data split

Question

data split

Closed this issue 3 years ago · 7 comments

Hi,

Thanks for the code, it's very helpful.
I was wondering is which script you split the data into train, validation, and test? I noticed that in MIMIC-CXR-JPG there is already an official csv called data_split, but all the data are labeled as "train" in that csv.

Thank you!

best,
Zixiao

Answer 1 · 2021-08-23T17:18:30.000Z

They have a very large amount of data of data labeled as the train which does not make sense if we use them all for training purposes and do test on very small portion. I mixed them all and did a 80-10-10 train validation test split such that no patient is shared between these 3 sets. Best Laleh

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On Mon, Aug 23, 2021 at 1:12 PM Zixiao Chen ***@***.***> wrote: Hi, Thanks for the code, it's very helpful. I was wondering is which script you split the data into train, validation, and test? I noticed that in MIMIC-CXR-JPG there is already an official csv called data_split, but all the data are labeled as "train" in that csv. Thank you! best, Zixiao — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIYJR7QUHHP46SSGCPVYYD3T6J6QLANCNFSM5CVANUQQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

-- Best Laleh

Answer 2 · 2021-08-23T17:29:05.000Z

Hi Laleh,

Thank you very much for the quick reply. Yes I agree and I noticed the same problem, the training dataset is more than 97%.
I was wondering in which script did you put the code of data splitting? I couldn't find it.
Thank you!

Best,
Zixiao

Answer 3 · 2021-08-23T17:37:09.000Z

Check function random_split() in this path: https://github.com/LalehSeyyed/CheXclusion/blob/main/NIH/nih.py A similar function may exist on other dataset folders, though if you did not find them the idea is the same. You can make your own split and do the train as well, just make sure to do it based on patient IDs not images.

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On Mon, Aug 23, 2021 at 1:29 PM Zixiao Chen ***@***.***> wrote: Hi Laleh, Thank you very much for the quick reply. Yes I agree and I noticed the same problem, the training dataset is more than 97%. I was wondering in which script did you put the code of data splitting? I couldn't find it. Thank you! Best, Zixiao — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIYJR7QADTXMIBEA2CG5YW3T6KAOZANCNFSM5CVANUQQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

-- Best Laleh

Answer 4 · 2021-08-23T17:58:37.000Z

That's very helpful, thank you Laleh!

Answer 5 · 2021-08-26T22:57:29.000Z

Hi Laleh,

I was wonering what's the input of the random_split() function? Is it a ratio (such as 0.8 if the train set is 80)?
Thank you!

Answer 6 · 2021-08-27T12:25:12.000Z

No we used a fix random seed for all split. We have not kept the seed but the list of patient ID in the test are available and have been posted in the github.

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On Thu., Aug. 26, 2021, 6:57 p.m. Zixiao Chen, ***@***.***> wrote: Hi Laleh, I was wonering what's the input of the random_split() function? Is it a ratio (such as 0.8 if the train set is 80)? Thank you! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIYJR7QOGEDPVA5CZRC6LCLT63BGHANCNFSM5CVANUQQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

Answer 7 · 2021-08-29T22:23:35.000Z

Thank you! That's very helpful