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Life sciences · Preprint
arXiv · September 17, 2026
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In extractive document question answering whose questions were generated from the passages that contain their answers -- so that retrieval recovers 92-99.8% of what any mode combination could reach, whatever its absolute accuracy -- confidence-driven mechanisms have little to gain. Fine-tuning an open language model on a specialized domain corpus yields a model whose own confidence is a tempting control signal: it could decide which queries warrant further adaptation, and which answers to trust. We evaluate both uses under criteria fixed before the runs were executed, across four 7-9B model families whose adaptation moved closed-book F1 by at most +0.03, and both fail: a distillation trigger on all four families, under its pre-specified three-step transfer budget, and a routing-and-abstention policy in its single-model pilot. Retrieval alone recovers 92-99.8% of best-case combined accuracy under every correctness criterion we test, leaving routers no meaningful gain. The sequence-likelihood signal is insufficient relative to that mode -- area under the receiver operating characteristic curve 0.65-0.81 under the registered criterion -- before adaptation as well as after, unchanged by scalar recalibration and not consistently improved by token-level temperature rescaling. And the finer diagnostics depend on the correctness criterion and on answer length; on the three adapted combinations where we could test it, selector ablations show no statistically detectable downstream benefit from the confidence term on any seed; on Gemma, removing it changes the selector from failing to passing both registered criteria. The usable product is a set of pre-specified negatives with their dependencies made explicit.