This paper introduces a computer-based training program for enhancing numerical cognition aimed at children with developmental dyscalculia. Through modelling cognitive processes and controlling the level of their stimulation, the system optimizes the learning process. Domain knowledge is represented with a dynamic Bayesian network on which the mechanism of automatic control operates. Accumulated knowledge is estimated to select informative tasks and to evaluate student actions. This adaptive training environment equally improves success and motivation. Large-scale experimental data quantifies substantial improvement and validates the advantages of the optimized training.