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

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.

First-Order Geometry, Spectral Compression, and Structural Compatibility under Bounded Computation

Optimization under structural constraints is typically analyzed through projection or penalty methods, obscuring the geometric mechanism by which constraints shape admissible dynamics. We propose an operator-theoretic formulation in which computational or feasibility limitations are encoded by self-adjoint operators defining locally reachable subspaces. In this setting, the optimal first-order improvement direction emerges as a pseudoinverse-weighted gradient, revealing how constraints induce a distorted ascent geometry. We further demonstrate that effective dynamics concentrate along dominant spectral modes, yielding a principled notion of spectral compression, and establish a compatibility principle that characterizes the existence of common admissible directions across multiple objectives. The resulting framework unifies gradient projection, spectral truncation, and multi-objective feasibility within a single geometric structure.