Olga Ovcharenko

Olga Ovcharenko, Rita Sevastjanova, Valentina Boeva

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 eliminates 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 library.

Jiale Lao, Andreas Zimmerer, Olga Ovcharenko et al.

We present a benchmark targeting a novel class of systems: semantic query processing engines. Those systems rely inherently on generative and reasoning capabilities of state-of-the-art large language models (LLMs). They extend SQL with semantic operators, configured by natural language instructions, that are evaluated via LLMs and enable users to perform various operations on multimodal data. Our benchmark introduces diversity across three key dimensions: scenarios, modalities, and operators. Included are scenarios ranging from movie review analysis to medical question-answering. Within these scenarios, we cover different data modalities, including images, audio, and text. Finally, the queries involve a diverse set of operators, including semantic filters, joins, mappings, ranking, and classification operators. We evaluated our benchmark on three academic systems (LOTUS, Palimpzest, and ThalamusDB) and one industrial system, Google BigQuery. Although these results reflect a snapshot of systems under continuous development, our study offers crucial insights into their current strengths and weaknesses, illuminating promising directions for future research.

Olga Ovcharenko, Florian Barkmann, Philip Toma et al.

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.

Olga Ovcharenko, Sebastian Schelter

Ensuring data quality at scale remains a persistent challenge for large organizations. Despite recent advances, maintaining accurate and consistent data is still complex, especially when dealing with multiple data modalities. Traditional error detection and correction methods tend to focus on a single modality, typically a table, and often miss cross-modal errors that are common in domains like e-Commerce and healthcare, where image, tabular, and text data co-exist. To address this gap, we take an initial step towards cross-modal error detection in tabular data, by benchmarking several methods. Our evaluation spans four datasets and five baseline approaches. Among them, Cleanlab, a label error detection framework, and DataScope, a data valuation method, perform the best when paired with a strong AutoML framework, achieving the highest F1 scores. Our findings indicate that current methods remain limited, particularly when applied to heavy-tailed real-world data, motivating further research in this area.