[vip-help] Brain Tumor Detection Code suggestion for UNet
Bhagtani, Kratika
kbhagtan at purdue.edu
Fri Nov 3 14:49:39 EDT 2023
Hi All,
I will join this meeting too. Thank you!
Sincerely,
============================================================
Kratika Bhagtani
Ph.D. Student
Research Assistant
Video and Image Processing Laboratory (VIPER)
School of Electrical and Computer Engineering
Purdue University
465 Northwestern Avenue
West Lafayette, IN 47907-2035
U.S.A.
Telephone: +1 765 714 7091
email: kbhagtan at purdue.edu
From: vip-help <vip-help-bounces at ecn.purdue.edu> on behalf of Chen, Alain <chen2967 at purdue.edu>
Date: Friday, November 3, 2023 at 12:50 PM
To: Mathur, Anika <mathur57 at purdue.edu>, Arin Asawa <aasawa at purdue.edu>, Cheung, Chingwo <cheung59 at purdue.edu>, Delp, Edward J <ace at purdue.edu>
Cc: Ignacio, Lourdes Ramos <lignaci at purdue.edu>, Matthew Glenn Roxas <mroxas at purdue.edu>, vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Great, thanks!
Here is the Zoom invite:
Alain Chen is inviting you to a scheduled Zoom meeting.
Topic: Brain Tumor VIP
Time: Nov 4, 2023 03:00 PM Eastern Time (US and Canada)
Join Zoom Meeting
https://purdue-edu.zoom.us/j/98203890649?pwd=ZVUrOExOV0hYdGdZb2V0enYwYW1Kdz09
Meeting ID: 982 0389 0649
Passcode: 538272
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Find your local number: https://purdue-edu.zoom.us/u/abEA9PnM1W
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Meeting ID: 982 0389 0649
Passcode: 538272
*****
Alain Chen
Ph.D. Student
Research Assistant
Video and Image Processing Laboratory (VIPER)
School of Electrical and Computer Engineering
Purdue University
465 Northwestern Avenue
West Lafayette, IN 47907-2035
U.S.A.
email: chen2967 at purdue.edu<mailto:chen2967 at purdue.edu>
URL: https://skynet.ecn.purdue.edu/~chen2967/
VIPER Lab Telephone: +1 765 494 3351
*****
________________________________
From: Mathur, Anika <mathur57 at purdue.edu>
Sent: Thursday, November 2, 2023 7:25 PM
To: Chen, Alain <chen2967 at purdue.edu>; Arin Asawa <aasawa at purdue.edu>; Cheung, Chingwo <cheung59 at purdue.edu>; Delp, Edward J <ace at purdue.edu>
Cc: Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
That time would work for our team, thank you!
Which zoom link should we plan to use?
Thanks,
Anika Mathur
________________________________
From: Chen, Alain <chen2967 at purdue.edu>
Sent: Thursday, November 2, 2023 6:31 PM
To: Arin Asawa <aasawa at purdue.edu>; Mathur, Anika <mathur57 at purdue.edu>; Cheung, Chingwo <cheung59 at purdue.edu>; Delp, Edward J <ace at purdue.edu>
Cc: Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Fine, is 3pm good?
*****
Alain Chen
Ph.D. Student
Research Assistant
Video and Image Processing Laboratory (VIPER)
School of Electrical and Computer Engineering
Purdue University
465 Northwestern Avenue
West Lafayette, IN 47907-2035
U.S.A.
email: chen2967 at purdue.edu
URL: https://skynet.ecn.purdue.edu/~chen2967/
VIPER Lab Telephone: +1 765 494 3351
*****
________________________________
From: Arin Asawa <aasawa at purdue.edu>
Sent: Thursday, November 2, 2023 3:10:00 PM
To: Chen, Alain <chen2967 at purdue.edu>; Mathur, Anika <mathur57 at purdue.edu>; Cheung, Chingwo <cheung59 at purdue.edu>; Delp, Edward J <ace at purdue.edu>
Cc: Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Would it be possible to meet after 3PM Saturday?
From: Chen, Alain <chen2967 at purdue.edu>
Date: Wednesday, November 1, 2023 at 9:42 PM
To: Mathur, Anika <mathur57 at purdue.edu>, Cheung, Chingwo <cheung59 at purdue.edu>, Delp, Edward J <ace at purdue.edu>
Cc: Arin Asawa <aasawa at purdue.edu>, Ignacio, Lourdes Ramos <lignaci at purdue.edu>, Matthew Glenn Roxas <mroxas at purdue.edu>, vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
How does 10:30am Saturday sound?
Thanks,
*****
Alain Chen
Ph.D. Student
Research Assistant
Video and Image Processing Laboratory (VIPER)
School of Electrical and Computer Engineering
Purdue University
465 Northwestern Avenue
West Lafayette, IN 47907-2035
U.S.A.
email: chen2967 at purdue.edu<mailto:chen2967 at purdue.edu>
URL: https://skynet.ecn.purdue.edu/~chen2967/
VIPER Lab Telephone: +1 765 494 3351
*****
________________________________
From: Mathur, Anika <mathur57 at purdue.edu>
Sent: Wednesday, November 1, 2023 6:33 PM
To: Chen, Alain <chen2967 at purdue.edu>; Cheung, Chingwo <cheung59 at purdue.edu>; Delp, Edward J <ace at purdue.edu>
Cc: Arin Asawa <aasawa at purdue.edu>; Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Hello,
We should be able to meet on Saturday anytime besides 12 to 3 pm.
Is there any time that works best for you?
Thanks,
Anika Mathur
________________________________
From: Chen, Alain <chen2967 at purdue.edu>
Sent: Wednesday, November 1, 2023 1:11 PM
To: Mathur, Anika <mathur57 at purdue.edu>; Cheung, Chingwo <cheung59 at purdue.edu>; Delp, Edward J <ace at purdue.edu>
Cc: Arin Asawa <aasawa at purdue.edu>; Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Hello team,
Actually I think we need to meet for a longer period of time. Is there any possibility of meeting on the weekend , say, Saturday? Let me know.
Thanks
*****
Alain Chen
Ph.D. Student
Research Assistant
Video and Image Processing Laboratory (VIPER)
School of Electrical and Computer Engineering
Purdue University
465 Northwestern Avenue
West Lafayette, IN 47907-2035
U.S.A.
email: chen2967 at purdue.edu
URL: https://skynet.ecn.purdue.edu/~chen2967/
VIPER Lab Telephone: +1 765 494 3351
*****
________________________________
From: vip-help <vip-help-bounces at ecn.purdue.edu> on behalf of Chen, Alain <chen2967 at purdue.edu>
Sent: Tuesday, October 31, 2023 7:41:52 PM
To: Mathur, Anika <mathur57 at purdue.edu>; Cheung, Chingwo <cheung59 at purdue.edu>; Delp, Edward J <ace at purdue.edu>
Cc: Arin Asawa <aasawa at purdue.edu>; Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Hello Brain Tumor Team,
Oof, both of those times are tough for me.
But let's plan on 1pm Friday for now. I can probably meet for about 15 to 25 minutes.
Thanks,
*****
Alain Chen
Ph.D. Student
Research Assistant
Video and Image Processing Laboratory (VIPER)
School of Electrical and Computer Engineering
Purdue University
465 Northwestern Avenue
West Lafayette, IN 47907-2035
U.S.A.
email: chen2967 at purdue.edu<mailto:chen2967 at purdue.edu>
URL: https://skynet.ecn.purdue.edu/~chen2967/
VIPER Lab Telephone: +1 765 494 3351
*****
________________________________
From: Mathur, Anika <mathur57 at purdue.edu>
Sent: Tuesday, October 31, 2023 6:23 PM
To: Chen, Alain <chen2967 at purdue.edu>; Cheung, Chingwo <cheung59 at purdue.edu>; Delp, Edward J <ace at purdue.edu>
Cc: Arin Asawa <aasawa at purdue.edu>; Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Hello,
We are free on Thursday from 4:30 to 5:20 pm, but if this does not work, Friday between 1pm to 5pm also works.
Would sometime in that range work well?
Thank you,
Anika Mathur
________________________________
From: Chen, Alain <chen2967 at purdue.edu>
Sent: Monday, October 30, 2023 8:04 PM
To: Cheung, Chingwo <cheung59 at purdue.edu>; Delp, Edward J <ace at purdue.edu>
Cc: Arin Asawa <aasawa at purdue.edu>; Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; Mathur, Anika <mathur57 at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Hello Chingwo,
I suggest that you and your group have a zoom call some time with either Yue or me to discuss this. Can you and your group come up with a few times that you could meet?
Thanks,
*****
Alain Chen
Ph.D. Student
Research Assistant
Video and Image Processing Laboratory (VIPER)
School of Electrical and Computer Engineering
Purdue University
465 Northwestern Avenue
West Lafayette, IN 47907-2035
U.S.A.
email: chen2967 at purdue.edu<mailto:chen2967 at purdue.edu>
URL: https://skynet.ecn.purdue.edu/~chen2967/
VIPER Lab Telephone: +1 765 494 3351
*****
________________________________
From: Cheung, Chingwo <cheung59 at purdue.edu>
Sent: Monday, October 30, 2023 12:30 PM
To: Chen, Alain <chen2967 at purdue.edu>; Delp, Edward J <ace at purdue.edu>
Cc: Arin Asawa <aasawa at purdue.edu>; Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; Mathur, Anika <mathur57 at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Hi, Alain
Originally, I am trying to use a vector size of 5 and later I changed it to 4 to see if the performance gets better. The first index is just saying the tumor is positive/negative. I used a very small dataset with only 40+ tagged images to train the model and it doesn't generate good result (loss does not decrease after a certain point). There’s not a specific reason why we used UNet. We can definitely try other architectures. Here's a list of possible problems:
1. Model architecture problem
2. Dataset too small
3. Training configuration
4. Bugs in the code
Would you say the model architecture is the greatest problem?
Best,
Chingwo Cheung
________________________________
发件人: Chen, Alain <chen2967 at purdue.edu>
发送时间: Monday, October 30, 2023 10:05:09 AM
收件人: Delp, Edward J <ace at purdue.edu>; Cheung, Chingwo <cheung59 at purdue.edu>
抄送: Arin Asawa <aasawa at purdue.edu>; Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; Mathur, Anika <mathur57 at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
主题: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Hi Chingwo,
Here are some comments Yue and I have for you:
1.Are you trying to output a 4 or 5 value vector? We are seeing conflicting information in the comments in your code
2. Unets are usually used for segmentation tasks and not for bounding box detection. Is there a reason why you chose Unet for this? (we discussed this after class last Tuesday)
Thanks,
*****
Alain Chen
Ph.D. Student
Research Assistant
Video and Image Processing Laboratory (VIPER)
School of Electrical and Computer Engineering
Purdue University
465 Northwestern Avenue
West Lafayette, IN 47907-2035
U.S.A.
email: chen2967 at purdue.edu<mailto:chen2967 at purdue.edu>
URL: https://skynet.ecn.purdue.edu/~chen2967/
VIPER Lab Telephone: +1 765 494 3351
*****
________________________________
From: vip-help <vip-help-bounces at ecn.purdue.edu> on behalf of Edward J. Delp <ace at purdue.edu>
Sent: Monday, October 30, 2023 8:35 AM
To: Cheung, Chingwo <cheung59 at purdue.edu>
Cc: Arin Asawa <aasawa at purdue.edu>; Ignacio, Lourdes Ramos <lignaci at purdue.edu>; Matthew Glenn Roxas <mroxas at purdue.edu>; Mathur, Anika <mathur57 at purdue.edu>; vip-help at ecn.purdue.edu <vip-help at ecn.purdue.edu>
Subject: Re: [vip-help] Brain Tumor Detection Code suggestion for UNet
Ok we respond soon.
On 10/30/2023 12:07 AM, Cheung, Chingwo wrote:
Good evening,
We have trouble getting a good result using UNet for bounding box detection. Could you take a look at our code and give us some suggestions on what could be potential mistakes? The code for UNet architecture is in the UNetBackbone.py and UNetForBoundingboxDetection.py files in the VIP-IPA/TumorDetection_F23 - VIP Gogs (purdue.edu)<https://buddy-boy4.ecn.purdue.edu:3000/VIP-IPA/TumorDetection_F23> repository.
Best,
Chingwo Cheung
--
============================================================
Note: my email address has changed slightly,
in the future please use: ace at purdue.edu<mailto:ace at purdue.edu>
Professor Edward J. Delp
The Charles William Harrison Distinguished Professor of
Electrical and Computer Engineering
and
Professor of Biomedical Engineering
and
Professor of Computer Science (Courtesy)
and
Professor of Psychological Sciences (Courtesy)
Purdue University
School of Electrical and Computer Engineering
465 Northwestern Avenue
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Telephone: +1 765 494 1740
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