PONE-D-24-18061Computing nasalance with MFCCs and Convolutional Neural NetworksPLOS ONE

Dear Dr. Lozano Durán,

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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: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: No

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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: No

Reviewer #2: Yes

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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: No

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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: Questions:

"Based on these dual-channel recordings, it is possible to compute Nasalance, which is the ratio of nose energy to mouth and nose energy in a small 300 Hz band centered around 600 Hz. [5, 7]."

Q1) Why the center frequency reduced to 500Hz (in method) instead of 600Hz according to the reference [5, 7] as mentioned in the Introduction?

Q2) According to the method described by Mathad et al. (2021), MFCCs and their first and second deltas were utilized to train the DNN. In contrast, your method includes only MFCCs without the deltas, which requires further explanation. [if there is no justification provided, please implement R2]

For Revision:

R1) In comparison to the reference study by Mathad et al. 2021, which utilized a substantial 100-hour database, the training model in that study is robust enough to mitigate any subset effects. However, the current paper relies on only 2 hours of data without employing cross-validation. To enhance the reliability of the results, I recommend implementing cross-validation and conducting a straightforward comparison of accuracy (%) means to strengthen the statistical validity of the findings.

R2) The deltas of MFCCs are crucial, as demonstrated in numerous studies, for capturing the temporal dynamics that are often lost during time windowing. By including the deltas, the current spectral dimension would be expanded to a three-dimensional matrix: 2 (channels) × 39 MFCC features (13 MFCCs + 13 first deltas + 13 second deltas) × 26 timeframes. This addition would enhance the model's ability to recover temporal information.

Typos/Corrections:

T1) Ensure that all graphs include labels on the y-axis. Currently, they are missing.

T2) Address the numerous typos throughout the paper, with particular attention to consistent capitalization and formatting of "MFCCs."

Reviewer #2: The utilization of CNN on MFCC for classification and nasal and oral radiated energy based classification are well-established. So, the article has lack of novelty. The description of the optimized kernel is confusing. The author should represent the kernel with respect to individual MFCC and their derivatives. The word and phrase selection should be unified. For an example, the spectrogram and MFCC are used same purpose, which made the reader confused.

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Reviewer #1: No

Reviewer #2: Yes: Md Mahbub Hasan

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PONE-D-24-18061R1Computing nasalance with MFCCs and Convolutional Neural NetworksPLOS ONE

Dear Dr. Lozano Durán,

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.

Because neither of the original reviewers were able to re-review this manuscript, a third reviewer was recruited. This reviewer raises some important points that should be addressed, including coverage of relevant literature, data coding and analysis, and interpretation of results.  Please revise the manuscript to address the points raised by R3 and it will be reassessed for suitability for publication in PLOS One.

Please submit your revised manuscript by Nov 22 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.

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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.

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We look forward to receiving your revised manuscript.

Kind regards,

Laura Morett

Academic Editor

PLOS ONE

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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 #3: (No Response)

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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 #3: Partly

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: 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 #3: Yes

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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 #3: Yes

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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 #3: This study attempt to create a nasalance-like metric directly from acoustics, using deep learning models. The study is quite nice in many respects, but there are issues that would need to be addressed before publication can be considered. These issues are listed below in the order (broadly) that they appear in the paper.

Abstract, Table 1, elsewhere: "The test data were recorded in Spain and included short words (-dynamic), sentences (+dynamic), and diakinetic syllables (+dynamic)"

-What do these +/- labels mean? Why is the /ka/ in "ka" considered "dynamic" but the /ka/ in "boka" isn't? These terms are never defined or justified.

-I am not familiar with the term "diakinetic". Do you mean "diadochokinetic"?

p.3: "To our knowledge, only one ML model has the flexibility of Nasometry [18]"

-The authors may want to be aware of similar works that have previous been carried out, for example Siriwardena et al. (2024) and Carignan (2021), the latter of which has been extended to low-resource languages (Carignan et al., 2023) and hyper-nasality in children (Fagniart et al., 2024), two goals which the current study also aims to meet.

Carignan, C. (2021). "A practical method of estimating the time-varying degree of vowel nasalization from acoustic features", J. Acoust. Soc. Am. 149 (2), 911–922. doi: https://doi.org/10.1121/10.0002925

Carignan, C., Chen, J., Harvey, M., Stockigt, C., Simpson, J. & Strangways, S. (2023). "An investigation of the dynamics of vowel nasalization in Arabana using machine learning of acoustic features”, Laboratory Phonology 14(1). doi: https://doi.org/10.16995/labphon.9152

Fagniart, S., Charlier, B., Delvaux, V., Huberlant, A., Harmegnies, B.G., Piccaluga, M., & Huet, K. (2024). "Consonant and vowel production in children with cochlear implants: acoustic measures and multiple factor analysis", Front. Audiol. Otol. 2:1425959. doi: 10.3389/fauot.2024.1425959

Siriwardena, Y.M., Boyce, S.E., Tiede, M.K., Oren, L., Fletcher, B., Stern, M., & Espy-Wilson, C.Y. (2024). "Speaker-independent speech inversion for recovery of velopharyngeal port constriction degree", J. Acoust. Soc. Am. 156 (2), 1380–1390. doi: https://doi.org/10.1121/10.0028124

-You say that European Spanish is "a non-nasal dialect" (p.3) and that "Costa Rican Spanish is known to be highly nasal, while European and Chilean Spanish are comparatively similarly oral" (p.15), but how do these statements align with the statement that "vowels in contact with nasal consonants tend to be nasalized (universally)" (p.2)?

p.4: "These signals are divided into 250 ms windows with 100 ms overlap (i.e., every window starts 100 ms after the previous one)"

-Based on this description, it would seem that every window starts 150 ms (not 100 ms) after the previous one.

p.6: "(/m/, /n/ and /ñ/)"

-"/ñ/" is not a symbol used in the IPA to denote any known consonant

p.6: "In this study, we assumed that the entire vowel was nasalized if it was shorter than 60 ms, 50% if it was between 60 and 90 ms, and 30% if it was longer than 90 ms."

-Based on what evidence?

p.7: "The transformation from a percentage to a 4-level scale required deciding the limits among classes. As we knew in advance how many children were classified perceptually as oral or nasal, or as Oral, Mild, Moderate or Severely nasal, we assumed that the same numbers would apply in the case of nasalance measures. Thus, after every simulation, the results were sorted per mfccNasalance, with the first N cases being categorized as Healthy, the next M cases as Mild, etc."

-This should be explained much more clearly, I don't understand this at all. Does this just meant that you assigned identical labels as the perceptual labels?

p.9: "Fiinally, the percentage ratings were recoded using a 4-level scale. Oral: nasality ≤ 0.05; Mild: 0.05 < nasality ≤ 0.25; Moderate: 0.25 < nasality ≤ 0.50; Severe: nasality > 0.50."

-Based on what evidence?

p.9: "Nasalance was computed as the ratio of nasal acoustic energy to the sum of oral and nasal energy"

-Please specify that you used RMS energy, as shown in the Praat script.

Fig.6, etc.: Why not two sets of box plots, or two sets of violin plots, etc.? Why one box plot and one line?

Fig.6, etc.: The caption says "Correlation between e-Nasalance [...] and mfccNasalance", but this is not accurate. They are separate correlations between e-Nasalance and perceptual scores, and mfccNasalance and perceptual scores.

p.10: "the scores are higher than eNasalance in most cases (i.e. all except the lower 25th percentile)."

-Are you referring to the lower whisker? The whisker is not the 25th percentile.

Table 2: Do you mean "p" instead of "s"? Also, what is "k11"?

p.13: "(Fig. 7 down right)" -> "bottom right"

p.14: "These results are compatible with the fact that nasalance is a poor approximation to perceptual nasality"

-Citation needed. Nasalance arose as a methodology precisely because it approximates perceptual nasality.

p.14: "in contrast, as we only need to know that a nasal sound was present (and not the exact location)"

-Maybe I've misunderstood, but this doesn't seem correct, because you based your labels off of phone-wise segmentation. In order to have phone-wise segmentation, you need to know the exact location of that phone in the speech stream.

-Punctuation errors throughout.

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Reviewer #3: No

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PONE-D-24-18061R2Computing nasalance with MFCCs and Convolutional Neural NetworksPLOS ONE

Dear Dr. Lozano Durán,

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 Dec 21 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,

Laura Morett

Academic Editor

PLOS ONE

Journal Requirements:

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.

Additional Editor Comments:

I thank the authors for their attention to the points raised in the last round of reviews. I agree with R3 that the revisions largely address the points raised by the reviewers, and I ask that they address the remaining points raised by R3. Provided they do so, I will render a decision without re-sending the manuscript for review.

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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 #3: (No Response)

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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 #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: 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 #3: Yes

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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 #3: Yes

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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 #3: Some minor issues still remain from my previous comments, but by and large the authors have done an admirable job with the revision!

p.2: "Furthermore, there are currently multiple machine learning (ML) algorithms that may serve to classify complex feature sets, such as MFCCs (see [12-14]), or high-speed nasopharyngoscopy [15]."

-The authors seem to have missed the point in providing these additional references, which are not simply for "classify[ing] complex feature sets". Carignan (2021) uses MFCCs in combination with other acoustic features to train an ML algorithm to create nasalance-like signals, and compares the results with nasometry measures. Siriwardena et al. (2024) use the full acoustic waveform to train an ML algorithm to create nasalance-like signals, and compare the results with nasopharyngoscopy. Therefore, both of these works have previously used speech acoustics to train ML algorithms to create nasalance-like signals, in a similar manner to Mathad et al. (2021) and to the current study, which is somewhat at odds with the claim that "only one ML model has the flexibility of Nasometry" (p. 2); both Carignan (2021) and Siriwardena et al. (2024) were carried out very specifically to generate nasalance-like signals from speech acoustics using ML algorithms.

Response 13: “s” is changed to “p”

-"s" still remains in the text at many different points

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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 #3: No

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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.

Computing nasalance with MFCCs and Convolutional Neural Networks

PONE-D-24-18061R3

Dear Dr. Lozano Durán,

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.

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Laura Morett

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

I thank the authors for their revisions in response to the remaining points raised by R3. The manuscript can now be accepted for publication in PLOS One.

Reviewers' comments: