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Commits on Dec 1, 2024

skyler update

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skyler original file

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Commits on Dec 4, 2024

Reproduce the oscillatory derivative

Shihao Yang
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Reproduce the oscillatory derivative with fast run time

Shihao Yang
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Shihao Yang
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there is some small oscillation in the simulated true trajectory. There might be some numerical instability in the ground truth simulation that you use to generate those data

Shihao Yang
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Shihao Yang
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The m matrix at the edge time points seem to be the problem. See attached for TF and pytorch comparison on GP derivative mapping applied on the same corrected data.

Shihao Yang
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The problem has been identified to be in the M-matrix.

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add back jitter

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Commits on Dec 5, 2024

add flag for use_fourier_prior

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allow phi_exo

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allow manual phi specification

Shihao Yang
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Qualitatively, the TensorFlow probability result does not agree with the PyTorch. The R component recovery is bad, but there is not much we can do about it. We will need to edit the experimental se…

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add trace plot

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Shihao Yang
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add skyler data generation

Shihao Yang
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seir simulation with log error

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log scale verified to be correct

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Commits on Dec 6, 2024

use 1.0 as N

Shihao Yang
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log error on SIR 3-component doesn't work

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refactor name. not working

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log using eir seems working

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low noise case works

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15% multiplicative noise for the SEIR model 3-component fully observed case is working. I am trying to generate the forecasting, but I think this picture alone we can already put into the paper.

Shihao Yang
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Shihao Yang
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15% multiplicative noise for the SEIR model 3-component fully observed case is working. I am trying to generate the forecasting, but I think this picture alone we can already put into the paper.

Shihao Yang
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prediction is working

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missing component runs but not performing well

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results are different every time, suggesting MCMC not converged yet

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Commits on Dec 7, 2024

add MLE that runs

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Shihao Yang
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add MLE to see identifiability problem

Shihao Yang
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print out loss so that I can compare different init value

Shihao Yang
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hessian approximation is not correct

Shihao Yang
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Shihao Yang
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add mcmc

Shihao Yang
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Shihao Yang
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add mcmc, it is working

Shihao Yang
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mcmc and UQ using MLE likelihood

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visualization labels

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UQ is under-estimated

Shihao Yang
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simplify plotting. more samples

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R0 reproduction number

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simulation for repetition

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save results with command line argument

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Commits on Dec 8, 2024

file update for repetition

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Commits on Dec 9, 2024

draft evaluation script

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evaluation script corrected

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add evaluation and generate tables and figures

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add visualizations

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add visualizations

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add visualizations

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ready to generate figures and tables

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add coverage

Shihao Yang
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Shihao Yang
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add R0

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Commits on Dec 11, 2024

6k early termination works the best

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try lmbda = 1000.0; remove sir file

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Commits on Dec 12, 2024

output pictures

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Commits on Dec 15, 2024

visualization update

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Commits on Dec 17, 2024

R0 = beta / (gamma)

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add pickle for plot data

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Commits on Dec 18, 2024

overall chart that is working

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two types of visualizations

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Commits on Dec 19, 2024

rmse on original scale

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add peak timing and intensity in MAGI

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bug fix

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add name

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bug fix

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results forecast

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bug fix

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bug fix

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add RMSPE

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Commits on Dec 23, 2024

final visualizations

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Commits on Dec 24, 2024

new data simulation under covid-19 setting

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phi2 init optim change

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magi to use new data

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output path

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bug in file path for SEIR MAGI

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Commits on Dec 27, 2024

move data

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add prediction rmse

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