Provable Joint Decontamination for Benchmarking Multiple Large Language Models
Authors: Zhenlong Liu, Hao Zeng, Hongxin Wei
Organizations: Department of Statistics and Data Science, Southern University of Science and Technology · Shanghai Innovation Institute
Abstract
Benchmark data contamination has become a central challenge in LLM evaluation: when evaluation examples appear in the training data of one or more audited models, reported performance can be inflated and cross-model comparisons become unreliable. A broad line of training-data detection work designs scores to quantify how strongly a model memorizes a given data point, but these score-based methods lack theoretical guarantees. Recent conformal approaches provide provable false-identification control for a single model; however, applying them separately to each model can produce model-specific benchmarks, undermining fair comparison across models. In this work, we formalize multi-model benchmark decontamination as a joint selection problem and propose Joint Envelope Conformal Selection (JECS), a conformal procedure that enables global contamination rate (GCR) control under stated assumptions. Specifically, JECS computes per-model conformal p-values, aggregates them by the per-item maximum, and reconstructs a conservative envelope of the max-p null distribution from right-tail observations above a data-driven threshold. By applying the adaptive Benjamini-Hochberg (BH) procedure to the envelope-rescaled values, we select a benchmark with provable GCR control. Extensive experiments across various models and benchmarks demonstrate that JECS achieves higher power than the max-p baseline while consistently maintaining the target GCR control.
Benchmark-based evaluation is the dominant paradigm for assessing large language model (LLM) capabilities, yet data contamination inflates reported performance and undermines fair comparison. Existing decontamination methods are evaluated solely through aggregate accuracy, which can obscure substantial differences in per-sample model behaviour, and many require access to an uncontaminated model. In this paper, we propose a sample-level evaluation framework for decontamination that complements accuracy-based assessment with distributional distance metrics, measuring how closely a decontaminated model recovers the output distribution of an uncontaminated model on each sample. Building on this framework, we introduce Uncertainty-Based Decontamination (UBD), a family of methods that leverage deep ensembles of the contaminated model to estimate per-sample memorization without requiring a uncontaminated model or knowledge of which samples are contaminated. UBD estimates a per-sample correction scalar from ensemble uncertainty, which is used to construct a debiased target distribution that suppresses the inflated probability mass on correct answers induced by contamination. This target is then used either as a post-hoc output correction (debiasing) or as a soft training signal for parameter update (unlearning). Experiments on MMLU-Pro and MATH-MCQA across multiple LLM backbones demonstrate that UBD produces per-sample output distributions substantially closer to those of an uncontaminated model than paraphrasing or choice-permutation baselines, while preserving model performance on uncontaminated data.
Benchmark datasets are critical for reproducible, reliable, and discriminative evaluation of LLMs. However, recent studies reveal that many benchmark datasets are included in pretraining corpora, i.e., contaminated, which diminishes their value as reliable measures of model generalization. In this paper, we argue that benchmark datasets should be contamination-resistant, i.e., unlearnable, but support inference. To accomplish this, we first highlight the wide prevalence of benchmark dataset contamination and outline the properties of contamination-resistant datasets. Second, we highlight how the asymmetry between the inference and training pipelines in the Transformer architecture can be leveraged to support contamination-resistance. Third, we outline mathematical advancements to make these datasets interoperable across various LLM architectures. Based on the above, we call on the community to ensure the reliability of LLM benchmarking by: (i) advancing novel contamination-resistant methodologies, (ii) developing supporting methods and platforms, and (iii) adopting contamination-resistant benchmarks into existing evaluation pipelines.
Benchmark contamination, where evaluation examples appear in a model's training data, threatens the validity of LLM assessment. Statistical tools for detecting training-data membership exist, but have been validated almost exclusively in controlled academic regimes: large, homogeneous pre-training corpora and transparent, single-stage training pipelines. Whether these methods remain reliable in realistic auditing scenarios remains unclear. We identify two under-studied failure modes: distribution shift, which arises when suspect and validation sets violate the IID assumption, and scale constraints, which arise because benchmarks are orders of magnitude smaller than pre-training corpora. We systematically evaluate three leading paradigms, LLM Dataset Inference, Post-Hoc Dataset Inference, and CoDeC, across 25 models from multiple families (including Pythia, OLMo 2, and specialised cultural and medical LLMs) and scales (up to 27B). We then further extend our analysis to frontier industry models. Across 335 evaluations, only 201 yield correct outcomes. LLM Dataset Inference results in false positives under distribution shift, Post-Hoc Dataset Inference is underpowered at benchmark scale, and CoDeC provides only coarse provenance signals that are insufficient to verify individual benchmark splits. Our results reveal a systematic reliability gap between controlled validation and practical benchmark auditing, and show that statistical detection cannot yet replace transparent data provenance. We open-source our benchmark for further research.