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why the shape of data.y is [1,]? Why isn't it the number of graphs? i.e. [num_graphs]?

That's because a graph is represented as a data object, where each data (graph) is associated with a scalar label y represented as a one-dimensional vector [1, *].

why the shape of data.y could be arbitrary?

This is an intentional design to provide more flexibility to accommodate different scenarios.
In certain cases, nodes may have multiple labels, such as in the PPI dataset. In such cases, the labels are represented as 2D vector.

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@evantianzg
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