scTranslation: A Comprehensive Benchmark for Single-Cell Multi-Omics Modality Translation

• URL: http://arxiv.org/abs/2606.03906v1
• Date: Tue, 02 Jun 2026 17:00:49 GMT
• Title: scTranslation: A Comprehensive Benchmark for Single-Cell Multi-Omics Modality Translation
• Abstract summary: scTranslation is a comprehensive benchmark for single-cell multi-omics modality translation tasks.<n>It includes diverse translation datasets, integrates state-of-the-art models, and provides a comprehensive evaluation metrics.
• Score: 61.97613474494102
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Simultaneous measurement of multiple omics modalities in single cells enables researchers to gain a more comprehensive understanding of cellular states and regulatory mechanisms. However, due to high experimental costs, significant noise, and incomplete modality coverage, a variety of computational methods for modality translation have emerged in recent years. Despite the development of translation models, there is still a lack of systematic benchmark evaluation in terms of datasets, evaluation metrics, and influencing factors. To address this, we present scTranslation, a comprehensive benchmark for single-cell multi-omics modality translation tasks. It includes diverse translation datasets, integrates state-of-the-art models, and provides a comprehensive evaluation metrics. In addition, we assess model performance under different scenarios, such as feature selection, feature quality, and few-shot settings. These factors significantly affect model performance but have rarely been systematically studied before. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark is open-sourced to facilitate future research. The code is anonymously released at https://github.com/Bunnybeibei/scTranslation.

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