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Date

Attendees

NameAttended
Jayashree Kalpathy-Cramer
Ulli WagnerYes
Carolyn KlingerYes
Benjamin BearceYes


Currently supported challenges

Name of ChallengeOrganization / MeetingMedici instance
used

Release
Training data

Release Validation dataRelease
Test data
Number of
Participants
Closing DateWill the challenge remain open?Comments

SIRPRISE Reconstruction Challenge

https://www.aapm.org/GrandChallenge/SIRPRISE/https://medici-codalab-main.eastus.cloudapp.azure.com/







Submitters will upload images to Medici. Did decide not to use FTP transfer but upload zipped images directly to Codalab. It was found out that the data size is not as large as anticipated.



Truth-based CT reconstruction challenge


https://medici-codalab-main.eastus.cloudapp.azure.com/







submitters will upload images to Dropbox, organizers will provide the scoring. Ben will create entries for each participants and enter the scores so that they can be shown on the leaderboard.

DL-sparse challenge #2

Ben is talking with Emil about using MedICI again for another DL-Sparse challenge









Previously supported challenges that remain open

Name of ChallengeOrganization / MeetingMedici instance
used

Release
Training data

Release Validation dataRelease
Test data
Number of
Participants
Closing DateWill the challenge remain open?Comments










Tasks / Deliverables


TaskDue DateDeliverableStatus

Supporting at least three challenges including one federated learning challenge

8/30/2022

Three challenges are DBTex2, SIRPRISE, and Truth-based CT reconstruction challenge.



Support organizers and participants (help desk, FAQ, training, presentations)

8/30/2022


Ongoing
Maintain and update the website8/30/2022
Ongoing

Capturing and providing metrics on the use of the MedICI website

8/30/2022
Ongoing

Capturing and providing metrics on the challenges

8/30/2022
Ongoing

Support at least three previously executed challenges

8/30/2022
Done

MedICI on the NCI Cloud Two (GCP) and Firecloud

8/30/2022

Task was suspended per discussion on  


Operations and Maintenance

8/30/2022
Ongoing

Changes to MedICI to support federated learning challenges



See Google doc


Discussion items


TimeItemWhoNotes

Notes 






 


Updated status of SOW tasks

Ben is supporting challenge organizers & participants

MIDRC test challenge will start soon including Docker submissions.

Supporting Codalab open source project.



 


SIRPRISE - active, users can download data. Challenge organizers will establish the scores and Ben will enter them at the end of the challenge. Scores will not be updated in real-time. No submissions yet.

Truth-based CT reconstruction challenge - is open

Submitters will upload the data to Dropbox

Organizers approve people in Codalab. After approval, the organizers will grant the participants access to a dropbox folder for the participants to upload the results. 


DL Sparse - version 2 will go live soon.


Action items



Meeting with Codalab developers

Ben is attending meetings. He is helping with fixing bugs. 

Ben to review the federated learning tasks and discuss with Codalab team.

Python3 


Responses to question about keeping challenges open

Bearce, Benjamin (NIH/NCI) [C]  - investigate options on how to keep challenges open, add phase or copy challenge, avoid having users add to the previous submissions

SPIE-AAPM-NCI DAIR Digital Breast Tomosynthesis Lesion Detection Challenge (DBTex) - Phase 1 - Bearce, Benjamin (NIH/NCI) [C] verify with submitters that decision of phase 2 applies to phase 1

SPIE-AAPM-NCI-DAIR & SPIE-AAPM-NCI-DAIR Phase 2  - TBD - (Nick Konz, Wed 11/24/2021 11:36 AM) "Maciej and I discussed this and an idea that we’ve been floating is to have some sort of ongoing validation phase, that would allow anyone to get validation results on their model. We would also want to have a periodic, occasional test phase for people to get test results.

BMMR2 - close on as previously planned. (David Newitt, Thu 10/28/2021 7:10 PM) - link to the challenge data will be de-activated on 12/1/2021. 
Update (01/20/2022): David Newitt retired. They want to keep the challenge open but without data. Only participants who had previously registered may continue to work and submit. Ben to check if the data is still accessible.

DL Sparse -  keep open (Emil Sidky, Thu 10/28/2021 11:42 PM) 

MICCAI 2020 - has already an open test phase

ISBI 2018 - has already an open test phase

AAPM RT-MAC Challenge - is open-ended


Upcoming challenges

MIDRC classification challenge (frontal/lateral views)

AAPM - SIPRISE challenge - Diane Alvares, Baptist Health. She filled out the submission form and sent instructions.

TrueCT - Truth-based CT reconstruction challenge - is being setup. Submitters need to upload images (30 GB per submission). Ben is investigating what the best method is e.g. submission to the cloud. Several options were discussed. Google workspace. 







Information sharing
Ben established connection with developers of Codalab/Codabench. He will join their meeting and potentially take a more active role in product development. These activities can be charged to the contract.

Monthly status reports
due on the 10th day of the following month

Contract / invoice status / SOW
  • the last invoice was for June 2021
  • Ben sent reminder emails to Peter Hickey on 10/25/2021. Resent it today.
  • New subcontracts administrator: Connor Cigrang
  • Connor pinged Lynne Benoit 01/05/2022 regarding invoice.

Paper
The draft will be submitted by September 15, 2020. - Not received

Videos
    • Hold the work on the video for now



Federated learning challenge - proposal for MICCAI, ACR confirmed that the data can be used

Wagner, Ulrike (NIH/NCI) [C] Change SOW, take cloud out, put federated learning modifications for Codalab in, send to Medici for review





Action items