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Deep Learning for Population Genetic Inference

Table 6

Confusion matrix for the selection predictions, compared between random initialization (top) and autoencoder initialization (bottom), for a deep network with 6 hidden layers.

Again, ideally we would like all 1’s down the diagonal, and 0’s in the off-diagonal entries. The largest number in each row is shown in boldface. When the network is initialized randomly, almost every dataset is classified as neutral; the network has not really learned anything meaningful from the input data. The overall percentage of misclassification is 74.8% for random initialization, while it is only 6.1% for autoencoder initialization.

Table 6