DVD: A Robust Method for Detecting Variant Contamination in Large Language Model Evaluation

Evaluating large language models (LLMs) is increasingly confounded by \emph{variant contamination}: the training corpus contains semantically equivalent yet lexically or syntactically altered versions of test items. Unlike verbatim leakage, these paraphrased or structurally transformed variants evade existing detectors based on sampling consistency or perplexity, thereby inflating benchmark scores via memorization rather than genuine reasoning. We formalize this problem and introduce \textbf{DVD} (\textbf{D}etection via \textbf{V}ariance of generation \textbf{D}istribution), a single-sample detector that models the local output distribution induced by temperature sampling. Our key insight is that contaminated items trigger alternation between a \emph{memory-adherence} state and a \emph{perturbation-drift} state, yielding abnormally high variance in the synthetic difficulty of low-probability tokens; uncontaminated items remain in drift with comparatively smooth variance. We construct the first benchmark for variant contamination across two domains Omni-MATH and SuperGPQA by generating and filtering semantically equivalent variants, and simulate contamination via fine-tuning models of different scales and architectures (Qwen2.5 and Llama3.1). Across datasets and models, \textbf{DVD} consistently outperforms perplexity-based, Min-$k$\%++, edit-distance (CDD), and embedding-similarity baselines, while exhibiting strong robustness to hyperparameters. Our results establish variance of the generation distribution as a principled and practical fingerprint for detecting variant contamination in LLM evaluation.

Unifying Sequences, Structures, and Descriptions for Any-to-Any Protein Generation with the Large Multimodal Model HelixProtX

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language models (LLMs) for protein research, current methodologies predominantly focus on limited specialized tasks -- often predicting one protein modality from another. These approaches restrict the understanding and generation of multimodal protein data. In contrast, large multimodal models have demonstrated potential capabilities in generating any-to-any content like text, images, and videos, thus enriching user interactions across various domains. Integrating these multimodal model technologies into protein research offers significant promise by potentially transforming how proteins are studied. To this end, we introduce HelixProtX, a system built upon the large multimodal model, aiming to offer a comprehensive solution to protein research by supporting any-to-any protein modality generation. Unlike existing methods, it allows for the transformation of any input protein modality into any desired protein modality. The experimental results affirm the advanced capabilities of HelixProtX, not only in generating functional descriptions from amino acid sequences but also in executing critical tasks such as designing protein sequences and structures from textual descriptions. Preliminary findings indicate that HelixProtX consistently achieves superior accuracy across a range of protein-related tasks, outperforming existing state-of-the-art models. By integrating multimodal large models into protein research, HelixProtX opens new avenues for understanding protein biology, thereby promising to accelerate scientific discovery.