Blaž Zupan

Pavlin G. Poličar, Andraž Pevcin, Blaž Zupan

Generating diverse, readable statistical charts from tabular data remains challenging for LLMs, as many failures become apparent after rendering and are not detectable from data or code alone. Existing chart datasets also rarely provide fully aligned artifacts, such as executable code, dataset context, and question-answer pairs. We present a structured LLM-based workflow that decomposes chart generation into dataset screening, plot proposal, code synthesis, rendering, validation-driven refinement, description generation, and question-answer generation. By incorporating rendered-output validation, the workflow addresses visualization-specific failure modes such as readability and semantic mismatch. It treats chart generation as an inspectable process rather than a one-shot prompt-to-code task, retaining each chart with its code, dataset context, description, and question-answer pairs. Applied to UCI datasets, the workflow produces 1,500 charts from 74 datasets, spanning 24 chart families and paired with 30,003 question-answer pairs. We evaluate 16 multimodal LLMs (MLLMs) on these chart-question pairs. The results show that chart-syntax questions are nearly saturated, while value extraction, comparison, and reasoning remain more challenging, illustrating the workflow's utility for diagnostic studies of chart-grounded multimodal reasoning.

Marinka Zitnik, Blaz Zupan

NIMFA is an open-source Python library that provides a unified interface to nonnegative matrix factorization algorithms. It includes implementations of state-of-the-art factorization methods, initialization approaches, and quality scoring. It supports both dense and sparse matrix representation. NIMFA's component-based implementation and hierarchical design should help the users to employ already implemented techniques or design and code new strategies for matrix factorization tasks.

Pavlin G. Poličar, Blaž Zupan

With the increasing availability of high-dimensional data, analysts often rely on exploratory data analysis to understand complex data sets. A key approach to exploring such data is dimensionality reduction, which embeds high-dimensional data in two dimensions to enable visual exploration. However, popular embedding techniques, such as t-SNE and UMAP, typically assume that data points are independent. When this assumption is violated, as in time-series data, the resulting visualizations may fail to reveal important temporal patterns and trends. To address this, we propose a formal extension to existing dimensionality reduction methods that incorporates two temporal loss terms that explicitly highlight temporal progression in the embedded visualizations. Through a series of experiments on both synthetic and real-world datasets, we demonstrate that our approach effectively uncovers temporal patterns and improves the interpretability of the visualizations. Furthermore, the method improves temporal coherence while preserving the fidelity of the embeddings, providing a robust tool for dynamic data analysis.

Pavlin G. Poličar, Blaž Zupan

Two-dimensional embeddings obtained from dimensionality reduction techniques, such as MDS, t-SNE, and UMAP, are widely used across various disciplines to visualize high-dimensional data. These visualizations provide a valuable tool for exploratory data analysis, allowing researchers to visually identify clusters, outliers, and other interesting patterns in the data. However, interpreting the resulting visualizations can be challenging, as it often requires additional manual inspection to understand the differences between data points in different regions of the embedding space. To address this issue, we propose Visual Explanations via Region Annotation (VERA), an automatic embedding-annotation approach that generates visual explanations for any two-dimensional embedding. VERA produces informative explanations that characterize distinct regions in the embedding space, allowing users to gain an overview of the embedding landscape at a glance. Unlike most existing approaches, which typically require some degree of manual user intervention, VERA produces static explanations, automatically identifying and selecting the most informative visual explanations to show to the user. We illustrate the usage of VERA on a real-world data set and validate the utility of our approach with a comparative user study. Our results demonstrate that the explanations generated by VERA are as useful as fully-fledged interactive tools on typical exploratory data analysis tasks but require significantly less time and effort from the user.

Primož Godec, Nikola Ðukić, Ajda Pretnar et al.

Two-dimensional data maps can visually reveal information about the relations between data instances. Popular techniques to construct data maps are t-SNE and UMAP. The resulting point-based visualizations, though, provide information only through their interpretation. We here consider a set of abstracts from the articles on longevity to argue for using keyword extraction methods to label clusters of documents in the map. Among the considered approaches, the best results were obtained by recently proposed YAKE!. Surprisingly, a classical TF-IDF term ranking outperformed graph and embedding-based techniques.

Marinka Zitnik, Blaz Zupan

Motivation: The rapid growth of diverse biological data allows us to consider interactions between a variety of objects, such as genes, chemicals, molecular signatures, diseases, pathways and environmental exposures. Often, any pair of objects--such as a gene and a disease--can be related in different ways, for example, directly via gene-disease associations or indirectly via functional annotations, chemicals and pathways. Different ways of relating these objects carry different semantic meanings. However, traditional methods disregard these semantics and thus cannot fully exploit their value in data modeling. Results: We present Medusa, an approach to detect size-k modules of objects that, taken together, appear most significant to another set of objects. Medusa operates on large-scale collections of heterogeneous data sets and explicitly distinguishes between diverse data semantics. It advances research along two dimensions: it builds on collective matrix factorization to derive different semantics, and it formulates the growing of the modules as a submodular optimization program. Medusa is flexible in choosing or combining semantic meanings and provides theoretical guarantees about detection quality. In a systematic study on 310 complex diseases, we show the effectiveness of Medusa in associating genes with diseases and detecting disease modules. We demonstrate that in predicting gene-disease associations Medusa compares favorably to methods that ignore diverse semantic meanings. We find that the utility of different semantics depends on disease categories and that, overall, Medusa recovers disease modules more accurately when combining different semantics.

Marinka Žitnik, Blaž Zupan

For most problems in science and engineering we can obtain data sets that describe the observed system from various perspectives and record the behavior of its individual components. Heterogeneous data sets can be collectively mined by data fusion. Fusion can focus on a specific target relation and exploit directly associated data together with contextual data and data about system's constraints. In the paper we describe a data fusion approach with penalized matrix tri-factorization (DFMF) that simultaneously factorizes data matrices to reveal hidden associations. The approach can directly consider any data that can be expressed in a matrix, including those from feature-based representations, ontologies, associations and networks. We demonstrate the utility of DFMF for gene function prediction task with eleven different data sources and for prediction of pharmacologic actions by fusing six data sources. Our data fusion algorithm compares favorably to alternative data integration approaches and achieves higher accuracy than can be obtained from any single data source alone.