Semantic Calibration Prevails Where Token Confidence Fails: Benchmarking Long-Form Scientific QA

Philip Müller, Nicholas Popovič, Michael Färber, Peter Steinbach


Abstract
Reliable uncertainty quantification (UQ) is essential for safe deployment of large language models (LLMs) in scientific question answering, where long-form outputs exceed practical human verification at scale. We introduce the first large-scale benchmark for UQ calibration in long-form, reasoning-demanding scientific QA, evaluating four UQ methods on 685,000 responses across up to 20 LLMs and seven datasets, supported by an extensible open-source framework whose shared-generation design enables reproducible cross-method comparisons. Instruction tuning is shown to associate with systematic token probability polarization, collapsing confidence distributions and undermining the reliability of token-level uncertainty signals. Reasoning model families diverge: some reproduce this polarization while others actively mitigate it, a pattern that clusters by provider and suggests training pipeline design as a key differentiating factor. Verbalized and token-aggregation sequence-level methods fail systematically. Only semantic consistency, as measured by consistency of the final answer, yields well-calibrated outputs, providing the first large-scale evidence that semantic calibration persists in multi-step, dependency-rich reasoning settings.
Anthology ID:
2026.uncertainlp-main.11
Volume:
The Proceedings of the Third Workshop on Uncertainty-Aware NLP
Month:
October
Year:
2026
Address:
Budapest, Hungary
Editors:
Wilker Aziz, Jonathan Berant, Bryan Eikema, Evgenia Ilia, Marie-Catherine de Marneffe, Barbara Plank, Artem Shelmanov, Swabha Swayamdipta, Jörg Tiedemann, Artem Vazhentsev, Raúl Vázquez, Chrysoula Zerva
Venues:
UncertaiNLP | WS
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
162–200
Language:
URL:
https://aclanthology.org/2026.uncertainlp-main.11/
DOI:
Bibkey:
Cite (ACL):
Philip Müller, Nicholas Popovič, Michael Färber, and Peter Steinbach. 2026. Semantic Calibration Prevails Where Token Confidence Fails: Benchmarking Long-Form Scientific QA. In The Proceedings of the Third Workshop on Uncertainty-Aware NLP, pages 162–200, Budapest, Hungary. Association for Computational Linguistics.
Cite (Informal):
Semantic Calibration Prevails Where Token Confidence Fails: Benchmarking Long-Form Scientific QA (Müller et al., UncertaiNLP 2026)
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PDF:
https://aclanthology.org/2026.uncertainlp-main.11.pdf