Unstructured clinical notes within the 24 hours since admission predict short, mid & long-term mortality in adult ICU patients

Maria Mahbub; Sudarshan Srinivasan; Ioana Danciu; Alina Peluso; Edmon Begoli; Suzanne Tamang; Gregory D. Peterson

doi:10.1371/journal.pone.0262182

Peer Review History

Original SubmissionSeptember 7, 2021
10 Dec 2021 Decision Letter - Wajid Mumtaz, Editor PONE-D-21-29049Unstructured clinical notes within the 24 hours since admission predict short, mid & long-term mortality in adult ICU patientsPLOS ONE Dear Dr. Maria Mehboob, 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 submit your revised manuscript by Jan 24 2022 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. 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Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: 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: The authors performed a retrospective analysis of MIMIC data using NLP to parse clinical notes written within 24 hours of admission in predicting mortality at several intervals (48 hours, 4 days, 7 days, 10 days, 15 days, and 30 days) with four different machine learning approaches (LR, GBM, RF, neural network), achieving strong discrimination using unstructured data alone. The authors also investigate three different NLP feature extraction techniques and explore interpretability mechanisms (feature importance). The topic is important. The methods are reasonable. The time horizons are appropriate. Why not use both unstructured and structured clinical data? As the authors note, their is some overlap between these entities, and also some unique information that is contained only in unstructured data and some that is contained only in unstructured data. Unstructured data has a theoretical advantage of greater objectivity. As you may know, a group from Boston and industry have shared the perspective that machine learning applications often learn clinicians' thought processes even when using structured data, producing outputs that tell the clinician that which they already knew (PMID: 33785839). Unstructured data from clinical notes seems to reflect clinicians' thought process to an even greater degree. Please discuss these perspectives and justify the use of clinical notes alone in prediction modeling. ****** 6. 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Revision 1
14 Dec 2021 Author Response Reviewer Points: - Why not use both unstructured and structured clinical data? As the authors note, their is some overlap between these entities, and also some unique information that is contained only in unstructured data and some that is contained only in unstructured data. Unstructured data has a theoretical advantage of greater objectivity. As you may know, a group from Boston and industry have shared the perspective that machine learning applications often learn clinicians' thought processes even when using structured data, producing outputs that tell the clinician that which they already knew (PMID: 33785839). Unstructured data from clinical notes seems to reflect clinicians' thought process to an even greater degree. Please discuss these perspectives and justify the use of clinical notes alone in prediction modeling. Answer: We agree with the reviewer. As the unstructured data occupy 80% of the EHR, they can capture more detailed information on patients, resulting in better performance of machine learning models. As such, models trained on these data may better capture the thought process of the clinicians and the conditions of the patients compared to models trained on structured data. However, to conclude the advantages of using unstructured clinical notes over structured data for predictive modeling in our problem setting, we need to further experiment with only structured data as well as both structured and unstructured data. But, since the focus of this study is to unveil the potential of raw unstructured clinical notes for predicting mortality in adult ICU patients, we use solely unstructured clinical notes in prediction modeling for this work and leave the comparative analysis for future work. We added a brief discussion on these perspectives of using only clinical notes in prediction modeling in the Introduction section of the paper. Editorial comments: Journal requirements: 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. Answer: We revised the manuscript to meet the style requirements of the journal, including section headings, figure captions and references, and table captions and references. 2. Please state what role the funders took in the study. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. Answer: We have added the role of funders in the study. Here is the amended Role of Funder statement: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” 3. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Answer: We have removed all funding-related texts from the manuscript. We have removed the acknowledgment section from the manuscript and would like to update the Funding statement in the online submission form. Here is the amended statement: “This research used resources of the Knowledge Discovery Infrastructure at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725 and the Department of Veterans Affairs Office of Information Technology Inter-Agency Agreement with the Department of Energy under IAA No. VA118-16-M-1062. This manuscript has been in part co-authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of all authors are articulated in the ‘author contributions’ section.” 4. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. Answer: We have added and validated the ORCID iD for the corresponding author in the Editorial Manager. 5. 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 delete it from any other section. Answer: We have edited the ethics statement in the Methods section of our manuscript and removed it from the other section(s). 6. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Answer: We have reviewed the reference list to check for quality. We have updated several references to be more complete. 7. While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool. Answer: We have used PACE to make appropriate corrections to the figure files. We have uploaded the corrected figure files. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0262182.r002
19 Dec 2021 Decision Letter - Wajid Mumtaz, Editor Unstructured clinical notes within the 24 hours since admission predict short, mid & long-term mortality in adult ICU patients PONE-D-21-29049R1 Dear Dr. Maria Mahbub, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Wajid Mumtaz Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ******** 2. 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 4. 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 ****** 5. 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 ****** 6. 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: Thank you for this excellent contribution to the literature. ****** 7. 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: No https://doi.org/10.1371/journal.pone.0262182.r003
Formally Accepted
27 Dec 2021 Acceptance Letter - Wajid Mumtaz, Editor PONE-D-21-29049R1 Unstructured clinical notes within the 24 hours since admission predict short, mid & long-term mortality in adult ICU patients Dear Dr. Mahbub: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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. Wajid Mumtaz Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0262182.r004

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