In process mining, extensive data about an organizational process is summarized by a formal mathematical model with well-grounded semantics. In recent years a number of successful algorithms have been developed that output Petri nets, and other related formalisms, from input event logs, as a way of describing process control flows. Such formalisms are inherently constrained when reasoning about the probabilities of the underlying organizational process, as they do not explicitly model probability. Accordingly, this paper introduces a framework for automatically discovering stochastic process models, in the form of Generalized Stochastic Petri Nets. We instantiate this Toothpaste Miner framework and introduce polynomial-time batch and increm...