Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Ensemble with Generalisation #11

Open
wants to merge 113 commits into
base: feature/hetero_ensemble
Choose a base branch
from
Open

Ensemble with Generalisation #11

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
113 commits
Select commit Hold shift + click to select a range
d9ee5e3
Merge branch 'feature/doc_datautils' into feature/direct_csv
NayanaBannur Jun 16, 2020
71cf811
Add direct csv data source
NayanaBannur Jun 16, 2020
395e8f1
Ensemble with Generalisation
Jul 11, 2020
f7a1251
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
NayanaBannur Jul 13, 2020
c1f506c
Add import
NayanaBannur Jul 13, 2020
6b04f79
SEIHRD with generalisation
Jul 13, 2020
a235931
SEIHRD with gen
Jul 13, 2020
6027f05
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
Jul 13, 2020
1dbcb1e
Testing new equations
Jul 13, 2020
ef737a1
Use subset of trials in ensemble
NayanaBannur Jul 14, 2020
0cb71df
Fix m2 plot dates
NayanaBannur Jul 15, 2020
907906e
Use subset of trials in ensemble
NayanaBannur Jul 15, 2020
5f54f70
Use local weights, not self.weights
NayanaBannur Jul 15, 2020
4096601
Tested train_eval_plot_ensemble
NayanaBannur Jul 15, 2020
54f05cd
Resolve merge conflicts
NayanaBannur Jul 15, 2020
5101907
Shift plots to plotting utils
NayanaBannur Jul 15, 2020
dead2b8
Manual merge
NayanaBannur Jul 15, 2020
70f481f
Include run name of previous runs in dataframe returned
NayanaBannur Jul 15, 2020
f4c8bf6
Add input filepath to config
NayanaBannur Jul 15, 2020
128d7b3
Accept input file path for csv
NayanaBannur Jul 15, 2020
8250efe
Clean up
NayanaBannur Jul 15, 2020
5977666
Update data source in configs
NayanaBannur Jul 15, 2020
973f5bd
Add filepath and code clean up
NayanaBannur Jul 15, 2020
52aadf4
Update utils
NayanaBannur Jul 15, 2020
0c0ff96
Update nb_utils and test notebook
NayanaBannur Jul 15, 2020
e373e70
Merge branch 'feature/direct_csv' into hetero_ensemble_generalised
NayanaBannur Jul 15, 2020
5c65529
generalised ensemble_utils and refactored predict_with_uncertainty
Jul 16, 2020
9092ad5
added get_params_for_percentiles func in hetero_ensemble class
Jul 16, 2020
89a3400
added is_tuning check while computing weights from beta
Jul 16, 2020
9cb8427
fixed bug of remultiplying weights
Jul 16, 2020
e5c5609
Add single variable and multivariate plots. Add m1 plots.
NayanaBannur Jul 16, 2020
19a7ab3
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
NayanaBannur Jul 16, 2020
d5fa748
Check if runs_df is empty
NayanaBannur Jul 17, 2020
06f91d7
Load only specific tables from Athena db
NayanaBannur Jul 17, 2020
5242fa8
Fix direct csv data fetcher
NayanaBannur Jul 17, 2020
f74205b
added predict with best fit functionality
Jul 18, 2020
1f48376
Change in import model_factory_alias
Jul 18, 2020
79c5575
Update configs
NayanaBannur Jul 19, 2020
f3b91d4
Fixed latent param issue
Jul 19, 2020
284187c
Add m2 plots. Update all plots.
NayanaBannur Jul 19, 2020
92e3abe
Update plotting in nb_utils. Add run day observations to predictions.
NayanaBannur Jul 19, 2020
8970f99
Prevent divide by zero
NayanaBannur Jul 19, 2020
d5397ad
center=true for rolling average
NayanaBannur Jul 19, 2020
0cc3306
Update predictions output format
NayanaBannur Jul 19, 2020
2589163
Return empty dataframe if no runs are available
NayanaBannur Jul 19, 2020
8c5579e
Rename predict with uncertainty mode
NayanaBannur Jul 19, 2020
c67b110
Test notebook with new plots
NayanaBannur Jul 19, 2020
1b0b168
Resolve conflicts and merge
NayanaBannur Jul 19, 2020
fd4dd8f
Add output paths for plots
NayanaBannur Jul 19, 2020
046af6d
Rename test as test1. Update some documentation.
NayanaBannur Jul 19, 2020
60bdc5d
Test notebook with latent param changes
NayanaBannur Jul 19, 2020
015adbb
Update official data to new covid case summary
NayanaBannur Jul 20, 2020
afb876e
Plot best fit
NayanaBannur Jul 20, 2020
20a0218
ModelBuildingSession notebook - init commit
shreyasshetty Jul 20, 2020
2124c4c
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
shreyasshetty Jul 20, 2020
1627fc0
Removed the default value for the date_of_interest parameter in uncer…
shreyasshetty Jul 20, 2020
78e3a93
Added the ModelBuildingSession class
shreyasshetty Jul 20, 2020
4add2b8
Moved nb_utils to src/ folder
shreyasshetty Jul 20, 2020
eafbfd2
Add report generation
NayanaBannur Jul 20, 2020
7d9f9aa
Add debug mode for additional plotting
NayanaBannur Jul 21, 2020
7a1bbf4
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
NayanaBannur Jul 21, 2020
614ae9f
Update src/nb_utils with plotting changes: best fit and debug mode fo…
NayanaBannur Jul 21, 2020
a79f423
added stats function in homogeneous ensemble class
Jul 21, 2020
0aa7ec2
Added output dir for plots. Added PDF,CDF plots.
NayanaBannur Jul 22, 2020
5b6851b
Placeholder function for fetching staffing ratios
NayanaBannur Jul 22, 2020
b4f5dee
Add function to return trials for a variable on planning date
NayanaBannur Jul 22, 2020
3073964
Update and test notebook
NayanaBannur Jul 22, 2020
e423205
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
NayanaBannur Jul 22, 2020
7cf4e07
changed get stats for correct weighted mean
harshm121 Jul 22, 2020
9388b4b
fixed set_dates
harshm121 Jul 23, 2020
7bce270
Updated PDF plot. Improved other plots.
NayanaBannur Jul 23, 2020
afd8b20
Bug fix in evaluation. Fix set_dates. Add messages.
NayanaBannur Jul 23, 2020
cb02079
Fix beta training start date
NayanaBannur Jul 23, 2020
ab1067e
Fix picking of run_day for latent params
NayanaBannur Jul 23, 2020
62375f9
Resolve merge conflicts
NayanaBannur Jul 23, 2020
8c96b32
Minor updates
NayanaBannur Jul 23, 2020
38d3a6c
Function to convert loss json to dataframe
NayanaBannur Jul 23, 2020
dcd1212
Handle pandas dataframes in report
NayanaBannur Jul 23, 2020
e90191d
Add loss dataframes to metrics for report
NayanaBannur Jul 23, 2020
6d0ef91
Link to forecast csv
NayanaBannur Jul 23, 2020
895425c
Display dicts as yaml in report
NayanaBannur Jul 23, 2020
b19c241
Model Building report generation added
shreyasshetty Jul 24, 2020
21482de
minor notebook cleanup
shreyasshetty Jul 24, 2020
0dbca2b
Added plots for planning configuration
shreyasshetty Jul 24, 2020
9d19830
Updated experiments on Pune
shreyasshetty Jul 24, 2020
0deceed
Updated model_building_utils for rendering markdown
shreyasshetty Jul 24, 2020
6094783
model building session experiments updated
shreyasshetty Jul 24, 2020
3cef7b7
Minor updates
NayanaBannur Jul 24, 2020
b22da8a
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
NayanaBannur Jul 24, 2020
76093f0
added patna's population
Jul 24, 2020
5b67b6d
updated planning output report generation
shreyasshetty Jul 24, 2020
fa8891f
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
shreyasshetty Jul 24, 2020
d44a237
Flatten dicts and log
NayanaBannur Jul 24, 2020
6e4e7f9
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
NayanaBannur Jul 24, 2020
286d8b1
updated model utils - version used in first internal demo
shreyasshetty Jul 25, 2020
3a79d93
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
shreyasshetty Jul 25, 2020
8897d42
Demo notebook
shreyasshetty Jul 25, 2020
9b7e0b9
Minor updates
NayanaBannur Jul 26, 2020
e087bdc
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
NayanaBannur Jul 26, 2020
4a7ff75
Update mlflow. Delete unwanted files.
NayanaBannur Jul 26, 2020
2483774
staffing matrix computations
shreyasshetty Jul 26, 2020
d98d8a3
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
shreyasshetty Jul 27, 2020
f4621ae
updated model_building_utils to consume train and forecast intervals
shreyasshetty Jul 28, 2020
a70f7f4
fixed the assert checks
shreyasshetty Jul 28, 2020
b76763e
Initial commit for data_all tracker data source
NayanaBannur Jul 29, 2020
43f7490
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
NayanaBannur Jul 29, 2020
6c6db3f
Data all source format conversion
Jul 29, 2020
9dc9904
Bug fix in data fetcher
Jul 29, 2020
93e6f83
Auto Capitalise region_name
Jul 30, 2020
e045884
Auto Capitalise region_name
Jul 30, 2020
4748908
Minor bug fix in get_mean_params
harshm121 Aug 2, 2020
1b02990
Fix rmsle loss function
NayanaBannur Aug 26, 2020
997025f
Merge branch 'hetero_ensemble_generalised' of https://github.com/dsin…
NayanaBannur Aug 26, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 11 additions & 6 deletions config/sample_homogeneous_train_config.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,24 +7,29 @@
"model_class": "homogeneous_ensemble",
"model_parameters": {
"child_model":{
"model_class": "SEIHRD",
"model_class": "SEIR_gen",
"model_parameters": {
"incubation_period": 5,
"F_icu" : 0.05
"F_icu" : 0.05,
"latent_information":{
"latent_variables": ["exposed", "active"],
"latent_on": "confirmed"
}
}
},

"modes":{
"training_mode": "constituent_models",
"predict_mode": "mean_predictions"
}
},
"search_space": {
"r0": [0.5, 3],
"EbyCRatio": [0.001, 70],
"IbyCRatio": [0.001, 2],
"exposed_ratio": [0.001, 70],
"active_ratio": [0.001, 2],
"infectious_period": [1, 10],
"F_hospitalization" : [0, 0.125],
"F_fatalities" : [0.02, 0.12],
"hospitalization_period" : [10, 20],
"deceased_ratio" : [0, 1],
"beta": [0, 2]
},
"search_parameters": {
Expand Down
Loading