Dear Shuo,

Thank you for submitting your manuscript entitled "Neural computations of visual, semantic, and memorability features in the human brain" for consideration as a Research Article by PLOS Biology. Please allow me to apologize for the long delay in getting back to you. It took us a bit longer than usual to discuss your appeal with an Academic Editor.

In any case, your manuscript has now been evaluated by the PLOS Biology editorial staff as well as by an academic editor with relevant expertise and I am writing to let you know that we would like to send your submission back for external peer review. I should say that we are not fully convinced that all reviewer concerns are sufficiently addressed and the revision leaves a sufficiently strong manuscript for PLOS Biology, but we would like to see what the reviewers think about the revision. We will be looking for strong support from the reviewers.

However, before we can send your manuscript to reviewers, we need you to complete your submission by providing the metadata that is required for full assessment. To this end, please login to Editorial Manager where you will find the paper in the 'Submissions Needing Revisions' folder on your homepage. Please click 'Revise Submission' from the Action Links and complete all additional questions in the submission questionnaire.

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Feel free to email us at plosbiology@plos.org if you have any queries relating to your submission.

Kind regards,

Christian

Christian Schnell, PhD

Senior Editor

PLOS Biology

cschnell@plos.org

Dear Dr Wang,

Thank you for your patience while we considered your revised manuscript "Neural computations of visual, semantic, and memorability features in the human brain" for publication as a Research Article at PLOS Biology. I am currently handling your manuscript while my colleague Christian Schnell is away from the office this week. Please accept my sincere apologies for the delays that you have experienced during this round of the peer review process. Your revised study has been evaluated by the PLOS Biology editors, the Academic Editor and two of the original reviewers.

In light of the reviews, which you will find at the end of this email, we would like to invite you to revise the work to thoroughly address the reviewers' reports.

As you can see, the reviewers agree that the revised version is strengthened and Reviewer #2 is now satisfied with the responses to the previous comments. However, Reviewer #1 continues to raise concerns about the analysis and interpretation of the data. Specifically, this includes the statistical models used to deal with multiple observations from the same subjects and that the HGP plots appear highly similar across brain regions.

Given the extent of revision needed, we cannot make a decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is likely to be sent for further evaluation by all or a subset of the reviewers.

In addition to these revisions, you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests shortly.

We expect to receive your revised manuscript within 3 months. Please email us (plosbiology@plos.org) if you have any questions or concerns, or would like to request an extension.

At this stage, your manuscript remains formally under active consideration at our journal; please notify us by email if you do not intend to submit a revision so that we may withdraw it.

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You should also cite any additional relevant literature that has been published since the original submission and mention any additional citations in your response.

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https://blogs.plos.org/plos/2019/05/plos-journals-now-open-for-published-peer-review/

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Thank you again for your submission to our journal. We hope that our editorial process has been constructive thus far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Best regards,

Richard

Richard Hodge, PhD

Senior Editor, PLOS Biology

rhodge@plos.org

On behalf of:

Christian Schnell, PhD

Senior Editor, PLOS Biology

cschnell@plos.org

------------------------------------

REVIEWS:

Reviewer #1: In this revised manuscript, the authors have made substantial changes to the presentation, reporting and interpretation of their findings, including new data. These updates have strengthened the authors' claims, however, there remain key issues regarding anatomical and physiological treatment/interpretation of the data.

Major:

PFC results and nested data: As intracranial data is nested, i.e. contains multiple observations from the same individuals, it is standard practice to deal with this violation of observation independence via mixed effects designs or collapsing observations within individuals. This issue was raised for PFC findings because it was clear that only a subset of data/subjects (10 electrodes) were driving the statistical effect. The authors have responded to these concerns, but I'm not sure the key issue has been adequately addressed. Firstly, I appreciate the authors focused only on responsive electrodes and have added more PFC data. However, of the 59 "added" electrodes (6 subjects), what is important are how many were responsive and made it into the analysis, for which it appears 29 responsive probes were actually added (with 12 total being significant). I might not have followed correctly as the authors didn't make this clear, but only 2 additional/significant PFC electrodes were actually added. Secondly, the authors note that 7/20 subjects contributed significant PFC channels, suggesting the results are not driven by individual differences. However, this is actually the concern being raised, namely that less than half of the sample shows the reported effect, suggesting it's driven by a subset of subjects and doesn't strongly replicate as an observation. In relation to this, I appreciate that the authors have tried alternative statistical methods to suggest that controlling for subject nesting isn't necessary, but this is more a basic principle of statistical testing than an empirical question. A mixed-effects model, with subjects as a random factor, is required to appropriately deal with multiple observations from the same subjects. I do acknowledge that the authors have adjusted the strength of their claims regarding this result. Finally, the authors note some subjects had repeated recording sessions, it's not clear if this means during the same implantation or a second surgery. If this is just a second session during the same invasive monitoring, it should not be treated as new electrodes/observations, simply more trials for those individuals.

Response timing: It is expected that responses in visual regions occur before those in the MTL and PFC, following a wealth of data. The concern raised regarding the timing of responses was about the data itself, rather than methods of response time detection (onset/peak). As is clear from revision Figure 1, mean HGP plots appear highly similar across brain regions, with changes occurring at/before time zero. This suggests that HGP data has been heavily smoothed, and raises concerns for how such data across brain regions can look so similar. While the authors might highlight their focus on latency of the peak response, this is still being estimated from data that suggests brain-wide response onset across regions immediately to stimulus presentation, which makes little physiological sense.

Minor:

Model comparison: I appreciate the authors' expanding their modeling analysis. This is very helpful, particularly for the ResNet (visual) and SGPT (semantic) models. However, should we be surprised or read into the finding that multiple layers of SBERT and ResMem outperform or are equal to the final layer in terms of significant channel %? Is that because earlier layers rely more on visual features, so we should expect a greater percentage than later layers?

Reviewer #2: The authors have done a fantastic job at thoroughly addressing my comments and those of the other reviewers. I greatly appreciated the updated introduction that makes the theoretical contribution of the work clearer. The many additional analyses (e.g., using other models, running additional 7T analyses, etc) have also really solidified the strength of the findings. Overall this work will be an important and impactful contribution to the literature and our understanding of how vision and memory work and interact. Great work.

Dear Shuo,

Thank you for your patience while we considered your revised manuscript "Neural computations of visual, semantic, and memorability features in the human brain" for publication as a Research Article at PLOS Biology. This revised version of your manuscript has been evaluated by the PLOS Biology editors and the Academic Editor.

Based on our Academic Editor's assessment of your revision, we are likely to accept this manuscript for publication, provided you satisfactorily address the following data and other policy-related requests:

* We would like to suggest a slightly different title to improve readability and accessibility for our broad audience. Would any of these two titles work for you?

Characterization of the spatiotemporal representations of visual, semantic, and memorability features in the human brain

OR

Dissociable spatiotemporal representation of visual, semantic and memorability features in the human brain shape object recognition and memory formation

* Please add the links to the funding agencies in the Financial Disclosure statement in the manuscript details.

* Please include the approval/license number of the ethical approval for the experiments.

* Please include information in the Methods section whether the study has been conducted according to the principles expressed in the Declaration of Helsinki.

DATA POLICY:

You may be aware of the PLOS Data Policy, which requires that all data be made available without restriction: http://journals.plos.org/plosbiology/s/data-availability. For more information, please also see this editorial: http://dx.doi.org/10.1371/journal.pbio.1001797

Note that we do not require all raw data. Rather, we ask that all individual quantitative observations that underlie the data summarized in the figures and results of your paper be made available in one of the following forms:

1) Supplementary files (e.g., excel). Please ensure that all data files are uploaded as 'Supporting Information' and are invariably referred to (in the manuscript, figure legends, and the Description field when uploading your files) using the following format verbatim: S1 Data, S2 Data, etc. Multiple panels of a single or even several figures can be included as multiple sheets in one excel file that is saved using exactly the following convention: S1_Data.xlsx (using an underscore).

2) Deposition in a publicly available repository. Please also provide the accession code or a reviewer link so that we may view your data before publication.

Regardless of the method selected, please ensure that you provide the individual numerical values that underlie the summary data displayed in the following figure panels as they are essential for readers to assess your analysis and to reproduce it: 3D, 4BCDEGHIJLMNO, and 6ABCDFHI

NOTE: the numerical data provided should include all replicates AND the way in which the plotted mean and errors were derived (it should not present only the mean/average values).

Please also ensure that figure legends in your manuscript include information on where the underlying data can be found, and ensure your supplemental data file/s has a legend.

Please ensure that your Data Statement in the submission system accurately describes where your data can be found.

* CODE POLICY

Per journal policy, if you have generated any custom code during the course of this investigation, please make it available without restrictions. Please ensure that the code is sufficiently well documented and reusable, and that your Data Statement in the Editorial Manager submission system accurately describes where your code can be found.

Please note that we cannot accept sole deposition of code in GitHub, as this could be changed after publication. However, you can archive this version of your publicly available GitHub code to Zenodo. Once you do this, it will generate a DOI number, which you will need to provide in the Data Accessibility Statement (you are welcome to also provide the GitHub access information). See the process for doing this here: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content

As you address these items, please take this last chance to 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 cover letter that accompanies your revised manuscript.

In addition to these revisions, you may need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests shortly. If you do not receive a separate email within a few days, please assume that checks have been completed, and no additional changes are required.

We expect to receive your revised manuscript within two weeks.

To submit your revision, please go to https://www.editorialmanager.com/pbiology/ and log in as an Author. Click the link labelled 'Submissions Needing Revision' to find your submission record. Your revised submission must include the following:

- a cover letter that should detail your responses to any editorial requests, if applicable, and whether changes have been made to the reference list

- a Response to Reviewers file that provides a detailed response to the reviewers' comments (if applicable, if not applicable please do not delete your existing 'Response to Reviewers' file.)

- a track-changes file indicating any changes that you have made to the manuscript.

NOTE: If Supporting Information files are included with your article, note that these are not copyedited and will be published as they are submitted. Please ensure that these files are legible and of high quality (at least 300 dpi) in an easily accessible file format. For this reason, please be aware that any references listed in an SI file will not be indexed. For more information, see our Supporting Information guidelines:

https://journals.plos.org/plosbiology/s/supporting-information

*Published Peer Review History*

Please note that you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. Please see here for more details:

https://plos.org/published-peer-review-history/

*Press*

Should you, your institution's press office or the journal office choose to press release your paper, please ensure you have opted out of Early Article Posting on the submission form. We ask that you notify us as soon as possible if you or your institution is planning to press release the article.

*Protocols deposition*

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. 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

Please do not hesitate to contact me should you have any questions.

Sincerely,

Christian

Christian Schnell, PhD,

Senior Editor

cschnell@plos.org

PLOS Biology

------------------------------------------------------------------------

Reviewer remarks:

Reviewer #1: I appreciate the author's additional responses to the prior round of review, I have no further comments.

Dear Shuo,

Thank you for your patience while we considered your revised manuscript "Characterization of the spatiotemporal representations of visual, semantic, and memorability features in the human brain" for publication as a Research Article at PLOS Biology. This revised version of your manuscript including the updated source data file has been evaluated by the PLOS Biology editors.

Unfortunately, I still could not fully match the source data to the figure plots, and some of the plots were also different to the original plots in the paper. I have checked this only carefully for Figure 3D. Because our editorial office will be closed from Monday Dec 22nd to Jan 4th, I am returning the manuscript back to you for a careful check. Please have a look through the figures and make sure that the source data match the data presented in the figures. Please also provide a short rationale for any changes to the figures that need to be made, including the one you have already provided. I have not updated the figure yet, but you can do this now yourself.

As you address these items, please take this last chance to 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 cover letter that accompanies your revised manuscript.

In addition to these revisions, you may need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests shortly. If you do not receive a separate email within a few days, please assume that checks have been completed, and no additional changes are required.

We expect to receive your revised manuscript within three weeks.

To submit your revision, please go to https://www.editorialmanager.com/pbiology/ and log in as an Author. Click the link labelled 'Submissions Needing Revision' to find your submission record. Your revised submission must include the following:

- a cover letter that should detail your responses to any editorial requests, if applicable, and whether changes have been made to the reference list

- a Response to Reviewers file that provides a detailed response to the reviewers' comments (if applicable, if not applicable please do not delete your existing 'Response to Reviewers' file.)

- a track-changes file indicating any changes that you have made to the manuscript.

NOTE: If Supporting Information files are included with your article, note that these are not copyedited and will be published as they are submitted. Please ensure that these files are legible and of high quality (at least 300 dpi) in an easily accessible file format. For this reason, please be aware that any references listed in an SI file will not be indexed. For more information, see our Supporting Information guidelines:

https://journals.plos.org/plosbiology/s/supporting-information

*Published Peer Review History*

Please note that you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. Please see here for more details:

https://plos.org/published-peer-review-history/

*Press*

Should you, your institution's press office or the journal office choose to press release your paper, please ensure you have opted out of Early Article Posting on the submission form. We ask that you notify us as soon as possible if you or your institution is planning to press release the article.

*Protocols deposition*

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. 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

Please do not hesitate to contact me should you have any questions.

Sincerely,

Christian

Christian Schnell, PhD

Senior Editor

cschnell@plos.org

PLOS Biology

Dear Shuo,

Happy new year and thank you for the submission of your revised Research Article "Characterization of the spatiotemporal representations of visual, semantic, and memorability features in the human brain" for publication in PLOS Biology. On behalf of my colleagues and the Academic Editor, Christopher Pack, I am pleased to say that we can in principle accept your manuscript for publication, provided you address any remaining formatting and reporting issues. These will be detailed in an email you should receive within 2-3 business days from our colleagues in the journal operations team; no action is required from you until then. Please note that we will not be able to formally accept your manuscript and schedule it for publication until you have completed any requested changes.

Please take a minute to log into Editorial Manager at http://www.editorialmanager.com/pbiology/, click the "Update My Information" link at the top of the page, and update your user information to ensure an efficient production process.

PRESS

We frequently collaborate with press offices. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If the press office is planning to promote your findings, we would be grateful if they could coordinate with biologypress@plos.org. If you have previously opted in to the early version process, we ask that you notify us immediately of any press plans so that we may opt out on your behalf.

We also ask that you take this opportunity to read our Embargo Policy regarding the discussion, promotion and media coverage of work that is yet to be published by PLOS. As your manuscript is not yet published, it is bound by the conditions of our Embargo Policy. Please be aware that this policy is in place both to ensure that any press coverage of your article is fully substantiated and to provide a direct link between such coverage and the published work. For full details of our Embargo Policy, please visit http://www.plos.org/about/media-inquiries/embargo-policy/.

Thank you again for choosing PLOS Biology for publication and supporting Open Access publishing. We look forward to publishing your study.

Sincerely,

Christian

Christian Schnell, PhD

Senior Editor

PLOS Biology

cschnell@plos.org