This paper presents a neural scheme for the topology-aware interpolation of time-varying scalar fields. Given a time-varying sequence of persistence diagrams, along with a sparse temporal sampling of the corresponding scalar fields, denoted as keyframes, our interpolation approach aims at "inverting" the non-keyframe diagrams to produce plausible estimations of the corresponding, missing data. For this, we rely on a neural architecture which learns the relation from a time value to the corresponding scalar field, based on the keyframe examples, and reliably extends this relation to the non-keyframe time steps. We show how augmenting this architecture with specific topological losses exploiting the input diagrams both improves the geometrical and topological reconstruction of the non-keyframe time steps. At query time, given an input time value for which an interpolation is desired, our approach instantaneously produces an output, via a single propagation of the time input through the network. Experiments interpolating 2D and 3D time-varying datasets show our approach superiority, both in terms of data and topological fitting, with regard to reference interpolation schemes. Our implementation is available at this GitHub link : https://github.com/MohamedKISSI/Topology-Aware-Neural-Interpolation-of-Scalar-Fields.git.

We investigate tasks that can be accomplished with unlabelled graphs, which are graphs with nodes that do not have attached persistent or semantically meaningful labels. New visualization techniques to represent unlabelled graphs have been proposed, but more understanding of unlabelled graph tasks is required before these techniques can be adequately evaluated. Some tasks apply to both labelled and unlabelled graphs, but many do not translate between these contexts. We propose a data abstraction model that distinguishes the Unlabelled context from the increasingly semantically rich Labelled, Attributed, and Augmented contexts. We filter tasks collected and gleaned from the literature according to our data abstraction and analyze the surfaced tasks, leading to a taxonomy of abstract tasks for unlabelled graphs. Our task taxonomy is organized according to the Scope of the data at play, the Action intended by the user, and the Target data under consideration. We show the descriptive power of this task abstraction by connecting to concrete examples from previous frameworks, and connect these abstractions to real-world problems. To showcase the evaluative power of the taxonomy, we perform a preliminary assessment of 6 visualizations for each task. For each combination of task and visual encoding, we consider the effort required from viewers, the likelihood of task success, and how both factors vary between small-scale and large-scale graphs.

Misuses of t-SNE and UMAP in visual analytics have become increasingly common. For example, although t-SNE and UMAP projections often do not faithfully reflect the original distances between clusters, practitioners frequently use them to investigate inter-cluster relationships. We investigate why this misuse occurs, and discuss methods to prevent it. To that end, we first review 136 papers to verify the prevalence of the misuse. We then interview researchers who have used dimensionality reduction (DR) to understand why such misuse occurs. Finally, we interview DR experts to examine why previous efforts failed to address the misuse. We find that the misuse of t-SNE and UMAP stems primarily from limited DR literacy among practitioners, and that existing attempts to address this issue have been ineffective. Based on these insights, we discuss potential paths forward, including the controversial but pragmatic option of automating the selection of optimal DR projections to prevent misleading analyses.

Item ranking systems support users in multi-criteria decision-making tasks. Users need to trust rankings and ranking algorithms to reflect user preferences nicely while avoiding systematic errors and biases. However, today only few approaches help end users, model developers, and analysts to explain rankings. We report on the study of explanation approaches from the perspectives of recommender systems, explainable AI, and visualization research and propose the first cross-domain design space for explainers of item rankings. In addition, we leverage the descriptive power of the design space to characterize a) existing explainers and b) three main user groups involved in ranking explanation tasks. The generative power of the design space is a means for future designers and developers to create more target-oriented solutions in this only weakly exploited space.

Multidimensional data is often associated with uncertainties that are not well-described by normal distributions. In this work, we describe how such distributions can be projected to a low-dimensional space using uncertainty-aware principal component analysis (UAPCA). We propose to model multidimensional distributions using Gaussian mixture models (GMMs) and derive the projection from a general formulation that allows projecting arbitrary probability density functions. The low-dimensional projections of the densities exhibit more details about the distributions and represent them more faithfully compared to UAPCA mappings. Further, we support including user-defined weights between the different distributions, which allows for varying the importance of the multidimensional distributions. We evaluate our approach by comparing the distributions in low-dimensional space obtained by our method and UAPCA to those obtained by sample-based projections.

Designing and building visual analytics (VA) systems is a complex, iterative process that requires the seamless integration of data processing, analytics capabilities, and visualization techniques. While prior research has extensively examined the social and collaborative aspects of VA system authoring, the practical challenges of developing these systems remain underexplored. As a result, despite the growing number of VA systems, there are only a few structured knowledge bases to guide their design and development. To tackle this gap, we propose VA-Blueprint, a methodology and knowledge base that systematically reviews and categorizes the fundamental building blocks of urban VA systems, a domain particularly rich and representative due to its intricate data and unique problem sets. Applying this methodology to an initial set of 20 systems, we identify and organize their core components into a multi-level structure, forming an initial knowledge base with a structured blueprint for VA system development. To scale this effort, we leverage a large language model to automate the extraction of these components for other 81 papers (completing a corpus of 101 papers), assessing its effectiveness in scaling knowledge base construction. We evaluate our method through interviews with experts and a quantitative analysis of annotation metrics. Our contributions provide a deeper understanding of VA systems' composition and establish a practical foundation to support more structured, reproducible, and efficient system development. VA-Blueprint is available at https://urbantk.org/va-blueprint.

Systems relying on ML have become ubiquitous, but so has biased behavior within them. Research shows that bias significantly affects stakeholders' trust in systems and how they use them. Further, stakeholders of different backgrounds view and trust the same systems differently. Thus, how ML models' behavior is explained plays a key role in comprehension and trust. We survey explainability visualizations, creating a taxonomy of design characteristics. We conduct user studies to evaluate five state-of-the-art visualization tools (LIME, SHAP, CP, Anchors, and ELI5) for model explainability, measuring how taxonomy characteristics affect comprehension, bias perception, and trust for non-expert ML users. Surprisingly, we find an inverse relationship between comprehension and trust: the better users understand the models, the less they trust them. We investigate the cause and find that this relationship is strongly mediated by bias perception: more comprehensible visualizations increase people's perception of bias, and increased bias perception reduces trust. We confirm this relationship is causal: Manipulating explainability visualizations to control comprehension, bias perception, and trust, we show that visualization design can significantly (p < 0.001) increase comprehension, increase perceived bias, and reduce trust. Conversely, reducing perceived model bias, either by improving model fairness or by adjusting visualization design, significantly increases trust even when comprehension remains high. Our work advances understanding of how comprehension affects trust and systematically investigates visualization's role in facilitating responsible ML applications.

We assume a scenario where a practitioner wants to select DR techniques that produce projections suitable for analyzing their dataset. It is crucial to select projections with high faithfulness for reliable analysis, but practitioners tend to be more biased towards the visual interestingness. We verify the existence of such bias and investigate its underlying causes, providing a grounded basis for mitigating the biases. Selecting the dimensionality reduction technique that faithfully represents the structure is essential for reliable visual communication and analytics. In reality, however, practitioners favor projections for other attractions, such as aesthetics and visual saliency, over the projection's structural faithfulness, a bias we define as visual interestingness. In this research, we conduct a user study that (1) verifies the existence of such bias and (2) explains why the bias exists. Our study suggests that visual interestingness biases practitioners' preferences when selecting projections for analysis, and this bias intensifies with color-encoded labels and shorter exposure time. Based on our findings, we discuss strategies to mitigate bias in perceiving and interpreting DR projections.

This application paper investigates the stability of hydrogen bonds (H-bonds), as characterized by the Quantum Theory of Atoms in Molecules (QTAIM). First, we contribute a database of 4544 electron densities associated to four isomers of water hexamers (the so-called Ring, Book, Cage and Prism), generated by distorting their equilibrium geometry under various structural perturbations, modeling the natural dynamic behavior of molecular systems. Second, we present a new stability measure, called bond occurrence rate, associating each bond path present at equilibrium with its rate of occurrence within the input ensemble. We also provide an algorithm, called BondMatcher, for its automatic computation, based on a tailored, geometry-aware partial isomorphism estimation between the extremum graphs of the considered electron densities. Our new stability measure allows for the automatic identification of densities lacking H-bond paths, enabling further visual inspections. Specifically, the topological analysis enabled by our framework corroborates experimental observations and provides refined geometrical criteria for characterizing the disappearance of H-bond paths. Our electron density database and our C++ implementation are available at this address: https://github.com/thom-dani/BondMatcher.

Visual analytics using dimensionality reduction (DR) can easily be unreliable for various reasons, e.g., inherent distortions in representing the original data. The literature has thus proposed a wide range of methodologies to make DR-based visual analytics reliable. However, the diversity and extensiveness of the literature can leave novice analysts and researchers uncertain about where to begin and proceed. To address this problem, we propose a guide for reading papers for reliable visual analytics with DR. Relying on the previous classification of the relevant literature, our guide helps both practitioners to (1) assess their current DR expertise and (2) identify papers that will further enhance their understanding. Interview studies with three experts in DR and data visualizations validate the significance, comprehensiveness, and usefulness of our guide.