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Carola-Bibiane Schönlieb

Carola-Bibiane Schönlieb contributes to research discovery and scholarly infrastructure.

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Published work

49 published item(s)

preprint2026arXiv

Bridging Input Feature Spaces Towards Graph Foundation Models

Unlike vision and language domains, graph learning lacks a shared input space, as input features differ across graph datasets not only in semantics, but also in value ranges and dimensionality. This misalignment prevents graph models from generalizing across datasets, limiting their use as foundation models. In this work, we propose ALL-IN, a simple and theoretically grounded method that enables transferability across datasets with different input features. Our approach projects node features into a shared random space and constructs representations via covariance-based statistics, thus eliminating dependence on the original feature space. We show that the computed node-covariance operators and the resulting node representations are invariant in distribution to permutations of the input features. We further demonstrate that the expected operator exhibits invariance to general orthogonal transformations of the input features. Empirically, ALL-IN achieves strong performance across diverse node- and graph-level tasks on unseen datasets with new input features, without requiring architecture changes or retraining. These results point to a promising direction for input-agnostic, transferable graph models.

preprint2026arXiv

CATO: Charted Attention for Neural PDE Operators

Neural operators have emerged as powerful data-driven solvers for PDEs, offering substantial acceleration over classical numerical methods. However, existing transformer-based operators still face critical challenges when modeling PDEs on complex geometries: directly processing over massive mesh points is computationally expensive, while operating in raw discretization coordinates may obscure the intrinsic geometry where physical interactions are more naturally expressed. To address these limitations, we introduce the Charted Axial Transformer Operator (CATO), a geometry-adaptive and derivative-aware neural operator for PDEs on general geometries. Instead of applying attention directly in the physical coordinate system, CATO learns a continuous latent chart that maps mesh coordinates into a learned chart space, where chart-conditioned axial attention efficiently captures long-range dependencies with reduced computational cost. In addition, CATO introduces a derivative-aware physics loss for steady-state PDEs that jointly supervises solution values, mesh-consistent gradients, and an auxiliary flux-like field, improving physical fidelity and reducing oversmoothing. We further provide a theoretical approximation result showing that, under a favorable chart, charted axial attention can represent low-rank axial solution operators with controlled error, and that small chart perturbations induce bounded approximation degradation. CATO achieves the best performance across all evaluated datasets, yielding an average improvement of approximately 26.76\% over the strongest competing baselines while reducing the number of parameters by 81.98\%. These results highlight the effectiveness of learning geometry-adaptive charts and derivative-aware physical supervision for accurate and efficient PDE operator learning.

preprint2026arXiv

Christoffel-DPS: Optimal sensor placement in diffusion posterior sampling for arbitrary distributions

State estimation is a critical task in scientific, engineering and control applications. Since the reliability of reconstructions depends on the number and position of sensors, optimal sensor placement (OSP) is essential in scenarios where measurements are sparse and expensive. Classical OSP approaches rely on Gaussian assumptions and are consequently unable to account for the complex distributions encountered in many real-world systems. Generative-model-based reconstruction using sensor guided diffusion posterior sampling (DPS) has emerged as a promising technique for reconstructing states from highly complex distributions. However, existing sensor-selection methods either require unrealistically many sensors or emulate classical OSP, creating a mismatch between modern recovery models with classical OSP tools motivating the need for fundamentally new ideas towards OSP that match the recent advances made in powerful recovery models. We introduce a distribution-free sensor placement framework based on the Christoffel function: a mathematical formulation of optimal sampling and recovery guarantees for posterior sampling with arbitrary sensors and signal distributions, from which we derive a new OSP strategy with non-asymptotic bounds on the number of sensors needed for recovery. We develop Christoffel-DPS, with offline and online variants, instantiating Christoffel sampling for generative models. Christoffel-DPS outperforms Gaussian OSP baselines and existing generative-model placement methods, validating that distribution-free sensing is both theoretically principled and practically superior. The framework is model-agnostic; we demonstrate its application to a range of unconditional DPS and flow-matching models on structurally non-Gaussian benchmarks, showing the efficacy of Christoffel-DPS in low sensor budget regimes.

preprint2026arXiv

Expressivity of Bi-Lipschitz Normalizing Flows: A Score-Based Diffusion Perspective

Many normalizing flow architectures impose regularity constraints, yet their distributional approximation properties are not fully characterized. We study the expressivity of bi-Lipschitz normalizing flows through the lens of score-based diffusion models. For the probability flow ODE of a variance-preserving diffusion, Lipschitz regularity of the score induces a flow of bi-Lipschitz diffeomorphic transport maps. This ODE bridge allows us to analyze the distributional approximation power of bi-Lipschitz normalizing flows and, conversely, derive deterministic convergence guarantees for diffusion-based transport. Our key idea is to use the probability flow ODE to link regularity of the score to regularity of the induced transport maps. We verify score regularity for broad target densities, including compactly supported densities, Gaussian convolutions of compactly supported measures and finite Gaussian mixtures. We obtain a universal distributional approximation result: Gaussian pullbacks induced by bi-Lipschitz variance-preserving transport maps are $L^1$-dense among all probability densities. For Gaussian convolution targets, we further obtain convergence in Kullback-Leibler divergence without early stopping.

preprint2026arXiv

GRIFDIR: Graph Resolution-Invariant FEM Diffusion Models in Function Spaces over Irregular Domains

Score-based diffusion models in infinite-dimensional function spaces provide a mathematically principled framework for modelling function-valued data, offering key advantages such as resolution invariance and the ability to handle irregular discretisations. However, practical implementations have struggled to fully realise these benefits. Existing backbones like Fourier neural operators are often biased towards regular grids and fail to generalise to complex domain topologies. We propose a novel architecture for function-space diffusion models that represents generalised graph convolutional kernels as finite element functions, enabling the model to naturally handle unstructured meshes and complex geometries. We demonstrate the efficacy of our network architecture through a series of unconditional and conditional sampling experiments across diverse geometries, including non-convex and multiply-connected domains. Our results show that the proposed method maintains resolution invariance and achieves high fidelity in capturing functional distributions on non-trivial geometries.

preprint2026arXiv

Learning Regularization Functionals for Inverse Problems: A Comparative Study

In recent years, a variety of learned regularization frameworks for solving inverse problems in imaging have emerged. These offer flexible modeling together with mathematical insights. The proposed methods differ in their architectural design and training strategies, making direct comparison challenging due to non-modular implementations. We address this gap by collecting and unifying the available code into a common framework. This unified view allows us to systematically compare the approaches and highlight their strengths and limitations, providing valuable insights into their future potential. We also provide concise descriptions of each method, complemented by practical guidelines.

preprint2026arXiv

Multi-Headed Transformer Architectures as Time-dependent Wasserstein Gradient Flows

In recent years, transformer architectures have revolutionized the field of language processing, opening the door to previously unforeseen possibilities. However, from a theoretical point of view, the mathematical models proposed in the literature often lack direct contact with the actual architectures and depend on strong simplifying assumptions. In this paper, we reduce this gap by modelling the data flow in multi-headed transformer architectures as time-dependent gradient flows for a suitable interaction energy capturing the design of the attention mechanism. The explicit dependence on time allows us to consider different weights for each head and for each layer, without imposing constraints on the initialization method. Moreover, we prove that, under a suitable integrability assumption on the evolution of the weights, each element of the $ω$-limit set of the gradient flows is a stationary point of the interaction energy at a limiting weight distribution. Finally, we analyse the stability of the gradient flows considering perturbations of both the initial data and the weights. Specifically, on the one hand, we study the robustness of the proposed models with respect to noisy inputs, establishing a continuous dependence of the gradient flows on the initial data and uniqueness of the flows. On the other hand, we prove the $Γ$-convergence of the perturbed interaction energy to the unperturbed one, leading to the convergence of the corresponding gradient flows. We complement these theoretical results with numerical experiments that confirm the predicted energy-dissipation identity and clarify the asymptotic behavior of the dynamics in both the autonomous-like (Ornstein--Uhlenbeck) and the genuinely non-autonomous (oscillating-weights) regimes.

preprint2026arXiv

Muon is Not That Special: Random or Inverted Spectra Work Just as Well

The recent empirical success of the Muon optimizer has renewed interest in non-Euclidean optimization, typically justified by similarities with second-order methods, and linear minimization oracle (LMO) theory. In this paper, we challenge this geometric narrative through three contributions, demonstrating that precise geometric structure is not the key factor affecting optimization performance. First, we introduce Freon, a family of optimizers based on Schatten (quasi-)norms, powered by a novel, provably optimal QDWH-based iterative approximation. Freon naturally interpolates between SGD and Muon, while smoothly extrapolating into the quasi-norm regime. Empirically, the best-performing Schatten parameters for GPT-2 lie strictly within the quasi-norm regime, and thus cannot be represented by any unitarily invariant LMO. Second, noting that Freon performs well across a wide range of exponents, we introduce Kaon, an absurd optimizer that replaces singular values with random noise. Despite lacking any coherent geometric structure, Kaon matches Muon's performance and retains classical convergence guarantees, proving that strict adherence to a precise geometry is practically irrelevant. Third, having shown that geometry is not the primary driver of performance, we demonstrate it is instead controlled by two local quantities: alignment and descent potential. Ultimately, each optimizer must tune its step size around these two quantities. While their dynamics are difficult to predict a-priori, evaluating them within a stochastic random feature model yields a precise insight: Muon succeeds not by tracking an ideal global geometry, but by guaranteeing step-size optimality.

preprint2026arXiv

Neural Fields for Highly Accelerated 2D Cine Phase Contrast MRI

2D cine phase contrast (CPC) MRI provides quantitative information on blood velocity and flow within the human vasculature. However, data acquisition is time-consuming, motivating the reconstruction of the velocity field from undersampled measurements to reduce scan times. In this work, neural fields are proposed as a continuous spatiotemporal parametrization of complex-valued images, jointly modeling magnitude and phase across multiple echoes to enable velocity estimation, and leveraging their inductive bias for the reconstruction of the velocity data. Additionally, to compensate for the oversmoothing tendency observed in neural-field reconstructions under severe undersampling, a simple voxel-based postprocessing step is introduced. The method is validated numerically in Cartesian and radial k-space with both high and low temporal resolution data. This approach achieves accurate reconstructions at high acceleration factors, with low errors even at 32$\times$ and 64$\times$ undersampling for the high temporal resolution data, and 16$\times$ for the low temporal resolution data, and consistently outperforms classical locally low-rank regularized voxel-based methods in both flow estimates and anatomical depiction.

preprint2022arXiv

A Three-Stage Self-Training Framework for Semi-Supervised Semantic Segmentation

Semantic segmentation has been widely investigated in the community, in which the state of the art techniques are based on supervised models. Those models have reported unprecedented performance at the cost of requiring a large set of high quality segmentation masks. To obtain such annotations is highly expensive and time consuming, in particular, in semantic segmentation where pixel-level annotations are required. In this work, we address this problem by proposing a holistic solution framed as a three-stage self-training framework for semi-supervised semantic segmentation. The key idea of our technique is the extraction of the pseudo-masks statistical information to decrease uncertainty in the predicted probability whilst enforcing segmentation consistency in a multi-task fashion. We achieve this through a three-stage solution. Firstly, we train a segmentation network to produce rough pseudo-masks which predicted probability is highly uncertain. Secondly, we then decrease the uncertainty of the pseudo-masks using a multi-task model that enforces consistency whilst exploiting the rich statistical information of the data. We compare our approach with existing methods for semi-supervised semantic segmentation and demonstrate its state-of-the-art performance with extensive experiments.

preprint2022arXiv

Collaborative learning of images and geometrics for predicting isocitrate dehydrogenase status of glioma

The isocitrate dehydrogenase (IDH) gene mutation status is an important biomarker for glioma patients. The gold standard of IDH mutation detection requires tumour tissue obtained via invasive approaches and is usually expensive. Recent advancement in radiogenomics provides a non-invasive approach for predicting IDH mutation based on MRI. Meanwhile, tumor geometrics encompass crucial information for tumour phenotyping. Here we propose a collaborative learning framework that learns both tumor images and tumor geometrics using convolutional neural networks (CNN) and graph neural networks (GNN), respectively. Our results show that the proposed model outperforms the baseline model of 3D-DenseNet121. Further, the collaborative learning model achieves better performance than either the CNN or the GNN alone. The model interpretation shows that the CNN and GNN could identify common and unique regions of interest for IDH mutation prediction. In conclusion, collaborating image and geometric learners provides a novel approach for predicting genotype and characterising glioma.

preprint2022arXiv

Contrastive Registration for Unsupervised Medical Image Segmentation

Medical image segmentation is a relevant task as it serves as the first step for several diagnosis processes, thus it is indispensable in clinical usage. Whilst major success has been reported using supervised techniques, they assume a large and well-representative labelled set. This is a strong assumption in the medical domain where annotations are expensive, time-consuming, and inherent to human bias. To address this problem, unsupervised techniques have been proposed in the literature yet it is still an open problem due to the difficulty of learning any transformation pattern. In this work, we present a novel optimisation model framed into a new CNN-based contrastive registration architecture for unsupervised medical image segmentation. The core of our approach is to exploit image-level registration and feature-level from a contrastive learning mechanism, to perform registration-based segmentation. Firstly, we propose an architecture to capture the image-to-image transformation pattern via registration for unsupervised medical image segmentation. Secondly, we embed a contrastive learning mechanism into the registration architecture to enhance the discriminating capacity of the network in the feature-level. We show that our proposed technique mitigates the major drawbacks of existing unsupervised techniques. We demonstrate, through numerical and visual experiments, that our technique substantially outperforms the current state-of-the-art unsupervised segmentation methods on two major medical image datasets.

preprint2022arXiv

Gaussian random fields on non-separable Banach spaces

We study Gaussian random fields on certain Banach spaces and investigate conditions for their existence. Our results apply inter alia to spaces of Radon measures and Hölder functions. In the former case, we are able to define Gaussian white noise on the space of measures directly, avoiding, e.g., an embedding into a negative-order Sobolev space. In the latter case, we demonstrate how Hölder regularity of the samples is controlled by that of the covariance kernel and, thus, show a connection to the Theorem of Kolmogorov-Chentsov.

preprint2022arXiv

Learned reconstruction methods with convergence guarantees

In recent years, deep learning has achieved remarkable empirical success for image reconstruction. This has catalyzed an ongoing quest for precise characterization of correctness and reliability of data-driven methods in critical use-cases, for instance in medical imaging. Notwithstanding the excellent performance and efficacy of deep learning-based methods, concerns have been raised regarding their stability, or lack thereof, with serious practical implications. Significant advances have been made in recent years to unravel the inner workings of data-driven image recovery methods, challenging their widely perceived black-box nature. In this article, we will specify relevant notions of convergence for data-driven image reconstruction, which will form the basis of a survey of learned methods with mathematically rigorous reconstruction guarantees. An example that is highlighted is the role of ICNN, offering the possibility to combine the power of deep learning with classical convex regularization theory for devising methods that are provably convergent. This survey article is aimed at both methodological researchers seeking to advance the frontiers of our understanding of data-driven image reconstruction methods as well as practitioners, by providing an accessible description of useful convergence concepts and by placing some of the existing empirical practices on a solid mathematical foundation.

preprint2022arXiv

Multi-Modal Hypergraph Diffusion Network with Dual Prior for Alzheimer Classification

The automatic early diagnosis of prodromal stages of Alzheimer's disease is of great relevance for patient treatment to improve quality of life. We address this problem as a multi-modal classification task. Multi-modal data provides richer and complementary information. However, existing techniques only consider either lower order relations between the data and single/multi-modal imaging data. In this work, we introduce a novel semi-supervised hypergraph learning framework for Alzheimer's disease diagnosis. Our framework allows for higher-order relations among multi-modal imaging and non-imaging data whilst requiring a tiny labelled set. Firstly, we introduce a dual embedding strategy for constructing a robust hypergraph that preserves the data semantics. We achieve this by enforcing perturbation invariance at the image and graph levels using a contrastive based mechanism. Secondly, we present a dynamically adjusted hypergraph diffusion model, via a semi-explicit flow, to improve the predictive uncertainty. We demonstrate, through our experiments, that our framework is able to outperform current techniques for Alzheimer's disease diagnosis.

preprint2022arXiv

Multi-modal learning for predicting the genotype of glioma

The isocitrate dehydrogenase (IDH) gene mutation is an essential biomarker for the diagnosis and prognosis of glioma. It is promising to better predict glioma genotype by integrating focal tumor image and geometric features with brain network features derived from MRI. Convolutions neural networks show reasonable performance in predicting IDH mutation, which, however, cannot learn from non-Euclidean data, e.g., geometric and network data. In this study, we propose a multi-modal learning framework using three separate encoders to extract features of focal tumor image, tumor geometrics and global brain networks. To mitigate the limited availability of diffusion MRI, we develop a self-supervised approach to generate brain networks from anatomical multi-sequence MRI. Moreover, to extract tumor-related features from the brain network, we design a hierarchical attention module for the brain network encoder. Further, we design a bi-level multi-modal contrastive loss to align the multi-modal features and tackle the domain gap at the focal tumor and global brain. Finally, we propose a weighted population graph to integrate the multi-modal features for genotype prediction. Experimental results on the testing set show that the proposed model outperforms the baseline deep learning models. The ablation experiments validate the performance of different components of the framework. The visualized interpretation corresponds to clinical knowledge with further validation. In conclusion, the proposed learning framework provides a novel approach for predicting the genotype of glioma.

preprint2022arXiv

Non-Uniform Diffusion Models

Diffusion models have emerged as one of the most promising frameworks for deep generative modeling. In this work, we explore the potential of non-uniform diffusion models. We show that non-uniform diffusion leads to multi-scale diffusion models which have similar structure to this of multi-scale normalizing flows. We experimentally find that in the same or less training time, the multi-scale diffusion model achieves better FID score than the standard uniform diffusion model. More importantly, it generates samples $4.4$ times faster in $128\times 128$ resolution. The speed-up is expected to be higher in higher resolutions where more scales are used. Moreover, we show that non-uniform diffusion leads to a novel estimator for the conditional score function which achieves on par performance with the state-of-the-art conditional denoising estimator. Our theoretical and experimental findings are accompanied by an open source library MSDiff which can facilitate further research of non-uniform diffusion models.

preprint2022arXiv

Operator Sketching for Deep Unrolling Networks

In this work we propose a new paradigm for designing efficient deep unrolling networks using operator sketching. The deep unrolling networks are currently the state-of-the-art solutions for imaging inverse problems. However, for high-dimensional imaging tasks, especially the 3D cone-beam X-ray CT and 4D MRI imaging, the deep unrolling schemes typically become inefficient both in terms of memory and computation, due to the need of computing multiple times the high-dimensional forward and adjoint operators. Recently researchers have found that such limitations can be partially addressed by stochastic unrolling with subsets of operators, inspired by the success of stochastic first-order optimization. In this work, we propose a further acceleration upon stochastic unrolling, using sketching techniques to approximate products in the high-dimensional image space. The operator sketching can be jointly applied with stochastic unrolling for the best acceleration and compression performance. Our numerical experiments on X-ray CT image reconstruction demonstrate the remarkable effectiveness of our sketched unrolling schemes.

preprint2022arXiv

PC-SwinMorph: Patch Representation for Unsupervised Medical Image Registration and Segmentation

Medical image registration and segmentation are critical tasks for several clinical procedures. Manual realisation of those tasks is time-consuming and the quality is highly dependent on the level of expertise of the physician. To mitigate that laborious task, automatic tools have been developed where the majority of solutions are supervised techniques. However, in medical domain, the strong assumption of having a well-representative ground truth is far from being realistic. To overcome this challenge, unsupervised techniques have been investigated. However, they are still limited in performance and they fail to produce plausible results. In this work, we propose a novel unified unsupervised framework for image registration and segmentation that we called PC-SwinMorph. The core of our framework is two patch-based strategies, where we demonstrate that patch representation is key for performance gain. We first introduce a patch-based contrastive strategy that enforces locality conditions and richer feature representation. Secondly, we utilise a 3D window/shifted-window multi-head self-attention module as a patch stitching strategy to eliminate artifacts from the patch splitting. We demonstrate, through a set of numerical and visual results, that our technique outperforms current state-of-the-art unsupervised techniques.

preprint2022arXiv

Predicting conversion of mild cognitive impairment to Alzheimer's disease

Alzheimer's disease (AD) is the most common age-related dementia. Mild cognitive impairment (MCI) is the early stage of cognitive decline before AD. It is crucial to predict the MCI-to-AD conversion for precise management, which remains challenging due to the diversity of patients. Previous evidence shows that the brain network generated from diffusion MRI promises to classify dementia using deep learning. However, the limited availability of diffusion MRI challenges the model training. In this study, we develop a self-supervised contrastive learning approach to generate structural brain networks from routine anatomical MRI under the guidance of diffusion MRI. The generated brain networks are applied to train a learning framework for predicting the MCI-to-AD conversion. Instead of directly modelling the AD brain networks, we train a graph encoder and a variational autoencoder to model the healthy ageing trajectories from brain networks of healthy controls. To predict the MCI-to-AD conversion, we further design a recurrent neural networks based approach to model the longitudinal deviation of patients' brain networks from the healthy ageing trajectory. Numerical results show that the proposed methods outperform the benchmarks in the prediction task. We also visualize the model interpretation to explain the prediction and identify abnormal changes of white matter tracts.

preprint2022arXiv

Simultaneous Semantic and Instance Segmentation for Colon Nuclei Identification and Counting

We address the problem of automated nuclear segmentation, classification, and quantification from Haematoxylin and Eosin stained histology images, which is of great relevance for several downstream computational pathology applications. In this work, we present a solution framed as a simultaneous semantic and instance segmentation framework. Our solution is part of the Colon Nuclei Identification and Counting (CoNIC) Challenge. We first train a semantic and instance segmentation model separately. Our framework uses as backbone HoverNet and Cascade Mask-RCNN models. We then ensemble the results with a custom Non-Maximum Suppression embedding (NMS). In our framework, the semantic model computes a class prediction for the cells whilst the instance model provides a refined segmentation. We demonstrate, through our experimental results, that our model outperforms the provided baselines by a large margin.

preprint2022arXiv

Stochastic Primal-Dual Deep Unrolling

We propose a new type of efficient deep-unrolling networks for solving imaging inverse problems. Conventional deep-unrolling methods require full forward operator and its adjoint across each layer, and hence can be significantly more expensive computationally as compared with other end-to-end methods that are based on post-processing of model-based reconstructions, especially for 3D image reconstruction tasks. We develop a stochastic (ordered-subsets) variant of the classical learned primal-dual (LPD), which is a state-of-the-art unrolling network for tomographic image reconstruction. The proposed learned stochastic primal-dual (LSPD) network only uses subsets of the forward and adjoint operators and offers considerable computational efficiency. We provide theoretical analysis of a special case of our LSPD framework, suggesting that it has the potential to achieve image reconstruction quality competitive with the full-batch LPD while requiring only a fraction of the computation. The numerical results for two different X-ray computed tomography (CT) imaging tasks (namely, low-dose and sparse-view CT) corroborate this theoretical finding, demonstrating the promise of LSPD networks for large-scale imaging problems.

preprint2022arXiv

Unsupervised Clustering of Roman Potsherds via Variational Autoencoders

In this paper we propose an artificial intelligence imaging solution to support archaeologists in the classification task of Roman commonware potsherds. Usually, each potsherd is represented by its sectional profile as a two dimensional black-white image and printed in archaeological books related to specific archaeological excavations. The partiality and handcrafted variance of the fragments make their matching a challenging problem: we propose to pair similar profiles via the unsupervised hierarchical clustering of non-linear features learned in the latent space of a deep convolutional Variational Autoencoder (VAE) network. Our contribution also include the creation of a ROman COmmonware POTtery (ROCOPOT) database, with more than 4000 potsherds profiles extracted from 25 Roman pottery corpora, and a MATLAB GUI software for the easy inspection of shape similarities. Results are commented both from a mathematical and archaeological perspective so as to unlock new research directions in both communities.

preprint2021arXiv

Beyond Fine-tuning: Classifying High Resolution Mammograms using Function-Preserving Transformations

The task of classifying mammograms is very challenging because the lesion is usually small in the high resolution image. The current state-of-the-art approaches for medical image classification rely on using the de-facto method for ConvNets - fine-tuning. However, there are fundamental differences between natural images and medical images, which based on existing evidence from the literature, limits the overall performance gain when designed with algorithmic approaches. In this paper, we propose to go beyond fine-tuning by introducing a novel framework called MorphHR, in which we highlight a new transfer learning scheme. The idea behind the proposed framework is to integrate function-preserving transformations, for any continuous non-linear activation neurons, to internally regularise the network for improving mammograms classification. The proposed solution offers two major advantages over the existing techniques. Firstly and unlike fine-tuning, the proposed approach allows for modifying not only the last few layers but also several of the first ones on a deep ConvNet. By doing this, we can design the network front to be suitable for learning domain specific features. Secondly, the proposed scheme is scalable to hardware. Therefore, one can fit high resolution images on standard GPU memory. We show that by using high resolution images, one prevents losing relevant information. We demonstrate, through numerical and visual experiments, that the proposed approach yields to a significant improvement in the classification performance over state-of-the-art techniques, and is indeed on a par with radiology experts. Moreover and for generalisation purposes, we show the effectiveness of the proposed learning scheme on another large dataset, the ChestX-ray14, surpassing current state-of-the-art techniques.

preprint2021arXiv

Depthwise Separable Convolutions Allow for Fast and Memory-Efficient Spectral Normalization

An increasing number of models require the control of the spectral norm of convolutional layers of a neural network. While there is an abundance of methods for estimating and enforcing upper bounds on those during training, they are typically costly in either memory or time. In this work, we introduce a very simple method for spectral normalization of depthwise separable convolutions, which introduces negligible computational and memory overhead. We demonstrate the effectiveness of our method on image classification tasks using standard architectures like MobileNetV2.

preprint2021arXiv

Improving "Fast Iterative Shrinkage-Thresholding Algorithm": Faster, Smarter and Greedier

The "fast iterative shrinkage-thresholding algorithm", a.k.a. FISTA, is one of the most well-known first-order optimisation scheme in the literature, as it achieves the worst-case $O(1/k^2)$ optimal convergence rate in terms of objective function value. However, despite such an optimal theoretical convergence rate, in practice the (local) oscillatory behaviour of FISTA often damps its efficiency. Over the past years, various efforts are made in the literature to improve the practical performance of FISTA, such as monotone FISTA, restarting FISTA and backtracking strategies. In this paper, we propose a simple yet effective modification to the original FISTA scheme which has two advantages: it allows us to 1) prove the convergence of generated sequence; 2) design a so-called "lazy-start" strategy which can up to an order faster than the original scheme. Moreover, by exploring the properties of FISTA scheme, we propose novel adaptive and greedy strategies which probes the limit of the algorithm. The advantages of the proposed schemes are tested through problems arising from inverse problem, machine learning and signal/image processing.

preprint2021arXiv

Learned convex regularizers for inverse problems

We consider the variational reconstruction framework for inverse problems and propose to learn a data-adaptive input-convex neural network (ICNN) as the regularization functional. The ICNN-based convex regularizer is trained adversarially to discern ground-truth images from unregularized reconstructions. Convexity of the regularizer is desirable since (i) one can establish analytical convergence guarantees for the corresponding variational reconstruction problem and (ii) devise efficient and provable algorithms for reconstruction. In particular, we show that the optimal solution to the variational problem converges to the ground-truth if the penalty parameter decays sub-linearly with respect to the norm of the noise. Further, we prove the existence of a sub-gradient-based algorithm that leads to a monotonically decreasing error in the parameter space with iterations. To demonstrate the performance of our approach for solving inverse problems, we consider the tasks of deblurring natural images and reconstructing images in computed tomography (CT), and show that the proposed convex regularizer is at least competitive with and sometimes superior to state-of-the-art data-driven techniques for inverse problems.

preprint2021arXiv

SPRING: A fast stochastic proximal alternating method for non-smooth non-convex optimization

We introduce SPRING, a novel stochastic proximal alternating linearized minimization algorithm for solving a class of non-smooth and non-convex optimization problems. Large-scale imaging problems are becoming increasingly prevalent due to advances in data acquisition and computational capabilities. Motivated by the success of stochastic optimization methods, we propose a stochastic variant of proximal alternating linearized minimization (PALM) algorithm \cite{bolte2014proximal}. We provide global convergence guarantees, demonstrating that our proposed method with variance-reduced stochastic gradient estimators, such as SAGA \cite{SAGA} and SARAH \cite{sarah}, achieves state-of-the-art oracle complexities. We also demonstrate the efficacy of our algorithm via several numerical examples including sparse non-negative matrix factorization, sparse principal component analysis, and blind image deconvolution.

preprint2020arXiv

3D deformable registration of longitudinal abdominopelvic CT images using unsupervised deep learning

This study investigates the use of the unsupervised deep learning framework VoxelMorph for deformable registration of longitudinal abdominopelvic CT images acquired in patients with bone metastases from breast cancer. The CT images were refined prior to registration by automatically removing the CT table and all other extra-corporeal components. To improve the learning capabilities of VoxelMorph when only a limited amount of training data is available, a novel incremental training strategy is proposed based on simulated deformations of consecutive CT images. In a 4-fold cross-validation scheme, the incremental training strategy achieved significantly better registration performance compared to training on a single volume. Although our deformable image registration method did not outperform iterative registration using NiftyReg (considered as a benchmark) in terms of registration quality, the registrations were approximately 300 times faster. This study showed the feasibility of deep learning based deformable registration of longitudinal abdominopelvic CT images via a novel incremental training strategy based on simulated deformations.

preprint2020arXiv

Art Speaks Maths, Maths Speaks Art

Our interdisciplinary team Mathematics for Applications in Cultural Heritage (MACH) aims to use mathematical research for the benefit of the arts and humanities. Our ultimate goal is to create user-friendly software toolkits for artists, art conservators and archaeologists. In order for their underlying mathematical engines and functionality to be optimised for the needs of the end users, we pursue an iterative approach based on a continuous communication between the mathematicians and the cultural-heritage members of our team. Our paper illustrates how maths can speak art, but only if first art speaks maths.

preprint2020arXiv

Bregman Itoh--Abe methods for sparse optimisation

In this paper we propose optimisation methods for variational regularisation problems based on discretising the inverse scale space flow with discrete gradient methods. Inverse scale space flow generalises gradient flows by incorporating a generalised Bregman distance as the underlying metric. Its discrete-time counterparts, Bregman iterations and linearised Bregman iterations, are popular regularisation schemes for inverse problems that incorporate a priori information without loss of contrast. Discrete gradient methods are tools from geometric numerical integration for preserving energy dissipation of dissipative differential systems. The resultant Bregman discrete gradient methods are unconditionally dissipative, and achieve rapid convergence rates by exploiting structures of the problem such as sparsity. Building on previous work on discrete gradients for non-smooth, non-convex optimisation, we prove convergence guarantees for these methods in a Clarke subdifferential framework. Numerical results for convex and non-convex examples are presented.

preprint2020arXiv

GraphX$^{NET}-$ Chest X-Ray Classification Under Extreme Minimal Supervision

The task of classifying X-ray data is a problem of both theoretical and clinical interest. Whilst supervised deep learning methods rely upon huge amounts of labelled data, the critical problem of achieving a good classification accuracy when an extremely small amount of labelled data is available has yet to be tackled. In this work, we introduce a novel semi-supervised framework for X-ray classification which is based on a graph-based optimisation model. To the best of our knowledge, this is the first method that exploits graph-based semi-supervised learning for X-ray data classification. Furthermore, we introduce a new multi-class classification functional with carefully selected class priors which allows for a smooth solution that strengthens the synergy between the limited number of labels and the huge amount of unlabelled data. We demonstrate, through a set of numerical and visual experiments, that our method produces highly competitive results on the ChestX-ray14 data set whilst drastically reducing the need for annotated data.

preprint2020arXiv

Ground Truth Free Denoising by Optimal Transport

We present a learned unsupervised denoising method for arbitrary types of data, which we explore on images and one-dimensional signals. The training is solely based on samples of noisy data and examples of noise, which -- critically -- do not need to come in pairs. We only need the assumption that the noise is independent and additive (although we describe how this can be extended). The method rests on a Wasserstein Generative Adversarial Network setting, which utilizes two critics and one generator.

preprint2020arXiv

Higher-Order Total Directional Variation: Analysis

We analyse a new notion of total anisotropic higher-order variation which, differently from the Total Generalized Variation by Bredies et al., quantifies for possibly non-symmetric tensor fields their variations at arbitrary order weighted by possibly inhomogeneous, smooth elliptic anisotropies. We prove some properties of this total variation and of the associated spaces of tensors with finite variations. We show the existence of solutions to a related regularity-fidelity optimisation problem. We also prove a decomposition formula which appears to be helpful for the design of numerical schemes, as shown in a companion paper, where several applications to image processing are studied.

preprint2020arXiv

Higher-Order Total Directional Variation: Imaging Applications

We introduce a class of higher-order anisotropic total variation regularisers, which are defined for possibly inhomogeneous, smooth elliptic anisotropies, that extends the Total Generalized Variation (TGV) regulariser and its variants. We propose a primal-dual hybrid gradient approach to approximate numerically the associated gradient flow. This choice of regularisers allows to preserve and enhance intrinsic anisotropic features in images. This is illustrated on various examples from different imaging applications: image denoising, wavelet-based image zooming, and reconstruction of surfaces from scattered height measurements.

preprint2020arXiv

iUNets: Fully invertible U-Nets with Learnable Up- and Downsampling

U-Nets have been established as a standard architecture for image-to-image learning problems such as segmentation and inverse problems in imaging. For large-scale data, as it for example appears in 3D medical imaging, the U-Net however has prohibitive memory requirements. Here, we present a new fully-invertible U-Net-based architecture called the iUNet, which employs novel learnable and invertible up- and downsampling operations, thereby making the use of memory-efficient backpropagation possible. This allows us to train deeper and larger networks in practice, under the same GPU memory restrictions. Due to its invertibility, the iUNet can furthermore be used for constructing normalizing flows.

preprint2020arXiv

Learning the Sampling Pattern for MRI

The discovery of the theory of compressed sensing brought the realisation that many inverse problems can be solved even when measurements are "incomplete". This is particularly interesting in magnetic resonance imaging (MRI), where long acquisition times can limit its use. In this work, we consider the problem of learning a sparse sampling pattern that can be used to optimally balance acquisition time versus quality of the reconstructed image. We use a supervised learning approach, making the assumption that our training data is representative enough of new data acquisitions. We demonstrate that this is indeed the case, even if the training data consists of just 7 training pairs of measurements and ground-truth images; with a training set of brain images of size 192 by 192, for instance, one of the learned patterns samples only 35% of k-space, however results in reconstructions with mean SSIM 0.914 on a test set of similar images. The proposed framework is general enough to learn arbitrary sampling patterns, including common patterns such as Cartesian, spiral and radial sampling.

preprint2020arXiv

Learning to segment microscopy images with lazy labels

The need for labour intensive pixel-wise annotation is a major limitation of many fully supervised learning methods for segmenting bioimages that can contain numerous object instances with thin separations. In this paper, we introduce a deep convolutional neural network for microscopy image segmentation. Annotation issues are circumvented by letting the network being trainable on coarse labels combined with only a very small number of images with pixel-wise annotations. We call this new labelling strategy `lazy' labels. Image segmentation is stratified into three connected tasks: rough inner region detection, object separation and pixel-wise segmentation. These tasks are learned in an end-to-end multi-task learning framework. The method is demonstrated on two microscopy datasets, where we show that the model gives accurate segmentation results even if exact boundary labels are missing for a majority of annotated data. It brings more flexibility and efficiency for training deep neural networks that are data hungry and is applicable to biomedical images with poor contrast at the object boundaries or with diverse textures and repeated patterns.

preprint2020arXiv

On Biased Stochastic Gradient Estimation

We present a uniform analysis of biased stochastic gradient methods for minimizing convex, strongly convex, and non-convex composite objectives, and identify settings where bias is useful in stochastic gradient estimation. The framework we present allows us to extend proximal support to biased algorithms, including SAG and SARAH, for the first time in the convex setting. We also use our framework to develop a new algorithm, Stochastic Average Recursive GradiEnt (SARGE), that achieves the oracle complexity lower-bound for non-convex, finite-sum objectives and requires strictly fewer calls to a stochastic gradient oracle per iteration than SVRG and SARAH. We support our theoretical results with numerical experiments that demonstrate the benefits of certain biased gradient estimators.

preprint2020arXiv

Scanning electron diffraction tomography of strain

Strain engineering is used to obtain desirable materials properties in a range of modern technologies. Direct nanoscale measurement of the three-dimensional strain tensor field within these materials has however been limited by a lack of suitable experimental techniques and data analysis tools. Scanning electron diffraction has emerged as a powerful tool for obtaining two-dimensional maps of strain components perpendicular to the incident electron beam direction. Extension of this method to recover the full three-dimensional strain tensor field has been restricted though by the absence of a formal framework for tensor tomography using such data. Here, we show that it is possible to reconstruct the full non-symmetric strain tensor field as the solution to an ill-posed tensor tomography inverse problem. We then demonstrate the properties of this tomography problem both analytically and computationally, highlighting why incorporating precession to perform scanning precession electron diffraction may be important. We establish a general framework for non-symmetric tensor tomography and demonstrate computationally its applicability for achieving strain tomography with scanning precession electron diffraction data.

preprint2020arXiv

SLIC-UAV: A Method for monitoring recovery in tropical restoration projects through identification of signature species using UAVs

Logged forests cover four million square kilometres of the tropics and restoring these forests is essential if we are to avoid the worst impacts of climate change, yet monitoring recovery is challenging. Tracking the abundance of visually identifiable, early-successional species enables successional status and thereby restoration progress to be evaluated. Here we present a new pipeline, SLIC-UAV, for processing Unmanned Aerial Vehicle (UAV) imagery to map early-successional species in tropical forests. The pipeline is novel because it comprises: (a) a time-efficient approach for labelling crowns from UAV imagery; (b) machine learning of species based on spectral and textural features within individual tree crowns, and (c) automatic segmentation of orthomosaiced UAV imagery into 'superpixels', using Simple Linear Iterative Clustering (SLIC). Creating superpixels reduces the dataset's dimensionality and focuses prediction onto clusters of pixels, greatly improving accuracy. To demonstrate SLIC-UAV, support vector machines and random forests were used to predict the species of hand-labelled crowns in a restoration concession in Indonesia. Random forests were most accurate at discriminating species for whole crowns, with accuracy ranging from 79.3% when mapping five common species, to 90.5% when mapping the three most visually-distinctive species. In contrast, support vector machines proved better for labelling automatically segmented superpixels, with accuracy ranging from 74.3% to 91.7% for the same species. Models were extended to map species across 100 hectares of forest. The study demonstrates the power of SLIC-UAV for mapping characteristic early-successional tree species as an indicator of successional stage within tropical forest restoration areas. Continued effort is needed to develop easy-to-implement and low-cost technology to improve the affordability of project management.

preprint2020arXiv

Structure preserving deep learning

Over the past few years, deep learning has risen to the foreground as a topic of massive interest, mainly as a result of successes obtained in solving large-scale image processing tasks. There are multiple challenging mathematical problems involved in applying deep learning: most deep learning methods require the solution of hard optimisation problems, and a good understanding of the tradeoff between computational effort, amount of data and model complexity is required to successfully design a deep learning approach for a given problem. A large amount of progress made in deep learning has been based on heuristic explorations, but there is a growing effort to mathematically understand the structure in existing deep learning methods and to systematically design new deep learning methods to preserve certain types of structure in deep learning. In this article, we review a number of these directions: some deep neural networks can be understood as discretisations of dynamical systems, neural networks can be designed to have desirable properties such as invertibility or group equivariance, and new algorithmic frameworks based on conformal Hamiltonian systems and Riemannian manifolds to solve the optimisation problems have been proposed. We conclude our review of each of these topics by discussing some open problems that we consider to be interesting directions for future research.

preprint2020arXiv

Unsupervised clustering of Roman pottery profiles from their SSAE representation

In this paper we introduce the ROman COmmonware POTtery (ROCOPOT) database, which comprises of more than 2000 black and white imaging profiles of pottery shapes extracted from 11 Roman catalogues and related to different excavation sites. The partiality and the handcrafted variance of the shape fragments within this new database make their unsupervised clustering a very challenging problem: profile similarities are thus explored via the hierarchical clustering of non-linear features learned in the latent representation space of a stacked sparse autoencoder (SSAE) network, unveiling new profile matches. Results are commented both from a mathematical and archaeological perspective so as to unlock new research directions in the respective communities.

preprint2020arXiv

Variational Osmosis for Non-linear Image Fusion

We propose a new variational model for non-linear image fusion. Our approach is based on the use of an osmosis energy term related to the one studied in Vogel et al. (2013) and Weickert et al. (2013) The minimization of the proposed non-convex energy realizes visually plausible image data fusion, invariant to multiplicative brightness changes. On the practical side, it requires minimal supervision and parameter tuning and can encode prior information on the structure of the images to be fused. For the numerical solution of the proposed model, we develop a primal-dual algorithm and we apply the resulting minimization scheme to solve multi-modal face fusion, color transfer and cultural heritage conservation problems. Visual and quantitative comparisons to state-of-the-art approaches prove the out-performance and the flexibility of our method.

preprint2019arXiv

Faster PET Reconstruction with Non-Smooth Priors by Randomization and Preconditioning

Uncompressed clinical data from modern positron emission tomography (PET) scanners are very large, exceeding 350 million data points (projection bins). The last decades have seen tremendous advancements in mathematical imaging tools many of which lead to non-smooth (i.e. non-differentiable) optimization problems which are much harder to solve than smooth optimization problems. Most of these tools have not been translated to clinical PET data, as the state-of-the-art algorithms for non-smooth problems do not scale well to large data. In this work, inspired by big data machine learning applications, we use advanced randomized optimization algorithms to solve the PET reconstruction problem for a very large class of non-smooth priors which includes for example total variation, total generalized variation, directional total variation and various different physical constraints. The proposed algorithm randomly uses subsets of the data and only updates the variables associated with these. While this idea often leads to divergent algorithms, we show that the proposed algorithm does indeed converge for any proper subset selection. Numerically, we show on real PET data (FDG and florbetapir) from a Siemens Biograph mMR that about ten projections and backprojections are sufficient to solve the MAP optimisation problem related to many popular non-smooth priors; thus showing that the proposed algorithm is fast enough to bring these models into routine clinical practice.

preprint2019arXiv

Superpixel Contracted Graph-Based Learning for Hyperspectral Image Classification

A central problem in hyperspectral image classification is obtaining high classification accuracy when using a limited amount of labelled data. In this paper we present a novel graph-based framework, which aims to tackle this problem in the presence of large scale data input. Our approach utilises a novel superpixel method, specifically designed for hyperspectral data, to define meaningful local regions in an image, which with high probability share the same classification label. We then extract spectral and spatial features from these regions and use these to produce a contracted weighted graph-representation, where each node represents a region rather than a pixel. Our graph is then fed into a graph-based semi-supervised classifier which gives the final classification. We show that using superpixels in a graph representation is an effective tool for speeding up graphical classifiers applied to hyperspectral images. We demonstrate through exhaustive quantitative and qualitative results that our proposed method produces accurate classifications when an incredibly small amount of labelled data is used. We show that our approach mitigates the major drawbacks of existing approaches, resulting in our approach outperforming several comparative state-of-the-art techniques.

preprint2018arXiv

Blind Image Fusion for Hyperspectral Imaging with the Directional Total Variation

Hyperspectral imaging is a cutting-edge type of remote sensing used for mapping vegetation properties, rock minerals and other materials. A major drawback of hyperspectral imaging devices is their intrinsic low spatial resolution. In this paper, we propose a method for increasing the spatial resolution of a hyperspectral image by fusing it with an image of higher spatial resolution that was obtained with a different imaging modality. This is accomplished by solving a variational problem in which the regularization functional is the directional total variation. To accommodate for possible mis-registrations between the two images, we consider a non-convex blind super-resolution problem where both a fused image and the corresponding convolution kernel are estimated. Using this approach, our model can realign the given images if needed. Our experimental results indicate that the non-convexity is negligible in practice and that reliable solutions can be computed using a variety of different optimization algorithms. Numerical results on real remote sensing data from plant sciences and urban monitoring show the potential of the proposed method and suggests that it is robust with respect to the regularization parameters, mis-registration and the shape of the kernel.

preprint2015arXiv

Preconditioned ADMM with nonlinear operator constraint

We are presenting a modification of the well-known Alternating Direction Method of Multipliers (ADMM) algorithm with additional preconditioning that aims at solving convex optimisation problems with nonlinear operator constraints. Connections to the recently developed Nonlinear Primal-Dual Hybrid Gradient Method (NL-PDHGM) are presented, and the algorithm is demonstrated to handle the nonlinear inverse problem of parallel Magnetic Resonance Imaging (MRI).

preprint2015arXiv

The structure of optimal parameters for image restoration problems

We study the qualitative properties of optimal regularisation parameters in variational models for image restoration. The parameters are solutions of bilevel optimisation problems with the image restoration problem as constraint. A general type of regulariser is considered, which encompasses total variation (TV), total generalized variation (TGV) and infimal-convolution total variation (ICTV). We prove that under certain conditions on the given data optimal parameters derived by bilevel optimisation problems exist. A crucial point in the existence proof turns out to be the boundedness of the optimal parameters away from $0$ which we prove in this paper. The analysis is done on the original -- in image restoration typically non-smooth variational problem -- as well as on a smoothed approximation set in Hilbert space which is the one considered in numerical computations. For the smoothed bilevel problem we also prove that it $Γ$ converges to the original problem as the smoothing vanishes. All analysis is done in function spaces rather than on the discretised learning problem.