For large graphs, the performance bottleneck is usually rendering. To improve rendering speed, you can try to use simple shapes (i.e. rectangles only) and display as little text as possible (text rendering is horrendously slow). With regards to the latter point, yEd offers a feature called "Paint Details Threshold" (see "File" -> "Preferences", tab "Display"). If you increase the value of the threshold to something close to 1.0, then text will only be shown at fairly large zoom levels (which implies few visible elements) and will not affect rendering performance as much.
Can you quantify "large graph"? How many nodes and edges are there in your graph?
