Alkan_SciSignal2018: fix noise (sd_) parameters to be fixed, not estimated - #321
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Alkan_SciSignal2018: fix noise (sd_) parameters to be fixed, not estimated#321dilpath wants to merge 1 commit into
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…mated 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 <noreply@anthropic.com>
FFroehlich
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Sep 11, 2026
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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.