Google Summer of Code 2020 Weekly Feedback

What progress have you made this week?

In the seventh week of the coding period (July 11 - July 17), I worked on implementing local database in the app with the help ROOM sqlite database. There was a blockage which I had mentioned earlier. I was working on that, using the old version of the SDK and getting the app running. I’m still working on that. I, also started to make a document of the UI designs and will upload it on gitlab.

What do I plan to do next week?

  • I plan to resolve any issue which the SDK is thorwing. Report it. Try to get it working with server code.
  • In the mean time, complete the work on local database.
  • Also, implement dummy data onto the app.

Have you had any blockers or issues that are impeding your project?

The interaction of the SDK and the server is still a work in progress.

2 Likes

Week 7 : Coding Period

What progress have you made this week?

  1. Completed hybrid compression of models.
  2. Currently writing code for knowledge distillation by combining various pytorch and tf code sources.
  3. Implementing onnx conversion of pytorch models to onnx format and then to tf format.

What do I plan to do next week?

  1. Complete knowledge distillation.
  2. Convert pytorch models to tf format

Have you had any blockers or issues that are impeding your project?

NA

2 Likes

"10-july-2020 to 17-july-2020"

[ Progress ]

  1. Started the retinanet training. [Resnet152 base]
  2. Done the appropriate image augmentation to overcome the data shortage for object detection .

[ Next Week ]

  1. Complete the training.
  2. Produce the results.

[ Blockers ]

tf2 checkpoint restoration issue: “Link

2 Likes

This week’s Progress (07/13 - 07/17)

  1. I adjusted my plans for this week to increase efficiency. I created fourteen custom elements for FHIR Medication and Medication Statement resources with lit-element v2.3.1.
  2. Read about the open-wc unit testing as an alternative for polymer unit testing.
  3. Figured out the data binding challenges of the previous week.

Next week’s Plan(07/20- 07/24)

  1. Write unit testing for the created elements, write the README documents and request an MR to the monorepo
  2. Debug the unit tests for previous elements and make an MR to the monorepo
2 Likes

"18-july-2020 to 24-july-2020"

[ Progress ]

  1. Trained the Retinanet.
  2. Added Retinanet to the backend.

[ Next Week ]

  1. Start training the image segmentation.

[ Blockers ]

NA

1 Like

What progress have you made this week?

For App

  1. Completed View CDM Statewise screen

  2. Completed UI of compare hospitals screen

  3. Fixed bugs in download CDM screen

For Web Scraper

  1. Scraped Medicare Data
  1. Created process script for medicare data

What do I plan to do next week?

  1. Completing compare hospitals screen

  2. Adding search functionality in view cdm screen

  3. Discussing with @muarachmann for GUI of scraper

Have you had any blockers or issues that are impending your project?

No

1 Like

What progress have you made this week?

In the eighth week of the coding period (July 18 - July 24), there was plenty of code changes in the sample repo of Evernym SDK. I tried running it whenever there was any changes and also tried with test server. Once sample code to make connection via QR code was added, I tried and tested with our server and was able to see some connection made.

I was also able to receive the Credential Offer on the app, but was not able to “accept” the Credential Offer, due to some error either in app or the server.

What do I plan to do next week?

  • @iainbarclay and I would test the app with server and make sure the server is working.
  • Also, add a “demo” feature in the Settings Screen, to have the app run in 2 phase, one in demo mode with dummy credentials and the other with server, SDK connections.

Have you had any blockers or issues that are impeding your project?

The integration of the SDK with the app is now showing some progress.

1 Like

Week 8 : Coding Period

What progress have you made this week?

  1. Completed quantization post pruning and presented the results.
  2. Converted pytorch model to onnx format.
  3. Created keras model for chexnet to run on chest-xray14 dataset.
  4. Wrote docstrings for python scripts.

What do I plan to do next week?

  1. Discuss with my mentor and decide targets to focus on and which direction to proceed with.

Have you had any blockers or issues that are impeding your project?

Problems in converting onnx model to Tensorflow format due to insufficient support for pytorch and onnx. Also, keras model has less size, no classifying layer and variable results.

1 Like

This week’s Progress (07/20- 07/24)

  1. Wrote unit testing for the elements created for medication and Medication statement. They all passed.
  2. Wrote the README documentations for the above elements.
  3. I requested an MR for the Observation resource earlier today, once reviewed and accepted, I will create MRs for the Medication and medication statements.
  4. Debugged the unit tests for previous elements. All the elements except fhir-create-patient, fhir-create-practitioner, fhir-create-organizationandfhir-create-location` passed the tests. I will make a MR for the unit tests that passed.

Next week’s Plan(07/27 -07/31)

  1. Integrate the elements created for the FHIR Medication, Observation and Medication statement resources into the lh-toolkit app.
  2. Create 3-4 workflows using those elements

Blocker

Some of the unit tests for the elements listed above keeps failing. I will keep reviewing them.

1 Like

"25-july-2020 to 31-july-2020"

[ Progress ]

  1. Added support for segmentation in the Django API.
  2. Served Unet model for segmentation.
  3. Did some UI changes for Segmentation (still work in progress).

[ Next Week ]

  1. Not yet decided. (Everything as of now is finished)
  2. Do all the documentations.

[ Blockers ]

NA

1 Like

What progress have you made this week?

  1. Completed Compare Hospitals Functionality of App ( Used Medicare Open Data API )

  2. Created Search functionality for View CDM Screen

  3. Identified & fixed small bugs in app

What do I plan to do next week?

  1. Working on Share App, About, Report a bug, Screens

  2. Writing Readme of App

  3. Using Flutter Cache Manager to store CDM while downloading

  4. Writing Unit Test of Home Screen

Have you had any blockers or issues that are impending your project?

No

1 Like

What progress have you made this week?

Made changes to switch to demo mode for displaying demo data. If not in demo mode, will be using live credentials from server. Half way done through the integration part.

What do I plan to do next week?

  • Change the agency config and test it with the live server.
  • Clean the codebase and update it on gitlab.
  • If time permits, work on Child credential as well.

Have you had any blockers or issues that are impeding your project?

No

1 Like

Week 9 : Coding Period

What progress have you made this week?

  1. Added functionality to convert pruned models to quantized models in scripts
  2. Began compression of Chexnet based on ChestX-ray14 dataset

What do I plan to do next week?

  1. Work on suggestions from mentors
  2. Complete compression of Chexnet.

Have you had any blockers or issues that are impeding your project?

Re-tried conversion of onnx model to tensorflow without DataParallel and it did not work. Shifted to purely tensorflow model of chexnet.

1 Like

This week’s Progress (07/27 -07/31)

  1. MR for Medication Resource created and merged.
  2. MR for Medication statement and Dosage will be made. Currently writing the README files for these elements.
  3. Started working on the creation of different workflows using those elements.

Next week’s Plan(08/03 -08/07)

  1. Create workflows using the fhir custom elements based on the High Fidelity prototypes created by @parishmita.bora

Blocker

Ran into some difficulties with using the High Fidelity prototypes created to make the workflows. The HTML,CSS, JS codes contained too many lines of code. I plan to resolve these issue over the weekend. I will provide an update on my progress on Monday (08/03)

1 Like

"1-jAugust-2020 to 7-August-2020"

[ Progress ]

  1. Added CSV download feature.
  2. Improved retinanet model.
  3. Did UI changes as suggested by @geepriya

[ Next Week ]

  1. Build the Segmentation tool.

[ Blockers ]

NA

What progress have you made this week?

  1. Worked on Share App, About App screens.
  2. Used Flutter cache Manager to download & Save CDM to cache.
  3. Readme of App is in progress.
  4. Search functionality in view CDM Screen.

What do I plan to do next week?

  1. Decreasing size of data scraper repository
  2. Writing Unit Test of Home Screen, Download CDM screen, Saved CDM Screen
  3. Developing & discussing REST API with flask.

Have you had any blockers or issues that are impending your project?

No

Week 10 : Coding Period

What progress have you made this week?

  1. Finished quantization of ChexNet model based on CHest-XRay14.
  2. Pruning and evaluation of models is in progress.
  3. Rectified the directory structure of the scripts for RSNA Dataset and worked on my mentors’ comments.

What do I plan to do next week?

  1. Complete accuracy evaluation of pruned models.
  2. Start evaluation on emulation of ARM devices.
  3. Start scripts for Chest-XRay14 and make MR for the same.

Have you had any blockers or issues that are impeding your project?

No.

This week’s Progress (08/03 -08/07)

  1. MR for Medication statement and Dosage was made. Pending review and approval
  2. Created all the elements for FHIR Medication Requests. Currently writing unit tests and ReadMe documents to be completed tomorrow(08/08/2020)
  3. Read the documentations for creating a PWA using Polymer PWA starter’s Kit.

Next week’s Plan(08/10 -08/14)

  1. Create workflows using the fhir custom elements based on the High Fidelity prototypes created by @parishmita.bora

Blocker

N/A

What progress have you made this week?

We revised our plan for August. I started creating a dummy app for the informant. We were able to get help from Evernym and make successful initialization of the SDK in the mobile app. I was able to make a connection and accept the credential. However, there were few logical errors, that needs to be fixed in the coming week.

What do I plan to do next week?

  • Finish the informant app.
  • Work on shifting modes in between ‘LIVE’ and ‘DEMO’ in the app.
  • Resolve the error while receving CHILD credential.

Have you had any blockers or issues that are impeding your project?

There is an problem in the way Child credential is being issued. This would be discussed in the coming week.

1 Like

"8-August-2020 to 14-August-2020"

[ Progress ]

  1. Added Logging features.
  2. Started building the segmentation tool.
  3. Added height/width field to the downloaded csv
  4. Tweaked the colors to make the UI consistent with the LibreHealth Theme.

[ Next Week ]

  1. Complete the segmentation tool
  2. Start the final documentation.

[ Blockers ]

NA