A Guide to Revising and Explaining AI-Flagged Sections for Journals

A Guide to Revising and Explaining AI-Flagged Sections for Journals

Until very recently, most concerns about academic integrity focused on plagiarism, duplicate publication, data fabrication and undeclared conflicts of interest. In the last two years, however, editors have faced an additional challenge: the rapid spread of advanced AI language models capable of generating fluent, apparently scholarly text. These tools can be used responsibly for brainstorming or language support, but they can also produce inaccurate, fabricated or overly generic prose that undermines research quality.

In response, many journals now employ automated systems to flag text that appears AI-generated or heavily AI-edited. The resulting reports are not perfect—they may produce false positives and false negatives—but they have changed the editorial workflow. Authors are now receiving messages such as “Sections of your manuscript appear to have been generated by an AI system. Please explain and revise.”

If you receive such a notice, your first reaction may be stress or frustration. Perhaps you did not use AI at all and feel unfairly accused. Or perhaps you did experiment with AI during early drafting and are unsure how to explain that without damaging your chances of publication. This article is designed to help you navigate that situation calmly and ethically, and to turn a potentially awkward exchange into evidence of your professionalism.

What follows is a step-by-step guide that moves from understanding why AI flags appear, through revising the manuscript itself, to crafting response letters that satisfy editors and reviewers. The aim is not only to “pass the check” but to strengthen your paper and your credibility as an author.

1. Why Journals Flag AI-Generated Text

To respond effectively, it helps to understand the editors’ perspective. Journals do not typically screen for AI because they want to catch authors out; they do so because they are responsible for protecting the reliability of the scholarly record and the integrity of authorship. Editors and publishers are judged on what they allow into the literature, and the sudden availability of fluent AI text has introduced new kinds of risk.

Several risks motivate AI screening:

1.1. Factual errors and fabricated references

AI systems can generate plausible-sounding statements that are simply untrue. They may also invent references or misattribute quotations. Editors worry that uncritical use of AI will lead to papers that are grammatically correct but empirically unreliable. In extreme cases, AI-generated manuscripts have cited non-existent journals, fabricated datasets and imagined clinical trials. Even when authors did not intend to deceive, the presence of AI hallucinations damages trust in the article and, by extension, in the journal.

1.2. Undeclared assistance and authorship concerns

Publisher policies now generally state that AI cannot be an author and that substantial AI involvement must be disclosed. If AI generated long sections of the manuscript, but the paper lists only human authors, questions arise about accountability. Who is responsible for the claims made? Who can respond to post-publication queries or corrections? Editors are obliged to ensure that listed authors genuinely stand behind the text.

1.3. Generic language and lack of scholarly voice

Some AI-generated text is vague, repetitive or stylistically similar across different manuscripts. Editors may worry that such text lacks the critical nuance or originality expected of peer-reviewed research. Repeated use of generic phrases can make a manuscript seem like a template rather than a record of specific new work. Journals want to publish articles where the writing reflects a particular set of data, a particular argument and a real human perspective on the topic.

1.4. Legal, ethical and reputational obligations

Journals and publishers are under pressure from universities, funders and the public to maintain high ethical standards. If an article is later revealed to be largely AI-generated or to contain fabricated content, questions are asked: why was this not detected? how rigorous is this publisher’s review process? AI-detection and AI-flagging are therefore part of a wider attempt to show due diligence and protect the journal’s reputation.

When you recognise these concerns as legitimate, it becomes easier to frame your response letter not as a defensive argument but as a contribution to a shared goal: maintaining quality and trust.

2. First Steps When You Receive an AI-Flag Notice

When an editor or reviewer indicates that parts of your paper appear AI-generated, do not reply immediately. It is tempting to respond with a quick denial or a short explanation, but a careful, reflective reply will always serve you better. Instead, follow a short, deliberate process before you begin drafting your response letter.

2.1. Read the editor’s message slowly

Check exactly what they are asking. Are they requesting a general statement about AI use? Are they pointing to specific sections (for example, the introduction or discussion)? Are they asking for revisions, an explanation, or both? Some messages are very general, while others include detailed reports from detection tools. Understanding the scope of the concern will shape how much detail you need to provide.

2.2. Identify which sections might be of concern

Some journals provide a marked-up file; others simply note that “certain paragraphs” appear algorithmic. Read your own paper as if you were an editor seeing it for the first time. Look for parts that feel unusually generic, stylistically inconsistent with the rest of the text or overly polished compared with your typical writing. Pay particular attention to passages drafted late at night, last-minute additions or text that multiple co-authors edited in different tools. These are likely to be the sections that triggered concern.

2.3. Reflect honestly on how the text was created

If you used AI tools at any stage, decide exactly how. Did you ask a system to rewrite your sentences for grammar and clarity? Did you paste in bullet points and ask for a paragraph draft that you then revised? Did you let the tool generate entire sections that you only lightly edited? Did a co-author use AI for a section you have not reviewed in detail?

This reflection is crucial. The content and tone of your response letter will depend on whether AI played a minimal supportive role or a substantial drafting role. Honesty at this stage is the foundation of an ethical response. It also helps you decide how much rewriting is required: light polishing of phrasing or a full re-authoring of entire paragraphs.

2.4. Consult co-authors and align your narrative

In multi-author work, one person’s recollection may not be complete. Someone might have experimented with an AI assistant for a small subsection without mentioning it at the time. Before replying to the editor, ensure that all authors share the same understanding of how the manuscript was produced. This is essential both for integrity and for avoiding contradictions in later correspondence.

3. Principles for Transparent, Professional Responses

Regardless of your specific situation, good responses share several principles. They are:

3.1. Transparent – They clearly state whether AI was used, in what way and to what extent. They do not try to conceal or minimise relevant information. Editors are usually more comfortable with limited AI use that is disclosed than with a defensive denial that seems incomplete or evasive.

3.2. Responsible – They emphasise that the human authors remain fully accountable for the content, have checked all claims and references and have revised or replaced any potentially problematic text. Even if AI helped shape early drafts, you should be able to demonstrate that the final manuscript is under your full intellectual control.

3.3. Solution-oriented – They describe concrete changes made in the revised manuscript (for example, rewriting flagged sections in the authors’ own words, verifying references and adding clarifying details). The emphasis should be on what you have done to resolve the problem, not merely on explaining how it happened.

3.4. Respectful – They acknowledge the editor’s responsibility and the reviewers’ time, even if you believe a flag is a false positive. A respectful tone signals that you see the journal as a partner, not an adversary.

3.5. Consistent – They align with the journal’s AI policy and with the content of the manuscript itself. If you write that you have removed all AI-generated text, your revisions should clearly reflect that effort.

Combining these principles will help you craft a response that reassures editors and reviewers that your paper can be trusted.

4. Rewriting AI-Flagged Text in Your Own Voice

One of the most practical ways to respond to AI concerns is to reduce or eliminate the dependency on AI-influenced text. Even if you used AI only for grammar, rewriting key passages yourself gives you more control and makes it easier to stand behind every sentence. The goal is not simply to “hide” AI involvement, but to make sure the writing genuinely reflects your thinking.

4.1. Start from your ideas, not from AI-generated phrasing

Instead of editing the questionable text directly, return to your core notes, datasets or conceptual outline. Write a fresh version of the paragraph based on your own understanding. This may take more time, but it ensures that the language reflects your reasoning rather than an algorithm’s pattern-matching.

A useful technique is to close the manuscript completely and talk through the point out loud, as if explaining it to a colleague. Then write the explanation you just gave, in your own words, and only later bring it back into the manuscript. This breaks your dependence on any prior AI-produced formulation.

4.2. Focus on specificity, not generic phrases

AI-generated prose often relies on vague formulations such as “It is important to note that…” or “In recent years, there has been growing interest in…”. Replace such generalities with specific statements about your context, your data and your contribution. Instead of “There is a growing interest in X”, write “Between 2015 and 2024, published studies on X increased from N to M, particularly in the contexts of Y and Z.” Specific details signal human authorship and deepen the content.

4.3. Check all references and factual claims

If you ever asked a system to provide or summarise references, ensure that every citation in the flagged sections corresponds to an actual, relevant source that you have read. Remove any reference you cannot verify independently. Editors are particularly concerned about AI hallucinations in bibliographies, and one fabricated citation can call all the others into question.

4.4. Maintain consistency with the rest of your manuscript

Compare the rewritten sections to your methods and results. Do they match in tone and depth? Does the introduction promise what the study can actually deliver? Aligning style across the manuscript helps reduce the appearance of patchwork authorship. When your revised sections sound like you, and fit the logic and rhythm of the rest of the paper, AI concerns naturally recede.

4.5. Keep track of your changes

As you revise, it is wise to keep a brief record of which paragraphs you rewrote and why. This can be as simple as a bulleted list in a private document. When you later draft your response letter, you will be able to refer to this list to describe your changes accurately and succinctly.

5. Explaining AI Use Without Undermining Your Work

After you have revised flagged sections, you still need to explain AI use, if any. The key is to be clear and precise without framing AI as the main architect of the paper. Focus on the following elements.

5.1. Distinguish between language-level and content-level assistance

There is a difference between asking an AI tool to tighten grammar in a paragraph you wrote and asking it to generate a paragraph from scratch based on a brief prompt. Journals are generally more comfortable with limited language-level assistance, provided it is disclosed, than with content-level drafting that authors do not fully control.

In your letter, distinguish these roles. For example: “We used an AI-based grammar tool to suggest minor language edits in early drafts of the introduction. All conceptual content and final wording has been authored, checked and revised by the human authors.” This shows that AI was a tool, not a co-author.

5.2. Emphasise verification and human responsibility

Whatever the level of AI involvement, editors want reassurance that you have personally verified every statement. Explicitly state that all data interpretations, methodological descriptions and conclusions were generated and checked by the authors. Make clear that no unverified AI text remains in the manuscript and that you fully understand and stand behind every part of the article.

5.3. Align your explanation with journal policy

Before responding, re-read the journal’s AI policy. Many publishers provide short guidance documents stating what they consider acceptable and how they want AI use disclosed (for example, in acknowledgements or methods). Referencing these expectations can show that you are engaging in good faith with their standards: “In line with the journal’s AI policy, we have now added a brief disclosure in the acknowledgements section describing our limited use of AI for language suggestions.”

5.4. Avoid over-explaining or self-incriminating language

While honesty is essential, you do not need to provide exhaustive technical detail about every experimental prompt you tried in a private notebook months ago. Focus on what matters for the manuscript in its current form. The editor is primarily interested in what the text now contains and how you have ensured its reliability.

6. When You Believe the Flagging Is a False Positive

Sometimes, journals flag text as potentially AI-generated even when you have not used AI at all. This can happen when your writing style is very formal, when you use standard phrases common in your field, or when automated detection tools misclassify high-quality human writing. It is understandably frustrating, but it is still important to respond calmly and professionally.

In these cases, you still need to respond carefully. Avoid anger or sarcasm; the editor is simply following protocol. A calm explanation can resolve the issue.

6.1. Explain your drafting process

Briefly describe how you wrote the manuscript—for example, that you drafted all sections manually, possibly with feedback from co-authors or human editors. If English is your second language, you may note that you have practised academic writing extensively or used non-AI tools (such as traditional grammar checkers) that the system might not distinguish easily.

Be factual rather than emotional: “The manuscript was drafted manually by the authors, and no generative AI tools were used at any stage. We used only standard spellcheck and grammar-check functions built into our word processor.” Clear, simple statements are more persuasive than defensive ones.

6.2. Offer to revise for clarity and style

Even if you are confident that no AI was involved, you can still offer minor revisions to make the style less reminiscent of generic templates. Rephrasing certain sentences in more distinctive, field-specific ways can help reassure reviewers that you are the genuine author. It also demonstrates your willingness to collaborate in improving the manuscript.

6.3. Accept that detection tools are imperfect

It can be helpful to acknowledge that automated tools are evolving and that you understand the editor’s need to investigate. This shifts the tone from confrontation to collaboration: “We appreciate the journal’s efforts to ensure the integrity of submissions and understand that detection tools may occasionally flag conventional academic phrasing. We hope the explanation above clarifies our authorship practices.”

7. The Role of Professional Human Editing

One of the paradoxes of the current climate is that authors are encouraged to improve their English and clarity but discouraged from relying on AI text generators. One way to navigate this tension is to use professional human editing rather than algorithmic drafting. Human editors can improve grammar, style and structure without introducing fabricated content or generic language.

For example, journal article editing, academic proofreading and scientific editing services rely on experienced human editors who respect your voice and arguments while correcting errors and improving clarity.

In a response letter, you can legitimately state that you used professional human editing support instead of AI systems. This can reassure editors that improvements in language quality did not come at the cost of authenticity or control.

8. Structuring Your Response Letter

A well-organised response letter helps the editor see quickly what you have done to address their concerns. You can use a structure such as the following:

8.1. Opening acknowledgement

Thank the editor for their message, acknowledge their responsibility to ensure research integrity and state that you take the concerns seriously. One or two sentences are enough; the goal is to set a cooperative tone.

8.2. Summary of AI use (or non-use)

Provide a clear statement about whether you used AI tools, and if so, for what purpose and to what extent. Distinguish between language editing and content generation. This section should be factual, not apologetic.

8.3. Description of revisions

Explain what changes you have made to the manuscript. Highlight rewritten sections, verification of references and any stylistic adjustments to clarity and specificity. If the editor mentioned particular paragraphs, address them directly.

8.4. Closing reassurance

Reiterate that the authors take full responsibility for the content and that they are committed to meeting the journal’s standards. Thank the editor again for their consideration and invite further questions if needed.

Keeping your letter concise but thorough shows respect for the editor’s time while still providing the necessary detail.

9. Long-Term Strategies for Avoiding AI-Related Problems

Rather than treating AI-flagged sections as a one-off crisis, it is helpful to develop long-term habits that reduce the likelihood of similar issues in future submissions.

These habits include:

• drafting your own text whenever possible, using AI (if at all) for local suggestions rather than full paragraphs;
• relying on human editors instead of generative tools for complex revisions;
• keeping notes about any AI interactions during manuscript preparation;
• reading and following the AI policies of your target journals before submission;
• treating AI as a prompt or mirror for your own thinking, not as a ghost-writer.

As publishers refine their policies and tools, transparency and documentation will become standard parts of scholarly practice, much like ethics approvals and data availability statements are today.

10. How AI-Detection Tools Actually Work (and Why That Matters)

Understanding the basics of how AI-detection tools function can help you interpret flags more calmly. Most systems do not “know” whether a piece of text is human or AI with certainty. Instead, they estimate probabilities based on statistical features such as predictability, sentence length, vocabulary variety and resemblance to known AI outputs.

AI-generated text tends to have relatively low variation in sentence structure and uses common phrases that appear frequently in model training data. Human writing, particularly when done under time pressure, often contains more irregularities, idiosyncratic turns of phrase and local variations in tone. Detection tools look for these patterns—and sometimes misclassify very polished human writing or revised text as “AI-like”.

This is important because it means that an AI flag is the beginning of a conversation, not a verdict. Editors are aware of detection limitations and often use flags as prompts for clarification, not as grounds for automatic rejection. A calm, well-structured response acknowledges the tool’s role while focusing on what you have done to ensure the manuscript’s integrity.

11. Evolving Publisher Policies: A Moving Target

Publisher policies on AI are still evolving. Some are strict, others more permissive, but most share a core set of principles: AI cannot be listed as an author; authors must disclose significant AI use; and responsibility for every part of the manuscript rests with the humans who sign it.

Some journals now provide standard disclosure templates along the lines of: “The authors used AI-tool X to assist with language editing of early drafts. The authors reviewed and edited the content and take full responsibility for the final version.” Familiarising yourself with these templates ahead of time can make both manuscript preparation and response letters easier.

Because policies change, it is wise to check the journal website again even if you read it months earlier. If your manuscript has been under review for a long time, the AI policy may have been updated in the meantime.

12. Ethical Disclosure Statements: How Much Detail Is Enough?

Authors often struggle with how detailed their AI disclosures should be. Too vague, and editors may feel that important information is being concealed; too detailed, and the letter may read like a confession, undermining confidence in the work

Sample Letter 1: Limited AI Assistance, Fully Disclosed

Dear [Editor’s Name],

Thank you for your message regarding potential AI-generated text in our manuscript, “[Manuscript Title]” (Manuscript ID: [ID]). We appreciate your commitment to upholding high standards of research integrity and understand the importance of transparency in this area.

In preparing early drafts, we used an AI-assisted language tool to suggest minor grammar and style improvements in sections of the introduction and discussion. The conceptual content, structure and final wording were written, reviewed and revised by the human authors. No parts of the manuscript were generated solely by AI and left unverified.

In light of your concerns, we have taken the following steps:

1. We carefully reviewed all sections where we previously used AI for language suggestions and have now rewritten those paragraphs entirely in our own words to ensure that the text reflects our authorial voice and reasoning.

2. We verified all references and factual statements in the rewritten sections to confirm that they accurately represent the underlying sources and data.

3. We confirmed that no AI system was used to generate new content, interpret results or propose arguments. All scientific claims and interpretations arise from our own analysis of the data.

We respect the journal’s policy that AI cannot be listed as an author and must not replace human responsibility for the manuscript. We can confirm that the human authors take full responsibility for the work as submitted and for all revisions made in response to your message.

We hope that these clarifications and revisions adequately address your concerns. We would, of course, be happy to provide any additional information you may require.

Sincerely,
[Name], on behalf of all authors
[Affiliation]
[Email address]

Sample Letter 2: Significant Rewrite of AI-Influenced Sections

Dear [Editor’s Name],

Thank you for informing us that portions of our manuscript, “[Manuscript Title]” (Manuscript ID: [ID]), appear to have been influenced by AI-generated text. We appreciate the opportunity to revise the manuscript and to clarify our use of digital tools.

In the initial stages of drafting, we experimented with an AI language model to generate preliminary phrasing for some background sentences in the introduction and for a small number of generic linking sentences in the discussion. We recognise that this was not fully aligned with emerging best practices in academic writing and that it may have contributed to the concerns raised.

To address this issue comprehensively, we have:

1. Identified all sections where AI-generated phrasing might have been present (primarily in the first two paragraphs of the introduction and in the final paragraph of the discussion).

2. Deleted these passages and rewritten them from scratch based on our own notes, using our own wording. The revised text reflects our direct engagement with the literature and our interpretation of the study’s implications.

3. Checked all cited references in the affected sections to ensure they correspond to genuine, relevant sources we have read and integrated carefully. Any reference that we could not verify has been removed.

4. Reviewed the entire manuscript to ensure that no remaining sentences rely on AI-generated wording. The current version is the result of human drafting, revision and proofreading only.

We fully accept that ultimate responsibility for the content lies with the authors. We are committed to meeting the journal’s standards and to avoiding over-reliance on AI systems in future work. We hope that the significant revisions we have made, together with this explanation, reassure you that the manuscript now meets your expectations regarding authorship and research integrity.

Thank you again for your careful attention to this matter and for the opportunity to revise our submission.

Sincerely,
[Name], on behalf of all authors
[Affiliation]
[Email address]

Sample Letter 3: Responding to a Likely False Positive (No AI Used)

Dear [Editor’s Name],

Thank you for your message about potential AI-generated passages in our manuscript, “[Manuscript Title]” (Manuscript ID: [ID]). We understand the importance of ensuring that published work reflects genuine human authorship and careful scholarly practice.

We would like to clarify that we did not use any AI text-generation or AI rewriting tools at any stage of preparing this manuscript. All sections were drafted manually by the authors, with revisions carried out through our usual internal review process. The manuscript has not been processed by generative AI systems for content or language.

We appreciate that automated detection tools are still developing and may occasionally identify highly formal or conventional academic phrasing as “AI-like.” To reduce the possibility of confusion, we have nonetheless taken your concerns seriously and have:

1. Carefully re-read the sections that might appear algorithmic in style, particularly the introduction and parts of the discussion, and rephrased some sentences to make our authorial voice more distinct and specific to our study.

2. Verified that all references and factual claims in those sections accurately reflect the underlying sources and data.

3. Confirmed among all co-authors that no AI tools were used to draft or edit the text, beyond standard, non-AI spellcheck and grammar-check functions built into common word-processing software.

We fully support the journal’s efforts to uphold high standards of research integrity and we recognise that it can be difficult to balance these efforts with the realities of evolving technology. We hope that this clarification, along with the minor stylistic revisions we have made, addresses the concerns raised.

Please let us know if you require any further information. We remain grateful for your consideration of our work.

Sincerely,
[Name], on behalf of all authors
[Affiliation]
[Email address]