Google Summer of Code 2020 Weekly Feedback

[Kislay_Singh]

"13-june-2020 to 19-june-2020"

[ Progress ]

1. Read about asyncio module in python.
2. Made the python middleware script asynchronous using asyncio.
3. Did a research on open source file storage system for dataset storage.

[ Next Week ]

1. Train the NIH Xray dataset on a different object detection algo and add a support for selecting different ML algos.
2. Complete all the documentation.

[ Blockers ]

N/A

[prajwal27]

What progress have you made this week?

In the third week of coding period (June 6 - June 12), I have developed most of the UI screens of the app. I had currently written the code without following any pattern, which I realised and have started to follow MVVM design pattern and modify the codebase.

What do I plan to do next week?

• Complete the codebase without the implementation of the SDK.
• Work with dummy data.

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

I had my college exams in the current and the following week, due to which the work would be a bit slow and have informed my mentor as well.

[aishwhereya (Aishwarya Harpale)]

Week 3 : Coding Period

What progress have you made this week?

1. Fine-tuned models till they reached their highest accuracy without overfitting.
2. Derived model evaluation parameters - Accuracy, Loss, Confusion matrix, Precision, Recall, F1 score, ROC curve.
3. Implemented dynamic range and F16 quantization methods on all models and evaluated their accuracy.

What do I plan to do next week?

1. Implement Int8 quantization and model pruning.
2. Migrate notebook to the plhi server for pruning.
3. Conduct feasibility analysis of the system architecture and experiment with the available options to get the most suitable one.

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

Tried implementing pruning on Kaggle notebook but it had compatibility issues with their python version. This will most likely get solved on the plhi server.

[bolu (Bolu Oluwalade)]

This week’s Plan (06/15 - 06/20)

1. Completed the upgrade for nine elements and initiate the MR.
2. Created four new custom element for the Observation resource.
3. Currently working on the Unit testing of the element

Next week’s Plan (06/21 - 06/26)

1. Create 3 new web components with lit-element v2.3.1 and perform unit testing.

[Kislay_Singh]

"19-june-2020 to 26-june-2020"

[ Progress ]

1. Read up about different docker and docker-compose feature.
2. Dockerized all the micro services.
3. Modified config for the tf-Serving, now any number of models can be served simultaneously.
4. Started working training a inception network.

[ Next Week ]

1. Add support for the react app.

[ Blockers ]

N/A

[Darshpreet2000 (Darshpreet)]

What progress have you made this week?

1. Worked on new tab in bottom navigation which will download cdm

2. Currently working on saving data from GitLab API to database using sqflite

3. Used Hive to store local data

4. Currently working on Scraping CDM of New York State

What do I plan to do next week?

1. Work on Search Screen & Saved screen backend

2. Scraping CDM of California State

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

No

[prajwal27]

What progress have you made this week?

In the fourth week of the coding period (June 21 - June 27), I have implemented the app design using Figma tool. The link to that is here. I implemented the credential screen and the notification screen in the app.

What do I plan to do next week?

• Test the app with the server-side .
• Implement some kind of local auth like fingerprint or passcode.

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

None as of now.

[aishwhereya (Aishwarya Harpale)]

Week 4 : Coding Period

What progress have you made this week?

1. Trained models with balanced dataset.
2. Implemented model pruning. Currently converting these models to tflite format and implementing int8 quantization.
3. Surveyed available datasets and trained models for next task.

What do I plan to do next week?

1. Complete model compression over 1st dataset.
2. Migrate notebook to Colab.
3. Start work on the next dataset.

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

Notebook had issues on the plhi server. Migrating it to Colab/Kaggle again to finish the pending tasks.

[bolu (Bolu Oluwalade)]

This week’s Plan (06/21 - 06/26)

1. Created three new custom elements for FHIR Observation resource
2. Created Unit testing for the four custom elements created last week
3. MR created and accepted for the upgrade of the previous custom elements to LitElement v.2.3.1

Next week’s Plan (06/29 - 07/03)

1. Create 3 new web components with lit-element v2.3.1 and perform unit testing.

Blockers

Got stuck Unit testing a few of the custom elements especially fhir-coding. Working to resolve it

[Darshpreet2000 (Darshpreet)]

What progress have you made this week?

1. Worked on Search Screen of App.

2. Made DAO ( Data Access Object ) class which uses SQL queries to query database.

3. Made Comparing Hospitals procedures functionality

4. Worked on Filter functionality, user can sort prices in Ascending or descending order & can sort by category.

5. Worked on Saved Screen Backed which displays saved chargemaster in database.

I am fixing some bugs, & some tasks are pending, I will soon make Merge Request for these.

What do I plan to do next week?

For Web Scraper

1. Scraping CDM of California State

   • Making Separate Spider class for it

   • Generating “process.py” script for each hospital

2. Making generate.py file by which user can generate “process.py” scripts which will parse CDM to proper columns

For App

1. Working on View CDM Statewise screen.

2. Making seperate BLoC for it.

3. Using GitLab API to get CDM of each state

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

No

[prajwal27]

What progress have you made this week?

In the fifth week of the coding period (June 28 - July 3), I finished coding all the screens of the app as designed in the Figma tool. I filled it with dummy data. I have pushed it to a separate branch feature-ui. We also tested the app with the server code and found that there were few things changed from the Evernym side. Also, we had a discussion on a few changes in the UI of the app, web app.

I’m also working on documenting the decisions taken in designing the UI.

What do I plan to do next week?

• Create a different branch feature-ui-mhbs, and to make it look similar to that. I plan to do this over the weekend.
• I plan to integrate the dummy data which @iainbarclay has shared.
• I also will integrate the connections part in the app.

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

The Evernym SDK and the wiki which I used did not work when tested with the live server. It’s not exactly a blocker, as I have the test server to work on.

[aishwhereya (Aishwarya Harpale)]

Week 5 : Coding Period

What progress have you made this week?

1. Implemented python scripts for training, quantizing and pruning the models.
2. Implemented int8 quantization by migrating notebook to Colab.
3. Currently implementing inference scripts and quantization of pruned models.

What do I plan to do next week?

1. Present complete results of 1st dataset.
2. Begin next set of models or Knowledge Distillation/int4 quantization

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

NA

[Kislay_Singh]

"27-june-2020 to 4-june-2020"

[ Progress ]

1. Made changes to the backend to accommodate multiple models.(Had to change the SQL schema and update the api’s accordingly)
2. Added login feature to the frontend app.
3. Fixed a bug in my docker setup. (Sometimes the docker-compose up would work sometimes it would fail, fixed it!)

[ Next Week ]

1. Complete the integration of the React app.

[ Blockers ]

N/A

[bolu (Bolu Oluwalade)]

This week’s Progress (06/29 - 07/03)

1. Created three new custom elements for FHIR Observation resource
2. Created Unit testing for the custom elements created
3. Prepared the README documentations for all the created elements.
4. Removed the material web components submodule and replaced it with material web components 0.15.0 in the Librehealth lh-toolkit-webcomponents monorepo. I made an MR that contains this changes and was accepted.

Next week’s Plan(07/06 - 07/10)

1. Create the remaining FHIR Observation Resource custom elements with lit-element v2.3.1 and perform unit testing.
2. Write the README documents for the elements.
3. Make the MR to merge the Observation custom elements to the Librehealth lh-toolkit-webcomponents monorepo.

[Darshpreet2000 (Darshpreet)]

What progress have you made this week?

1. Tested both IOS & Android App
2. Scraped CDM of California State
   • Made Separate Spider class for it
3. Wrote Readme.md file for scraper
4. Separated “process.py” from “Data” Directory, so that user don’t need to clone large repository.

What do I plan to do next week?

For Web Scraper

• Generating “process.py” script for each hospital

For App

• Working on View CDM Statewise screen.

GitLab CI Pipeline

• I have to setup chromedriver & chromebrowser in CI Pipeline & then make this project run properly

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

It is not a blocker but I have tried a lot but chromedriver & chromebrowser are not working in Linux CI Pipeline, I am getting exception in pipeline,but its working on my windows, maybe I am not installing them properly , I will search more on this, & will discuss with @muarachmann

[prajwal27]

What progress have you made this week?

In the fifth week of the coding period (July 4 - July 10), I modified the UI to make it look similar to mHBS training app. It has been pushed to feature-ui-mhbs branch. I tried working on the updated SDK with the test server, but it wasn’t responding. I tried debuggind the source code and still wasn’t able to conclude as to why the updated sample app was not working with the test server.

What do I plan to do next week?

• I plan to integrate the app with realistic dummy data.
• I plan to use the old version of the SDK and code to run with the test server

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

The Evernym Mobile SDK is being continuously changed which doesn’t support the verity UI test server. We plan to communicate with the Evernym Team in the coming week.

[Kislay_Singh]

"5-july-2020 to 11-july-2020"

[ Progress ]

1. Completed the integration of UI with django backend.
2. Converted the dataset into proper protocol buffers for training on ResNet50 base of Retinanet model.

[ Next Week ]

1. Complete the training.
2. Serve the model on our tf serving server.

[ Blockers ]

N/A

[aishwhereya (Aishwarya Harpale)]

Week 6 : Coding Period

What progress have you made this week?

1. Resolved discrepancies in pruned models.Found out their actual evaluation parameters.
2. Experimenting with Knowledge Distillation and hybrid compression techniques.

What do I plan to do next week?

1. Perform traditional compression on chestx-ray14 models.
2. Give substantial results on hybrid techniques.

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

Int8 model evaluation is taking >12 hours. Working to produce the results faster.

[bolu (Bolu Oluwalade)]

This week’s Progress (07/06 - 07/10)

1. Created three more FHIR Observation Resource custom elements with lit-element v2.3.1 and performed unit testing.
2. Started writing the README documents for the elements and should be completed over the weekend

Next week’s Plan(07/13 - 07/17)

1. Make the MR to merge the Observation custom elements to the Librehealth lh-toolkit-webcomponents monorepo.
2. Start creating wen components for the FHIR medication resources after the Observation MR is accepted.

Blockers

I ran into some challenges while implementing some of the created components within other components. While the components works as expected while implemented alone, there seems to be some data binding problems when used with other components. This is as a result of the attribute/property relationship in LitElement. I am currently reading on how to solve this and hopefully come up with a solution over the weekend Here is a guide to property handling in LitElement https://lit-element.polymer-project.org/guide/properties

[Darshpreet2000 (Darshpreet)]

What progress have you made this week?

For App

1. I worked on Showing progress indicator while downloading CDM & saving to SQL database.
2. Work on View CDM Statewise screen is in progress, I will complete it by tomorrow.
3. Fixed Network exceptions while downloading CDM in app.

Web Scraper

1. Made “process.py” scripts for each hospital in California to process CDM to proper columns.
2. Made Readme.md & troubleshoot.md
3. Fixed the blocker, After trying & seraching a lot , I successfully installed chromebrowser & chromedriver in Linux CI, & it is also working correctly now.

@Darshpreet2000

It is not a blocker but I have tried a lot but chromedriver & chromebrowser are not working in Linux CI Pipeline, I am getting exception in pipeline,but its working on my windows, maybe I am not installing them properly , I will search more on this, & will discuss with @muarachmann

What do I plan to do next week?

For Web Scraper

1.Scraping & making process script for following data.

Inpatient Data of 3000 Hospitals

https://data.cms.gov/Medicare-Inpatient/Inpatient-Prospective-Payment-System-IPPS-Provider/tcsp-6e99

Outpatient Data of Hospitals

https://data.cms.gov/Medicare-Outpatient/Provider-Outpatient-Hospital-Charge-Data-by-APC-CY/fmbt-qrrw

For App

1.Completing view CDM Statewise screen.

2.Working on Compare Hospitals Functionality of App

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

I don’t have any blocker, but my only one MR is merged till now, I will discuss with @muarachmann about any improvement needed in the Merge Requests I have created so far.