Development and validation of an automated machine for self-injury assessment via young Koreans’ natural writings

Seoyoung Kim; Dong-gwi Lee

doi:10.1371/journal.pone.0316619

Peer Review History

Original SubmissionJuly 10, 2024
28 Aug 2024 Decision Letter - Agnieszka Konys, Editor PONE-D-24-27189Development and validation of an automated machine for self-injury assessment via young Koreans’ natural writingsPLOS ONE Dear Dr. Lee, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please carefully check the Reviewers' comments and improve the manuscript. Reviews provide details into areas that require improvements. Please submit your revised manuscript by Oct 12 2024 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. Please include the following items when submitting your revised manuscript: 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, Agnieszka Konys, Ph.D. Academic Editor PLOS ONE Journal requirements: 1. When submitting your revision, we need you to address these additional requirements. 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. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. [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? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. 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 requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This paper provides empirical results on the K-SITR software, developed by the authors, for assessing self-harm in individuals from their writing and forecasting the resulting outcomes. The authors developed this natural language processing software using off-the-shelf methods and in collaboration with counsellors and therapists. An analysis of K-SITR results with several questionnaire-based scoring mechanisms was provided. Overall, the paper seems scientifically sound and could be published with minor revisions. 1. It is never made clear how the matching is actually done (e.g., on Page 11). Is it cosine similarity or some kind of common word count? Is there a projection onto topic space occurring? This should be spelled out. 2. Similar question on Page 12: It seems like a raw word count comparison was performed. There are other ways of doing this, including projection methods (onto the reduced topic space). Were they considered? 3. On Page 28, the authors suggest acquiring a writing sample on intake for patients. However, an arbitrary writing sample may not be sufficient. What prompts are suggested and what (future work) methods could be used to identify prompts that do not provoke self-censoring? Since K-SITR was developed for open-ended writing with no prompt, what changes adjustments, if any, may need to be made? Minor Comments: Page 7, Line 133: "Raw corpus..." should be "The raw corpus..." Page 9, Line 181: There is a tense inconsistency. The sentence should read, "Each training dataset was subjected..." Page 10, Line 193: "opinions" should be "topics". Page 10, Line 199: "find more..." should be: "See Blei et al. [41] for more on LDA." Page 10, Line 201: "...and within-topic..." should be "...and small within-topic..." Page 11, Line 213, "of the machine..." should be "of the machine learning algorithm..." Page 13, Line 264: "0.64 a more..." should be "0.64 higher..." or something like it. Page 17, Line 319: "eliciting urges" is not right. Do you mean, "encouraging"? Reviewer #2: The following issues should be considered: 1. Abstract: The abstract is too long. You should check the journal's format. 2. Keywords: Please add 5 keywords. It is advisable to avoid abbreviations in this section. 3. Introduction: This section is too long. Please rewrite the main contributions of the research at the end of the Introduction. It is better to write it more concisely and in a more substantial form. Currently, this part resembles a related work section. You should add a new section titled 'Related Work,' move the relevant text there, and then write a new Introduction. 4. Related Work: The related work section must be completed and updated with recent articles from reputable journals. 5. Methodology and Proposed Work: This section must be added. Also, the applications of this method have yet to be mentioned. 6. Section Numbering: The sections should be numbered. 7. Comparative Analysis: One of the fundamental questions is, what are the advantages and disadvantages of your method compared to recent methods? 8. Conclusion: The conclusion section is acceptable. 9. Article Formatting: In general, the format of articles may vary across different fields. Therefore, I suggest reading several articles within the current field of study and considering their format for structuring the various sections of your paper. For example, this could include aspects such as: 1. Naming the sections, 2. Ordering the sections, 3. Numbering the sections. 10. Additional Work: There are some other works on semantic analysis by LDA that should be considered: https://doi.org/10.1155/2022/7612276 https://doi.org/10.1142/S0219622022500584 https://doi.org/10.1111/exsy.12527 ****** 6. PLOS authors have the option to publish the peer review history of their article (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: Christopher Griffin Reviewer #2: No ******** [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. https://doi.org/10.1371/journal.pone.0316619.r001
Revision 1
28 Nov 2024 Author Response We sincerely appreciate the opportunity to revise our manuscript. We attached our response to each review comment along with our revised manuscript. Plus, we are submitting our response here too: Response to Reviewer 1 Comment 1: It is never made clear how the matching is actually done (e.g., on Page 11). Is it cosine similarity or some kind of common word count? Is there a projection onto topic space occurring? This should be spelled out. Response 1: Thank you for your help in clarifying the matching process. We have clarified the two-step matching process of the K-SITR machine (visualized in Fig. 2 as H1 and H2) and elaborated it with examples, on pages 16-18, lines 310-360 in our revised manuscript with track changes. The H1 matching aimed to match a new text case (presumably, a new counseling client’s writing) to one of the subsets to tentatively assess the severity of the new case. To do this, the K-SITR counts the frequencies of word-to-word matches. And within the subset, the H2 matching aimed to match the new case with a specific case that the K-SITR has as training data. To do this, the K-SITR compares the topic profile of the new case with the topic profile of each training data case until it finds the most similar training data case. As a result of this matching, the K-SITR can retrieve the professional counselor judgements that were made on the subset and the best matching training data case for the new client’s case. Comment 2: Similar question on Page 12: It seems like a raw word count comparison was performed. There are other ways of doing this, including projection methods (onto the reduced topic space). Were they considered? Response 2: The reason for choosing the LDA method is now explained with supporting references on page 15 lines 293-297. Following your kind suggestion, we have also mentioned the random projection method for short text data as an alternative topic modeling method for future studies in our Discussion on page 35, lines 691-696. Comment 3: On Page 28, the authors suggest acquiring a writing sample on intake for patients. However, an arbitrary writing sample may not be sufficient. What prompts are suggested and what (future work) methods could be used to identify prompts that do not provoke self-censoring? Since K-SITR was developed for open-ended writing with no prompt, what changes adjustments, if any, may need to be made? Response 3: Thank you for bringing up a very important point. We have added a guide for counselors on the verbal prompts that can help self-injuring clients feel as open as possible, on pages 35-36, lines 702-710. Comment 4: Minor Comments: Page 7, Line 133: "Raw corpus..." should be "The raw corpus..." Page 9, Line 181: There is a tense inconsistency. The sentence should read, "Each training dataset was subjected..." Page 10, Line 193: "opinions" should be "topics". Page 10, Line 199: "find more..." should be: "See Blei et al. [41] for more on LDA." Page 10, Line 201: "...and within-topic..." should be "...and small within-topic..." Page 11, Line 213, "of the machine..." should be "of the machine learning algorithm..." Page 13, Line 264: "0.64 a more..." should be "0.64 higher..." or something like it. Page 17, Line 319: "eliciting urges" is not right. Do you mean, "encouraging"? Response 4: Thanks for your kind suggestions, all sentences are now revised except one on page 15, line 298. We meant to say, “An efficient topic model has small between-topic similarities and large within-topic similarities,” and the previous sentence had typos. We apologize for the confusion. Response to Reviewer 2 Comment 1: The abstract is too long. You should check the journal's format. Response 1: Following your advice and PLOS ONE’s recent publications, our abstract has now been shortened and revised. Comment 2: Please add 5 keywords. It is advisable to avoid abbreviations in this section Response 2: Five keywords are added after the abstract. Comment 3: This section is too long. Please rewrite the main contributions of the research at the end of the Introduction. It is better to write it more concisely and in a more substantial form. Currently, this part resembles a related work section. You should add a new section titled 'Related Work,' move the relevant text there, and then write a new Introduction. Response 3: Thank you for helping us restructure the Introduction to improve readability. We have revised the entire Introduction from page 4 to page 11. Specifically, we made the Introduction more concise by omitting parts that had unclear relevance to our research topic and objectives. Following your suggestion, we added the sections “Efforts to Assess Self-Injury and Related Work” (on page 6 line 99 in our revised manuscript with track change) and “Methodology and Proposed Work” (on page 7, line 127) to distinguish the background and literature review from the part where we introduce our study and expected implications. Comment 4: The related work section must be completed and updated with recent articles from reputable journals. Response 4: Following your suggestion, we added the section “Efforts to Assess Self-Injury and Related Work” (on page 6, line 99) and a new reference [22]. Also, in the following “Methodology and Proposed Work” section, we have elaborated on our methodological approach by adding research information from some of the previous studies that we have referenced (e.g., [30, 31]). Comment 5: This section (“Methodology and Proposed Work”) must be added. Also, the applications of this method have yet to be mentioned. Response 5: Regarding your third suggestion, we have added the sections “Efforts to Assess Self-Injury and Related Work” (on page 6, line 99) and “Methodology and Proposed Work” (on page 7, line 127) to distinguish the background and literature review from the part where we present our study (objectives and methods) and expected impact. Comment 6: The sections should be numbered. Response 6: We have revised our heading format based on the PLOS ONE submission guidelines. (We found the PLOS ONE does not allow psychology articles to use numbered sections/headings. Please see: https://doi.org/10.1371/journal.pone.0290756) Comment 7: One of the fundamental questions is, what are the advantages and disadvantages of your method compared to recent methods? Response 7: Thank you for your help in assuring us of the benefits of taking the text-mining approach to self-injury assessment. We have added a paragraph on the methodological advantages on page 10, lines 185-198, compared to other methods including the self-report surveys and previous text-mining results that did not reflect the opinions of psychologists. Potential disadvantages/limitations are explained in the Discussion, primarily on pages 34-35, lines 678-696. Comment 8: The conclusion section is acceptable. Response 8: N/A Comment 9: In general, the format of articles may vary across different fields. Therefore, I suggest reading several articles within the current field of study and considering their format for structuring the various sections of your paper. For example, this could include aspects such as: 1. Naming the sections, 2. Ordering the sections, 3. Numbering the sections. Reseponse 9: We have reconstructed and revised our sections/headings based on the recent PLOS ONE publications in the field of psychology (e.g., https://doi.org/10.1371/journal.pone.0290756). Comment 10: There are some other works on semantic analysis by LDA that should be considered: https://doi.org/10.1155/2022/7612276 https://doi.org/10.1142/S0219622022500584 https://doi.org/10.1111/exsy.12527 Response 10: Thank you for your thoughtful suggestion. Attachments Attachment Submitted filename: (final) K-SITR_review response.docx https://doi.org/10.1371/journal.pone.0316619.r002
15 Dec 2024 Decision Letter - Agnieszka Konys, Editor Development and validation of an automated machine for self-injury assessment via young Koreans’ natural writings PONE-D-24-27189R1 Dear Dr. Lee, 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. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. 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, Agnieszka Konys, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0316619.r003
Formally Accepted
19 Dec 2024 Acceptance Letter - Agnieszka Konys, Editor PONE-D-24-27189R1 PLOS ONE Dear Dr. Lee, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Agnieszka Konys Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0316619.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .