Extended Data Fig. 1: Evoracle model properties.
From: Reconstruction of evolving gene variants and fitness from short sequencing reads
a, Regularization strategies. Comparison of loss incurred by L2 norm, variance, normalized statistical skew, and unnormalized statistical skew (our skew) regularizers for distributions of three variables. b, Synthetic data to demonstrate the utility of the skew regularizer. The top left graph shows a ground-truth simulated population containing only a wild-type genotype and a double mutant. Observed single-mutation frequencies from the ground-truth simulation were used by Evoracle to infer full-length genotype trajectories of the wild-type genotype, both single mutants, and the double mutant. Evoracle was performed with varying values of beta (top right, bottom left, and bottom right). When beta is higher, Evoracle more correctly infers the ground-truth trajectories. Inferred genotype frequencies are plotted with a small jitter to show overlapping lines clearly. c, Robustness to hyperparameters. Performance while varying hyperparameters alpha and beta for Cry1Ac data. Reported statistics summarize performance across ten replicates with random parameter initializations.
