arXiv subjects

Carola-Bibiane Schönlieb

Publications and source records attributed to Carola-Bibiane Schönlieb.

At least 181 records · Page 10Linked to original sources

arXiv2022

Navigating the challenges in creating complex data systems: a development philosophy

In this perspective, we argue that despite the democratization of powerful tools for data science and machine learning over the last decade, developing the code for a trustworthy and effective data science system (DSS) is getting harder. Perverse incentives and a lack of widespread software engineering (SE) skills are among many root causes we identify that naturally give rise to the current systemic crisis in reproducibility of DSSs. We analyze why SE and building large complex systems is, in general, hard. Based on these insights, we identify how SE addresses those difficulties and how we can apply and generalize SE methods to construct DSSs that are fit for purpose. We advocate two key development philosophies, namely that one should incrementally grow -- not biphasically plan and build -- DSSs, and one should always employ two types of feedback loops during development: one which tests the code's correctness and another that evaluates the code's efficacy.

cs.SE↗

arXiv2022

Mutual Contrastive Low-rank Learning to Disentangle Whole Slide Image Representations for Glioma Grading

Whole slide images (WSI) provide valuable phenotypic information for histological assessment and malignancy grading of tumors. The WSI-based grading promises to provide rapid diagnostic support and facilitate digital health. Currently, the most commonly used WSIs are derived from formalin-fixed paraffin-embedded (FFPE) and Frozen section. The majority of automatic tumor grading models are developed based on FFPE sections, which could be affected by the artifacts introduced by tissue processing. The frozen section exists problems such as low quality that might influence training within single modality as well. To overcome this problem in a single modal training and achieve better multi-modal and discriminative representation disentanglement in brain tumor, we propose a mutual contrastive low-rank learning (MCL) scheme to integrate FFPE and frozen sections for glioma grading. We first design a mutual learning scheme to jointly optimize the model training based on FFPE and frozen sections. In this proposed scheme, we design a normalized modality contrastive loss (NMC-loss), which could promote to disentangle multi-modality complementary representation of FFPE and frozen sections from the same patient. To reduce intra-class variance, and increase inter-class margin at intra- and inter-patient levels, we conduct a low-rank (LR) loss. Our experiments show that the proposed scheme achieves better performance than the model trained based on each single modality or mixed modalities and even improves the feature extraction in classical attention-based multiple instances learning methods (MIL). The combination of NMC-loss and low-rank loss outperforms other typical contrastive loss functions.

eess.IV↗

arXiv2022

LaplaceNet: A Hybrid Graph-Energy Neural Network for Deep Semi-Supervised Classification

Semi-supervised learning has received a lot of recent attention as it alleviates the need for large amounts of labelled data which can often be expensive, requires expert knowledge and be time consuming to collect. Recent developments in deep semi-supervised classification have reached unprecedented performance and the gap between supervised and semi-supervised learning is ever-decreasing. This improvement in performance has been based on the inclusion of numerous technical tricks, strong augmentation techniques and costly optimisation schemes with multi-term loss functions. We propose a new framework, LaplaceNet, for deep semi-supervised classification that has a greatly reduced model complexity. We utilise a hybrid approach where pseudolabels are produced by minimising the Laplacian energy on a graph. These pseudo-labels are then used to iteratively train a neural-network backbone. Our model outperforms state-of-the art methods for deep semi-supervised classification, over several benchmark datasets. Furthermore, we consider the application of strong-augmentations to neural networks theoretically and justify the use of a multi-sampling approach for semi-supervised learning. We demonstrate, through rigorous experimentation, that a multi-sampling augmentation approach improves generalisation and reduces the sensitivity of the network to augmentation.

cs.LG↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

cs.LG↗

arXiv2022

Imaging with Equivariant Deep Learning

From early image processing to modern computational imaging, successful models and algorithms have relied on a fundamental property of natural signals: symmetry. Here symmetry refers to the invariance property of signal sets to transformations such as translation, rotation or scaling. Symmetry can also be incorporated into deep neural networks in the form of equivariance, allowing for more data-efficient learning. While there has been important advances in the design of end-to-end equivariant networks for image classification in recent years, computational imaging introduces unique challenges for equivariant network solutions since we typically only observe the image through some noisy ill-conditioned forward operator that itself may not be equivariant. We review the emerging field of equivariant imaging and show how it can provide improved generalization and new imaging opportunities. Along the way we show the interplay between the acquisition physics and group actions and links to iterative reconstruction, blind compressed sensing and self-supervised learning.

eess.SP↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

cs.LG↗

arXiv2022

Classification of datasets with imputed missing values: does imputation quality matter?

Classifying samples in incomplete datasets is a common aim for machine learning practitioners, but is non-trivial. Missing data is found in most real-world datasets and these missing values are typically imputed using established methods, followed by classification of the now complete, imputed, samples. The focus of the machine learning researcher is then to optimise the downstream classification performance. In this study, we highlight that it is imperative to consider the quality of the imputation. We demonstrate how the commonly used measures for assessing quality are flawed and propose a new class of discrepancy scores which focus on how well the method recreates the overall distribution of the data. To conclude, we highlight the compromised interpretability of classifier models trained using poorly imputed data.

cs.LG↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

math.PR↗

arXiv2022

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.

eess.IV↗

arXiv2022

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.

eess.IV↗

arXiv2022

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.

cs.LG↗