This is a known bug in Android Studio
I've been facing this problem for a long time and I came across a Reddit thread that explains the actual cause of the problem...
Here's the link to the Thread:
https://m.reddit.com/r/androiddev/comments/4m2v25/instant_run_causing_incredibly_long_app_start/

Until the problem has been resolved perform any of the following :
1. Turn off Instant Run
2. Revert back to version 2.8 of Gradle
Things you should do:
1. Wait until the problem is fixed
Sorry, this is a known issue right now. We are working on improving it
in 2.3. The reason this happens is that: Initially, we split all your
code into multiple dex files, and put them all inside a
instant-run.zip file After the first install, we unzip that file and
add all those classes to the classpath. This is the step that takes
time, you see a white screen. In the worst case, you may even get an
ANR. We split it up so that on subsequent updates, we only send out
the dex files that have changed. In Android N, we have some more
platform support via split APKs, which we leverage and should be
faster.