Dear Dr Park,

Thank you for submitting your manuscript entitled "Sound reconstruction from human brain activity via a generative model with hierarchical auditory features" for consideration as a Research Article by PLOS Biology.

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 revised manuscript back to the peer reviewer.

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Kind regards,

Christian

Christian Schnell, PhD

Senior Editor

PLOS Biology

cschnell@plos.org

Dear Dr Park,

Thank you for your patience while we considered your revised manuscript "Sound reconstruction from human brain activity via a generative model with hierarchical auditory features" for consideration as a Research Article at PLOS Biology. Your revised study has now been evaluated by the PLOS Biology editors, the Academic Editor and one of the original reviewers.

In light of the reviews, which you will find at the end of this email, we are pleased to offer you the opportunity to address the remaining points from Reviewer 1 in a revision that we anticipate should not take you very long. We will then assess your revised manuscript and your response to the reviewers' comments with our Academic Editor aiming to avoid further rounds of peer-review, although we might need to consult with the reviewers, depending on the nature of the revisions.

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 1 month. 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 withdraw the manuscript.

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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.

Sincerely,

Christian

Christian Schnell, PhD

Senior Editor

PLOS Biology

cschnell@plos.org

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REVIEWS:

Reviewer #1: I thank the authors for making a substantial effort to improve the quality of the paper. Overall, the thorough revisions and additions have strengthened the contribution. I especially appreciated the effort taken to run a behavioral study on the generated sounds. For the most part, my concerns have been well addressed, and I found the paper a fascinating read and an impressive engineering feat.

A few remaining things that I believe would help the paper before publication, which can be addressed with fairly minor wording changes:

- I still don't think the claim of lack of hierarchical correspondence for decoding (line 566-568) is appropriately backed up by the presented results. Is this statement just referring to Figure S10A, with the single layer of the DNN decoding each region? Overall, lines 566-576 seem very bold to be making from just this result, and one would have to do substantial control analysis beyond what is currently in the paper to make sure that there are not additional confounds. I encourage the authors to significantly tone down this section.

- It is still not clear how the reconstruction of input provides "crucial insights" into neural coding (first line of the introduction, lines 57-58). This was also brought up in Reviewer 2's concern #8. I appreciate the authors' response to my concern #14; however, the response addresses linear decoding, which is not what the reconstruction process is doing. The main text now seems generally clear what the scientific contribution of the decoder vs. the reconstruction says, but I think some of the abstract and introduction should be modified with this in mind (i.e. first sentence mentioned above).

- The identifiability result with textured and scrambled stimuli at different lengths provides interesting insights into how the reconstructions are performing, however result this is not well captured in the abstract (the line "despite its ability to reconstruct exact temporal sequences" on 52 seems vague). I appreciated the authors interpretation of this result in the discussion and relating it to the nature of the fMRI signal, so perhaps using some similar wording in the abstract would help with clarity.

- For the category specific analysis of the behavioral results (lines 292-294), is the randomly selected alternative always from the same category? Or is this just the average across the same and different categories (I think it is probably this)? As written, it is a little unclear in the main text.

- Also, regarding the behavioral results, can any within-category confusions be reported (i.e. something similar to Fig S6 for the modeling results). For instance, it seems likely that a speech sound is easy to tell apart from thunder, but then the identification of one speech sound from another speech sound is close to chance. This would be good to know and would help the interpretation of the behavioral results.

- I do not think there is enough data to validate lines 326-328. This observation could perhaps be mentioned in the discussion as a future direction, but it seems inappropriate for the results.

- Error bars are not included in Fig 8C. If there is a reason they are not included (for instance if they are too small as mentioned in the rebuttal for other plots), then this should be mentioned in the caption, especially for the human ratings.

Dear Dr Park,

Thank you for your patience while we considered your revised manuscript "Sound reconstruction from human brain activity via a generative model with hierarchical auditory features" 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 different title to improve its accessibility for our broad audience:

Natural sounds can be reconstructed from human neuroimaging data using a deep neural network

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

* Please specify whether the participants provided written or oral consent.

* 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).

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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: 3CD, 4DG, 5CF, 6, 7, 8C, S3B, S4B, S5C, S6, S7, S8, S9B, S10, S12B, S13B, S14AC, S15 and S16B.

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).

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

* CODE POLICY

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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 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 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

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*Published Peer Review History*

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*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 Dr Park,

Thank you for the submission of your revised Research Article "Natural sounds can be reconstructed from human neuroimaging data using deep neural network representation" for publication in PLOS Biology. On behalf of my colleagues and the Academic Editor, Manuel Malmierca, 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