| | --- |
| | 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 |
| | ```python |
| | 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/) <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: 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/) <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> |
