diff --git a/testing/manual/model-configuration-extracting-variables.md b/testing/manual/model-configuration-extracting-variables.md index fa0c729810..e8d7f34036 100644 --- a/testing/manual/model-configuration-extracting-variables.md +++ b/testing/manual/model-configuration-extracting-variables.md @@ -12,16 +12,18 @@ Report any issues into GitHub: [open an issue](https://github.com/DARPA-ASKEM/te ### 2. Upload assets 1. From the manual testing [data folder](https://drive.google.com/drive/folders/14z6WAldQky0xgOAM69f6hakXhyHobYMe), add these resources to your project by clicking the `Upload` button and dragging these downloaded files onto the popup: - a. [SIR Document 1](https://drive.google.com/file/d/1ZQXSGhesif_G0bjQiB9nx0B_BJ1xV1Wx/view?usp=sharing) - b. [SIR Document 2](https://drive.google.com/file/d/1U1h5YCBxom9k475QSOzkiIwyi5V159dV/view?usp=sharing) - c. [SIR Model](https://drive.google.com/file/d/1F9UWuvwJPZY_XAGflsOIYy4Qrl56KS91/view?usp=sharing) - d. [Stratified SIR model](https://drive.google.com/file/d/1r-zfKmHrOub7QT9BfdQEZabfZqveLhIq/view?usp=sharing) - e. [SIDARTHE model](https://drive.google.com/drive/folders/14z6WAldQky0xgOAM69f6hakXhyHobYMe) - f. [SIDARTHE paper](https://drive.google.com/file/d/1pOb1MuarNEyrDf6I6z96Pdf_hQ9Q3_v0/view?usp=drive_link) - g. [SIR timeseries Dataset 1](https://drive.google.com/file/d/1QM2TL6XrBHIlFOVSavugKAQErls7XtY8/view?usp=sharing) - h. [SIR timeseries Dataset 2](https://drive.google.com/file/d/1zKySIpyPN_aa-icxy1e8NHmVtkZs51Fn/view?usp=sharing) - i. [SIR contact matrix dataset](https://drive.google.com/file/d/17TByirv-LwunB0gDq46-Ww-SyJZYaHKD/view?usp=sharing) -2. Wait a minute or two for the Document Intelligence service to finish extracting artifacts from the uploaded document. + 1. [SIR Document 1](https://drive.google.com/file/d/1ZQXSGhesif_G0bjQiB9nx0B_BJ1xV1Wx/view?usp=sharing) + 2. [SIR Document 2](https://drive.google.com/file/d/1U1h5YCBxom9k475QSOzkiIwyi5V159dV/view?usp=sharing) + 3. [SIR Model](https://drive.google.com/file/d/1F9UWuvwJPZY_XAGflsOIYy4Qrl56KS91/view?usp=sharing) + 4. [Stratified SIR model](https://drive.google.com/file/d/1r-zfKmHrOub7QT9BfdQEZabfZqveLhIq/view?usp=sharing) + 5. [SIDARTHE model](https://drive.google.com/drive/folders/14z6WAldQky0xgOAM69f6hakXhyHobYMe) + 6. [SIDARTHE paper](https://drive.google.com/file/d/1pOb1MuarNEyrDf6I6z96Pdf_hQ9Q3_v0/view?usp=drive_link) + 7. [SIR timeseries Dataset 1](https://drive.google.com/file/d/1QM2TL6XrBHIlFOVSavugKAQErls7XtY8/view?usp=sharing) + 8. [SIR timeseries Dataset 2](https://drive.google.com/file/d/1zKySIpyPN_aa-icxy1e8NHmVtkZs51Fn/view?usp=sharing) + 9. [SIR contact matrix dataset](https://drive.google.com/file/d/17TByirv-LwunB0gDq46-Ww-SyJZYaHKD/view?usp=sharing) + 10. [Prob 5 Model C](https://drive.google.com/file/d/1CF-n8OUroRaaNCaRTwvOgrPuASrktj1P/view?usp=drive_link) + 11. [Rosenblatt 2024](https://drive.google.com/file/d/1mGU2HwXG5ZWjgo24DNaNkq2oS5ipL6_V/view?usp=drive_link) +3. Wait a minute or two for the Document Intelligence service to finish extracting artifacts from the uploaded document. ### 3. Extracting configurations from multiple documents and timeseries datasets 1. Create a new workflow @@ -85,3 +87,64 @@ Report any issues into GitHub: [open an issue](https://github.com/DARPA-ASKEM/te - `Restrictive NPIs Scenario` - Initial expressions for S, I, D, A, R, T, H, and E should be extracted for all configurations - Parameter values for alpha, beta, delta, epsilon, eta, gamma, kappa, lambda, mu, nu, rho, theta, xi, zeta, tau, and sigma should be extracted for all configurations + +### 6. Extracting configuration from a table with probability distributions (Not supported yet) + +This is difficult test case since it involves extracting values from a table _and_ some of the parameters are probability distributions. + +1. Add `Prob 5 Model C` model and `Rosenblatt 2024` document to the workflow +2. Create a new "Configure model" operator +3. Connect the model and document to this operator +4. Open the operator and click "Extract configuration from inputs" +5. There should be only one model configuration that is extracted +6. Confirm the values + + | Parameters | Type | Distribution Parameter(s) | + | --- | --- | --- | + | α | LogNormal1 | meanLog = 4.72, stdevLog = 0.63 | + | AER | Constant | 4 | + | Aw | Constant | 100 | + | Ci | Constant | 0.0014 | + | Nw | Constant | 1000 | + | S | Constant | 0.24 | + | Vair | Constant | 7.03 | + | Vdrop | Constant | 0.01 | + | e | Constant | 2.71828 | + | kappa | Constant | 11.35 | + | lambda | Constant | 0.63 | + | q | Constant | 0.34 | + | rhoA | LogNormal1 | meanLog = 3.47, stdevLog = 0.23 | + | theta | LogNormal1 | meanLog = 0.28, stdevLog = 0.27 | + | epsilonD | LogitNormal1 | location = -1.46, scale = 0.71 | + | k | Constant | 410 | + | y | Constant | 0.1666 | + | IR_W_W | Constant | 0.85 | + | IR_W_C | Constant | 0.85 | + | IR_W_H | Constant | 0.85 | + | IR_C_W | Constant | 0.85 | + | IR_C_C | Constant | 0.85 | + | IR_C_H | Constant | 0.85 | + | IR_H_W | Constant | 0.53 | + | IR_H_C | Constant | 0.53 | + | IR_H_H | Constant | 0.53 | + | omega_W_C | Constant | 0.00072 | + | omega_C_W | Constant | 0.00072 | + | omega_C_C | LogNormal1 | meanLog = 3.47, stdevLog = 0.91 | + | omega_H_W | LogNormal1 | meanLog = -1.59, stdevLog = 1.70 | + | omega_W_H | LogNormal1 | meanLog = -1.59, stdevLog = 1.70 | + | omega_H_C | LogNormal1 | meanLog = 2.52, stdevLog = 1.13 | + | omega_C_H | LogNormal1 | meanLog = 2.52, stdevLog = 1.13 | + | tContact_W_W | LogNormal1 | meanLog = 1.55, stdevLog = 1.27 | + | tContact_W_C | LogNormal1 | meanLog = 1.55, stdevLog = 1.27 | + | tContact_C_W | LogNormal1 | meanLog = 1.55, stdevLog = 1.27 | + | tContact_C_C | LogNormal1 | meanLog = 1.55, stdevLog = 1.27 | + | tContact_C_H | LogNormal1 | meanLog = 1.79, stdevLog = 1.15 | + | tContact_W_H | LogNormal1 | meanLog = -0.36, stdevLog = 0.98 | + | Cvs | LogNormal1 | meanLog = 0.22, stdevLog = 0.34 | + | Cv_C_C | LogNormal1 | meanLog = 0.22, stdevLog = 0.34 | + | Cv_C_W | LogNormal1 | meanLog = 0.22, stdevLog = 0.34 | + | Cv_W_C | LogNormal1 | meanLog = 0.22, stdevLog = 0.34 | + | Cv_C_H | LogNormal1 | meanLog = 5.6 * log(10), stdevLog = 1.2 * log(10) | + + | Cv_W_H | LogNormal1 | meanLog = 5.6 * log(10), stdevLog = 1.2 * log(10) | + | Vsputum | Constant | 100 |