"Citation" is the topic being discussed. It's a technical term that refers to how scientific papers refer to other scientific papers.
"Modality" is the concept I've been introducing for three paragraphs. You're supposed to know what it means by then, or I've not been clear enough.
"Present as" is an intransitive verb phrase. I could say the same thing, perhaps more simply, by saying "you can think of a citation as a modality". Perhaps it's this phrase that has thrown you?
[EDIT: I've changed the article to try and make the sentence clearer. Thanks for your feedback.]
It seems to me that "degree of confidence" is clear enough, and that it's clear enough that a modality can have a degree of confidence associated with it.
So the article introduces two technical terms you're perhaps not familiar with, but I'd suppose someone who can read a CS paper or write a program can cope with that much.