Stars
Demographic inference from Ancestral Recombination Graphs (ARGs)
A framework for simulation-based inference in evolutionary biology
Geometric kernels on manifolds, meshes and graphs
Application of machine learning methods for approximate prediction of demographic history parameters by the allele-frequency spectrum
Standalone python scripts to do pairwise AFS analysis for population differentiation using Moments (http://www.genetics.org/content/early/2017/05/08/genetics.117.200493)
Two-locus selection moments (scripts to create figures in manuscript)
CHMM History-Inference ML Procedure - Infers population size histories from genomic data
Simulate genealogical trees and genomic sequence data using population genetic models
SMAC3: A Versatile Bayesian Optimization Package for Hyperparameter Optimization
Here are all the materials on our first semester project.
Supplementary code for the AISTATS 2021 paper "Matern Gaussian Processes on Graphs".
A Julia implementation of sparse Gaussian processes via path-wise doubly stochastic variational inference.
Code for efficiently sampling functions from GP(flow) posteriors
SFS-Based Demographic Inference with Inbreeding
Gaussian Process Optimization using GPy
Supplementary code for the NeurIPS 2020 paper "Matern Gaussian processes on Riemannian manifolds".
Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
Bayesian optimization for the derivation of the demographic population history
Infer demographic history with the Moran model
An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.