Stef van Buuren

Stef van Buuren

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 $R^2$ gap up to 0.057). We further introduce a black-box diagnostic $ρ_R(α)$ 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.

Stef van Buuren

Minimizing the Mean Squared Error (MSE) is a key objective in machine learning and is commonly used for imputing missing values. While this approach provides accurate point estimates, it introduces systematic biases in downstream analyses. These biases affect key parameters such as variance, prevalence, correlation, slope, and explained variance. The root cause is that imputed values optimized for MSE are averages, which reduce the natural variability in the data. This paper demonstrates that adding noise to imputed values can effectively eliminate these biases. The required noise level is proportional to the MSE. Using a toy example in a multivariate normal setting, we compare two methods: predictive imputation, which minimizes MSE, and stochastic imputation, which incorporates random noise. Simulation results show that predictive methods systematically introduce bias, while stochastic methods preserve the data's natural variability and produce unbiased estimates. We also evaluate three popular imputation tools -- missForest, softImpute, and mice -- and observe consistent biases in predictive methods. These findings highlight that MSE is an inadequate measure of imputation quality, as it prioritizes accuracy over variability. Incorporating noise into imputation methods is essential to prevent biases and ensure valid downstream analyses, underscoring the importance of stochastic approaches for handling incomplete data.