[JHonaker]

Unfortunately, it's just something you start to notice once you become more familiar with the fundamental math underlying all of this.

The book, Machine Learning: A Probabilistic Perspective by Kevin Murphy (the original book everyone in this thread is talking about) is probably the closest thing I can think of. Its goal is to frame everything around graphical models and probability. It's quite a tome. Still, despite its breadth, it can't possibly cover everything.