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In modern information infrastructures, diagnosis must be able to assess the status or the extent of the damage of individual components. Traditional one-shot diagnosis is not adequate, but streams of data on component behavior need to be collected and filtered over time as done by some existing heuristics. This paper proposes instead a general framework and a formalism to model such over-time diagnosis scenarios, and to find appropriate solutions. As such, it is very beneficial to system designers to support design choices. Taking advantage of the characteristics of the hidden Markov models formalism, widely used in pattern recognition, the paper proposes a formalization of the diagnosis process, addressing the complete chain constituted by monitored component, deviation detection and state diagnosis. Hidden Markov models are well suited to represent problems where the internal state of a certain entity is not known and can only be inferred from external observations of what this entity emits. Such over-time diagnosis is a first class representative of this category of problems. The accuracy of diagnosis carried out through the proposed formalization is then discussed, as well as how to concretely use it to perform state diagnosis and allow direct comparison of alternative solutions.