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In this paper a neuro-fuzzy modeling framework is proposed, which is devoted to discover knowledge from data and represent it in the form of fuzzy rules. The core of the framework is a knowledge extraction procedure that is aimed to identify the structure and the parameters of a fuzzy rule base, through a two-phase learning of a neuro-fuzzy network. In order to obtain reliable and readable knowledge, two further stages are integrated with the knowledge extraction procedure: a pre-processing stage, performing variable selection on the available data to obtain simpler and more reliable fuzzy rules, and a post-processing stage, that granulates outputs of the extracted fuzzy rules so as to provide a validity range of estimated outputs. Moreover, the framework can address complex multi-input multi-output problems. In such case, two distinct modeling strategies can be followed with the opportunity of producing both a single MIMO model or a collection of MISO models. The proposed framework is verified on a real-world case study, involving prediction of chemical composition of ashes produced by combustion processes carried out in thermo-electric generators located in Italy.