From 2ef1a0840d55d85bdc8f21495980a1fd808951fd Mon Sep 17 00:00:00 2001 From: Dilan Pathirana Date: Fri, 11 Sep 2026 12:27:43 +0000 Subject: [PATCH] Alkan_SciSignal2018: fix noise (sd_) parameters to be fixed, not estimated Closes #320. The 12 noise standard-deviation parameters were marked estimate=1, but in the canonical d2d implementation they are fixed (qFit=0), not fitted. Their PEtab nominalValues already equal the d2d fixed values exactly, so only the estimate flag was wrong. Fix: set estimate=0 for all 12. Verified against d2d (arFramework3/Examples/Alkan_DDRP_SciSignal2018, Results/final_fit/workspace_pars_only.mat: ar.qFit / ar.p). All 71 PEtab parameters map 1:1 to d2d; the ONLY estimate-vs-qFit mismatches were exactly these 12, and every nominalValue matches the d2d fixed value: sd_count_abs=0.1 sd_count_casp_abs=0.1 sd_pchk1_au=0.1 (10^-1) sd_patm_au=0.0794328234724 (10^-1.1) sd_yh2ax_au=0.125892541179 (10^-0.9) sd_pdnapk_au=sd_pp53_au=sd_tp53_au=0.199526231497 (10^-0.7) sd_pchk2_au=sd_tp21_au=0.316227766017 (10^-0.5) sd_p21_mRNA_fold=sd_wip1_mRNA_fold=1.0 (10^0) Result: 44 estimated / 27 fixed parameters, matching d2d (44 qFit=1 / 27 qFit=0). PEtab lint passes. Co-Authored-By: Claude Opus 4.8 --- .../parameters_Alkan_SciSignal2018.tsv | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/Benchmark-Models/Alkan_SciSignal2018/parameters_Alkan_SciSignal2018.tsv b/Benchmark-Models/Alkan_SciSignal2018/parameters_Alkan_SciSignal2018.tsv index bc8303d1..c40f5020 100644 --- a/Benchmark-Models/Alkan_SciSignal2018/parameters_Alkan_SciSignal2018.tsv +++ b/Benchmark-Models/Alkan_SciSignal2018/parameters_Alkan_SciSignal2018.tsv @@ -58,15 +58,15 @@ scale_tp21_au scale_tp21_au log10 1e-05 1000.0 3.9178550677340596 1 scale_tp53_au scale_tp53_au log10 1e-05 1000.0 1.4313361828755429 1 scale_wip1_mRNA_fold scale_wip1_mRNA_fold log10 1e-05 1000.0 2.2770003237741387 1 scale_yh2ax_au scale_yh2ax_au log10 1e-05 1000.0 60.50316673653378 1 -sd_count_abs sd_count_abs log10 1e-05 1000.0 0.1 1 -sd_count_casp_abs sd_count_casp_abs log10 1e-05 1000.0 0.1 1 -sd_p21_mRNA_fold sd_p21_mRNA_fold log10 1e-05 1000.0 1.0 1 -sd_patm_au sd_patm_au log10 1e-05 1000.0 0.07943282347242814 1 -sd_pchk1_au sd_pchk1_au log10 1e-05 1000.0 0.1 1 -sd_pchk2_au sd_pchk2_au log10 1e-05 1000.0 0.31622776601683794 1 -sd_pdnapk_au sd_pdnapk_au log10 1e-05 1000.0 0.19952623149688797 1 -sd_pp53_au sd_pp53_au log10 1e-05 1000.0 0.19952623149688797 1 -sd_tp21_au sd_tp21_au log10 1e-05 1000.0 0.31622776601683794 1 -sd_tp53_au sd_tp53_au log10 1e-05 1000.0 0.19952623149688797 1 -sd_wip1_mRNA_fold sd_wip1_mRNA_fold log10 1e-05 1000.0 1.0 1 -sd_yh2ax_au sd_yh2ax_au log10 1e-05 1000.0 0.12589254117941673 1 +sd_count_abs sd_count_abs log10 1e-05 1000.0 0.1 0 +sd_count_casp_abs sd_count_casp_abs log10 1e-05 1000.0 0.1 0 +sd_p21_mRNA_fold sd_p21_mRNA_fold log10 1e-05 1000.0 1.0 0 +sd_patm_au sd_patm_au log10 1e-05 1000.0 0.07943282347242814 0 +sd_pchk1_au sd_pchk1_au log10 1e-05 1000.0 0.1 0 +sd_pchk2_au sd_pchk2_au log10 1e-05 1000.0 0.31622776601683794 0 +sd_pdnapk_au sd_pdnapk_au log10 1e-05 1000.0 0.19952623149688797 0 +sd_pp53_au sd_pp53_au log10 1e-05 1000.0 0.19952623149688797 0 +sd_tp21_au sd_tp21_au log10 1e-05 1000.0 0.31622776601683794 0 +sd_tp53_au sd_tp53_au log10 1e-05 1000.0 0.19952623149688797 0 +sd_wip1_mRNA_fold sd_wip1_mRNA_fold log10 1e-05 1000.0 1.0 0 +sd_yh2ax_au sd_yh2ax_au log10 1e-05 1000.0 0.12589254117941673 0