Software-based solutions may mitigate physical damage to multi-layer networks, such as neural networks having shortcut (residual) connections. An example includes: providing a multi-layer network comprising a plurality of nodes; for each of a plurality of training cases: determining a set of dropout nodes, based at least on a damage model having a probability of a node being selected for dropout that is based at least on a target operating environment of the multi-layer network, wherein the probability of a node being selected is spatially correlated; and training the multi-layer network with the determined set of dropout nodes disabled (with a different set of dropout nodes for different training cases). In some examples the damage model involves expected physical radiation damage to a computing device hosting the multi-layer network, such as on board an aircraft or an earth-orbiting satellite. Thus, multiple degrees of expected damage may be addressed.