Reviewer’s report
Title: 
Deep Learning for Sensitive Detection of Helicobacter Pylori in Gastric
Biopsies
Version: 
0 
Date: 
01 Jan 2020
Reviewer: 
Chun-Rong Huang
Reviewer's report:
1. The authors proposed using deep learning VGG network to detect
Helicobacter pylori (HP) from gastric biopsy images. Many works proposed
artificial intelligence methods to detect HP directly from endoscopic images
without invasive biopsies instead of from gastric biopsy images. Please give
some reviews and discussions for the differences between two kinds of methods. 
2. The following paper also uses the deep learning method in the diagnosis of
inflammatory gastrointestinal pathology including HP. Please give some
discussions for the paper. 
Martin, DR, Hanson, JA, Gullapalli, RR, Schultz, FA, Sethi, A, and Clark, DP, A
Deep Learning Convolutional Neural Network Can Recognize Common Patterns
of Injury in Gastric Pathology. Arch Pathol Lab Med. 2019.
https://www.ncbi.nlm.nih.gov/pubmed/31246112
3. Cropping the image into non-overlapping patches of 224x224 may lead to
mis-detect the small regions that contain HP. In addition, did the authors use pre-
trained VGG models?
4. In the results, please discuss the reason why the method performs better for
modified Giemsa stains compared with H&E stains.
5. Figure 5 seems missing in the manuscript. 
6. Some typos need to be corrected. For example, "we provide first evidence…"
should be "we provide the first evidence…" 
"gastric mucosa [6, 7] It" should be
"gastric mucosa [6, 7]. It" 
In Figure S2, figure legends A,B, C and D should be
provided. Please revise the paper.
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
Yes
Does the work include the necessary controls?
If not, please specify which controls are required in your comments to the
authors.
Unable to assess
Are the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
Yes
Are you able to assess any statistics in the manuscript or would you
recommend an additional statistical review?
If an additional statistical review is recommended, please specify what aspects
require further assessment in your comments to the editors.
Not relevant to this manuscript
Quality of written English
Please indicate the quality of language in the manuscript:
Needs some language corrections before being published
Declaration of competing interests
Please complete a declaration of competing interests, considering the following
questions:
1
. 
Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially
from the publication of this manuscript, either now or in the future?
2
. 
Do you hold any stocks or shares in an organisation that may in any way
gain or lose financially from the publication of this manuscript, either now
or in the future?
3
. 
Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
4
. 
Have you received reimbursements, fees, funding, or salary from an
organization that holds or has applied for patents relating to the content of
the manuscript?
5
. 
Do you have any other financial competing interests?
6
. 
Do you have any non-financial competing interests in relation to this
paper?
If you can answer no to all of the above, write 'I declare that I have no competing
interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests
I agree to the open peer review policy of the journal. I understand that my name
will be included on my report to the authors and, if the manuscript is accepted
for publication, my named report including any attachments I upload will be
posted on the website along with the authors' responses. I agree for my report to
be made available under an Open Access Creative Commons CC-BY license
(
http://creativecommons.org/licenses/by/4.0/
). I understand that any comments
which I do not wish to be included in my named report can be included as
confidential comments to the editors, which will not be published.
I agree to the open peer review policy of the journal
Reviewer’s report
Title: 
Deep Learning for Sensitive Detection of Helicobacter Pylori in Gastric
Biopsies
Version: 
0 
Date: 
01 Jan 2020
Reviewer: 
Chun-Rong Huang
Reviewer's report:
1. The authors proposed using deep learning VGG network to detect
Helicobacter pylori (HP) from gastric biopsy images. Many works proposed
artificial intelligence methods to detect HP directly from endoscopic images
without invasive biopsies instead of from gastric biopsy images. Please give
some reviews and discussions for the differences between two kinds of methods. 
2. The following paper also uses the deep learning method in the diagnosis of
inflammatory gastrointestinal pathology including HP. Please give some
discussions for the paper. 
Martin, DR, Hanson, JA, Gullapalli, RR, Schultz, FA, Sethi, A, and Clark, DP, A
Deep Learning Convolutional Neural Network Can Recognize Common Patterns
of Injury in Gastric Pathology. Arch Pathol Lab Med. 2019.
https://www.ncbi.nlm.nih.gov/pubmed/31246112
3. Cropping the image into non-overlapping patches of 224x224 may lead to
mis-detect the small regions that contain HP. In addition, did the authors use pre-
trained VGG models?
4. In the results, please discuss the reason why the method performs better for
modified Giemsa stains compared with H&E stains.
5. Figure 5 seems missing in the manuscript. 
6. Some typos need to be corrected. For example, "we provide first evidence…"
should be "we provide the first evidence…" 
"gastric mucosa [6, 7] It" should be
"gastric mucosa [6, 7]. It" 
In Figure S2, figure legends A,B, C and D should be
provided. Please revise the paper.
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
Yes
Does the work include the necessary controls?
If not, please specify which controls are required in your comments to the
authors.
Unable to assess
Are the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
Yes
Are you able to assess any statistics in the manuscript or would you
recommend an additional statistical review?
If an additional statistical review is recommended, please specify what aspects
require further assessment in your comments to the editors.
Not relevant to this manuscript
Quality of written English
Please indicate the quality of language in the manuscript:
Needs some language corrections before being published
Declaration of competing interests
Please complete a declaration of competing interests, considering the following
questions:
1
. 
Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially
from the publication of this manuscript, either now or in the future?
2
. 
Do you hold any stocks or shares in an organisation that may in any way
gain or lose financially from the publication of this manuscript, either now
or in the future?
3
. 
Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
4
. 
Have you received reimbursements, fees, funding, or salary from an
organization that holds or has applied for patents relating to the content of
the manuscript?
5
. 
Do you have any other financial competing interests?
6
. 
Do you have any non-financial competing interests in relation to this
paper?
If you can answer no to all of the above, write 'I declare that I have no competing
interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests
I agree to the open peer review policy of the journal. I understand that my name
will be included on my report to the authors and, if the manuscript is accepted
for publication, my named report including any attachments I upload will be
posted on the website along with the authors' responses. I agree for my report to
be made available under an Open Access Creative Commons CC-BY license
(
http://creativecommons.org/licenses/by/4.0/
). I understand that any comments
which I do not wish to be included in my named report can be included as
confidential comments to the editors, which will not be published.
I agree to the open peer review policy of the journal
Please review this paper.
user
Reviewer’s report
Title: 
Deep Learning for Sensitive Detection of Helicobacter Pylori in Gastric
Biopsies
Version: 
0 
Date: 
01 Jan 2020
Reviewer: 
Chun-Rong Huang
Reviewer's report:
1. The authors proposed using deep learning VGG network to detect
Helicobacter pylori (HP) from gastric biopsy images. Many works proposed
artificial intelligence methods to detect HP directly from endoscopic images
without invasive biopsies instead of from gastric biopsy images. Please give
some reviews and discussions for the differences between two kinds of methods. 
2. The following paper also uses the deep learning method in the diagnosis of
inflammatory gastrointestinal pathology including HP. Please give some
discussions for the paper. 
Martin, DR, Hanson, JA, Gullapalli, RR, Schultz, FA, Sethi, A, and Clark, DP, A
Deep Learning Convolutional Neural Network Can Recognize Common Patterns
of Injury in Gastric Pathology. Arch Pathol Lab Med. 2019.
https://www.ncbi.nlm.nih.gov/pubmed/31246112
3. Cropping the image into non-overlapping patches of 224x224 may lead to
mis-detect the small regions that contain HP. In addition, did the authors use pre-
trained VGG models?
4. In the results, please discuss the reason why the method performs better for
modified Giemsa stains compared with H&E stains.
5. Figure 5 seems missing in the manuscript. 
6. Some typos need to be corrected. For example, "we provide first evidence…"
should be "we provide the first evidence…" 
"gastric mucosa [6, 7] It" should be
"gastric mucosa [6, 7]. It" 
In Figure S2, figure legends A,B, C and D should be
provided. Please revise the paper.
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
Yes
Does the work include the necessary controls?
If not, please specify which controls are required in your comments to the
authors.
Unable to assess
Are the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
Yes
Are you able to assess any statistics in the manuscript or would you
recommend an additional statistical review?
If an additional statistical review is recommended, please specify what aspects
require further assessment in your comments to the editors.
Not relevant to this manuscript
Quality of written English
Please indicate the quality of language in the manuscript:
Needs some language corrections before being published
Declaration of competing interests
Please complete a declaration of competing interests, considering the following
questions:
1
. 
Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially
from the publication of this manuscript, either now or in the future?
2
. 
Do you hold any stocks or shares in an organisation that may in any way
gain or lose financially from the publication of this manuscript, either now
or in the future?
3
. 
Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
4
. 
Have you received reimbursements, fees, funding, or salary from an
organization that holds or has applied for patents relating to the content of
the manuscript?
5
. 
Do you have any other financial competing interests?
6
. 
Do you have any non-financial competing interests in relation to this
paper?
If you can answer no to all of the above, write 'I declare that I have no competing
interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests
I agree to the open peer review policy of the journal. I understand that my name
will be included on my report to the authors and, if the manuscript is accepted
for publication, my named report including any attachments I upload will be
posted on the website along with the authors' responses. I agree for my report to
be made available under an Open Access Creative Commons CC-BY license
(
http://creativecommons.org/licenses/by/4.0/
). I understand that any comments
which I do not wish to be included in my named report can be included as
confidential comments to the editors, which will not be published.
I agree to the open peer review policy of the journal
assistant