | 47136 | 4803 | 4803 |
| gene_exp.oryza_sativa | 31244 | 3702 | 3702 |
| gene_exp.solanum_lycopersicum | 27321 | 3827 | 3827 |
| gene_exp.zea_mays | 34493 | 4483 | 4483 |
| gene_exp.arabidopsis_thaliana | 25731 | 3401 | 3402 |
| chromatin_access.oryza_sativa_MH63_RS2 | 5120000 | 14848 | 14848 |
| chromatin_access.setaria_italica | 5120000 | 19968 | 19968 |
| chromatin_access.oryza_sativa_ZS97_RS2 | 5120000 | 14848 | 14848 |
| chromatin_access.arabidopis_thaliana | 5120000 | 9984 | 9984 |
| chromatin_access.brachypodium_distachyon | 5120000 | 14848 | 14848 |
| chromatin_access.sorghum_bicolor | 5120000 | 29952 | 29952 |
| chromatin_access.zea_mays | 6400000 | 79872 | 79872 |
| pro_seq.m_esculenta | 16852 | 1229 | 812 |
*** It is important to note that fine-tuning for lncrna was carried out using all datasets in a single training. The reason for this is that the datasets are small and combining them helped to improve learning.
Example Usage
from datasets import load_dataset
task_name='terminator_strength.protoplast' # one of the task names from the above table
dataset = load_dataset("InstaDeepAI/plant-genomic-benchmark",task_name=task_name)
In Silico Saturation Mutagensis
File structure for: ISM_Tables/Mesculenta_305_v6_PROseq_ISM_LOG2FC.txt.gz
Intergenic enhancer regions based on Lozano et al. 2021 (https://pubmed.ncbi.nlm.nih.gov/34499719/)
Genome version: Manihot esculenta reference genome v6.1 from Phytozome
CHR: Chromosome
POS: Physical position (bp)
REF: Reference allele
ALT: Alternative allele
LOG2FC: Log fold change in Intergenic enhancer probability (log2(p_mutated_sequence / p_original_sequence))
File structure for: ISM_Tables/Mesculenta_v6_GeneExpression_ISM_LOG2FC.txt.gz
Gene expression prediction based on: Wilson et al. 2016 (https://pubmed.ncbi.nlm.nih.gov/28116755/)
Genome version: Manihot esculenta reference genome v6 from Ensembl 56
CHR: Chromosome
POS: Physical position (bp)
REF: Reference allele
ALT: Alternative allele
GENE: Gene ID
STRAND: Gene strand
TISSUE: Tissue type (Acronyms detailed in Figure 1 of Wilson et al.)
LOG2FC: Gene expression log fold change (log2(gene_exp_mutated_sequence / gene_exp_original_sequence))
Data source for Figures 2-8
File structure for: Figures/Figure[FIGURE_NUMBER]_panel[PANEL_LETTER].txt
Text files containing the data used to plot Figures 2 to 8 from Mendoza-Revilla & Trop et al., 2024. The text files are named using the following format: Figure[FIGURE_NUMBER]_panel[PANEL_LETTER].txt [FIGURE_NUMBER]: This is the number of the figure in the publication. For example, if the data corresponds to Figure 3, this part of the file name will be "Figure3". [PANEL_LETTER]: This is the letter corresponding to a specific panel within the figure. Figures often contain multiple panels labeled with letters (e.g., a, b, c). For example, if the data corresponds to panel b of Figure 3, this part of the file name will be "panelb".