arXiv subjects

Anna Vilanova

Publications and source records attributed to Anna Vilanova.

At least 19 recordsLinked to original sources

arXiv2026

SIINR: Structurally Informed Implicit Neural Representations for super-resolution with uncertainty quantification of clinical quality diffusion MRI datasets

Diffusion Magnetic Resonance Imaging (dMRI) is a powerful tool for probing brain microstructure, but clinical acquisitions are often limited by low out-of-plane resolution, resulting in degraded structural information and reduced utility for advanced analysis. We introduce SIINR (Structurally Informed Implicit Neural Representations), a general framework for super-resoltion of clinical dMRI datasets while quantifying uncertainty in the reconstructed outputs. SIINR utilizes a supervised 3D U-net as a prior and combines it with a self-supervised implicit neural representation (INR) that fuses the high-resolution prior and the original low-resolution data. The INR enables joint modeling across spatial and angular domains, enforces data consistency, and provides analytic approximate posterior distributions for downstream uncertainty quantification. We validate the framework on a diverse set of open-access dMRI datasets, demonstrating that SIINR outperforms standard interpolation methods in both quantitative error metrics and qualitative anatomical fidelity. Experiments on clinical cases, including subjects with multiple sclerosis and brain lesions, illustrate the framework its ability to propagate intensity changes and flag uncertain regions in challenging scenarios. SIINR is flexible, modular, and can be adapted to different upsampling ratios and downstream tasks, providing a principled approach for enhancing clinical dMRI and supporting robust interpretation of derived neuroimaging metrics.

cs.CV↗

arXiv2026

Visualizing Lagrangian Heat Transport Paths and Density Structures in Unsteady Heat Transfer

Convective heat transfer is traditionally visualized from a Eulerian perspective using scalar temperature fields, offering limited insight into the underlying transport mechanisms. A Lagrangian view, analogous to mass transport along fluid paths, can reveal coherent structures and transport routes invisible from a Eulerian view of temperature. However, heat transport is aperiodic and non-conservative, hampering the application of fluid mixing and transport visualization techniques, developed primarily for time-periodic, conservative transport. We present a particle-based visualization technique that addresses these challenges by advecting massless particles along a time-reparameterized spacetime formulation of thermal transport, accumulating path contributions to reveal coherent transport routes and finite-time attracting and repelling structures that conventional methods cannot show.

physics.flu-dyn↗

arXiv2026

Manifold-Preserving Superpixel Hierarchies and Embeddings for the Exploration of High-Dimensional Images

High-dimensional images, or images with a high-dimensional attribute vector per pixel, are commonly explored with coordinated views of a low-dimensional embedding of the attribute space and a conventional image representation. Nowadays, such images can easily contain several million pixels. For such large datasets, hierarchical embedding techniques are better suited to represent the high-dimensional attribute space than flat dimensionality reduction methods. However, available hierarchical dimensionality reduction methods construct the hierarchy purely based on the attribute information and ignore the spatial layout of pixels in the images. This impedes the exploration of regions of interest in the image space, since there is no congruence between a region of interest in image space and the associated attribute abstractions in the hierarchy. In this paper, we present a superpixel hierarchy for high-dimensional images that takes the high-dimensional attribute manifold into account during construction. Through this, our method enables consistent exploration of high-dimensional images in both image and attribute space. We show the effectiveness of this new image-guided hierarchy in the context of embedding exploration by comparing it with classical hierarchical embedding-based image exploration in two use cases.

cs.CV↗

arXiv2025

Real-Time Rendering of Dynamic Line Sets using Voxel Ray Tracing

Real-time rendering of dynamic line sets is relevant in many visualization tasks, including unsteady flow visualization and interactive white matter reconstruction from Magnetic Resonance Imaging. High-quality global illumination and transparency are important for conveying the spatial structure of dense line sets, yet remain difficult to achieve at interactive rates. We propose an efficient voxel-based ray-tracing framework for rendering large dynamic line sets with ambient occlusion and ground-truth transparency. We introduce a voxelization algorithm that supports efficient on-the-fly construction of acceleration structures for both voxel cone tracing and ray tracing. To further reduce per-frame preprocessing cost, we propose a voxel-based culling method that restricts acceleration structure construction to camera-visible voxels. Together, these contributions enable real-time rendering of large-scale dynamic line sets with high quality and physically accurate transparency. We demonstrate that our method outperforms the state of the art in quality and performance when rendering (semi-)opaque dynamic line sets.

cs.GR↗

arXiv2025

Characterizing Multimodal Interaction in Visualization Authoring Tools

Multimodal interaction has been increasingly considered in designing visualization authoring tools. However, multimodal interaction has a broad meaning in visualization authoring, according to our literature review. Although some previous studies compare different authoring tools, a comprehensive overview of the diverse characteristics of multimodal interaction in visualization authoring tools is still missing. This paper seeks to offer a systematic perspective on how multimodal interaction is integrated within visualization authoring tools. Such an overview can enhance understanding of current practices, highlight distinguishing features among tools, and help identify future research directions, guiding designers in developing more accessible and effective authoring systems. We review 20 visualization authoring tools that incorporate multimodal interaction and characterize how multimodal interaction is applied in these tools. Based on the review results, we discuss design implications and future directions.

cs.HC↗

arXiv2025

NerT-CA: Efficient Dynamic Reconstruction from Sparse-view X-ray Coronary Angiography

Three-dimensional (3D) and dynamic 3D+time (4D) reconstruction of coronary arteries from X-ray coronary angiography (CA) has the potential to improve clinical procedures. However, there are multiple challenges to be addressed, most notably, blood-vessel structure sparsity, poor background and blood vessel distinction, sparse-views, and intra-scan motion. State-of-the-art reconstruction approaches rely on time-consuming manual or error-prone automatic segmentations, limiting clinical usability. Recently, approaches based on Neural Radiance Fields (NeRF) have shown promise for automatic reconstructions in the sparse-view setting. However, they suffer from long training times due to their dependence on MLP-based representations. We propose NerT-CA, a hybrid approach of Neural and Tensorial representations for accelerated 4D reconstructions with sparse-view CA. Building on top of the previous NeRF-based work, we model the CA scene as a decomposition of low-rank and sparse components, utilizing fast tensorial fields for low-rank static reconstruction and neural fields for dynamic sparse reconstruction. Our approach outperforms previous works in both training time and reconstruction accuracy, yielding reasonable reconstructions from as few as three angiogram views. We validate our approach quantitatively and qualitatively on representative 4D phantom datasets.

eess.IV↗

arXiv2025

Towards Difficulty-Aware Analysis of Deep Neural Networks

Traditional instance-based model analysis focuses mainly on misclassified instances. However, this approach overlooks the varying difficulty associated with different instances. Ideally, a robust model should recognize and reflect the challenges presented by intrinsically difficult instances. It is also valuable to investigate whether the difficulty perceived by the model aligns with that perceived by humans. To address this, we propose incorporating instance difficulty into the deep neural network evaluation process, specifically for supervised classification tasks on image data. Specifically, we consider difficulty measures from three perspectives -- data, model, and human -- to facilitate comprehensive evaluation and comparison. Additionally, we develop an interactive visual tool, DifficultyEyes, to support the identification of instances of interest based on various difficulty patterns and to aid in analyzing potential data or model issues. Case studies demonstrate the effectiveness of our approach.

cs.HC↗

arXiv2025

Implicit neural representations for accurate estimation of the standard model of white matter

Diffusion magnetic resonance imaging (dMRI) enables non-invasive investigation of tissue microstructure. The Standard Model (SM) of white matter aims to disentangle dMRI signal contributions from intra- and extra-axonal water compartments. However, due to the model its high-dimensional nature, accurately estimating its parameters poses a complex problem and remains an active field of research, in which different (machine learning) strategies have been proposed. This work introduces an estimation framework based on implicit neural representations (INRs), which incorporate spatial regularization through the sinusoidal encoding of the input coordinates. The INR method is evaluated on both synthetic and in vivo datasets and compared to existing methods. Results demonstrate superior accuracy of the INR method in estimating SM parameters, particularly in low signal-to-noise conditions. Additionally, spatial upsampling of the INR can represent the underlying dataset anatomically plausibly in a continuous way. The INR is self-supervised, eliminating the need for labeled training data. It achieves fast inference, is robust to noise, supports joint estimation of SM kernel parameters and the fiber orientation distribution function with spherical harmonics orders up to at least 8, and accommodates gradient non-uniformity corrections. The combination of these properties positions INRs as a potentially important tool for analyzing and interpreting diffusion MRI data.

eess.IV↗

arXiv2025

NeRF-CA: Dynamic Reconstruction of X-ray Coronary Angiography with Extremely Sparse-views

Dynamic three-dimensional (4D) reconstruction from two-dimensional X-ray coronary angiography (CA) remains a significant clinical problem. Existing CA reconstruction methods often require extensive user interaction or large training datasets. Recently, Neural Radiance Field (NeRF) has successfully reconstructed high-fidelity scenes in natural and medical contexts without these requirements. However, challenges such as sparse-views, intra-scan motion, and complex vessel morphology hinder its direct application to CA data. We introduce NeRF-CA, a first step toward a fully automatic 4D CA reconstruction that achieves reconstructions from sparse coronary angiograms. To the best of our knowledge, we are the first to address the challenges of sparse-views and cardiac motion by decoupling the scene into the moving coronary artery and the static background, effectively translating the problem of motion into a strength. NeRF-CA serves as a first stepping stone for solving the 4D CA reconstruction problem, achieving adequate 4D reconstructions from as few as four angiograms, as required by clinical practice, while significantly outperforming state-of-the-art sparse-view X-ray NeRF. We validate our approach quantitatively and qualitatively using representative 4D phantom datasets and ablation studies. To accelerate research in this domain, we made our codebase public: https://github.com/kirstenmaas/NeRF-CA.

eess.IV↗

arXiv2024

Progressive Monitoring of Generative Model Training Evolution

While deep generative models (DGMs) have gained popularity, their susceptibility to biases and other inefficiencies that lead to undesirable outcomes remains an issue. With their growing complexity, there is a critical need for early detection of issues to achieve desired results and optimize resources. Hence, we introduce a progressive analysis framework to monitor the training process of DGMs. Our method utilizes dimensionality reduction techniques to facilitate the inspection of latent representations, the generated and real distributions, and their evolution across training iterations. This monitoring allows us to pause and fix the training method if the representations or distributions progress undesirably. This approach allows for the analysis of a models' training dynamics and the timely identification of biases and failures, minimizing computational loads. We demonstrate how our method supports identifying and mitigating biases early in training a Generative Adversarial Network (GAN) and improving the quality of the generated data distribution.

cs.LG↗

arXiv2024

EvolvED: Evolutionary Embeddings to Understand the Generation Process of Diffusion Models

Diffusion models, widely used in image generation, rely on iterative refinement to generate images from noise. Understanding this data evolution is important for model development and interpretability, yet challenging due to its high-dimensional, iterative nature. Prior works often focus on static or instance-level analyses, missing the iterative and holistic aspects of the generative path. While dimensionality reduction can visualize image evolution for few instances, it does preserve the iterative structure. To address these gaps, we introduce EvolvED, a method that presents a holistic view of the iterative generative process in diffusion models. EvolvED goes beyond instance exploration by leveraging predefined research questions to streamline generative space exploration. Tailored prompts aligned with these questions are used to extract intermediate images, preserving iterative context. Targeted feature extractors trace the evolution of key image attribute evolution, addressing the complexity of high-dimensional outputs. Central to EvolvED is a novel evolutionary embedding algorithm that encodes iterative steps while maintaining semantic relations. It enhances the visualization of data evolution by clustering semantically similar elements within each iteration with t-SNE, grouping elements by iteration, and aligning an instance's elements across iterations. We present rectilinear and radial layouts to represent iterations and support exploration. We apply EvolvED to diffusion models like GLIDE and Stable Diffusion, demonstrating its ability to provide valuable insights into the generative process.

cs.CV↗

arXiv2024

MICCAI-CDMRI 2023 QuantConn Challenge Findings on Achieving Robust Quantitative Connectivity through Harmonized Preprocessing of Diffusion MRI

White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.

physics.med-ph↗

arXiv2024

Multi-dimensional Parameter Space Exploration for Streamline-specific Tractography

One of the unspoken challenges of tractography is choosing the right parameters for a given dataset or bundle. In order to tackle this challenge, we explore the multi-dimensional parameter space of tractography using streamline-specific parameters (SSP). We 1) validate a state-of-the-art probabilistic tracking method using per-streamline parameters on synthetic data, and 2) show how we can gain insights into the parameter space by focusing on streamline acceptance using real-world data. We demonstrate the potential added value of SSP to the current state of tractography by showing how SSP can be used to reveal patterns in the parameter space.

eess.IV↗

arXiv2023

Unraveling the Temporal Dynamics of the Unet in Diffusion Models

Diffusion models have garnered significant attention since they can effectively learn complex multivariate Gaussian distributions, resulting in diverse, high-quality outcomes. They introduce Gaussian noise into training data and reconstruct the original data iteratively. Central to this iterative process is a single Unet, adapting across time steps to facilitate generation. Recent work revealed the presence of composition and denoising phases in this generation process, raising questions about the Unets' varying roles. Our study dives into the dynamic behavior of Unets within denoising diffusion probabilistic models (DDPM), focusing on (de)convolutional blocks and skip connections across time steps. We propose an analytical method to systematically assess the impact of time steps and core Unet components on the final output. This method eliminates components to study causal relations and investigate their influence on output changes. The main purpose is to understand the temporal dynamics and identify potential shortcuts during inference. Our findings provide valuable insights into the various generation phases during inference and shed light on the Unets' usage patterns across these phases. Leveraging these insights, we identify redundancies in GLIDE (an improved DDPM) and improve inference time by ~27% with minimal degradation in output quality. Our ultimate goal is to guide more informed optimization strategies for inference and influence new model designs.

cs.CV↗

arXiv2023

ManiVault: A Flexible and Extensible Visual Analytics Framework for High-Dimensional Data

Exploration and analysis of high-dimensional data are important tasks in many fields that produce large and complex data, like the financial sector, systems biology, or cultural heritage. Tailor-made visual analytics software is developed for each specific application, limiting their applicability in other fields. However, as diverse as these fields are, their characteristics and requirements for data analysis are conceptually similar. Many applications share abstract tasks and data types and are often constructed with similar building blocks. Developing such applications, even when based mostly on existing building blocks, requires significant engineering efforts. We developed ManiVault, a flexible and extensible open-source visual analytics framework for analyzing high-dimensional data. The primary objective of ManiVault is to facilitate rapid prototyping of visual analytics workflows for visualization software developers and practitioners alike. ManiVault is built using a plugin-based architecture that offers easy extensibility. While our architecture deliberately keeps plugins self-contained, to guarantee maximum flexibility and re-usability, we have designed and implemented a messaging API for tight integration and linking of modules to support common visual analytics design patterns. We provide several visualization and analytics plugins, and ManiVault's API makes the integration of new plugins easy for developers. ManiVault facilitates the distribution of visualization and analysis pipelines and results for practitioners through saving and reproducing complete application states. As such, ManiVault can be used as a communication tool among researchers to discuss workflows and results. A copy of this paper and all supplemental material is available at https://osf.io/9k6jw and source code at https://github.com/ManiVaultStudio.

cs.HC↗

arXiv2023

Class-constrained t-SNE: Combining Data Features and Class Probabilities

Data features and class probabilities are two main perspectives when, e.g., evaluating model results and identifying problematic items. Class probabilities represent the likelihood that each instance belongs to a particular class, which can be produced by probabilistic classifiers or even human labeling with uncertainty. Since both perspectives are multi-dimensional data, dimensionality reduction (DR) techniques are commonly used to extract informative characteristics from them. However, existing methods either focus solely on the data feature perspective or rely on class probability estimates to guide the DR process. In contrast to previous work where separate views are linked to conduct the analysis, we propose a novel approach, class-constrained t-SNE, that combines data features and class probabilities in the same DR result. Specifically, we combine them by balancing two corresponding components in a cost function to optimize the positions of data points and iconic representation of classes -- class landmarks. Furthermore, an interactive user-adjustable parameter balances these two components so that users can focus on the weighted perspectives of interest and also empowers a smooth visual transition between varying perspectives to preserve the mental map. We illustrate its application potential in model evaluation and visual-interactive labeling. A comparative analysis is performed to evaluate the DR results.

cs.HC↗

arXiv2023

Neural Spherical Harmonics for structurally coherent continuous representation of diffusion MRI signal

We present a novel way to model diffusion magnetic resonance imaging (dMRI) datasets, that benefits from the structural coherence of the human brain while only using data from a single subject. Current methods model the dMRI signal in individual voxels, disregarding the intervoxel coherence that is present. We use a neural network to parameterize a spherical harmonics series (NeSH) to represent the dMRI signal of a single subject from the Human Connectome Project dataset, continuous in both the angular and spatial domain. The reconstructed dMRI signal using this method shows a more structurally coherent representation of the data. Noise in gradient images is removed and the fiber orientation distribution functions show a smooth change in direction along a fiber tract. We showcase how the reconstruction can be used to calculate mean diffusivity, fractional anisotropy, and total apparent fiber density. These results can be achieved with a single model architecture, tuning only one hyperparameter. In this paper we also demonstrate how upsampling in both the angular and spatial domain yields reconstructions that are on par or better than existing methods.

eess.IV↗

arXiv2022

ProtoFold Neighborhood Inspector

Post-translational modifications (PTMs) affecting a protein's residues (amino acids) can disturb its function, leading to illness. Whether or not a PTM is pathogenic depends on its type and the status of neighboring residues. In this paper, we present the ProtoFold Neighborhood Inspector (PFNI), a visualization system for analyzing residues neighborhoods. The main contribution is a visualization idiom, the Residue Constellation (RC), for identifying and comparing three-dimensional neighborhoods based on per-residue features and spatial characteristics. The RC leverages two-dimensional representations of the protein's three-dimensional structure to overcome problems like occlusion, easing the analysis of neighborhoods that often have complicated spatial arrangements. Using the PFNI, we explored proteins' structural PTM data, which allowed us to identify patterns in the distribution and quantity of per-neighborhood PTMs that might be related to their pathogenic status. In the following, we define the tasks that guided the development of the PFNI and describe the data sources we derived and used. Then, we introduce the PFNI and illustrate its usage through an example of an analysis workflow. We conclude by reflecting on preliminary findings obtained while using the tool on the provided data and future directions concerning the development of the PFNI.

q-bio.QM↗