zhengtong-liu / cs-m226-project

Non-linear Genetic Effects for Complex Traits

CS M226: Machine Learning for Bioinformatics

This is the repo documenting the project Non-linear Genetic Effects for Complex Traits.

Group Members:

Yu-Wei Chen, Zhengtong Liu, Jacob Wallin

Main work:

• Study Variational Inference for the Polygenetic Risk Scores models (Bayesian Networks, Spike and Slab Priors, Evidence Lower Bound, etc.);
• Modify the Biologically Annotated Neural Networks (BANNs) architecture to capture non-linear genetic effects within genes;
• Compare BANNs with Variational Inference of Polygenic Risk Scores;
• Apply Polygenetic Risk Scores models to genotype data from 1000 Genomes Project and simulated phenotype (experience with PLINK).