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Peer-Review Record

Prediction of Intrinsically Disordered Proteins Using Machine Learning Algorithms Based on Fuzzy Entropy Feature

Algorithms 2021, 14(4), 102; https://doi.org/10.3390/a14040102
by Lin Zhang 1, Haiyuan Liu 1,* and Hao He 2
Reviewer 1: Anonymous
Reviewer 2: Anonymous
Algorithms 2021, 14(4), 102; https://doi.org/10.3390/a14040102
Submission received: 7 March 2021 / Revised: 20 March 2021 / Accepted: 21 March 2021 / Published: 24 March 2021
(This article belongs to the Section Evolutionary Algorithms and Machine Learning)

Round 1

Reviewer 1 Report

This study proposed a predictor for intrinsically disordered proteins using machine learning algorithms based on fuzzy entropy features. It is a resubmitted manuscript, the authors have addressed some previous comments. However, there are some comments that need room for improvement:

1. Did the authors remove similar sequences before training? What was the similarity cut-off level?

2. Some machine learning algorithms are simple and well-known, thus the authors don't need to re-describe them in every detail.

3. Since there are a lot of machine learning algorithms, what is the idea behind the use of SVM, LDA, and BP rather than the others?

4. PSSM is a 2D matrix, how did the authors fit it into machine learning models?

5. When comparing different models/methods, it is suggested to have some statistical tests to see the significant differences. p-value also needs to be shown.

6. The authors should have more discussions on the biological insights of their models/findings.

7. For this kind of problem, it is mandatory to provide a web server to support users to use the prediction models.

8. "Data preprocessing" could be moved to "Methods".

9. The authors should combine Tables 5-6-7 into one.

10. Source codes should be provided for replicating the methods.

Author Response

Dear reviewer

 

Thank you for your efforts in the review of our manuscript.

Please see the attachment.

 

Best regards 

 

Author Response File: Author Response.docx

Reviewer 2 Report

Thanks, authors for developing the paper considerably. All required modifications are applied and the paper can be published.

Author Response

Dear reviewer

Thank you very much for your recognition of our work!

Please see the attachment.

Best regards 

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

My previous comments have been addressed well.

Reviewer 2 Report

Thanks authors to apply all required modifications.

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