Novel feature extraction method for signal analysis based on independent component analysis and wavelet transform

Mariusz Topolski; Jędrzej Kozal

doi:10.1371/journal.pone.0260764

Peer Review History

Original SubmissionJuly 27, 2021
28 Sep 2021 Decision Letter - Mahmoud Al Ahmad, Editor PONE-D-21-24171Novel Feature Extraction Method for Signal Analysis based on Independent Component Analysis and Wavelet TransformPLOS ONE Dear Dr. Topolski, 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 Nov 12 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. 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If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only [Note: HTML markup is below. Please do not edit.] 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: Yes 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: No 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 authors propose a novel method for signal feature extraction that combines analysis of the signal waveform and separation of its sources. A wavelet transform is used to modify a mixing matric in the independent component analysis. The approach was validated using an ECG heartbeat classification, against 4 target classes; normal, vestibular ectopic beats and ventricular ectopic beats and fusion strikes. A 95.79% recall was obtained and the authors claim the method performance is close to that of convolutional neural networks for classes with limited number of learning examples and can be easily deployed in environments with limited computing power. Interesting research questions. 1. Include references for the following; Line 11 “… well-established datasets and evaluation procedures” Line 12”… well-performing algorithms developed specifically for this field.” Line126 “In principal component analysis correlation coefficient…” Line 314 “The proportion of data in train 314 and test split is defined by stratified 5-fold cross validation.” Line 405 “In years 2006-2007 first approaches that combined DWT with ICA were proposed.” Line 410 “Due to this fact, we were able to 410 obtain better results compared to other feature extraction methods.” 2. Several abbreviations should be defined before use; ECG, EMG, TP, TN, FN, FP, MLP 3. Certain sentences require commas to read better. Grammatical errors should be corrected; line 27-28, 58-60, 67-68, 73-75,90-91,138-139, 311-312, 469 (This is not an exhaustive list. Authors are advised to re-read the manuscript) 4. Section 1.1 and section 1.2 are both discussed as feature extraction methods. Section 1.1 should therefore be renamed appropriately perhaps as Independent Component Analysis 5. Consistency should be maintained. Equation (17) D is undefined. Does it refer to the width of the window which was defined as d in the text? Ensure all variables used in equations are defined e.g Df in eqn 24 & 25. 6. Justification for using negentropy should be included. 7. Line 276 ci? 8. Table 5 and 6 should be swapped to correspond with the order in which they are discussed in the text to reduce confusion. 9. Table headings could be more descriptive e.g “Table 5 Best MLP network for heart beat classification compared to selected convolutional networks reported in the literature” 10. Authors argue that in low data regimes the proposed method is comparable to convolutional neural networks, this could be included in the comparison tables for ease of comparison. 11. Justification for some choice of algorithms should be included e.g why stratified 5-fold cross validation, Pan-Tompkins algorithm etc… were these selected because they are commonly used in the literature? Could the technique benefit from other choices? Reviewer #2: The contribution of this paper is exciting and original. The proposed method seems to be valid for signal feature extraction. The procedure using signal processing can successfully lead to separation between the signal waveform from its resources. Experiments were carried out with an MIT-BIH database to illustrate the four classifications(Normal, Vestibular ectopic beats, Ventricular ectopic beats, and Fusion strikes). The derivations, experimental setup, and discussion section are clear to the readers. I think this paper will exhibit a better understanding of ECG heartbeat classification. Therefore, I recommend accepting this manuscript as it is with some polishing comments: C1. The abstract shall be rewritten to reflect all results yielded. C2. The Introduction could be shorter with more concentration on state of the art and the advantage of the proposed methodology. C3: In any case, profound grammatical revisions are needed to render the document useful for readers. C4: The article should have clear arguments regarding the proposed method's rationale and motivations and explicit discussions of the advances versus the prior art. ****** 6. 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 Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] 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. Attachments Attachment Submitted filename: Reviewers comments _Nedal Al Taradeh.pdf https://doi.org/10.1371/journal.pone.0260764.r001
Revision 1
23 Oct 2021 Author Response Reviewer #1 Thank you very much for your substantive comments allowing us to improve our article. RV: Reviewer AA: Author Answer RV: 1. Include references for the following; Line 11 “… well-established datasets and evaluation procedures” AA: Proper references were added. RV: 1. Include references for the following; Line 12”… well-performing algorithms developed specifically for this field.” AA: Proper references were added. RV: 1. Include references for the following; Line126 “In principal component analysis correlation coefficient…” AA: Proper reference was included. RV: 1. Include references for the following; Line 314 “The proportion of data in train 314 and test split is defined by stratified 5-fold cross validation.” AA: Proper reference was included. RV: 1. Include references for the following; Line 405 “In years 2006-2007 first approaches that combined DWT with ICA were proposed.” AA: This line was removed due to remarks provided by second reviewer. RV: 1. Include references for the following; Line 410 “Due to this fact, we were able to 410 obtain better results compared to other feature extraction methods.” AA: Proper citations were added. RV: 2. Several abbreviations should be defined before use; ECG, EMG, TP, TN, FN, FP, MLP AA: We added definitions of abbreviations mentioned above. We made sure that definitions were provided before the first appearance of abbreviation. RV: 3. Certain sentences require commas to read better. Grammatical errors should be corrected; line 27-28, 58-60, 67-68, 73-75,90-91,138-139, 311-312, 469 (This is not an exhaustive list. Authors are advised to re-read the manuscript) AA: All lines pointed out were checked and corrected. We have re-read the manuscript, corrected errors, and also asked one of our colleague for a fresh look. RV: 4. Section 1.1 and section 1.2 are both discussed as feature extraction methods. Section 1.1 should therefore be renamed appropriately perhaps as Independent Component Analysis AA: Introduction structure was changed. We believe that the current names of subsections in the introduction should be more informative. RV: 5. Consistency should be maintained. Equation (17) D is undefined. Does it refer to the width of the window which was defined as d in the text? Ensure all variables used in equations are defined e.g Df in eqn 24 & 25. AA: D is the width of the window. Naming was changed to improve consistency. All equations were checked for missing references. RV: 6. Justification for using negentropy should be included. AA: Justification for negentropy usage was added to text. RV: 7. Line 276 ci? AA: This is some error introduced during editing of our article. It was removed. RV: 8. Table 5 and 6 should be swapped to correspond with the order in which they are discussed in the text to reduce confusion. AA: I am sorry, but there was no Table 6 in the submitted paper. There is one reference to table 6, but this should be in fact reference to figure 6 (previously data in these plots were presented as a table). This error was corrected. Sorry for confusion. All other references were checked and corrected if needed. RV: 9. Table headings could be more descriptive e.g “Table 5 Best MLP network for heart beat classification compared to selected convolutional networks reported in the literature” AA: Thank you very much for your attention. We have supplemented the descriptions for the tables. RV: 10. Authors argue that in low data regimes the proposed method is comparable to convolutional neural networks, this could be included in the comparison tables for ease of comparison. AA: Information about performance for classes with low number of learning examples is presented in Figure 9. For clarity we included information about the number of beats available with a short conclusion. This should justify our claims about performance in low data regimes. RV: 11. Justification for some choice of algorithms should be included e.g why stratified 5-fold cross validation, Pan-Tompkins algorithm etc… were these selected because they are commonly used in the literature? Could the technique benefit from other choices? AA: Pan-Tompkins is commonly used algorithm for finding R wave in ECG signal. Proper mention was added. A 5-fold cross-validation was used because it ensures the statistical representability of larger data sets. This validation allows for the lowest bias and variance. Reviewer #2 Thank you very much for your substantive comments allowing us to improve our article. RV: Reviewer AA: Author Answer RV: C1. The abstract shall be rewritten to reflect all results yielded. AA: Abstract was rewritten to include most important result and conclusions. RV: C2. The Introduction could be shorter with more concentration on state of the art and the advantage of the proposed methodology. AA: Introduction was reorganized, and unnecessary information was removed to improve clarity. Subsection with ECG classification methods was rewritten to contain more recent approaches. RV: C3: In any case, profound grammatical revisions are needed to render the document useful for readers. AA: Document was checked for grammar, readability and clarity. We belive that major errors were removed and article in current form should be easier to follow. RV: C4: The article should have clear arguments regarding the proposed method's rationale and motivations and explicit discussions of the advances versus the prior art. AA: Separate subsection for aims and contributions in Introduction was created to highlight goals of our work and possible benefits of our method. Detailed discussion of benefits and obtained results is given in section 4. https://doi.org/10.1371/journal.pone.0260764.r002
17 Nov 2021 Decision Letter - Mahmoud Al Ahmad, Editor Novel Feature Extraction Method for Signal Analysis based on Independent Component Analysis and Wavelet Transform PONE-D-21-24171R1 Dear Dr. Topolski, 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, Mahmoud Al Ahmad, PhD 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 Reviewer #2: 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: (No Response) Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: (No Response) Reviewer #2: 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: (No Response) Reviewer #2: 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: (No Response) Reviewer #2: 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: (No Response) Reviewer #2: After considering all of the raised comments , I recommend to accept this article to be published in PLOS ONE journal. ****** 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 Reviewer #2: No https://doi.org/10.1371/journal.pone.0260764.r003
Formally Accepted
23 Nov 2021 Acceptance Letter - Mahmoud Al Ahmad, Editor PONE-D-21-24171R1 Novel Feature Extraction Method for Signal Analysis based on Independent Component Analysis and Wavelet Transform Dear Dr. Topolski: 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. Mahmoud Al Ahmad Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0260764.r004

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