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## Dataset Overview
This dataset features the 7 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.
| Task 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 |
| Chromatin Accessibility | 7 | Multi-label Classification | 1000 |
| Gene Expression | 6 | Multi-Variable Regression | 6000 |
| Ehancer Region | 1 | Binary Classification | 1000 |
## Dataset Sizes
| Config 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|
|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|
|pro_seq.m_esculenta|16852|1229|812|
## In Silico Saturation Mutagensis
### File structure for: Mesculenta_305_v6_PROseq_ISM_LOG2FC.txt.gz
Intergenic enhancer regions based on Lozano et al. 2021 (https://pubmed.ncbi.nlm.nih.gov/34499719/) <br>
Genome version: Manihot esculenta reference genome v6.1 from Phytozome <br>
CHR: Chromosome <br>
POS: Physical position (bp) <br>
REF: Reference allele <br>
ALT: Alternative allele <br>
LOG2FC: Log fold change in Intergenic enhancer probability (log2(p_mutated_sequence / p_original_sequence)) <br>
### File structure for: Mesculenta_v6_GeneExpression_ISM_LOG2FC.txt.gz
Gene expression prediction based on: Wilson et al. 2016 (https://pubmed.ncbi.nlm.nih.gov/28116755/) <br>
Genome version: Manihot esculenta reference genome v6 from Ensembl 56 <br>
CHR: Chromosome <br>
POS: Physical position (bp) <br>
REF: Reference allele <br>
ALT: Alternative allele <br>
GENE: Gene ID <br>
STRAND: Gene strand <br>
TISSUE: Tissue type (Acronyms detailed in Figure 1 of Wilson et al.) <br>
LOG2FC: Gene expression log fold change (log2(gene_exp_mutated_sequence / gene_exp_original_sequence)) <br> |