From 91c59d60d3a1f9ad0faf8c15308e96eeab5a6ea9 Mon Sep 17 00:00:00 2001 From: "Jose P. Faria" Date: Wed, 9 Sep 2026 10:40:48 -0500 Subject: [PATCH] Methods: fill the abstention rate from the completed run The full-database run finished after #290 was merged, so the placeholder in that section can now be replaced with the measured value. The ensemble abstains on 1.7% of the 45,644 reactions, against the existing rules declining on 48.7% of them, so both halves of that contrast are measured. The only remaining TBD in the section is the supplementary reference, which waits on final numbering. --- .../latex/sections/methods_council_direction.tex | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/Papers/NAR_Update_2026/latex/sections/methods_council_direction.tex b/Papers/NAR_Update_2026/latex/sections/methods_council_direction.tex index 38592599..698a602f 100644 --- a/Papers/NAR_Update_2026/latex/sections/methods_council_direction.tex +++ b/Papers/NAR_Update_2026/latex/sections/methods_council_direction.tex @@ -1,5 +1,6 @@ %% Direction assignment from reaction chemistry (LLM ensemble). -%% \TBD values pending the full-database run, in progress. +%% Run complete over all 45,644 reactions. The one remaining \TBD is the +%% supplementary reference, pending final numbering. \subsection{Direction assignment from reaction chemistry}\label{sec:methods-council} Thermodynamic direction assignment is bounded by estimate coverage: a reaction @@ -53,11 +54,11 @@ \subsection{Direction assignment from reaction chemistry}\label{sec:methods-coun so individual assignments can be reviewed rather than accepted in aggregate. Two properties of the method bear on how the calls should be used. The ensemble commits to a direction far more readily than the thermodynamic rules -do, abstaining on \TBD[pct]\% of reactions where the rules decline on a -substantial fraction of the database, so it supplies calls where none -currently exist rather than reproducing the ones that do. And its stated -confidence does not distinguish its correct calls from its incorrect ones, so -confidence is not a usable filter for downstream integration. A systematic +do, abstaining on 1.7\% of the reaction set where the existing rules decline +on 48.7\% of it, so it supplies calls where none currently exist rather than +reproducing the ones that do. And its stated confidence does not distinguish +its correct calls from its incorrect ones, so confidence is not a usable +filter for downstream integration. A systematic evaluation against measured equilibrium constants, and against the model-level consequences of adopting these calls, is deferred to follow-up work.