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# System prepended metadata

title: July 3 TODO

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# July 3 TODO

- run [normalization script on TWILIGHT-RAIN](https://github.com/Covi-Canada/simulator/blob/master/docs/src/notes/distribution_normalization.md)

### Martin:
- Experiments:
    - Compare TWILIGHT-RAIN experiments with Refactor branch results to ensure I didn't break anything (so we can merge it)
    - Run unmitigated with 1k, 3k, 5k, 10k, 20k population
- Bugfixes:
    - Check that when someone in a household quarantines, the rest of the poeple in the house try to avoid them and also go into quarantine
- Features:
    - Add demographics / epidemiological results to victor's script
    - Add day of infection of the infector (like generation times)
    - re-tune based off unmitigated experiment results
- DevOps:
    - Add human and day idx then send Nasim a mini dataset with the new hdf5 format
- align with epidemiological data:
    - Load and visualize the [historical case and hospitalization counts for montreal](https://docs.google.com/spreadsheets/d/1F98IwKdO5dDdhhALnURsANPCqS6AP6uCYeqsX0JoArI/edit#gid=1889102279)
    - Implement dynamic change in mixing to align with real-world data 
    - Add more pre-existing conditions (heart disease, diabetes, obesity, smoking and chronic kidney disease). You can find the [% on p.26 of the shared google doc](https://docs.google.com/document/d/1QE05BBJI-zD0Qt08_O72y2iFb6LJP-35DOC-xD0AMPU/edit), under "Prevalence in the general population" 
- Parallelism / Real-world maps
    - Partition graph in [CityGraph](https://github.com/MPI-IS/CityGraph) for multiprocessing
    - Decide whether we 1) use CityGraph as an imported package and heavily modify it, 2) install it from source and heavily modify it, 3) re-implement some of its functionality in our codebase. Need to do a huge merge of City and Location.

### Victor

### Meng
- integrate SpyHumansPro notebook with victor scripts

### PLSC
- throw out logged events (4kb each) after some time for postmortem debugging/baseball plots
- analyze memory usage in long simulations while running with tune=True only
    - if necessary, modify the tracking code to progressively dump data to disk using hdf5 utils in opened PR
- finish wrapping the geospatial utilities for zone-based boundary/statistics usage in simulator
- ...finish merging/testing opened PRs (code violence might be necessary) >:(
- move repo from covi-canada to mila-iqia (!!!)

### Prateek
- Submit PR for contact mixing changes
- improving hospitalization model (prateek + francois)

### Tegan
- Fix clipping of infectiousness_onset (and incubation_days?)
- shift and reduce mean instead of clipping
- check beta with Eilif 
- “Cohort Ro” look at % infected for has_app vs not 


### Nasim
- Experiments:
    - Find out if predicting Viral Load and multiplier separately helps (need plotting scripts for eval in the loop)
    - Find out if factorizing $P(C | D, Data) = P(C | D) P(D | Data)$ helps, where $C$ is contagiousness, $D$ is days since exposure and $Data$ includes contacts, PEC, symptoms, etc. 
    - Integrate city-wide hospitalizations and case counts into predictor and train model
    - Integrate GT prevalence into predictor and train model
    - Mu + alpha sigma experiment takes more thought (nasim)


### Eilif
- Write Cisco Grant (pair w/ martin)

DONE:
- debug current pareto plots
- integrate wandb with plot scripts
- remove plots each run
- have plot dir
- add way to compare multiple transformers with different weights and/or rec level maps
- enable Transformer and Oracle pareto plots to work
- Get datasets to nasim for retraining (narrower DR, no DR, perfect clustering)
- Fix legend / colors in pareto all_adoption
- expand width of pareto adoption figure
- make jellybean uptake 2 wide
- make pre-symptomatic plot be allowed to select just 1 vertical
- Create an example experiment (markdown + images) on hackmd
