LLMs as Implicit Imputers: Uncertainty Should Scale with Missing Information
Authors: Stef van Buuren
Organizations: 1. TNO - Netherlands Organization for Applied Scientific Research, Leiden · 2. Dept. of Methodology and Statistics, University of Utrecht
Abstract
Large language models (LLMs) are increasingly deployed in settings where the available context is incomplete or degraded. We argue that an LLM generating answers under incomplete context can be viewed as an implicit imputer, and evaluated against a criterion from the multiple imputation (MI) literature: uncertainty should scale with the amount of missing information. We assess this criterion on SQuAD, using a controlled framework in which context availability is varied across five levels. We evaluate two answer-level uncertainty measures that can be estimated from repeated sampling: sampling-based confidence (empirical mode frequency) and response entropy. Confidence fails to reflect increasing missingness: it remains high even as accuracy collapses. Entropy, by contrast, increases with context removal, consistent with the MI analogy, and explains substantially more variance in accuracy than confidence across all evidence levels (quadratic R2 gap up to 0.057). We further introduce a black-box diagnostic ρR(α) that estimates the proportion of baseline uncertainty resolved by context level α, requiring only repeated sampling with and without context. These results suggest that entropy is a more responsive black-box uncertainty measure than confidence under incomplete context.
Large language models (LLMs) are powerful black-box systems, making it difficult to discern whether their answers reflect stable internal beliefs or superficial pattern matching. We identify cross-contextual consistency as an underutilized behavioral property of LLMs: a credible answer should remain stable when the same task is placed under topic-aligned, content-neutral contextual variation. Building on this intuition, we operationalize Cross-Contextual Consistency (C3) by comparing model generations under original and perturbed prompts. Across 26 models and six benchmarks spanning reasoning, factuality, and code generation, we find that answers with smaller cross-contextual shifts are more likely to be correct or factual. We demonstrate that C3 provides a complementary axis of evaluation and can serve as a benchmark usefulness diagnostic, identifying which portions of a benchmark remain informative even when aggregated scores are widely considered "saturate".
LLMs' overconfidence, particularly when hallucinating, poses a significant challenge for the deployment of the models in safety-critical settings and makes a reliable estimation of uncertainty necessary. Existing approaches for uncertainty quantification typically prioritize lexical or probabilistic measures; however, these techniques often ignore the semantic variance of different responses with similar meaning. In this paper, we propose Adaptive Conformal Semantic Entropy (ACSE), a method for estimating prompt-level uncertainty by adaptively measuring semantic dispersion in LLMs outputs. Our uncertainty scoring function is based on clustering semantic entropy of multiple diverse responses to the same prompt. The function adaptively adjusts the uncertainty score based on semantic features of each cluster. To ensure statistical reliability of our score, we use conformal calibration to apply a decision rule to accept/abstain the prompts, providing a finite-sample, distribution-free guarantee such that the error rate among the accepted responses remains bounded by a user-specified tolerance. Our extensive experimental evaluations using different LLMs and datasets, demonstrate that our approach consistently outperforms state-of-the-art uncertainty quantification baselines using discriminative performance, conformal guarantees, and probabilistic calibration indicators. As a highlight, for TriviaQA dataset, AUROC of our approach is 0.88 compared to 0.65 produced by the token entropy approach.
Large language models hallucinate confidently, making uncertainty quantification (UQ) essential for reliable deployment. Existing methods rely predominantly on token-level signals, leaving the geometric structure of intermediate hidden states underused. In this paper, we take the geometric complexity of hidden-state matrices as a measure of the global uncertainty of LLMs, while treating token-level uncertainty estimation as a local metric. We show that hidden-state geometric entropy (global uncertainty) and token-level entropy (local uncertainty) are statistically near-orthogonal, capturing distinct failure regimes for reliability prediction. In particular, global geometry recovers the confident-but-wrong failure mode that local signals systematically miss. Building on this, we propose Global-Local Uncertainty (GLU), an unsupervised, single-pass score that fuses the two signals via a multiplicative gate. Across three model families and six benchmarks, GLU matches or outperforms all unsupervised baselines while requiring only a single forward pass and remaining length-normalized and architecture-agnostic.