One main theme can be tied to the novels The Perks of Being a Wallflower and Speak: sexual violence.
In the novel Speak, Melinda is raped at a party which takes place over the summer prior to her freshman year in high school. Melinda faces alienation, resentment, and the inability to self-define. Over the course of the novel, she comes to find herself and face the reality of what happened to her.
As for the novel The Perks of Being a Wallflower, Charlie, the protagonist of the story, witnesses a rape. While very different from experiencing a rape, Charlie runs through the scene in his mind trying to dissect it. The impact the rape has upon him, as a witness, is very different from the one which haunts Melinda.
Therefore, one could easily take the theme of sexual violence from both novels and compare and contrast how each Melinda and Charlie react to rape.