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Growth rate predictor
Predicting a population's growth rate from genetic data with an MLP and a CNN trained on simulated populations.
Till it's ready, here's the GitHub repo: github.com/simran-malik/growth-rate-predictor ↗
StackPython · PyTorch · msprime
What it is
A pipeline that simulates populations with the msprime coalescent simulator, turns each one into a matrix of genetic variants (SNPs), and trains two models to predict how fast the population was growing: a small MLP on summary statistics (the site frequency spectrum) and a 2-D CNN on the full SNP matrix.