Training the document page layout and classifying good/bad layouts
When you're talking about layout, I am assuming you are talking about the way elements are arranged in the page. In that case, dividing your page into grids and having each element represented into grid numbers should solve your problem. Let's assume your page is divided into 9 x 9 grids, then you can have this data frame as an input. Grids can be replaced with your co-ordinates. You can add in more features like font-size, font-style, colour, etc.,

number header1 header2 header3 paragraph1 font-size-h1 font-size-h2 target
1      (2,3)      4     (4,2)     3           12           8           0


The tuple represents the co-ordinates and the individual number represents the grid number. The font-size can be added for each element which will increase  the dimensions of the dataset. May be try running a simpler algorithm like Random Forest first and then move onto deep learning techniques. Sometimes, simpler algorithms work better than complex algorithms. 

Aesthetic Value of a Webpage, Layout Classification