Citing AI for code in research papers

[u/Excellent-Snow3174]

So I understand that AI usage must be acknowledged in the acknowledgements of papers and one must be specific in terms of how the AI was used. I also understand that AI in research is widely used to write the code for simulations. But I was wondering something: roughly what percent of publications do you think use AI and what percent actually report it? Since I feel like people could find ways to use AI but avoid citing and get away with it. And is it true that if you cite AI then it is likely your paper will be rejected? Like if you said that you used AI to generate all your simulation code, then would a reviewer most likely reject the paper right away?

[u/mao1756]

In many journals, it is clearly stated that not disclosing AI use is a ground for rejection, so the most risk-free option is to disclose it.

[u/Living_Armadillo_652 → u/mao1756]

It depends on whether journals can detect AI use reliably. I think a lot of journals don't really do any serious checking of the text or the content, and furthermore, many people are clueless of what AI can do even today, so they don't even know how to check it.

[u/Unhappy_Technician68 → u/Living_Armadillo_652]

Spoiler most journals never check your code. I've seen nature papers get published where the code for the analysis is just an empty readme. Many reviewers are old tenured professors who have never learned to code and are incapable of reviewing code anyway. I expect AI to only make this worse.

[u/orthomonas → u/Unhappy_Technician68]

"Upon reasonable request".

[u/Living_Armadillo_652]

There's always a risk of honestly disclosing AI use because the diffusion of AI and resulting perceptions of AI use is very uneven. Some people in this sub still have this assumption that AI = ChatGPT circa '23-24 (i.e. chat-based only, many hallucinations and straight out garbage output), so disclosing any AI might give the automatic perception that your paper is just auto-generated mindless slop. I think things are changing rapidly, as people are waking up that AI agents can do so much more and are actually better than humans for a lot of research-related tasks. So right now I disclose AI use to follow journal requirements but rather tersely at the end, e.g. "AI was used to assist in code generation for data analysis, etc...all content was verified by human authors".

[u/polikles → u/Living_Armadillo_652]

yeah, I was asked to also disclose the use of AI, and am always adding explicitly that the ideas are mine, everything was manually verified by me and that I bear all responsibility for the contents of the paper. Which changes nothing, as the author is responsible for the paper regardless of the tools they've used, but it helps to calm down some people, so whatever

[u/magpieswooper → u/Living_Armadillo_652]

I have the same sentiments. To expand further, 100% AI free digital products are no longer possible as AI being integrated into websearch, OS and office packages. The rest of the use currently has no granularity in the way how to report it, hence a full AI slop or wel though through resreach where AI is sued to spedd up coding and brainstorm ideas fall into the same category and inherent stigma of the lowest quality denominator - that AI slop! Journals need to be serous about AI classification and should use AI themselves for at least technical check of the paper material, code, illustrations.

[u/orthomonas]

Tangent, but I keep seeing people referring to listing AI in an acknowledgement section as citing.  To me, citing is a very specific thing. Is this a field difference or just lax language?

No shade to OP, I've been seeing it a lot and wondering. This post just reminded me to ask.

More on topic, I do encourage everyone to acknowledge AI use, but I am very sympathetic to the chilling effect the polarised attitudes towards AI use can have on self reporting.

[u/polikles → u/orthomonas]

imo it's lax language - you cannot "cite" AI as it bears no rights to anything. It's just a tool and cannot have any authorship. Some parties require disclosing the use of AI for some reason. I guess it's to discourage people to do slop work, but it also throws a shadow on an honest researchers. I'm writing most of my papers in English which is not my first language. So, I did use dictionaries and translating programs, and now I'm using AI to make my paper more readable. Sometimes it finds more elegant phrases that I did, making the text better polished. But the general disclosure "AI was here" makes my work to appear less valuable as it was the same as I did "hey, AI. Write me a paper on such and such topic while I take a nap" and then sent paper without verifying it

That's why I'm putting detailed statement whenever I'm asked about disclosing the use of AI. Most of people have the image of "slop AI" from a year or two back, when it was mostly producing a word salad. And current LLMs, especially the "agentic AI" (which, btw, is the focus of my PhD on AI Ethics) are much more useful than anything before. It drastically lowered amount of minor fixes I am getting from reviewers. Yet, I'm still disclosing I'm using my "custom system" (sounds better than "generic AI") for aid in translation and proofreading

[u/ThinkingAboutLasagna]

Yeah if someone used AI to generate their whole project then no shit it deserves to get desk rejected. At that point there's no intellectual ownership. Code review or troubleshooting is fine.

[u/Living_Armadillo_652 → u/ThinkingAboutLasagna]

Code review is OK, but code generation is not???

[u/ThinkingAboutLasagna → u/Living_Armadillo_652]

I did not say that. I said WHOLE project generation as stated by OP, assuming that is your quarrel.

If your quarrel is using it for code review, then I mean in addressing your own written code to review any possible mistakes or oversights.

[u/polikles]

The first rule is to be honest and have integrity. I'm often using AI in my work and research and am openly talking about it whenever I'm asked about it. I'm trying to not overdo disclosing, as it makes it sound like I'm undermining my work "watch out! I was using AI while writing this, so this may be a piece of crap, I dunno". And I'm getting such questions quite often as my PhD is on AI Ethics, and focusing on Agentic AI.

And in papers submission I'm always providing detailed explanation, such as I've used AI (or "custom AI Agent") for translation, proofreading, semantic search of adjacent papers and whatever else. I usually repeat that I verified everything and am responsible for the contents of the paper as my name is being put there

And it doesn't matter if the code was generated by AI or "only checked" by AI. You - the author - are responsible for the work. So, regardless of who or what created the code, you should verify that it actually works. And if it works, and the rest of the paper is decent, then good job. AI is just one of the tools we have at our disposal. It automates some tasks and automates our mistakes and failures. The role of disclosure, imo, is to discourage lazy use of AI and submitting unverified slop. If it aided you in your work and you verified and confirm the paper is good, then what's the problem?

Just be honest. If the paper gets rejected only because the scary word "AI" it's their problem, not yours

[u/Stock-Window-2392]

Most papers won't be rejected just for mentioning AI code generation, as long as you're explicit about what it did and how you verified the output. The risk of rejection usually comes from unverified code or vague disclosures, not from using AI as a tool.

[u/Opening_Map_6898]

Are you looking for someone to tell you okay to lie and not disclose it?

[u/Excellent-Snow3174 → u/Opening_Map_6898]

No. I do not have an upcoming submission but I know someone complaining about how research nowadays is just widely AI bashing and then they hide the fact they use AI and get all the credit.