These are two different things, actually. The graph you are talking about is constructed using the inputs of the attention layer (ie, nodes=tokens, edges=affini

These are two different things, actually. The graph you are talking about is constructed using the inputs of the attention layer (ie, nodes=tokens, edges=affinity), while the article talks about graphs that represent the actual operations performed in the attention layer (ie, nodes=weights and intermediate results, edges=mathematical operations that combine them).