Nicola Pezzotti

Kirsten W. H. Maas, Danny Ruijters, Anna Vilanova et al.

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.

Linhao Meng, Stef van den Elzen, Nicola Pezzotti et al.

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.

Segrey Kastryulin, Jamil Zakirov, Nicola Pezzotti et al.

Image quality assessment (IQA) algorithms aim to reproduce the human's perception of the image quality. The growing popularity of image enhancement, generation, and recovery models instigated the development of many methods to assess their performance. However, most IQA solutions are designed to predict image quality in the general domain, with the applicability to specific areas, such as medical imaging, remaining questionable. Moreover, the selection of these IQA metrics for a specific task typically involves intentionally induced distortions, such as manually added noise or artificial blurring; yet, the chosen metrics are then used to judge the output of real-life computer vision models. In this work, we aspire to fill these gaps by carrying out the most extensive IQA evaluation study for Magnetic Resonance Imaging (MRI) to date (14,700 subjective scores). We use outputs of neural network models trained to solve problems relevant to MRI, including image reconstruction in the scan acceleration, motion correction, and denoising. Our emphasis is on reflecting the radiologist's perception of the reconstructed images, gauging the most diagnostically influential criteria for the quality of MRI scans: signal-to-noise ratio, contrast-to-noise ratio, and the presence of artifacts. Seven trained radiologists assess these distorted images, with their verdicts then correlated with 35 different image quality metrics (full-reference, no-reference, and distribution-based metrics considered). The top performers -- DISTS, HaarPSI, VSI, and FID-VGG16 -- are found to be efficient across three proposed quality criteria, for all considered anatomies and the target tasks.

Chinmay Rao, Matthias van Osch, Nicola Pezzotti et al.

Since multiple MRI contrasts of the same anatomy contain redundant information, one contrast can guide the reconstruction of an undersampled subsequent contrast. To this end, several end-to-end learning-based guided reconstruction methods have been proposed. However, a key challenge is the requirement of large paired training datasets comprising raw data and aligned reference images. We propose a modular two-stage approach that does not require any k-space training data, relying solely on image-domain datasets, a large part of which can be unpaired. Additionally, our approach provides an explanatory framework for the multi-contrast problem based on the shared and non-shared generative factors underlying two given contrasts. A content/style model of two-contrast image data is learned from a largely unpaired image-domain dataset and is subsequently applied as a plug-and-play operator in iterative reconstruction. The disentanglement of content and style allows explicit representation of contrast-independent and contrast-specific factors. Consequently, incorporating prior information into the reconstruction reduces to a simple replacement of the aliased content of the reconstruction iterate with high-quality content derived from the reference scan. Combining this component with a data consistency step and introducing a general corrective process for the content yields an iterative scheme. We name this novel approach PnP-CoSMo. Various aspects like interpretability and convergence are explored via simulations. Furthermore, its practicality is demonstrated on the public NYU fastMRI DICOM dataset, showing improved generalizability compared to end-to-end methods, and on two in-house multi-coil raw datasets, offering up to 32.6\% more acceleration over learning-based non-guided reconstruction for a given SSIM.

Vidya Prasad, Chen Zhu-Tian, Anna Vilanova et al.

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.

Donghang Lyu, Chinmay Rao, Marius Staring et al.

Cardiac magnetic resonance imaging (CMR) is vital for diagnosing heart diseases, but long scan time remains a major drawback. To address this, accelerated imaging techniques have been introduced by undersampling k-space, which reduces the quality of the resulting images. Recent deep learning advancements aim to speed up scanning while preserving quality, but adapting to various sampling modes and undersampling factors remains challenging. Therefore, building a universal model is a promising direction. In this work, we introduce UPCMR, a universal unrolled model designed for CMR reconstruction. This model incorporates two kinds of learnable prompts, undersampling-specific prompt and spatial-specific prompt, and integrates them with a UNet structure in each block. Overall, by using the CMRxRecon2024 challenge dataset for training and validation, the UPCMR model highly enhances reconstructed image quality across all random sampling scenarios through an effective training strategy compared to some traditional methods, demonstrating strong adaptability potential for this task.

Donghang Lyu, Marius Staring, Mariya Doneva et al.

Cardiac Magnetic Resonance (CMR) imaging is a non-invasive method for assessing cardiac structure, function, and blood flow. Cine MRI extends this by capturing heart motion, providing detailed insights into cardiac mechanics. To reduce scan time and breath-hold discomfort, fast acquisition techniques have been utilized at the cost of lowering image quality. Recently, Implicit Neural Representation (INR) methods have shown promise in unsupervised reconstruction by learning coordinate-to-value mappings from undersampled data, enabling high-quality image recovery. However, current existing INR methods primarily focus on using coordinate-based positional embeddings to learn the mapping, while overlooking the feature representations of the target point and its neighboring context. In this work, we propose KP-INR, a dual-branch INR method operating in k-space for cardiac cine MRI reconstruction: one branch processes the positional embedding of k-space coordinates, while the other learns from local multi-scale k-space feature representations at those coordinates. By enabling cross-branch interaction and approximating the target k-space values from both branches, KP-INR can achieve strong performance on challenging Cartesian k-space data. Experiments on the CMRxRecon2024 dataset confirms its improved performance over baseline models and highlights its potential in this field.

Kirsten W. H. Maas, Danny Ruijters, Nicola Pezzotti et al.

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.

Vidya Prasad, Anna Vilanova, Nicola Pezzotti

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.

Vidya Prasad, Hans van Gorp, Christina Humer et al.

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.

Nicola Pezzotti

This paper describe an hybrid agent trained to play in Fantasy Football AI which participated in the Bot Bowl III competition. The agent, MimicBot, is implemented using a specifically designed deep policy network and trained using a combination of imitation and reinforcement learning. Previous attempts in using a reinforcement learning approach in such context failed for a number of reasons, e.g. due to the intrinsic randomness in the environment and the large and uneven number of actions available, with a curriculum learning approach failing to consistently beat a randomly paying agent. Currently no machine learning approach can beat a scripted bot which makes use of the domain knowledge on the game. Our solution, thanks to an imitation learning and a hybrid decision-making process, consistently beat such scripted agents. Moreover we shed lights on how to more efficiently train in a reinforcement learning setting while drastically increasing sample efficiency. MimicBot is the winner of the Bot Bowl III competition, and it is currently the state-of-the-art solution.

Nicola Pezzotti, Sahar Yousefi, Mohamed S. Elmahdy et al.

Adaptive intelligence aims at empowering machine learning techniques with the additional use of domain knowledge. In this work, we present the application of adaptive intelligence to accelerate MR acquisition. Starting from undersampled k-space data, an iterative learning-based reconstruction scheme inspired by compressed sensing theory is used to reconstruct the images. We adopt deep neural networks to refine and correct prior reconstruction assumptions given the training data. The network was trained and tested on a knee MRI dataset from the 2019 fastMRI challenge organized by Facebook AI Research and NYU Langone Health. All submissions to the challenge were initially ranked based on similarity with a known groundtruth, after which the top 4 submissions were evaluated radiologically. Our method was evaluated by the fastMRI organizers on an independent challenge dataset. It ranked #1, shared #1, and #3 on respectively the 8x accelerated multi-coil, the 4x multi-coil, and the 4x single-coil track. This demonstrates the superior performance and wide applicability of the method.

Shi Hu, Nicola Pezzotti, Max Welling

In healthcare applications, predictive uncertainty has been used to assess predictive accuracy. In this paper, we demonstrate that predictive uncertainty estimated by the current methods does not highly correlate with prediction error by decomposing the latter into random and systematic errors, and showing that the former is equivalent to the variance of the random error. In addition, we observe that current methods unnecessarily compromise performance by modifying the model and training loss to estimate the target and uncertainty jointly. We show that estimating them separately without modifications improves performance. Following this, we propose a novel method that estimates the target labels and magnitude of the prediction error in two steps. We demonstrate this method on a large-scale MRI reconstruction task, and achieve significantly better results than the state-of-the-art uncertainty estimation methods.

Cagatay Turkay, Nicola Pezzotti, Carsten Binnig et al.

Data science requires time-consuming iterative manual activities. In particular, activities such as data selection, preprocessing, transformation, and mining, highly depend on iterative trial-and-error processes that could be sped-up significantly by providing quick feedback on the impact of changes. The idea of progressive data science is to compute the results of changes in a progressive manner, returning a first approximation of results quickly and allow iterative refinements until converging to a final result. Enabling the user to interact with the intermediate results allows an early detection of erroneous or suboptimal choices, the guided definition of modifications to the pipeline and their quick assessment. In this paper, we discuss the progressiveness challenges arising in different steps of the data science pipeline. We describe how changes in each step of the pipeline impact the subsequent steps and outline why progressive data science will help to make the process more effective. Computing progressive approximations of outcomes resulting from changes creates numerous research challenges, especially if the changes are made in the early steps of the pipeline. We discuss these challenges and outline first steps towards progressiveness, which, we argue, will ultimately help to significantly speed-up the overall data science process.

Nicola Pezzotti, Julian Thijssen, Alexander Mordvintsev et al.

The t-distributed Stochastic Neighbor Embedding (tSNE) algorithm has become in recent years one of the most used and insightful techniques for the exploratory data analysis of high-dimensional data. tSNE reveals clusters of high-dimensional data points at different scales while it requires only minimal tuning of its parameters. Despite these advantages, the computational complexity of the algorithm limits its application to relatively small datasets. To address this problem, several evolutions of tSNE have been developed in recent years, mainly focusing on the scalability of the similarity computations between data points. However, these contributions are insufficient to achieve interactive rates when visualizing the evolution of the tSNE embedding for large datasets. In this work, we present a novel approach to the minimization of the tSNE objective function that heavily relies on modern graphics hardware and has linear computational complexity. Our technique does not only beat the state of the art, but can even be executed on the client side in a browser. We propose to approximate the repulsion forces between data points using adaptive-resolution textures that are drawn at every iteration with WebGL. This approximation allows us to reformulate the tSNE minimization problem as a series of tensor operation that are computed with TensorFlow.js, a JavaScript library for scalable tensor computations.

Nicola Pezzotti, Boudewijn P. F. Lelieveldt, Laurens van der Maaten et al.

Progressive Visual Analytics aims at improving the interactivity in existing analytics techniques by means of visualization as well as interaction with intermediate results. One key method for data analysis is dimensionality reduction, for example, to produce 2D embeddings that can be visualized and analyzed efficiently. t-Distributed Stochastic Neighbor Embedding (tSNE) is a well-suited technique for the visualization of several high-dimensional data. tSNE can create meaningful intermediate results but suffers from a slow initialization that constrains its application in Progressive Visual Analytics. We introduce a controllable tSNE approximation (A-tSNE), which trades off speed and accuracy, to enable interactive data exploration. We offer real-time visualization techniques, including a density-based solution and a Magic Lens to inspect the degree of approximation. With this feedback, the user can decide on local refinements and steer the approximation level during the analysis. We demonstrate our technique with several datasets, in a real-world research scenario and for the real-time analysis of high-dimensional streams to illustrate its effectiveness for interactive data analysis.