Tips for useful note-making when learning by oneself
Here's the method I found works best for me:


Read a section
Put the paper down, summarize verbally (mentally or out loud)
If you can't summarize, re-read the section. If you can summarize, write down the summary.


This method has the benefit that your notes don't reflect the stream of consciousness that I found went through my brain as I read the paper, but rather only a concise summary of what I actually understood from the paper.

Note that there were definitely papers where I read a particular section numerous times and had no idea what it was talking about, and I wrote that in my notes (e.g., "The authors then performed a mathematical transform involving  technique, and I was not able to figure out how it works from reading the paper.").