Classification and Visualization of Genotype x Phenotype Interactions in Biomass Sorghum
We introduce a simple approach to understanding the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. The pipeline involves training deep convolutional neural networks (CNNs) to differentiate between images of plants with reference and alternate versions of various SNPs, and then using visualization approaches to highlight what the classification networks key on. We demonstrate the capacity of deep CNNs at performing this classification task, and show the utility of these visualizations on RGB imagery of biomass sorghum captured by the TERRA-REF gantry. We focus on several different genetic markers with known phenotypic expression, and discuss the possibilities of using this approach to uncover genotype x phenotype relationships.
Code (0)
등록된 구현이 없습니다.
Tasks
ClassificationSimilar Papers 제목 키워드 기반
Inferring genotype-phenotype maps using attention models
Predicting phenotype from genotype is a central challenge in genetics. Traditional approaches in quantitative genetics typically analyze this problem using methods based on linear regression. These methods generally assu…
Transfer LearningSG×P : A Sorghum Genotype × Phenotype Prediction Dataset and Benchmark
Large scale field-phenotyping approaches have the potential to solve important questions about the relationship of plant genotype to plant phenotype. Computational approaches to measuring the phenotype (the observable p…
Significance and Stability Analysis of Gene-Environment Interaction using RGxEStat
Genotype-by-Environment (GxE) interactions influence the performance of genotypes across diverse environments, reducing the predictability of phenotypes in target environments. In-depth analysis of GxE interactions facil…
Evolutionary Shaping of Low-Dimensional Path Facilitates Robust and Plastic Switching Between Phenotypes
Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is es…
Integrating Hypertension Phenotype and Genotype with Hybrid Non-negative Matrix Factorization
Hypertension is a heterogeneous syndrome in need of improved subtyping using phenotypic and genetic measurements so that patients in different subtypes share similar pathophysiologic mechanisms and respond more uniformly…