Peer Review History
| Original SubmissionNovember 4, 2020 |
|---|
|
PONE-D-20-34763 Neural representation of words within phrases: Temporal evolution of color-adjectives and object-nouns during simple composition PLOS ONE Dear Dr. Fyshe, 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. Both Reviewers noticed some critical aspects and required clarifications that should be addressed to improve the overall quality of the Manuscript. 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 Feb 05 2021 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:
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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Nicola Molinaro, 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 2.In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 3.Thank you for stating the following in your Competing Interests section: "No" Please complete your Competing Interests on the online submission form to state any Competing Interests. If you have no competing interests, please state "The authors have declared that no competing interests exist.", as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now This information should be included in your cover letter; we will change the online submission form on your behalf. Please know it is PLOS ONE policy for corresponding authors to declare, on behalf of all authors, all potential competing interests for the purposes of transparency. PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests 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: I Don't Know 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: Yes ********** 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: The present study proposes a decoding approach to study noun adjective brain representations from MEG recordings during a production task. The original data corresponds to a previously published study in which pictures had to be described only using nouns, adjectives, or noun adjectives in a compositional or list manner. The authors track the neural representations of noun and adjectives over time, and explore the similarity between the representation of noun and adjectives before producing the words in isolation compared to the representation of the same words produced during compositional or list like contexts by training and testing the regression models across conditions. They conclude that noun and adjective representations behave differently: nouns are more decodable and their representation is more consistent across time and context, whereas adjectives are less decodable across contexts and time, and hence their representation is more variable. The manuscript is well written, the objectives and hypothesis are clearly stated, the methodological approach seems correctly conducted and is consistent with the author's questions. I specially value the collaboration between research groups and the repurpose of already collected data. Overall the paper is good but I would suggest the authors to make more explicit some specifications of the statistical analyses (see below) as well as to enrich the discussion on the following points: Variability of noun adjective representations in comprehension and production tasks. Invariability of noun representation across time in this production task is somewhat unexpected. In the phrasal context the combination of noun and adjective would elicit a different representation of the noun (a lamp that is red, not any lamp), and the combined representation would have to be broken down into their constituent representations (red, lamp) to produce the correct articulation. Considering that the original article shows a composition activity, noun representation when modified by the adjective should correspond to a different representation than the noun in isolation. In this sense brain representation of noun and adjective in the list context would be expected to be more consistent across time than noun in phrases. Moreover, how does this result on adjective variability and noun robustness of representation in the production task relate to the somewhat symmetrical result in the comprehension task studied in Fyshe et al., 2019. Finally, did the authors explore how are the decoding accuracies for nouns and adjectives when training and testing the models across the context conditions? This could provide important information on the effect of composition on noun and adjective representation. Accuracy before speech onset The authors mention that the increased decoding accuracy for the adjective representation prior to word articulation is motor related. This would mean that the early representation of adjectives is also partly motor related? The hypothesis suggested by the authors would benefit from some discussion on word multimodal representation at early stages of word processing. In relation to the methods sections some points should be made more clear and detailed so reproduction is possible: M1. The preprocessing parameters seem to be different from the original paper (i.e: epochs length, filters). If this is the case, the authors should specify all of the information concerned with the preprocessing (i.e: trial rejection, all filter specifications). If the authors did not start their study from raw data I would suggest the authors to refer the readers to the original paper for the preprocessing details. Although note that in the original paper filter specifications that would allow replicating the preprocessing are missing (filter type, cutoff frequency, filter order, roll-off or transition bandwidth, direction of computation). M2. Authors should be more explicit on the details of the permutation cluster analysis. The null distribution was constructed taking the cluster with the maximum statistic sum? or all clusters F sum were included?. If the statistic F corresponds to the interaction obtained by a 3x2 ANOVA for the time points 100-190ms, how were the main effect cluster times determined?, this should be more thoroughly explained and justified. M3. I would suggest the authors to incorporate the statistical results for the 2x2 ANOVAs contrasting the isolated word stimuli to the phrases and list trials Minor issues are detailed below separated by sections METHODS M4. Please specify the order of presentation for the different condition blocks M5. “with a sampling frequency of 1000Hz” This refers to the recording parameters not the filter specifications? M6. Note 40HZ in all caps M7. Misphrased: total of N choose 2 pairs in p.7 M8. Authors should cite software and statistical packages used to carry the analyses, providing information on versions, etc. RESULTS R1. This phrase is not clear: “A main effect of word-category was significant at 240-395ms, with higher decoding accuracies for nouns than adjectives and at 580-650, with higher decoding accuracies for adjectives than nouns (Figure 2, gray shading).” R2. As separate models for each participant were trained authors should report the variability across subjects on top of the average model performance. R3. Misphrased: “Isolated noun representations HAD DID not generalize well to list contexts, and did not show generalization across time” DISCUSSION D1. Replace an for a in “of an adjectives” in p.15 D2. Misphrased “which no sustained activations” in p.15 Reviewer #2: The paper by Honari-Jahromi and colleagues presents an important and under-researched question in cognitive neuroscience of language – how stable are the neural representations of the semantic properties of adjectives and nouns across both temporal, contextual and combinatorial dimensions. To answer this question they use a MEG data and a combination of decoding techniques. Results they present are interesting and compelling. Overall I am very happy with both the quality of the paper, novelty of the question and the analysis used to answer it, however there are several areas that would require improvement and clarifications. Major 1. The methods section describing the analysis used (p. 7) requires a lot of clarification. The stages of the decoding analysis are not clear from the text and at present it would be difficult to replicate it. For instance, what is the dimensionality of the data and predictor matrixes? What distance d was used for vector comparison (Cosine? Mahalanobis?)? In each regression (n=300) the predicted single value (the nth dimension of the semantic vector) is derived/estimated from channel x time matrix? Was the data averaged over these 100ms? Was here some dimensionality reduction performed on the sensors? Or was the stimulus value estimated by integration over all 100 time points and channels (multiplied by the learned decoder matrix)? I think for the benefit of the reader an explanatory figure (showing data dimensionality and schematic representation of steps) and formula describing the model as well as references to the exact method are necessary. 2. Semantic vectors/embeddings when derived from collocational matrixes or with neural networks to some degree reflect the frequency of the words they encode. Vectors of more frequent words tend to be more similar to each other than vectors of less frequent words. In this dataset, were the adjectives and nouns matched on word form / lemma frequency? Could better decodability of nouns across contexts and times be simply due to their higher frequency and greater vector similarity (to each other), when comped to adjectives? 3. Since decoding happened within participants (not on pooled data) and the accuracies were simply averaged, this means that decoding variability between participants was not “accounted for” and observed effects cannot be generalised outside of this sample – the models trained on one participant cannot be used to predict data in another participant/s – and this needs to be acknowledged explicitly. Minor 1. Introduction p.3 para.2 - “complex effects of ambiguity” is a bit ambiguous. Do you mean in sentences or in narratives? In complex and naturalistic listening conditions. Please clarify. 2. Methods section p.5 “spoken and signed language as regards to the neural correlates ..” did you mean “with regards to”? 3. Did any artefact rejection or blink / heart beat removal with ICA take place? I appreciate that when using decoding artefact rejection is not strictly compulsivity as with ERPs but it is good to state this explicitly and give some references. 4. The Statistical significance section on p. 8 is somewhat difficult to read, especially the second paragraph. Was ANOVA done first across all time points and then 0.05 cutoff applied (seems that way since F values were summed for cluster mass estimate)? The word ‘label’ is ambiguous, please clarify. 5. p.9 para 2 “… similar patterns will be picked out by regression.. ” not clear, not sure ‘patterns’ is the right word. Do you mean to say regression weights learned in one window will also generate above-chance performance in another window. 6. Results p.10 was responce accuracy above 90% for all participants? 7. Figure 2 – most of the figure 1 caption text belongs in the text of the results section, not in the figure caption. Also please explain exactly why you think the demand to attend to the background colour improved decodability for adjectives in lists. 8. p.11 “we found an interaction effect...” please explain 9. Figure 3 and 4 – does the black contouring indicate statistical significance? Again, please consider putting text that describes results out of the caption and into main text. 10. It would be useful throughout the manuscript to refer to not simply ‘representations’ but semantic or lexicon-semantics representation, since this is what model was trained to decode (as opposed to say phonological representations). 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. |
| Revision 1 |
|
Neural representation of words within phrases: Temporal evolution of color-adjectives and object-nouns during simple composition PONE-D-20-34763R1 Dear Dr. Fyshe, 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, Nicola Molinaro, Ph.D. Academic Editor PLOS ONE |
| Formally Accepted |
|
PONE-D-20-34763R1 Neural representation of words within phrases:Temporal evolution of color-adjectives and object-nouns during simple composition Dear Dr. Fyshe: 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. Nicola Molinaro Academic Editor PLOS ONE |
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 .