arXiv:2512.02471v1 Announce Type: cross Abstract: Cell clustering is crucial for uncovering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data by identifying cell types and marker genes. Despite its importance, benchmarks for scRNA-seq clustering methods remain fragmented, often lacking standardized protocols and failing to incorporate recent advances in artificial intelligence. To fill these gaps, we present scCluBench, a comprehensive benchmark of clustering algorithms for scRNA-seq data. First, scCluBench provides 36 scRNA-seq datasets collected from diverse public sources, covering multiple tissues, which are uniformly processed and standardized to ensure consistency for systematic evaluation and downstream analyses. To evaluate performance, we collect and reproduce a range of scRNA-seq clustering methods, including traditional, deep learning-based, graph-based, and biological foundation models. We comprehensively evaluate each method both quantitatively and qualitatively, using core performance metrics as well as visualization analyses. Furthermore, we construct representative downstream biological tasks, such as marker gene identification and cell type annotation, to further assess the practical utility. scCluBench then investigates the performance differences and applicability boundaries of various clustering models across diverse analytical tasks, systematically assessing their robustness and scalability in real-world scenarios. Overall, scCluBench offers a standardized and user-friendly benchmark for scRNA-seq clustering, with curated datasets, unified evaluation protocols, and transparent analyses, facilitating informed method selection and providing valuable insights into model generalizability and application scope.

npj Digital Medicine, Published online: 24 November 2025; doi:10.1038/s41746-025-02095-y

Multimodal analysis of whole slide images in colorectal cancer

arXiv:2508.13234v2 Announce Type: replace-cross Abstract: The acceleration of artificial intelligence (AI) in science is recognized and many scholars have begun to explore its role in interdisciplinary collaboration. However, the mechanisms and extent of this impact are still unclear. This study, using AlphaFold's impact on structural biologists, examines how AI technologies influence interdisciplinary collaborative patterns. By analyzing 1,247 AlphaFold-related papers and 7,700 authors from Scopus, we employ bibliometric analysis and causal inference to compare interdisciplinary collaboration between AlphaFold adopters and non-adopters. Contrary to the widespread belief that AI facilitates interdisciplinary collaboration, our findings show that AlphaFold increased structural biology-computer science collaborations by just 0.48%, with no measurable effect on other disciplines. Specifically, AI creates interdisciplinary collaboration demands with specific disciplines due to its technical characteristics, but this demand is weakened by technological democratization and other factors. These findings demonstrate that artificial intelligence (AI) alone has limited efficacy in bridging disciplinary divides or fostering meaningful interdisciplinary collaboration.