Update README.md

README.md

@@ -1,4 +1,52 @@
-## File description for: Mesculenta_305_v6_PROseq_ISM_LOG2FC.txt.gz
+
+## 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
+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> 
@@ -7,7 +55,7 @@ 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 description for: Mesculenta_v6_GeneExpression_ISM_LOG2FC.txt.gz
+### 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>