Self-supervised learning (SSL) has proven to be a powerful approach for extracting biologically meaningful representations from single-cell data. To advance our understanding of SSL methods applied to single-cell data, we present scSSL-Bench, a comprehensive benchmark that evaluates nineteen SSL methods. Our evaluation spans nine datasets and focuses on three common downstream tasks: batch correction, cell type annotation, and missing modality prediction. Furthermore, we systematically assess various data augmentation strategies. Our analysis reveals task-specific trade-offs: the specialized single-cell frameworks, scVI, CLAIRE, and the finetuned scGPT excel at uni-modal batch correction, while generic SSL methods, such as VICReg and SimCLR, demonstrate superior performance in cell typing and multi-modal data integration. Random masking emerges as the most effective augmentation technique across all tasks, surpassing domain-specific augmentations. Notably, our results indicate the need for a specialized single-cell multi-modal data integration framework. scSSL-Bench provides a standardized evaluation platform and concrete recommendations for applying SSL to single-cell analysis, advancing the convergence of deep learning and single-cell genomics.

Humans struggle to perceive and interpret high-dimensional data. Therefore, high-dimensional data are often projected into two dimensions for visualization. Many applications benefit from complex nonlinear dimensionality reduction techniques, but the effects of individual high-dimensional features are hard to explain in the two-dimensional space. Most visualization solutions use multiple two-dimensional plots, each showing the effect of one high-dimensional feature in two dimensions; this approach creates a need for a visual inspection of k plots for a k-dimensional input space. Our solution, Feature Clock, provides a novel approach that reduces the need to inspect these k plots to grasp the influence of original features on the data structure depicted in two dimensions. Feature Clock enhances the explainability and compactness of visualizations of embedded data and is available in an open-source Python library1.

Federated learning allows training machine learning (ML) models without central consolidation of the raw data. Variants of such federated learning systems enable privacy-preserving ML, and address data ownership and/or sharing constraints. However, existing work mostly adopt data-parallel parameter-server architectures for mini-batch training, require manual construction of federated runtime plans, and largely ignore the broad variety of data preparation, ML algorithms, and model debugging. Over the last years, we extended Apache SystemDS by an additional federated runtime backend for federated linear-algebra programs, federated parameter servers, and federated data preparation. In this paper, we share the system-level compiler and runtime integration, new features such as multi-tenant federated learning, selected federated primitives, multi-key homomorphic encryption, and our monitoring infrastructure. Our demonstrator showcases how composite ML pipelines can be compiled into federated runtime plans with low overhead.

Data science workflows are largely exploratory, dealing with under-specified objectives, open-ended problems, and unknown business value. Therefore, little investment is made in systematic acquisition, integration, and pre-processing of data. This lack of infrastructure results in redundant manual effort and computation. Furthermore, central data consolidation is not always technically or economically desirable or even feasible (e.g., due to privacy, and/or data ownership). The ExDRa system aims to provide system infrastructure for this exploratory data science process on federated and heterogeneous, raw data sources. Technical focus areas include (1) ad-hoc and federated data integration on raw data, (2) data organization and reuse of intermediates, and (3) optimization of the data science lifecycle, under awareness of partially accessible data. In this paper, we describe use cases, the overall system architecture, selected features of SystemDS' new federated backend (for federated linear algebra programs, federated parameter servers, and federated data preparation), as well as promising initial results. Beyond existing work on federated learning, ExDRa focuses on enterprise federated ML and related data pre-processing challenges. In this context, federated ML has the potential to create a more fine-grained spectrum of data ownership and thus, even new markets.