For modern large-scale structure survey techniques it has become standard practice to test data analysis pipelines on large suites of mock simulations, a task which is currently prohibitively expensive for full N-body simulations. Instead of calculating this costly gravitational evolution, we have trained a three-dimensional deep Convolutional Neural Network (CNN) to identify dark matter protohalos directly from the cosmological initial conditions. Training on halo catalogues from the Peak Patch semi-analytic code, we test various CNN architectures and find they generically achieve a Dice coefficient of ~92% in only 24 hours of training. We present a simple and fast geometric halo finding algorithm to extract halos from this powerful pixel-wise binary classifier and find that the predicted catalogues match the mass function and power spectra of the ground truth simulations to within ~10%. We investigate the effect of long-range tidal forces on an object-by-object basis and find that the network's predictions are consistent with the non-linear ellipsoidal collapse equations used explicitly by the Peak Patch algorithm.
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