The Reliability Gap in Benchmark Auditing: Distribution Shift and Scale as Failure Modes of Contamination Detection

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 27 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 199 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.

seqme: a Python library for evaluating biological sequence design

Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their attainment of desired properties. However, a single software library implementing these metrics was lacking. In this work we introduce seqme, a modular and highly extendable open-source Python library, containing model-agnostic metrics for evaluating computational methods for biological sequence design. seqme considers three groups of metrics: sequence-based, embedding-based, and property-based, and is applicable to a wide range of biological sequences: small molecules, DNA, ncRNA, mRNA, peptides and proteins. The library offers a number of embedding and property models for biological sequences, as well as diagnostics and visualization functions to inspect the results. seqme can be used to evaluate both one-shot and iterative computational design methods.