For MOE 1.x this is not easy. One option is to try and enable method tracing on the Java side using the Dalvik
VMDebug interface, then you can analyze that trace log. I am not sure if method tracing works correctly on the current MOE, we had some issues with it in the past.
For MOE 2.x, you will see the actual Java methods from the native side as well, so you will be able to use Instruments as you would with any native app. We are finalizing the first alpha of MOE 2.x, so you should be able to try this out real soon now.