Asking Is Not Enough: Protocol Sensitivity in LLM Confidence Calibration

LLM confidence calibration is often evaluated by comparing two signals: token-probability scores and verbalized confidence. These signals are sometimes treated as direct readouts of model uncertainty, but their comparison depends on measurement choices that are rarely made explicit. In the main analysis, we hold the verbalized-confidence elicitation fixed: a single prompt template, probability scale, and output format. We then vary the measurement axes that define the verbalized-vs-token comparison: which answer string receives the token-probability score, how that score is read from the answer tokens, and under which conditioning context it is measured. We evaluate this design on four QA benchmarks across three open 7--8B base/Instruct model families, with larger Qwen2.5 variants as same-family robustness checks. The resulting comparison is sensitive to these choices: conditioning context changes the sign or magnitude of the ECE gap across settings, token readout produces smaller but still sign-moving changes, and changing the ECE estimator has little effect. Under the default generated-answer, bare-context protocol, Instruct settings are close to parity rather than showing a large calibration gain for verbalized confidence. In a separate supplied-answer analysis, surface-plausible wrong answers receive nearly the same confidence as supplied gold answers, suggesting that verbalized confidence also reflects answer plausibility and provenance rather than correctness alone. We argue that both confidence signals should be treated as protocol-dependent behavioral measurements, and provide a reporting checklist covering elicitation provenance, scored answer, token-probability readout, and conditioning context.

naPINN: Noise-Adaptive Physics-Informed Neural Networks for Recovering Physics from Corrupted Measurement

Physics-Informed Neural Networks (PINNs) are effective methods for solving inverse problems and discovering governing equations from observational data. However, their performance degrades significantly under complex measurement noise and gross outliers. To address this issue, we propose the Noise-Adaptive Physics-Informed Neural Network (naPINN), which robustly recovers physical solutions from corrupted measurements without prior knowledge of the noise distribution. naPINN embeds an energy-based model into the training loop to learn the latent distribution of prediction residuals. Leveraging the learned energy landscape, a trainable reliability gate adaptively filters data points exhibiting high energy, while a rejection cost regularization prevents trivial solutions where valid data are discarded. We demonstrate the efficacy of naPINN on various benchmark partial differential equations corrupted by non-Gaussian noise and varying rates of outliers. The results show that naPINN significantly outperforms existing robust PINN baselines, successfully isolating outliers and accurately reconstructing the dynamics under severe data corruption.