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Implicit Neural Representations (INRs) have emerged as a paradigm in knowledge representation, offering exceptional flexibility and performance across a diverse range of applications. INRs leverage multilayer perceptrons (MLPs) to model data as continuous implicit functions, providing critical advantages such as resolution independence, memory efficiency, and generalisation beyond discretised data structures. Their ability to solve complex inverse problems makes them particularly effective for tasks including audio reconstruction, image representation, 3D object reconstruction, and high-dimensional data synthesis. This survey provides a comprehensive review of state-of-the-art INR methods, introducing a clear taxonomy that categorises them into four key areas: activation functions, position encoding, combined strategies, and network structure optimisation. We rigorously analyse their critical properties, such as full differentiability, smoothness, compactness, and adaptability to varying resolutions while also examining their strengths and limitations in addressing locality biases and capturing fine details. Our experimental comparison offers new insights into the trade-offs between different approaches, showcasing the capabilities and challenges of the latest INR techniques across various tasks. In addition to identifying areas where current methods excel, we highlight key limitations and potential avenues for improvement, such as developing more expressive activation functions, enhancing positional encoding mechanisms, and improving scalability for complex, high-dimensional data. This survey serves as a roadmap for researchers, offering practical guidance for future exploration in the field of INRs. We aim to foster new methodologies by outlining promising research directions for INRs and applications.

Graph neural networks have inherent representational limitations due to their message-passing structure. Recent work has suggested that these limitations can be overcome by using unique node identifiers (UIDs). Here we argue that despite the advantages of UIDs, one of their disadvantages is that they lose the desirable property of permutation-equivariance. We thus propose to focus on UID models that are permutation-equivariant, and present theoretical arguments for their advantages. Motivated by this, we propose a method to regularize UID models towards permutation equivariance, via a contrastive loss. We empirically demonstrate that our approach improves generalization and extrapolation abilities while providing faster training convergence. On the recent BREC expressiveness benchmark, our proposed method achieves state-of-the-art performance compared to other random-based approaches.

When developing machine learning models, image quality assessment (IQA) measures are a crucial component for evaluation. However, commonly used IQA measures have been primarily developed and optimized for natural images. In many specialized settings, such as medical images, this poses an often-overlooked problem regarding suitability. In previous studies, the IQA measure HaarPSI showed promising behavior for natural and medical images. HaarPSI is based on Haar wavelet representations and the framework allows optimization of two parameters. So far, these parameters have been aligned for natural images. Here, we optimize these parameters for two annotated medical data sets, a photoacoustic and a chest X-Ray data set. We observe that they are more sensitive to the parameter choices than the employed natural images, and on the other hand both medical data sets lead to similar parameter values when optimized. We denote the optimized setting, which improves the performance for the medical images notably, by HaarPSI$_{MED}$. The results suggest that adapting common IQA measures within their frameworks for medical images can provide a valuable, generalizable addition to the employment of more specific task-based measures., Comment: 5 pages, 3 figures, 2 tables

Hamilton's equations of motion form a fundamental framework in various branches of physics, including astronomy, quantum mechanics, particle physics, and climate science. Classical numerical solvers are typically employed to compute the time evolution of these systems. However, when the system spans multiple spatial and temporal scales numerical errors can accumulate, leading to reduced accuracy. To address the challenges of evolving such systems over long timescales, we propose SympFlow, a novel neural network-based symplectic integrator, which is the composition of a sequence of exact flow maps of parametrised time-dependent Hamiltonian functions. This architecture allows for a backward error analysis: we can identify an underlying Hamiltonian function of the architecture and use it to define a Hamiltonian matching objective function, which we use for training. In numerical experiments, we show that SympFlow exhibits promising results, with qualitative energy conservation behaviour similar to that of time-stepping symplectic integrators., Comment: NeurReps 2024

We propose Pullback Flow Matching (PFM), a novel framework for generative modeling on data manifolds. Unlike existing methods that assume or learn restrictive closed-form manifold mappings for training Riemannian Flow Matching (RFM) models, PFM leverages pullback geometry and isometric learning to preserve the underlying manifold's geometry while enabling efficient generation and precise interpolation in latent space. This approach not only facilitates closed-form mappings on the data manifold but also allows for designable latent spaces, using assumed metrics on both data and latent manifolds. By enhancing isometric learning through Neural ODEs and proposing a scalable training objective, we achieve a latent space more suitable for interpolation, leading to improved manifold learning and generative performance. We demonstrate PFM's effectiveness through applications in synthetic data, protein dynamics and protein sequence data, generating novel proteins with specific properties. This method shows strong potential for drug discovery and materials science, where generating novel samples with specific properties is of great interest.

The quest for robust and generalizable machine learning models has driven recent interest in exploiting symmetries through equivariant neural networks. In the context of PDE solvers, recent works have shown that Lie point symmetries can be a useful inductive bias for Physics-Informed Neural Networks (PINNs) through data and loss augmentation. Despite this, directly enforcing equivariance within the model architecture for these problems remains elusive. This is because many PDEs admit non-compact symmetry groups, oftentimes not studied beyond their infinitesimal generators, making them incompatible with most existing equivariant architectures. In this work, we propose Lie aLgebrA Canonicalization (LieLAC), a novel approach that exploits only the action of infinitesimal generators of the symmetry group, circumventing the need for knowledge of the full group structure. To achieve this, we address existing theoretical issues in the canonicalization literature, establishing connections with frame averaging in the case of continuous non-compact groups. Operating within the framework of canonicalization, LieLAC can easily be integrated with unconstrained pre-trained models, transforming inputs to a canonical form before feeding them into the existing model, effectively aligning the input for model inference according to allowed symmetries. LieLAC utilizes standard Lie group descent schemes, achieving equivariance in pre-trained models. Finally, we showcase LieLAC's efficacy on tasks of invariant image classification and Lie point symmetry equivariant neural PDE solvers using pre-trained models., Comment: 40 pages; preprint

Partial differential equations (PDEs) are widely used to model complex physical systems, but solving them efficiently remains a significant challenge. Recently, Transformers have emerged as the preferred architecture for PDEs due to their ability to capture intricate dependencies. However, they struggle with representing continuous dynamics and long-range interactions. To overcome these limitations, we introduce the Mamba Neural Operator (MNO), a novel framework that enhances neural operator-based techniques for solving PDEs. MNO establishes a formal theoretical connection between structured state-space models (SSMs) and neural operators, offering a unified structure that can adapt to diverse architectures, including Transformer-based models. By leveraging the structured design of SSMs, MNO captures long-range dependencies and continuous dynamics more effectively than traditional Transformers. Through extensive analysis, we show that MNO significantly boosts the expressive power and accuracy of neural operators, making it not just a complement but a superior framework for PDE-related tasks, bridging the gap between efficient representation and accurate solution approximation.

Data-driven Riemannian geometry has emerged as a powerful tool for interpretable representation learning, offering improved efficiency in downstream tasks. Moving forward, it is crucial to balance cheap manifold mappings with efficient training algorithms. In this work, we integrate concepts from pullback Riemannian geometry and generative models to propose a framework for data-driven Riemannian geometry that is scalable in both geometry and learning: score-based pullback Riemannian geometry. Focusing on unimodal distributions as a first step, we propose a score-based Riemannian structure with closed-form geodesics that pass through the data probability density. With this structure, we construct a Riemannian autoencoder (RAE) with error bounds for discovering the correct data manifold dimension. This framework can naturally be used with anisotropic normalizing flows by adopting isometry regularization during training. Through numerical experiments on various datasets, we demonstrate that our framework not only produces high-quality geodesics through the data support, but also reliably estimates the intrinsic dimension of the data manifold and provides a global chart of the manifold, even in high-dimensional ambient spaces.

Deep Generative Models (DGMs), including Energy-Based Models (EBMs) and Score-based Generative Models (SGMs), have advanced high-fidelity data generation and complex continuous distribution approximation. However, their application in Markov Decision Processes (MDPs), particularly in distributional Reinforcement Learning (RL), remains underexplored, with conventional histogram-based methods dominating the field. This paper rigorously highlights that this application gap is caused by the nonlinearity of modern DGMs, which conflicts with the linearity required by the Bellman equation in MDPs. For instance, EBMs involve nonlinear operations such as exponentiating energy functions and normalizing constants. To address this, we introduce Bellman Diffusion, a novel DGM framework that maintains linearity in MDPs through gradient and scalar field modeling. With divergence-based training techniques to optimize neural network proxies and a new type of stochastic differential equation (SDE) for sampling, Bellman Diffusion is guaranteed to converge to the target distribution. Our empirical results show that Bellman Diffusion achieves accurate field estimations and is a capable image generator, converging 1.5x faster than the traditional histogram-based baseline in distributional RL tasks. This work enables the effective integration of DGMs into MDP applications, unlocking new avenues for advanced decision-making frameworks., Comment: Paper under review

We demonstrate the Patterns of Life Simulation to create realistic simulations of human mobility in a city. This simulation has recently been used to generate massive amounts of trajectory and check-in data. Our demonstration focuses on using the simulation twofold: (1) using the graphical user interface (GUI), and (2) running the simulation headless by disabling the GUI for faster data generation. We further demonstrate how the Patterns of Life simulation can be used to simulate any region on Earth by using publicly available data from OpenStreetMap. Finally, we also demonstrate recent improvements to the scalability of the simulation allows simulating up to 100,000 individual agents for years of simulation time. During our demonstration, as well as offline using our guides on GitHub, participants will learn: (1) The theories of human behavior driving the Patters of Life simulation, (2) how to simulate to generate massive amounts of synthetic yet realistic trajectory data, (3) running the simulation for a region of interest chosen by participants using OSM data, (4) learn the scalability of the simulation and understand the properties of generated data, and (5) manage thousands of parallel simulation instances running concurrently., Comment: Accepted paper to SIGSPATIAL 2024 main conference

Artificial intelligence (AI) systems have substantially improved dermatologists' diagnostic accuracy for melanoma, with explainable AI (XAI) systems further enhancing clinicians' confidence and trust in AI-driven decisions. Despite these advancements, there remains a critical need for objective evaluation of how dermatologists engage with both AI and XAI tools. In this study, 76 dermatologists participated in a reader study, diagnosing 16 dermoscopic images of melanomas and nevi using an XAI system that provides detailed, domain-specific explanations. Eye-tracking technology was employed to assess their interactions. Diagnostic performance was compared with that of a standard AI system lacking explanatory features. Our findings reveal that XAI systems improved balanced diagnostic accuracy by 2.8 percentage points relative to standard AI. Moreover, diagnostic disagreements with AI/XAI systems and complex lesions were associated with elevated cognitive load, as evidenced by increased ocular fixations. These insights have significant implications for clinical practice, the design of AI tools for visual tasks, and the broader development of XAI in medical diagnostics.

Celcomen leverages a mathematical causality framework to disentangle intra- and inter- cellular gene regulation programs in spatial transcriptomics and single-cell data through a generative graph neural network. It can learn gene-gene interactions, as well as generate post-perturbation counterfactual spatial transcriptomics, thereby offering access to experimentally inaccessible samples. We validated its disentanglement, identifiability, and counterfactual prediction capabilities through simulations and in clinically relevant human glioblastoma, human fetal spleen, and mouse lung cancer samples. Celcomen provides the means to model disease and therapy induced changes allowing for new insights into single-cell spatially resolved tissue responses relevant to human health.

We consider the task of image reconstruction while simultaneously decomposing the reconstructed image into components with different features. A commonly used tool for this is a variational approach with an infimal convolution of appropriate functions as a regularizer. Especially for noise corrupted observations, incorporating these functionals into the classical method of Bregman iterations provides a robust method for obtaining an overall good approximation of the true image, by stopping early the iteration according to a discrepancy principle. However, crucially, the quality of the separate components depends further on the proper choice of the regularization weights associated to the infimally convoluted functionals. Here, we propose the method of Nested Bregman iterations to improve a decomposition in a structured way. This allows to transform the task of choosing the weights into the problem of stopping the iteration according to a meaningful criterion based on normalized cross-correlation. We discuss the well-definedness and the convergence behavior of the proposed method, and illustrate its strength numerically with various image decomposition tasks employing infimal convolution functionals.

Sparse-View Computed Tomography (SVCT) offers low-dose and fast imaging but suffers from severe artifacts. Optimizing the sampling strategy is an essential approach to improving the imaging quality of SVCT. However, current methods typically optimize a universal sampling strategy for all types of scans, overlooking the fact that the optimal strategy may vary depending on the specific scanning task, whether it involves particular body scans (e.g., chest CT scans) or downstream clinical applications (e.g., disease diagnosis). The optimal strategy for one scanning task may not perform as well when applied to other tasks. To address this problem, we propose a deep learning framework that learns task-specific sampling strategies with a multi-task approach to train a unified reconstruction network while tailoring optimal sampling strategies for each individual task. Thus, a task-specific sampling strategy can be applied for each type of scans to improve the quality of SVCT imaging and further assist in performance of downstream clinical usage. Extensive experiments across different scanning types provide validation for the effectiveness of task-specific sampling strategies in enhancing imaging quality. Experiments involving downstream tasks verify the clinical value of learned sampling strategies, as evidenced by notable improvements in downstream task performance. Furthermore, the utilization of a multi-task framework with a shared reconstruction network facilitates deployment on current imaging devices with switchable task-specific modules, and allows for easily integrate new tasks without retraining the entire model.

In real-world applications, users often favor structurally diverse design choices over one high-quality solution. It is hence important to consider more solutions that decision-makers can compare and further explore based on additional criteria. Alongside the existing approaches of evolutionary diversity optimization, quality diversity, and multimodal optimization, this paper presents a fresh perspective on this challenge by considering the problem of identifying a fixed number of solutions with a pairwise distance above a specified threshold while maximizing their average quality. We obtain first insight into these objectives by performing a subset selection on the search trajectories of different well-established search heuristics, whether specifically designed with diversity in mind or not. We emphasize that the main goal of our work is not to present a new algorithm but to look at the problem in a more fundamental and theoretically tractable way by asking the question: What trade-off exists between the minimum distance within batches of solutions and the average quality of their fitness? These insights also provide us with a way of making general claims concerning the properties of optimization problems that shall be useful in turn for benchmarking algorithms of the approaches enumerated above. A possibly surprising outcome of our empirical study is the observation that naive uniform random sampling establishes a very strong baseline for our problem, hardly ever outperformed by the search trajectories of the considered heuristics. We interpret these results as a motivation to develop algorithms tailored to produce diverse solutions of high average quality.

Equal access to health ensures that all citizens, regardless of socio-economic status, can achieve optimal health, leading to a more productive, equitable, and resilient society. Yet, migrant populations were frequently observed to have lower access to health. The reasons for this are not entirely clear and may include language barriers, a lack of knowledge of the healthcare system, and selective migration (a "healthy migrant" effect). We use extensive medical claims data from Austria (13 million hospital stays of approximately 4 million individuals) to compare the healthcare utilization patterns between Austrians and non-Austrians. We looked at the differences in primary diagnoses and hospital sections of initial hospital admission across different nationalities. We hypothesize that cohorts experiencing the healthy migrant effect show lower readmission rates after hospitalization compared to migrant populations that are in poorer health but show lower hospitalization rates due to barriers in access. We indeed find that all nationalities showed lower hospitalization rates than Austrians, except for Germans, who exhibit a similar healthcare usage to Austrians. Although around 20\% of the population has a migration background, non-Austrian citizens account for only 9.4% of the hospital patients and 9.79% of hospital nights. However, results for readmission rates are much more divergent. Nationalities like Hungary, Romania, and Turkey (females) show decreased readmission rates in line with the healthy migrant effect. Patients from Russia, Serbia, and Turkey (males) show increased readmissions, suggesting that their lower hospitalization rates are more likely due to access barriers. Considering the surge in migration, our findings shed light on healthcare access and usage behaviours across patients with different nationalities, offering new insights and perspectives.

We study the exact ground states of the Su--Schrieffer--Heeger open chain and of the Kitaev open chain, using the Variational Quantum Eigensolver (VQE) algorithm. These models host symmetry-protected topological phases, characterized by edge modes with vanishing single-particle energy in the thermodynamic limit. The same fact prevents the standard VQE algorithm from converging to the correct ground state for finite chains, since it is quasi-degenerate in energy with other many-body states. Notably, this quasi-degeneracy cannot be removed by small perturbations, as in typical spin systems. We address this issue by imposing appropriate constraints on the VQE evolution and constructing appropriate variational circuits, to restrict the probed portion of the Hilbert space along the same evolution. These constraints stem from both general properties of the topological phases and of the studied Hamiltonians. In this way, the improved VQE algorithm achieves an accurate convergence to the exact ground states in each phase. The present approach promises large applicability, also to realistic systems and possibly with different topology, thanks to the very high fidelity achieved also on systems with a relatively high number of qubits.

In recent years, Graph Neural Networks (GNNs) have been utilized for various applications ranging from drug discovery to network design and social networks. In many applications, it is impossible to observe some properties of the graph directly; instead, noisy and indirect measurements of these properties are available. These scenarios are coined as Graph Inverse Problems (GRIP). In this work, we introduce a framework leveraging GNNs to solve GRIPs. The framework is based on a combination of likelihood and prior terms, which are used to find a solution that fits the data while adhering to learned prior information. Specifically, we propose to combine recent deep learning techniques that were developed for inverse problems, together with GNN architectures, to formulate and solve GRIP. We study our approach on a number of representative problems that demonstrate the effectiveness of the framework.

Accurate classification of haematological cells is critical for diagnosing blood disorders, but presents significant challenges for machine automation owing to the complexity of cell morphology, heterogeneities of biological, pathological, and imaging characteristics, and the imbalance of cell type frequencies. We introduce CytoDiffusion, a diffusion-based classifier that effectively models blood cell morphology, combining accurate classification with robust anomaly detection, resistance to distributional shifts, interpretability, data efficiency, and superhuman uncertainty quantification. Our approach outperforms state-of-the-art discriminative models in anomaly detection (AUC 0.976 vs. 0.919), resistance to domain shifts (85.85% vs. 74.38% balanced accuracy), and performance in low-data regimes (95.88% vs. 94.95% balanced accuracy). Notably, our model generates synthetic blood cell images that are nearly indistinguishable from real images, as demonstrated by a Turing test in which expert haematologists achieved only 52.3% accuracy (95% CI: [50.5%, 54.2%]). Furthermore, we enhance model explainability through the generation of directly interpretable counterfactual heatmaps. Our comprehensive evaluation framework, encompassing these multiple performance dimensions, establishes a new benchmark for medical image analysis in haematology, ultimately enabling improved diagnostic accuracy in clinical settings. Our code is available at https://github.com/Deltadahl/CytoDiffusion.

Like in many other research fields, recent developments in computational imaging have focused on developing machine learning (ML) approaches to tackle its main challenges. To improve the performance of computational imaging algorithms, machine learning methods are used for image processing tasks such as noise reduction. Generally, these ML methods heavily rely on the availability of high-quality data on which they are trained. This work explores the application of ML methods, specifically convolutional neural networks (CNNs), in the context of noise reduction for computed tomography (CT) imaging. We utilize a large 2D computed tomography dataset for machine learning to carry out for the first time a comprehensive study on the differences between the observed performances of algorithms trained on simulated noisy data and on real-world experimental noisy data. The study compares the performance of two common CNN architectures, U-Net and MSD-Net, that are trained and evaluated on both simulated and experimental noisy data. The results show that while sinogram denoising performed better with simulated noisy data if evaluated in the sinogram domain, the performance did not carry over to the reconstruction domain where training on experimental noisy data shows a higher performance in denoising experimental noisy data. Training the algorithms in an end-to-end fashion from sinogram to reconstruction significantly improved model performance, emphasizing the importance of matching raw measurement data to high-quality CT reconstructions. The study furthermore suggests the need for more sophisticated noise simulation approaches to bridge the gap between simulated and real-world data in CT image denoising applications and gives insights into the challenges and opportunities in leveraging simulated data for machine learning in computational imaging.

The manifold hypothesis says that natural high-dimensional data is actually supported on or around a low-dimensional manifold. Recent success of statistical and learning-based methods empirically supports this hypothesis, due to outperforming classical statistical intuition in very high dimensions. A natural step for analysis is thus to assume the manifold hypothesis and derive bounds that are independent of any embedding space. Theoretical implications in this direction have recently been explored in terms of generalization of ReLU networks and convergence of Langevin methods. We complement existing results by providing theoretical statistical complexity results, which directly relates to generalization properties. In particular, we demonstrate that the statistical complexity required to approximate a class of bounded Sobolev functions on a compact manifold is bounded from below, and moreover that this bound is dependent only on the intrinsic properties of the manifold. These provide complementary bounds for existing approximation results for ReLU networks on manifolds, which give upper bounds on generalization capacity.

In the field of neuroimaging, accurate brain age prediction is pivotal for uncovering the complexities of brain aging and pinpointing early indicators of neurodegenerative conditions. Recent advancements in self-supervised learning, particularly in contrastive learning, have demonstrated greater robustness when dealing with complex datasets. However, current approaches often fall short in generalizing across non-uniformly distributed data, prevalent in medical imaging scenarios. To bridge this gap, we introduce a novel contrastive loss that adapts dynamically during the training process, focusing on the localized neighborhoods of samples. Moreover, we expand beyond traditional structural features by incorporating brain stiffness, a mechanical property previously underexplored yet promising due to its sensitivity to age-related changes. This work presents the first application of self-supervised learning to brain mechanical properties, using compiled stiffness maps from various clinical studies to predict brain age. Our approach, featuring dynamic localized loss, consistently outperforms existing state-of-the-art methods, demonstrating superior performance and laying the way for new directions in brain aging research.

Immunofluorescent (IF) imaging is crucial for visualizing biomarker expressions, cell morphology and assessing the effects of drug treatments on sub-cellular components. IF imaging needs extra staining process and often requiring cell fixation, therefore it may also introduce artefects and alter endogenouous cell morphology. Some IF stains are expensive or not readily available hence hindering experiments. Recent diffusion models, which synthesise high-fidelity IF images from easy-to-acquire brightfield (BF) images, offer a promising solution but are hindered by training instability and slow inference times due to the noise diffusion process. This paper presents a novel method for the conditional synthesis of IF images directly from BF images along with cell segmentation masks. Our approach employs a Residual Diffusion process that enhances stability and significantly reduces inference time. We performed a critical evaluation against other image-to-image synthesis models, including UNets, GANs, and advanced diffusion models. Our model demonstrates significant improvements in image quality (p<0.05 in MSE, PSNR, and SSIM), inference speed (26 times faster than competing diffusion models), and accurate segmentation results for both nuclei and cell bodies (0.77 and 0.63 mean IOU for nuclei and cell true positives, respectively). This paper is a substantial advancement in the field, providing robust and efficient tools for cell image analysis.

Low discrepancy point sets have been widely used as a tool to approximate continuous objects by discrete ones in numerical processes, for example in numerical integration. Following a century of research on the topic, it is still unclear how low the discrepancy of point sets can go; in other words, how regularly distributed can points be in a given space. Recent insights using optimization and machine learning techniques have led to substantial improvements in the construction of low-discrepancy point sets, resulting in configurations of much lower discrepancy values than previously known. Building on the optimal constructions, we present a simple way to obtain $L_{\infty}$-optimized placement of points that follow the same relative order as an (arbitrary) input set. Applying this approach to point sets in dimensions 2 and 3 for up to 400 and 50 points, respectively, we obtain point sets whose $L_{\infty}$ star discrepancies are up to 25% smaller than those of the current-best sets, and around 50% better than classical constructions such as the Fibonacci set.

In this paper, we consider the problem of prototype-based vision-language reasoning problem. We observe that existing methods encounter three major challenges: 1) escalating resource demands and prolonging training times, 2) contending with excessive learnable parameters, and 3) fine-tuning based only on a single modality. These challenges will hinder their capability to adapt Vision-Language Models (VLMs) to downstream tasks. Motivated by this critical observation, we propose a novel method called NODE-Adapter, which utilizes Neural Ordinary Differential Equations for better vision-language reasoning. To fully leverage both visual and textual modalities and estimate class prototypes more effectively and accurately, we divide our method into two stages: cross-modal prototype construction and cross-modal prototype optimization using neural ordinary differential equations. Specifically, we exploit VLM to encode hand-crafted prompts into textual features and few-shot support images into visual features. Then, we estimate the textual prototype and visual prototype by averaging the textual features and visual features, respectively, and adaptively combine the textual prototype and visual prototype to construct the cross-modal prototype. To alleviate the prototype bias, we then model the prototype optimization process as an initial value problem with Neural ODEs to estimate the continuous gradient flow. Our extensive experimental results, which cover few-shot classification, domain generalization, and visual reasoning on human-object interaction, demonstrate that the proposed method significantly outperforms existing state-of-the-art approaches.

Exploratory landscape analysis (ELA) is a well-established tool to characterize optimization problems via numerical features. ELA is used for problem comprehension, algorithm design, and applications such as automated algorithm selection and configuration. Until recently, however, ELA was limited to search spaces with either continuous or discrete variables, neglecting problems with mixed variable types. This gap was addressed in a recent study that uses an approach based on target-encoding to compute exploratory landscape features for mixedvariable problems. In this work, we investigate an alternative encoding scheme based on SHAP values. While these features do not lead to better results in the algorithm selection setting considered in previous work, the two different encoding mechanisms exhibit complementary performance. Combining both feature sets into a hybrid approach outperforms each encoding mechanism individually. Finally, we experiment with two different ways of meta-selecting between the two feature sets. Both approaches are capable of taking advantage of the performance complementarity of the models trained on target-encoded and SHAP-encoded feature sets, respectively., Comment: This version has been accepted for publication at the 18th International Conference on Parallel Problem Solving from Nature (PPSN 2024)

Point clouds are popular 3D representations for real-life objects (such as in LiDAR and Kinect) due to their detailed and compact representation of surface-based geometry. Recent approaches characterise the geometry of point clouds by bringing deep learning based techniques together with geometric fidelity metrics such as optimal transportation costs (e.g., Chamfer and Wasserstein metrics). In this paper, we propose a new surface geometry characterisation within this realm, namely a neural varifold representation of point clouds. Here the surface is represented as a measure/distribution over both point positions and tangent spaces of point clouds. The varifold representation quantifies not only the surface geometry of point clouds through the manifold-based discrimination, but also subtle geometric consistencies on the surface due to the combined product space. This study proposes neural varifold algorithms to compute the varifold norm between two point clouds using neural networks on point clouds and their neural tangent kernel representations. The proposed neural varifold is evaluated on three different sought-after tasks -- shape matching, few-shot shape classification and shape reconstruction. Detailed evaluation and comparison to the state-of-the-art methods demonstrate that the proposed versatile neural varifold is superior in shape matching and few-shot shape classification, and is competitive for shape reconstruction., Comment: The first author, Juheon Lee, is an unaffiliated, independent researcher. This work is a personal endeavor, unrelated to his current job

We present a novel, and effective, approach to the long-standing problem of mesh adaptivity in finite element methods (FEM). FE solvers are powerful tools for solving partial differential equations (PDEs), but their cost and accuracy are critically dependent on the choice of mesh points. To keep computational costs low, mesh relocation (r-adaptivity) seeks to optimise the position of a fixed number of mesh points to obtain the best FE solution accuracy. Classical approaches to this problem require the solution of a separate nonlinear "meshing" PDE to find the mesh point locations. This incurs significant cost at remeshing and relies on certain a-priori assumptions and guiding heuristics for optimal mesh point location. Recent machine learning approaches to r-adaptivity have mainly focused on the construction of fast surrogates for such classical methods. Our new approach combines a graph neural network (GNN) powered architecture, with training based on direct minimisation of the FE solution error with respect to the mesh point locations. The GNN employs graph neural diffusion (GRAND), closely aligning the mesh solution space to that of classical meshing methodologies, thus replacing heuristics with a learnable strategy, and providing a strong inductive bias. This allows for rapid and robust training and results in an extremely efficient and effective GNN approach to online r-adaptivity. This method outperforms classical and prior ML approaches to r-adaptive meshing on the test problems we consider, in particular achieving lower FE solution error, whilst retaining the significant speed-up over classical methods observed in prior ML work.

In this paper, we propose a novel activation function tailored specifically for graph data in Graph Neural Networks (GNNs). Motivated by the need for graph-adaptive and flexible activation functions, we introduce DiGRAF, leveraging Continuous Piecewise-Affine Based (CPAB) transformations, which we augment with an additional GNN to learn a graph-adaptive diffeomorphic activation function in an end-to-end manner. In addition to its graph-adaptivity and flexibility, DiGRAF also possesses properties that are widely recognized as desirable for activation functions, such as differentiability, boundness within the domain, and computational efficiency. We conduct an extensive set of experiments across diverse datasets and tasks, demonstrating a consistent and superior performance of DiGRAF compared to traditional and graph-specific activation functions, highlighting its effectiveness as an activation function for GNNs. Our code is available at https://github.com/ipsitmantri/DiGRAF., Comment: NeurIPS 2024

Cell imaging assays utilizing fluorescence stains are essential for observing sub-cellular organelles and their responses to perturbations. Immunofluorescent staining process is routinely in labs, however the recent innovations in generative AI is challenging the idea of IF staining are required. This is especially true when the availability and cost of specific fluorescence dyes is a problem to some labs. Furthermore, staining process takes time and leads to inter-intra technician and hinders downstream image and data analysis, and the reusability of image data for other projects. Recent studies showed the use of generated synthetic immunofluorescence (IF) images from brightfield (BF) images using generative AI algorithms in the literature. Therefore, in this study, we benchmark and compare five models from three types of IF generation backbones, CNN, GAN, and diffusion models, using a publicly available dataset. This paper not only serves as a comparative study to determine the best-performing model but also proposes a comprehensive analysis pipeline for evaluating the efficacy of generators in IF image synthesis. We highlighted the potential of deep learning-based generators for IF image synthesis, while also discussed potential issues and future research directions. Although generative AI shows promise in simplifying cell phenotyping using only BF images with IF staining, further research and validations are needed to address the key challenges of model generalisability, batch effects, feature relevance and computational costs.

Perfusion MRI (pMRI) offers valuable insights into tumor vascularity and promises to predict tumor genotypes, thus benefiting prognosis for glioma patients, yet effective models tailored to 4D pMRI are still lacking. This study presents the first attempt to model 4D pMRI using a GNN-based spatiotemporal model PerfGAT, integrating spatial information and temporal kinetics to predict Isocitrate DeHydrogenase (IDH) mutation status in glioma patients. Specifically, we propose a graph structure learning approach based on edge attention and negative graphs to optimize temporal correlations modeling. Moreover, we design a dual-attention feature fusion module to integrate spatiotemporal features while addressing tumor-related brain regions. Further, we develop a class-balanced augmentation methods tailored to spatiotemporal data, which could mitigate the common label imbalance issue in clinical datasets. Our experimental results demonstrate that the proposed method outperforms other state-of-the-art approaches, promising to model pMRI effectively for patient characterization., Comment: 11 pages, 2 figures

The selection of the most appropriate algorithm to solve a given problem instance, known as algorithm selection, is driven by the potential to capitalize on the complementary performance of different algorithms across sets of problem instances. However, determining the optimal algorithm for an unseen problem instance has been shown to be a challenging task, which has garnered significant attention from researchers in recent years. In this survey, we conduct an overview of the key contributions to algorithm selection in the field of single-objective continuous black-box optimization. We present ongoing work in representation learning of meta-features for optimization problem instances, algorithm instances, and their interactions. We also study machine learning models for automated algorithm selection, configuration, and performance prediction. Through this analysis, we identify gaps in the state of the art, based on which we present ideas for further development of meta-feature representations., Comment: 14 pages, 2 figures

Generative AI models are capable of performing a wide range of tasks that traditionally require creativity and human understanding. They learn patterns from existing data during training and can subsequently generate new content such as texts, images, and music that follow these patterns. Due to their versatility and generally high-quality results, they, on the one hand, represent an opportunity for digitalization. On the other hand, the use of generative AI models introduces novel IT security risks that need to be considered for a comprehensive analysis of the threat landscape in relation to IT security. In response to this risk potential, companies or authorities using them should conduct an individual risk analysis before integrating generative AI into their workflows. The same applies to developers and operators, as many risks in the context of generative AI have to be taken into account at the time of development or can only be influenced by the operating company. Based on this, existing security measures can be adjusted, and additional measures can be taken., Comment: 33 pages, 3 figures

Image restoration is typically addressed through non-convex inverse problems, which are often solved using first-order block-wise splitting methods. In this paper, we consider a general type of non-convex optimisation model that captures many inverse image problems and present an inertial block proximal linearised minimisation (iBPLM) algorithm. Our new method unifies the Jacobi-type parallel and the Gauss-Seidel-type alternating update rules, and extends beyond these approaches. The inertial technique is also incorporated into each block-wise subproblem update, which can accelerate numerical convergence. Furthermore, we extend this framework with a plug-and-play variant (PnP-iBPLM) that integrates deep gradient denoisers, offering a flexible and robust solution for complex imaging tasks. We provide comprehensive theoretical analysis, demonstrating both subsequential and global convergence of the proposed algorithms. To validate our methods, we apply them to multi-block dictionary learning problems in image denoising and deblurring. Experimental results show that both iBPLM and PnP-iBPLM significantly enhance numerical performance and robustness in these applications., Comment: 6 figures, 6 tables

In this paper, part of the DREAMING Challenge - Diminished Reality for Emerging Applications in Medicine through Inpainting, we introduce a refined video inpainting technique optimised from the ProPainter method to meet the specialised demands of medical imaging, specifically in the context of oral and maxillofacial surgery. Our enhanced algorithm employs the zero-shot ProPainter, featuring optimized parameters and pre-processing, to adeptly manage the complex task of inpainting surgical video sequences, without requiring any training process. It aims to produce temporally coherent and detail-rich reconstructions of occluded regions, facilitating clearer views of operative fields. The efficacy of our approach is evaluated using comprehensive metrics, positioning it as a significant advancement in the application of diminished reality for medical purposes., Comment: Accepted to ISBI 2024

Interlayer excitons in transition-metal dichalcogenide heterobilayers combine high binding energy and valley-contrasting physics with long optical lifetime and strong dipolar character. Their permanent electric dipole enables electric-field control of emission energy, lifetime, and location. Device material and geometry impacts the nature of the interlayer excitons via their real- and momentum-space configurations. Here, we show that interlayer excitons in MoS$_{2}$/MoSe$_{2}$ heterobilayers are formed by charge carriers residing at the Brillouin zone edges, with negligible interlayer hybridization. We find that the moir\'e superlattice leads to the reversal of the valley-dependent optical selection rules, yielding a positively valued g-factor and cross-polarized photoluminescence. Time-resolved photoluminescence measurements reveal that the interlayer exciton population retains the optically induced valley polarization throughout its microsecond-long lifetime. The combination of long optical lifetime and valley polarization retention makes MoS$_{2}$/MoSe$_{2}$ heterobilayers a promising platform for studying fundamental bosonic interactions and developing excitonic circuits for optical information processing.

Image quality assessment (IQA) is standard practice in the development stage of novel machine learning algorithms that operate on images. The most commonly used IQA measures have been developed and tested for natural images, but not in the medical setting. Reported inconsistencies arising in medical images are not surprising, as they have different properties than natural images. In this study, we test the applicability of common IQA measures for medical image data by comparing their assessment to manually rated chest X-ray (5 experts) and photoacoustic image data (2 experts). Moreover, we include supplementary studies on grayscale natural images and accelerated brain MRI data. The results of all experiments show a similar outcome in line with previous findings for medical images: PSNR and SSIM in the default setting are in the lower range of the result list and HaarPSI outperforms the other tested measures in the overall performance. Also among the top performers in our medical experiments are the full reference measures FSIM, LPIPS and MS-SSIM. Generally, the results on natural images yield considerably higher correlations, suggesting that additional employment of tailored IQA measures for medical imaging algorithms is needed.

Image quality assessment (IQA) is not just indispensable in clinical practice to ensure high standards, but also in the development stage of novel algorithms that operate on medical images with reference data. This paper provides a structured and comprehensive collection of examples where the two most common full reference (FR) image quality measures prove to be unsuitable for the assessment of novel algorithms using different kinds of medical images, including real-world MRI, CT, OCT, X-Ray, digital pathology and photoacoustic imaging data. In particular, the FR-IQA measures PSNR and SSIM are known and tested for working successfully in many natural imaging tasks, but discrepancies in medical scenarios have been noted in the literature. Inconsistencies arising in medical images are not surprising, as they have very different properties than natural images which have not been targeted nor tested in the development of the mentioned measures, and therefore might imply wrong judgement of novel methods for medical images. Therefore, improvement is urgently needed in particular in this era of AI to increase explainability, reproducibility and generalizability in machine learning for medical imaging and beyond. On top of the pitfalls we will provide ideas for future research as well as suggesting guidelines for the usage of FR-IQA measures applied to medical images.

Federated Learning (FL) enables collaborative training of machine learning models on decentralized data while preserving data privacy. However, data across clients often differs significantly due to class imbalance, feature distribution skew, sample size imbalance, and other phenomena. Leveraging information from these not identically distributed (non-IID) datasets poses substantial challenges. FL methods based on a single global model cannot effectively capture the variations in client data and underperform in non-IID settings. Consequently, Personalized FL (PFL) approaches that adapt to each client's data distribution but leverage other clients' data are essential but currently underexplored. We propose a novel Bayesian PFL framework using bi-level optimization to tackle the data heterogeneity challenges. Our proposed framework utilizes the global model as a prior distribution within a Maximum A Posteriori (MAP) estimation of personalized client models. This approach facilitates PFL by integrating shared knowledge from the prior, thereby enhancing local model performance, generalization ability, and communication efficiency. We extensively evaluated our bi-level optimization approach on real-world and synthetic datasets, demonstrating significant improvements in model accuracy compared to existing methods while reducing communication overhead. This study contributes to PFL by establishing a solid theoretical foundation for the proposed method and offering a robust, ready-to-use framework that effectively addresses the challenges posed by non-IID data in FL.

Deep learning has been extensively applied in medical image reconstruction, where Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) represent the predominant paradigms, each possessing distinct advantages and inherent limitations: CNNs exhibit linear complexity with local sensitivity, whereas ViTs demonstrate quadratic complexity with global sensitivity. The emerging Mamba has shown superiority in learning visual representation, which combines the advantages of linear scalability and global sensitivity. In this study, we introduce MambaMIR, an Arbitrary-Masked Mamba-based model with wavelet decomposition for joint medical image reconstruction and uncertainty estimation. A novel Arbitrary Scan Masking (ASM) mechanism "masks out" redundant information to introduce randomness for further uncertainty estimation. Compared to the commonly used Monte Carlo (MC) dropout, our proposed MC-ASM provides an uncertainty map without the need for hyperparameter tuning and mitigates the performance drop typically observed when applying dropout to low-level tasks. For further texture preservation and better perceptual quality, we employ the wavelet transformation into MambaMIR and explore its variant based on the Generative Adversarial Network, namely MambaMIR-GAN. Comprehensive experiments have been conducted for multiple representative medical image reconstruction tasks, demonstrating that the proposed MambaMIR and MambaMIR-GAN outperform other baseline and state-of-the-art methods in different reconstruction tasks, where MambaMIR achieves the best reconstruction fidelity and MambaMIR-GAN has the best perceptual quality. In addition, our MC-ASM provides uncertainty maps as an additional tool for clinicians, while mitigating the typical performance drop caused by the commonly used dropout.

This study examines the generalization ability of algorithm performance prediction models across various benchmark suites. Comparing the statistical similarity between the problem collections with the accuracy of performance prediction models that are based on exploratory landscape analysis features, we observe that there is a positive correlation between these two measures. Specifically, when the high-dimensional feature value distributions between training and testing suites lack statistical significance, the model tends to generalize well, in the sense that the testing errors are in the same range as the training errors. Two experiments validate these findings: one involving the standard benchmark suites, the BBOB and CEC collections, and another using five collections of affine combinations of BBOB problem instances., Comment: To appear in the Proc. of the 2024 IEEE World Congress on Computational - Congress on Evolutionary Computation

This study explores the influence of modules on the performance of modular optimization frameworks for continuous single-objective black-box optimization. There is an extensive variety of modules to choose from when designing algorithm variants, however, there is a rather limited understanding of how each module individually influences the algorithm performance and how the modules interact with each other when combined. We use the functional ANOVA (f-ANOVA) framework to quantify the influence of individual modules and module combinations for two algorithms, the modular Covariance Matrix Adaptation (modCMA) and the modular Differential Evolution (modDE). We analyze the performance data from 324 modCMA and 576 modDE variants on the BBOB benchmark collection, for two problem dimensions, and three computational budgets. Noteworthy findings include the identification of important modules that strongly influence the performance of modCMA, such as the~\textit{weights\ option} and~\textit{mirrored} modules for low dimensional problems, and the~\textit{base\ sampler} for high dimensional problems. The large individual influence of the~\textit{lpsr} module makes it very important for the performance of modDE, regardless of the problem dimensionality and the computational budget. When comparing modCMA and modDE, modDE undergoes a shift from individual modules being more influential, to module combinations being more influential, while modCMA follows the opposite pattern, with an increase in problem dimensionality and computational budget., Comment: To appear in the Proc. of IEEE Congress on Evolutionary Computation (WCCI CEC 2024)