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Climate change poses an existential threat to humanity. In order to mitigate this threat, a transition must be made towards a more sustainable energy system. Hydrogen is predicted to play an important role in this transition, as it can be used directly as a source of fuel and can function as an effective energy storage medium. Important strategic investment decisions will need to be made regarding the production and deployment of hydrogen at scale. Fortunately, we are able to use mathematical modeling techniques to determine an optimal transition path and aid this decision making. However, for such large and complex problems, there is much uncertainty regarding future developments in technology, economics, policymaking, etc. The main goal of this PhD project is to develop a robust optimization methodology for dealing with such uncertainties while optimizing long-term, large-scale energy system models.