I'm amazed they've all got prerequisites like that. At least half of the courses in the Stanford math department are the kind I describe as having a "suspicious lack of prerequisites". I suppose if you understand half the words in the course description, then you know whether or not you can take the class.
Some of the graph seems redundant. For example, math245a requires math135 and math113, but math135 already has math113 as a prerequisite. But checking, this seems that this isn't a bug in your graph, but rather a bug in the math course structure.
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