diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml new file mode 100644 index 0000000..c1697fd --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml @@ -0,0 +1,183 @@ + + + + + + + + + + + + + + + + + + + + + kappa + + + 1 + + + + + + + kappa + 400 + + 1 + + + + + + rho + + + + + + + + + + u_2 + + + + + + + 1 + 1000000000 + + + + + + + + + + + + rho + U + + + 1 + + + + + U + I + + kappa + + + + + + psi + V + U + + + + + + + + + + + + + rho + I + + + 1 + + + + + U + I + + kappa + + + + + + psi + V + U + + + + + alpha + I + + + + + + + + + + + + + alpha + beta + I + + + + psi + V + U + + + + + delta + V + + + + + + + + + + + + U + 1 -8 + + + + + + + 0 + + + + + + + diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml b/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml new file mode 100644 index 0000000..6e3a81a --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml @@ -0,0 +1,13 @@ +format_version: 1 +parameter_file: parameters.tsv +problems: + - condition_files: + - conditions.tsv + measurement_files: + - measurements_scaled.tsv + observable_files: + - observables.tsv + sbml_files: + - baseline_model.xml + visualization_files: + - visualizations.tsv \ No newline at end of file diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv new file mode 100644 index 0000000..05f8ba2 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv @@ -0,0 +1,3 @@ +conditionId conditionName u_2 +vvDD vvDD 1000000000.0 +ctrl ctrl 0.0 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv new file mode 100644 index 0000000..2fa1f20 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv @@ -0,0 +1,101 @@ +observableId simulationConditionId measurement time +tumor_num vvDD 451.73401707247393 0 +tumor_num vvDD 477.41006706423315 0 +tumor_num vvDD 509.5051295539299 0 +tumor_num vvDD 554.4382170395085 0 +tumor_num vvDD 852.9222981937005 0 +tumor_num vvDD 1016.607116891161 0 +tumor_num vvDD 1058.3306981277697 0 +tumor_num vvDD 1084.006748119529 0 +tumor_num vvDD 1241.2725543190497 0 +tumor_num vvDD 1263.7390980618388 0 +tumor_num vvDD 679.6089607493324 1 +tumor_num vvDD 817.6177294550338 1 +tumor_num vvDD 535.1811795456891 1 +tumor_num vvDD 824.0367419529714 1 +tumor_num vvDD 1055.1211918788 1 +tumor_num vvDD 926.740941920006 1 +tumor_num vvDD 1571.8516979629405 1 +tumor_num vvDD 1331.1387292902025 1 +tumor_num vvDD 1481.9855229917855 1 +tumor_num vvDD 968.4645231566146 1 +tumor_num vvDD 406.80092958689744 2 +tumor_num vvDD 483.82907956217286 2 +tumor_num vvDD 294.4682108729532 2 +tumor_num vvDD 885.0173606833995 2 +tumor_num vvDD 291.25870462398325 2 +tumor_num vvDD 814.4082232060639 2 +tumor_num vvDD 958.836004409705 2 +tumor_num vvDD 1119.3113168581956 2 +tumor_num vvDD 1132.1493418540751 2 +tumor_num vvDD 1000.5595856463136 2 +tumor_num vvDD 355.4488296033791 3 +tumor_num vvDD 349.0298171054393 3 +tumor_num vvDD 220.64956714664766 3 +tumor_num vvDD 194.97351715488847 3 +tumor_num vvDD 252.74462963634662 3 +tumor_num vvDD 422.84846083174693 3 +tumor_num vvDD 772.6846419694551 3 +tumor_num vvDD 464.5720420683534 3 +tumor_num vvDD 785.5226669653348 3 +tumor_num vvDD 339.40129835853173 3 +tumor_num vvDD 50.545735951247316 4 +tumor_num vvDD 101.89783593476568 4 +tumor_num vvDD 76.2217859430065 4 +tumor_num vvDD 53.75524220021722 4 +tumor_num vvDD 191.76401090591855 4 +tumor_num vvDD 262.3731483832563 4 +tumor_num vvDD 589.7427857781752 4 +tumor_num vvDD 345.8203108564694 4 +tumor_num vvDD 631.4663670147839 4 +tumor_num vvDD 374.7058670971985 4 +tumor_num ctrl 349.1039275702164 0 +tumor_num ctrl 370.50979635893606 0 +tumor_num ctrl 407.93829872021803 0 +tumor_num ctrl 552.3499369974998 0 +tumor_num ctrl 632.5786249293225 0 +tumor_num ctrl 657.550182543784 0 +tumor_num ctrl 945.4762838668787 0 +tumor_num ctrl 985.5848518293386 0 +tumor_num ctrl 1244.9967188123485 0 +tumor_num ctrl 1343.9454339282627 0 +tumor_num ctrl 508.3483427091911 1 +tumor_num ctrl 323.8108084590962 1 +tumor_num ctrl 516.3654354989194 1 +tumor_num ctrl 917.5146511614834 1 +tumor_num ctrl 965.6460879171242 1 +tumor_num ctrl 830.874501593137 1 +tumor_num ctrl 1345.400986797869 1 +tumor_num ctrl 1404.2411339513233 1 +tumor_num ctrl 1086.00067182176 1 +tumor_num ctrl 1372.138106771691 1 +tumor_num ctrl 648.8611786571674 2 +tumor_num ctrl 343.986388512792 2 +tumor_num ctrl 480.36360598998806 2 +tumor_num ctrl 1250.5821141492872 2 +tumor_num ctrl 1140.9304646390121 2 +tumor_num ctrl 771.4696645965797 2 +tumor_num ctrl 1400.3481076254745 2 +tumor_num ctrl 1357.553698058382 2 +tumor_num ctrl 1400.3423316220221 2 +tumor_num ctrl 1592.8854066549445 2 +tumor_num ctrl 612.8651251516885 3 +tumor_num ctrl 441.73369491093814 3 +tumor_num ctrl 449.7392356937657 3 +tumor_num ctrl 1091.5802911552485 3 +tumor_num ctrl 1265.4091150075299 3 +tumor_num ctrl 959.3493729329441 3 +tumor_num ctrl 1669.2210682609186 3 +tumor_num ctrl 1441.9064524540886 3 +tumor_num ctrl 1262.7232734028994 3 +tumor_num ctrl 1749.461308199642 3 +tumor_num ctrl 705.2811803647304 4 +tumor_num ctrl 416.469455817074 4 +tumor_num ctrl 496.70391975234486 4 +tumor_num ctrl 1499.550966893223 4 +tumor_num ctrl 1357.8136182136711 4 +tumor_num ctrl 1026.0423760760882 4 +tumor_num ctrl 1531.6539940728533 4 +tumor_num ctrl 1700.1226867227788 4 +tumor_num ctrl 1470.1280053147707 4 +tumor_num ctrl 1876.6258001727879 4 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv new file mode 100644 index 0000000..c6495a2 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv @@ -0,0 +1,2 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observableTransformation +tumor_num tumor_number U + I sqrt(sigma_a^2 + (sigma_b * (U + I))^2) normal lin diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv new file mode 100644 index 0000000..46cc17f --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv @@ -0,0 +1,9 @@ +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate parameterType +rho rho log10 0.42 1.66 1 1 +kappa kappa log10 100.0 100000.0 1 1 +psi psi log10 1e-10 0.01 1 1 +beta beta log10 1.0 10000.0 1 1 +alpha alpha log10 0.0001 1000.0 1 1 +delta delta log10 0.01 100.0 1 1 +sigma_a sigma_a log10 10.0 100000.0 1 1 +sigma_b sigma_b log10 0.0001 100.0 1 1 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv new file mode 100644 index 0000000..137103f --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv @@ -0,0 +1,2 @@ +plotId plotTypeData plotTypeSimulation xValues xLabel yValues yLabel legendEntry +plot1 MeanAndSD ScatterPlot condition Condition tumor_num Tumor Number Model