Why does assembleDebug takes much longer then project build and how to optimize it?

I've been dealing with gradle build time in Android Studio recently. I've managed to decrease the build time from about 3 mins to 10 seconds by removing some dependencies, but here's the thing:

When I rebuild project it takes about 10 seconds:

15:13:43 Executing tasks: [clean, :app:generateDebugSources, :app:generateDebugAndroidTestSources, :app:compileDebugSources, :app:compileDebugAndroidTestSources]
15:13:54 Gradle build finished in 11s 596ms

However when I launch the app, it takes a lot longer, about a minute:

15:15:09 Executing tasks: [:app:assembleDebug]
15:15:58 Gradle build finished in 49s 676ms

What is the cause of such big difference? Is this still because of the large amount of gradle dependencies or something else? Can I reduce the build time somehow?

Why:

Recently I enabled multidex in my app because I had over 65k methods. Dexing is what was taking a lot of time to complete.

How to speed up build:

Go to Settings (Ctrl + alt + s) -> Build, Execution, Deployment -> Compiler

Enabling compiling modules in parallel and adding --offline in compiler has decreased my execution time to about 15 seconds.