Dear Dr. Linh,

Please submit your revised manuscript by Nov 29 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols .

We look forward to receiving your revised manuscript.

Kind regards,

Musa Adekunle Ayanwale, Ph.D

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified (1) whether consent was informed and (2) what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). If your study included minors, state whether you obtained consent from parents or guardians. If the need for consent was waived by the ethics committee, please include this information.

3. Please note that PLOS One has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse

If you are reporting a retrospective study of medical records or archived samples, please ensure that you have discussed whether all data were fully anonymized before you accessed them and/or whether the IRB or ethics committee waived the requirement for informed consent. If patients provided informed written consent to have data from their medical records used in research, please include this information.

4. Please ensure that you include a title page within your main document. You should list all authors and all affiliations as per our author instructions and clearly indicate the corresponding author.

5. We notice that your supplementary figures are uploaded with the file type 'Figure'. Please amend the file type to 'Supporting Information'. Please ensure that each Supporting Information file has a legend listed in the manuscript after the references list.

6. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.

7. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: Yes

Reviewer #2: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

Reviewer #2: Yes

**********

Reviewer #1: It is a great pleasure to have reviewed this paper, “Evaluating Cognitive Depth in AI-Generated Multiple-Choice Questions: A Comparative Study of Modern Large Language Models Using Bloom’s Taxonomy”. The study has numerous merits, but for this review, I will unravel some grey areas that, after implementing the correction, will further strengthen the quality of the paper.

Title and Abstract

Title (L1–3): The title is informative and clearly indicates scope, methods, and framework. However, it is a little long. You might shorten to: “Evaluating Cognitive Depth of AI-Generated Multiple-Choice Questions with Bloom’s Taxonomy”. The “Short Title” already captures this succinctly.

Abstract (L4–30): The abstract is structured but slightly repetitive. The “Introduction” sentence could be condensed into one line (“While LLMs are used to generate medical and dental MCQs, their alignment with Bloom’s Taxonomy remains unexplored.”). The “Materials and Methods” section is clear, but you should specify that each model generated 60 MCQs (total 300) upfront for transparency. In the “Results,” provide exact p-values where significant, not just p < 0.05. In “Conclusions,” avoid subjective phrasing (“superior performance”) and instead state “Claude Sonnet 4 achieved the highest alignment at higher-order levels.”

Introduction

Opening (L31–38): The rationale for MCQs is well stated, but the phrasing is verbose. Consider shortening: “MCQs provide a cost-effective way to assess knowledge, comprehension, and problem-solving in large cohorts, but creating high-quality, cognitively targeted items requires expertise and resources.”

Bloom’s Taxonomy (L39–43): Good explanation. Ensure consistent naming (“Analyze,” “Evaluate/Create”) throughout the manuscript. Consider referencing updated frameworks (e.g., Anderson & Krathwohl’s 2001 revision).

AI and LLM background (L44–49): Strong context, but some citations are older (e.g., GPT-3 work). Since you are submitting in 2025, reference more recent reviews (e.g., Küchemann et al., 2025).

Research gap (L50–57): Well identified, but should emphasize novelty: “To date, no comparative evaluation of state-of-the-art LLMs has assessed their ability to generate MCQs across Bloom’s levels.”

Methods

Design (L60–67): Clear statement of cross-sectional comparative design. Consider explicitly noting IRB exemption if no human subjects were involved.

LLM Selection (L68–76): Strong justification, listing release dates and subscription status. Add citations or URLs to each model’s technical report for transparency.

Sample Size (L77–81): You correctly reference G*Power. Specify the test family (e.g., Kruskal–Wallis) and effect size convention. Good decision to use 60 items per LLM.

Source Material and Prompt (L82–99): Very detailed, which is a strength. However, Table 1 is overly long—condense to 1–2 illustrative examples. Avoid full explanations that overwhelm the reader.

Evaluation (L105–115): Well structured with two independent raters. Provide rater demographics (teaching years, academic level) for credibility.

Statistics (L117–123): You describe use of SPSS and Python. Good practice. Re-word sentence at L121–122 for clarity: “Inter-model comparisons were conducted using the Kruskal–Wallis test, followed by Bonferroni-corrected post hoc tests.”

Results

Inter-rater reliability (L126–133): Good reporting of weighted kappa values. Consider citing Yilmaz & Demirhan (2023) for weighted kappa interpretation.

Model comparison (L135–139): Table 3 is comprehensive. Ensure alignment in table formatting (some rows misaligned). Report effect sizes (η² or rank-biserial) alongside p-values.

Figures (L148–179): Figures 2–4 are useful but captions are too brief. Add interpretive context (e.g., “Claude Sonnet 4 scored highest at Applying, Analyzing, and Evaluating/Creating levels”).

Text results (L166–174): The within-model analysis is strong, but rephrase sentences for conciseness. Example: “For ChatGPT-4o, Remembering items scored higher than Analyzing and Evaluating/Creating (p < 0.01).”

Discussion

Strengths of study (L180–186): Clear articulation of novelty. Good acknowledgment that this is the first systematic LLM-Bloom evaluation.

Interpretation (L187–218): Insightful comparison, but avoid over-interpreting. For example, stating “Claude Sonnet 4 consistently outperformed…” should be softened: “Claude Sonnet 4 achieved higher alignment at higher levels.”

Integration with prior work (L193–200): Nicely cites medical/dental MCQ research. Ensure consistent referencing style (some journal abbreviations missing).

Mechanisms (L219–229): Well-reasoned discussion on architecture, training data, and fine-tuning. Ensure references to Vaswani (2017), Fedus (2022), and Kaplan (2020) are up to date.

Educational implications (L231–247): Strong discussion of healthcare education implications. Add practical takeaway: “Educators may selectively use Claude or Copilot for advanced assessments, while ChatGPT-4o may be more suitable for foundational testing.”

Limitations (L252–260): Limitations are acknowledged (subjectivity of raters, Bloom focus only, exclusion of multimodal tasks). Strengthen by explicitly noting: (1) only dental anatomy domain, (2) prompt design may bias outputs.

Conclusions

Concluding sentence (L263–269): Strong, but rephrase for precision: “Claude Sonnet 4 demonstrated the highest ability to generate higher-order questions, while all LLMs performed well at lower levels.” Avoid aspirational phrases (“fully realized”).

References

Strengths: Includes foundational MCQ literature and recent 2023–2025 LLM evaluations.

Weaknesses: Some inconsistencies (missing italics for journal names, inconsistent use of initials). Ensure uniform adherence to PLOS ONE reference style. Verify DOI formatting (should be lowercase “doi:” not capitalized).

Overall Assessment

Strengths:

Novel and timely evaluation of LLMs in education.

Strong methodological rigor (sample size, inter-rater reliability, nonparametric statistics).

Practical implications for dental/medical education.

Weaknesses:

Verbosity in Abstract, Introduction, and Methods.

Overly detailed Table 1 examples.

Need for clearer limitations (domain, prompt, subjective scoring).

Figures and tables require more explanatory captions.

References need style consistency.

Recommendations:

1. Shorten Abstract and Introduction for concision.

2. Reduce Table 1 to 1–2 examples; move others to Supplementary.

3. Add effect sizes to results.

4. Rephrase strong claims in Discussion and Conclusion.

5. Expand Limitations section explicitly.

6. Revise reference formatting per PLOS ONE guidelines.

Reviewer #2: This is an interesting research which has the potential of having direct impact on professional teaching similar course. I would like the authors to address of the thoughts I had as I read the manuscript in the hope to making it better for readers.

Provide some citation to back the statement in line 50-52

It will be more helpful to have the figures at the appropriate location they are mentioned in the manuscript instead of after reference. Not seeing those figures break flow of reading.

In table 3, I am not sure what the values in the parenthesis represents. Some clarification would be helpful to readers.

I was hoping so see some kind of quick highlight table showing the performance based on free and paid LLMs as stated in line 248. Is there any takeaway from that?

Can you provide some justification for the use of Kruskal-Wallis? Line 121

I am wondering if the use of LLM will reduce the usual time used for developing MCQ? Of course it would potentially reduce time it takes to write but what about need for editing? Would there be need for proficiency in prompt engineering? Could that be a roadblock for potential use?

**********

what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy

Reviewer #1: Yes: Oluwaseyi Aina Gbolade Opesemowo

Reviewer #2: Yes: Daniel Oyeniran

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step.

Title: Evaluating Cognitive Depth of AI-Generated Multiple-Choice Questions with Bloom’s Taxonomy

PONE-D-25-36938R1

Dear Dr. Nguyen,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager®  and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support .

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Musa Adekunle Ayanwale, Ph.D

Academic Editor

PLOS One

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #3: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions??>

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #3: Yes

**********

Reviewer #3: The article is well written, and the authors have addressed all reviewers' comments. However, there is a typo in the study design figure (Figure 1), Clinical revelence instead of clinical relevance.

**********

what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy

Reviewer #3: Yes: Mubarak Mojoyinola

**********