Calvin-Pang / MAg

MAg: a simple learning-based patient-level aggregation method for detecting microsatellite instability from whole-slide images
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About splitting the data #1

Open WayneWu01 opened 2 years ago

WayneWu01 commented 2 years ago

How to split data according to your files? The code you gave, he uses all the patients for random splitting. There are several images that are corresponding to 1 patient, should I put all of them in the same folder?

Calvin-Pang commented 2 years ago

If you mean the first stage patch-level training, the answer is YES. In the patch-level training, we put all MSS patches no matter which patient they belong to in one folder. So as MSI. So that in patch-level we only have six folders: train/MSI, train/MSS, validation/MSI, validation/MSS, test/MSI, test/MSI.

WayneWu01 commented 2 years ago

So for TCGA-AZ-4615 as an example in MSI test for CRC_DX, there are 61 pngs in the original dataset and I should put all of them in one folder for MSI test, right?

Calvin-Pang commented 2 years ago

Yes, just use your trained patch-level models to get the predicted scores of these 61 pngs. And you can use any aggregation method (MAg, counting, averaging and so on) to get the patient's predicted result (MSI or MSS).

PLMMZY67 commented 2 years ago

Sorry to bother you.why i find that there are 84 pngs of patient 'TCGA-AZ-4615' in the CRC_DX MSIMUT_test ?not 61 pngs.

WayneWu01 commented 2 years ago

But after searching there are only 61. Could you share the data with me(the already split one)?

PLMMZY67 @.***>于2022年3月25日 周五下午9:56写道:

Sorry to bother you.why i find that there are 84 pngs of patient 'TCGA-AZ-4615' in the CRC_DX MSIMUT_test ?not 61 pngs.

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PLMMZY67 commented 2 years ago

could you contact me by Wechat?my wechat:894052374.just for discussing this topic

WayneWu01 @.***> 于2022年3月26日周六 11:08写道:

But after searching there are only 61. Could you share the data with me(the already split one)?

PLMMZY67 @.***>于2022年3月25日 周五下午9:56写道:

Sorry to bother you.why i find that there are 84 pngs of patient 'TCGA-AZ-4615' in the CRC_DX MSIMUT_test ?not 61 pngs.

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WayneWu01 commented 2 years ago

Could you share the data with me? The already split one.

Calvin Pang @.***>于2022年3月21日 周一下午10:00写道:

If you mean the first stage patch-level training, the answer is YES. In the patch-level training, we put all MSS patches no matter which patient they belong to in one folder. So as MSI. So that in patch-level we only have six folders: train/MSI, train/MSS, validation/MSI, validation/MSS, test/MSI, test/MSI.

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Calvin-Pang commented 2 years ago

Could you share the data with me? The already split one. Calvin Pang @.>于2022年3月21日 周一下午10:00写道: If you mean the first stage patch-level training, the answer is YES. In the patch-level training, we put all MSS patches no matter which patient they belong to in one folder. So as MSI. So that in patch-level we only have six folders: train/MSI, train/MSS, validation/MSI, validation/MSS, test/MSI, test/MSI. — Reply to this email directly, view it on GitHub https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCalvin-Pang%2FMAg%2Fissues%2F1%23issuecomment-1074674153&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C8a8f4127cbd14ca8715108da0bb011e6%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637835148079539179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=CmOmG%2FRdjAUpSSGzN4pDUzRJEpPQJerHjAYl09ByVE4%3D&reserved=0, or unsubscribe https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQYEGJ7Z3LVDPFU2SIH26TLVBEZTLANCNFSM5RJPSG5A&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C8a8f4127cbd14ca8715108da0bb011e6%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637835148079539179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=brMOTNLpiHvipOtURqoPVJy8qnj1cirJqhZ998HOquk%3D&reserved=0 . You are receiving this because you authored the thread.Message ID: @.>

Hello, I checked my data again and I think in my experiment there is 84 pngs for TCGA-AZ-4615 in MSIMUT test. I think maybe you type the wrong id? Because I found there do have a patient with 61 pngs (TCGA-AZ-4315 in MSS test). And I am sorry that I cannot share any image data with you beacuse in my experiments I put all images in one folder and use file names in json or xlsx to call them and train or test them. And my split patient xlsx files is in https://github.com/Calvin-Pang/MAg/tree/main/name_patient

WayneWu01 commented 2 years ago

For 4315 I only find 29, why they are appeared much less?

Calvin Pang @.***>于2022年3月25日 周五下午11:40写道:

Could you share the data with me? The already split one. Calvin Pang @.

>于2022年3月21日 周一下午10:00写道: … <#m-1537933242082814649> If you mean the first stage patch-level training, the answer is YES. In the patch-level training, we put all MSS patches no matter which patient they belong to in one folder. So as MSI. So that in patch-level we only have six folders: train/MSI, train/MSS, validation/MSI, validation/MSS, test/MSI, test/MSI. — Reply to this email directly, view it on GitHub https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCalvin-Pang%2FMAg%2Fissues%2F1%23issuecomment-1074674153&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C8a8f4127cbd14ca8715108da0bb011e6%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637835148079539179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=CmOmG%2FRdjAUpSSGzN4pDUzRJEpPQJerHjAYl09ByVE4%3D&reserved=0 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCalvin-Pang%2FMAg%2Fissues%2F1%23issuecomment-1074674153&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C2185ab971a9c4ae9679508da0ee2ba97%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637838664211636016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Q7MdEhKyrnV56z7KEkWy8WGJaLJCdBGh19KKK6HX8vc%3D&reserved=0, or unsubscribe https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQYEGJ7Z3LVDPFU2SIH26TLVBEZTLANCNFSM5RJPSG5A&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C8a8f4127cbd14ca8715108da0bb011e6%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637835148079539179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=brMOTNLpiHvipOtURqoPVJy8qnj1cirJqhZ998HOquk%3D&reserved=0 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQYEGJ7Z3LVDPFU2SIH26TLVBEZTLANCNFSM5RJPSG5A&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C2185ab971a9c4ae9679508da0ee2ba97%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637838664211636016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=mfmJeNAP9wU5CfV6NKTgNlLZNXCvgwEPhMqPigFDlPA%3D&reserved=0 . You are receiving this because you authored the thread.Message ID: @.>

Hello, I checked my data again and I think in my experiment there is 84 pngs for TCGA-AZ-4615 in MSIMUT test. I think maybe you type the wrong id? Because I found there do have a patient with 61 pngs (TCGA-AZ-4315 in MSS test). And I am sorry that I cannot share any image data with you beacuse in my experiments I put all images in one folder and use file names in json or xlsx to call them and train or test them. And my split patient xlsx files is in https://github.com/Calvin-Pang/MAg/tree/main/name_patient https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCalvin-Pang%2FMAg%2Ftree%2Fmain%2Fname_patient&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C2185ab971a9c4ae9679508da0ee2ba97%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637838664211636016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=idAMuQhd14BXOoLFBoNZSmz2iTTSAK9uc8U9Vf5ZiKU%3D&reserved=0

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Calvin-Pang commented 2 years ago

I am sorry I don't know what's wrong with your split. I guess you have data loss when downloading and unzipping the dataset. I just found my split dataset in my Google Drive, you may download and I hope it can help you. CRC_DX: https://drive.google.com/drive/folders/1sQR_4_ZjOW8IWk8cMdsF2MTMOmfS9Y06?usp=sharing STAD: https://drive.google.com/drive/folders/1ntb9MLvBx7ptyEA3dGhpQiM1nKg-jVCH?usp=sharing

WayneWu01 commented 2 years ago

Do you have the train_mobilenet.py file? I could'nt find it.

On Sat, Mar 26, 2022 at 4:19 AM Calvin Pang @.***> wrote:

I am sorry I don't know what's wrong with your split. I guess you have data loss when downloading and unzipping the dataset. I just found my split dataset in my Google Drive, you may download and I hope it can help you. CRC_DX: https://drive.google.com/drive/folders/1sQR_4_ZjOW8IWk8cMdsF2MTMOmfS9Y06?usp=sharing https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1sQR_4_ZjOW8IWk8cMdsF2MTMOmfS9Y06%3Fusp%3Dsharing&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C7b41345f87614e5503f908da0f09c990%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637838831954767756%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2BOyCvdfcmRHh2UCIaiZyGM8qPP57tEMUfhh3ODg5OT0%3D&reserved=0 STAD: https://drive.google.com/drive/folders/1ntb9MLvBx7ptyEA3dGhpQiM1nKg-jVCH?usp=sharing https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1ntb9MLvBx7ptyEA3dGhpQiM1nKg-jVCH%3Fusp%3Dsharing&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C7b41345f87614e5503f908da0f09c990%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637838831954767756%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=hj%2FqA0LFT0kPfH57BKkTpjl%2F0UrPhNdEGC9YTcafCrg%3D&reserved=0

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Calvin-Pang commented 2 years ago

Do you have the train_mobilenet.py file? I could'nt find it. On Sat, Mar 26, 2022 at 4:19 AM Calvin Pang @.> wrote: I am sorry I don't know what's wrong with your split. I guess you have data loss when downloading and unzipping the dataset. I just found my split dataset in my Google Drive, you may download and I hope it can help you. CRC_DX: https://drive.google.com/drive/folders/1sQR_4_ZjOW8IWk8cMdsF2MTMOmfS9Y06?usp=sharing https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1sQR_4_ZjOW8IWk8cMdsF2MTMOmfS9Y06%3Fusp%3Dsharing&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C7b41345f87614e5503f908da0f09c990%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637838831954767756%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2BOyCvdfcmRHh2UCIaiZyGM8qPP57tEMUfhh3ODg5OT0%3D&reserved=0 STAD: https://drive.google.com/drive/folders/1ntb9MLvBx7ptyEA3dGhpQiM1nKg-jVCH?usp=sharing https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1ntb9MLvBx7ptyEA3dGhpQiM1nKg-jVCH%3Fusp%3Dsharing&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C7b41345f87614e5503f908da0f09c990%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637838831954767756%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=hj%2FqA0LFT0kPfH57BKkTpjl%2F0UrPhNdEGC9YTcafCrg%3D&reserved=0 — Reply to this email directly, view it on GitHub https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCalvin-Pang%2FMAg%2Fissues%2F1%23issuecomment-1079647323&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C7b41345f87614e5503f908da0f09c990%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637838831954767756%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=D1jsCKPAf42HuUV3EQiiUjzXWenjRWDOk66NDzb0e8A%3D&reserved=0, or unsubscribe https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAQYEGJY734QJXWAFTAW3MT3VB3JDTANCNFSM5RJPSG5A&data=04%7C01%7Czheng.wu%40mail-service-3-mx.vanderbilt.edu%7C7b41345f87614e5503f908da0f09c990%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637838831954767756%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Znp8sK3dwQkT9YvRp8q4TUeVHwuRp8CadAS4CVJ3Lts%3D&reserved=0 . You are receiving this because you authored the thread.Message ID: @.>

Hello, I checked my files and found that the file train_mobilenet.py is just a modified train.py which was a experiment for parameter-frozen processing. And the result showed that the frozen processing is meaningless. So please just use train.py for all model(resnet, mobilenet,......)