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changes.mady.by.user Unknown User (bearceba)

Saved on May 13, 2021

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changes.mady.by.user Unknown User (bearceba)

Saved on May 13, 2021

Activities completed this month
I have a ported version of codalab to python3 working with custom changes to python and jQuery to update those libraries...status? -BB Opened these Challenges: SPIE AAPM (http://spie-aapm-nci-dair.westus2.cloudapp.azure.com/competitions/4#participate-submit_results) - submissions working, but we need to change open validation phase to open ended phase after test. Will require a code update from main codalab branch....status -BB Demo docker submissions to Emily Townley who is designing a MIDRC challenge. I should have a non-gpu and a gpu submission ready soon: I did in fact get a cpu submission working and am fine tuning it. (http://medici-codalab-main.eastus.cloudapp.azure.com/) I testing briefly with a gpu machine and it works too. We are using the forum to go back and forth as people test my tutorial (https://github.com/QTIM-Lab/MedICI-Challenge-Bundles/tree/main/aks_MedNIST_bundle/README). There some interesting bugs that we are working out: Windows uploaded zip files are not behaving the same as ubuntu or mac based ones. While not an issue on my system, some parts of the training algorithm require some adjustments and the organizers (MDRC folks) are requesting that I make code changes to the tutorial so that users don't have to figure that out. Sounds reasonable.

Activities completed this month

I have a ported version of codalab to python3 working with custom changes to python and jQuery to update those libraries...status? -BB
Opened these Challenges:
1. SPIE AAPM (http://spie-aapm-nci-dair.westus2.cloudapp.azure.com/competitions/4#participate-submit_results) - submissions working, but we need to change open validation phase to open ended phase after test. Will require a code update from main codalab branch....status -BB
Demo docker submissions to Emily Townley who is designing a MIDRC challenge. I should have a non-gpu and a gpu submission ready soon:
1. I did in fact get a cpu submission working and am fine tuning it. (http://medici-codalab-main.eastus.cloudapp.azure.com/)
2. I testing briefly with a gpu machine and it works too.
3. We are using the forum to go back and forth as people test my tutorial (https://github.com/QTIM-Lab/MedICI-Challenge-Bundles/tree/main/aks_MedNIST_bundle/README). There some interesting bugs that we are working out:
  1. Windows uploaded zip files are not behaving the same as ubuntu or mac based ones.
  2. While not an issue on my system, some parts of the training algorithm require some adjustments and the organizers (MDRC folks) are requesting that I make code changes to the tutorial so that users don't have to figure that out. Sounds reasonable.

Planned for next month
Continue opening older challenges listed on https://medici-challenges.org so that people can still make submissions. (wrap up SPIE AAPM from above) I've been busy with MDRC project to fine tune the docker submission main platform and haven't had a chance to change code to add a phase. To elaborate, whatever code base I used for this codalab doesn't have an "add phase" button and so the only way to keep it open is to have the validation phase open indefinitely. Investigate Federated Learning Challenges (https://wiki.nci.nih.gov/display/NICC) presentation from Daniel Rubin, July 6th (under Presentations and Recordings from Previous Calls) Jayashree and I met with Daniel and they have a plan. The plan is to first spin up some VMs and perform the basic federated learning concepts Daniel has already built a framework for. .status? -BB Soon he will be reaching out and we will perform this. Add indication on website (medici-challenges.org) which challenges accept submissions. Pending completion. It's been a very busy month and adding this felt like a lower priority. Based on a discussion with Ulli and Carolyn, I will establish an appropriate priority.

Planned for next month

Continue opening older challenges listed on https://medici-challenges.org so that people can still make submissions. (wrap up SPIE AAPM from above)
1. I've been busy with MDRC project to fine tune the docker submission main platform and haven't had a chance to change code to add a phase. To elaborate, whatever code base I used for this codalab doesn't have an "add phase" button and so the only way to keep it open is to have the validation phase open indefinitely.
Investigate Federated Learning Challenges (https://wiki.nci.nih.gov/display/NICC) presentation from Daniel Rubin, July 6th (under Presentations and Recordings from Previous Calls)
1. Jayashree and I met with Daniel and they have a plan. The plan is to first spin up some VMs and perform the basic federated learning concepts Daniel has already built a framework for.
.status? -BB
2. Soon he will be reaching out and we will perform this.
Add indication on website (medici-challenges.org) which challenges accept submissions.
1. Pending completion. It's been a very busy month and adding this felt like a lower priority. Based on a discussion with Ulli and Carolyn, I will establish an appropriate priority.

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