arXiv subjects

Carola-Bibiane Schönlieb

Publications and source records attributed to Carola-Bibiane Schönlieb.

At least 199 records · Page 11Linked to original sources

arXiv2022

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.

cs.CV↗

arXiv2021

AI-based Reconstruction for Fast MRI -- A Systematic Review and Meta-analysis

Compressed sensing (CS) has been playing a key role in accelerating the magnetic resonance imaging (MRI) acquisition process. With the resurgence of artificial intelligence, deep neural networks and CS algorithms are being integrated to redefine the state of the art of fast MRI. The past several years have witnessed substantial growth in the complexity, diversity, and performance of deep learning-based CS techniques that are dedicated to fast MRI. In this meta-analysis, we systematically review the deep learning-based CS techniques for fast MRI, describe key model designs, highlight breakthroughs, and discuss promising directions. We have also introduced a comprehensive analysis framework and a classification system to assess the pivotal role of deep learning in CS-based acceleration for MRI.

eess.IV↗

arXiv2021

A Continuous-time Stochastic Gradient Descent Method for Continuous Data

Optimization problems with continuous data appear in, e.g., robust machine learning, functional data analysis, and variational inference. Here, the target function is given as an integral over a family of (continuously) indexed target functions - integrated with respect to a probability measure. Such problems can often be solved by stochastic optimization methods: performing optimization steps with respect to the indexed target function with randomly switched indices. In this work, we study a continuous-time variant of the stochastic gradient descent algorithm for optimization problems with continuous data. This so-called stochastic gradient process consists in a gradient flow minimizing an indexed target function that is coupled with a continuous-time index process determining the index. Index processes are, e.g., reflected diffusions, pure jump processes, or other Lévy processes on compact spaces. Thus, we study multiple sampling patterns for the continuous data space and allow for data simulated or streamed at runtime of the algorithm. We analyze the approximation properties of the stochastic gradient process and study its longtime behavior and ergodicity under constant and decreasing learning rates. We end with illustrating the applicability of the stochastic gradient process in a polynomial regression problem with noisy functional data, as well as in a physics-informed neural network.

cs.LG↗

arXiv2021

Conditional Image Generation with Score-Based Diffusion Models

Score-based diffusion models have emerged as one of the most promising frameworks for deep generative modelling. In this work we conduct a systematic comparison and theoretical analysis of different approaches to learning conditional probability distributions with score-based diffusion models. In particular, we prove results which provide a theoretical justification for one of the most successful estimators of the conditional score. Moreover, we introduce a multi-speed diffusion framework, which leads to a new estimator for the conditional score, performing on par with previous state-of-the-art approaches. Our theoretical and experimental findings are accompanied by an open source library MSDiff which allows for application and further research of multi-speed diffusion models.

cs.LG↗

arXiv2021

Unified Focal loss: Generalising Dice and cross entropy-based losses to handle class imbalanced medical image segmentation

Automatic segmentation methods are an important advancement in medical image analysis. Machine learning techniques, and deep neural networks in particular, are the state-of-the-art for most medical image segmentation tasks. Issues with class imbalance pose a significant challenge in medical datasets, with lesions often occupying a considerably smaller volume relative to the background. Loss functions used in the training of deep learning algorithms differ in their robustness to class imbalance, with direct consequences for model convergence. The most commonly used loss functions for segmentation are based on either the cross entropy loss, Dice loss or a combination of the two. We propose the Unified Focal loss, a new hierarchical framework that generalises Dice and cross entropy-based losses for handling class imbalance. We evaluate our proposed loss function on five publicly available, class imbalanced medical imaging datasets: CVC-ClinicDB, Digital Retinal Images for Vessel Extraction (DRIVE), Breast Ultrasound 2017 (BUS2017), Brain Tumour Segmentation 2020 (BraTS20) and Kidney Tumour Segmentation 2019 (KiTS19). We compare our loss function performance against six Dice or cross entropy-based loss functions, across 2D binary, 3D binary and 3D multiclass segmentation tasks, demonstrating that our proposed loss function is robust to class imbalance and consistently outperforms the other loss functions. Source code is available at: https://github.com/mlyg/unified-focal-loss

eess.IV↗

arXiv2021

HERS Superpixels: Deep Affinity Learning for Hierarchical Entropy Rate Segmentation

Superpixels serve as a powerful preprocessing tool in numerous computer vision tasks. By using superpixel representation, the number of image primitives can be largely reduced by orders of magnitudes. With the rise of deep learning in recent years, a few works have attempted to feed deeply learned features / graphs into existing classical superpixel techniques. However, none of them are able to produce superpixels in near real-time, which is crucial to the applicability of superpixels in practice. In this work, we propose a two-stage graph-based framework for superpixel segmentation. In the first stage, we introduce an efficient Deep Affinity Learning (DAL) network that learns pairwise pixel affinities by aggregating multi-scale information. In the second stage, we propose a highly efficient superpixel method called Hierarchical Entropy Rate Segmentation (HERS). Using the learned affinities from the first stage, HERS builds a hierarchical tree structure that can produce any number of highly adaptive superpixels instantaneously. We demonstrate, through visual and numerical experiments, the effectiveness and efficiency of our method compared to various state-of-the-art superpixel methods.

cs.CV↗

arXiv2021

Advancing COVID-19 Diagnosis with Privacy-Preserving Collaboration in Artificial Intelligence

Artificial intelligence (AI) provides a promising substitution for streamlining COVID-19 diagnoses. However, concerns surrounding security and trustworthiness impede the collection of large-scale representative medical data, posing a considerable challenge for training a well-generalised model in clinical practices. To address this, we launch the Unified CT-COVID AI Diagnostic Initiative (UCADI), where the AI model can be distributedly trained and independently executed at each host institution under a federated learning framework (FL) without data sharing. Here we show that our FL model outperformed all the local models by a large yield (test sensitivity /specificity in China: 0.973/0.951, in the UK: 0.730/0.942), achieving comparable performance with a panel of professional radiologists. We further evaluated the model on the hold-out (collected from another two hospitals leaving out the FL) and heterogeneous (acquired with contrast materials) data, provided visual explanations for decisions made by the model, and analysed the trade-offs between the model performance and the communication costs in the federated training process. Our study is based on 9,573 chest computed tomography scans (CTs) from 3,336 patients collected from 23 hospitals located in China and the UK. Collectively, our work advanced the prospects of utilising federated learning for privacy-preserving AI in digital health.

cs.AI↗

arXiv2021

Incorporating Boundary Uncertainty into loss functions for biomedical image segmentation

Manual segmentation is used as the gold-standard for evaluating neural networks on automated image segmentation tasks. Due to considerable heterogeneity in shapes, colours and textures, demarcating object boundaries is particularly difficult in biomedical images, resulting in significant inter and intra-rater variability. Approaches, such as soft labelling and distance penalty term, apply a global transformation to the ground truth, redefining the loss function with respect to uncertainty. However, global operations are computationally expensive, and neither approach accurately reflects the uncertainty underlying manual annotation. In this paper, we propose the Boundary Uncertainty, which uses morphological operations to restrict soft labelling to object boundaries, providing an appropriate representation of uncertainty in ground truth labels, and may be adapted to enable robust model training where systematic manual segmentation errors are present. We incorporate Boundary Uncertainty with the Dice loss, achieving consistently improved performance across three well-validated biomedical imaging datasets compared to soft labelling and distance-weighted penalty. Boundary Uncertainty not only more accurately reflects the segmentation process, but it is also efficient, robust to segmentation errors and exhibits better generalisation.

eess.IV↗

arXiv2021

Focal Attention Networks: optimising attention for biomedical image segmentation

In recent years, there has been increasing interest to incorporate attention into deep learning architectures for biomedical image segmentation. The modular design of attention mechanisms enables flexible integration into convolutional neural network architectures, such as the U-Net. Whether attention is appropriate to use, what type of attention to use, and where in the network to incorporate attention modules, are all important considerations that are currently overlooked. In this paper, we investigate the role of the Focal parameter in modulating attention, revealing a link between attention in loss functions and networks. By incorporating a Focal distance penalty term, we extend the Unified Focal loss framework to include boundary-based losses. Furthermore, we develop a simple and interpretable, dataset and model-specific heuristic to integrate the Focal parameter into the Squeeze-and-Excitation block and Attention Gate, achieving optimal performance with fewer number of attention modules on three well-validated biomedical imaging datasets, suggesting judicious use of attention modules results in better performance and efficiency.

eess.IV↗

arXiv2021

Energy Models for Better Pseudo-Labels: Improving Semi-Supervised Classification with the 1-Laplacian Graph Energy

Semi-supervised classification is a great focus of interest, as in real-world scenarios obtaining labels is expensive, time-consuming and might require expert knowledge. This has motivated the fast development of semi-supervised techniques, whose performance is on a par with or better than supervised approaches. A current major challenge for semi-supervised techniques is how to better handle the network calibration and confirmation bias problems for improving performance. In this work, we argue that energy models are an effective alternative to such problems. With this motivation in mind, we propose a hybrid framework for semi-supervised classification called CREPE model (1-Lapla$\mathbf{C}$ian g$\mathbf{R}$aph $\mathbf{E}$nergy for $\mathbf{P}$seudo-lab$\mathbf{E}$ls). Firstly, we introduce a new energy model based on the non-smooth $\ell_1$ norm of the normalised graph 1-Laplacian. Our functional enforces a sufficiently smooth solution and strengthens the intrinsic relation between the labelled and unlabelled data. Secondly, we provide a theoretical analysis for our proposed scheme and show that the solution trajectory does converge to a non-constant steady point. Thirdly, we derive the connection of our energy model for pseudo-labelling. We show that our energy model produces more meaningful pseudo-labels than the ones generated directly by a deep network. We extensively evaluate our framework, through numerical and visual experiments, using six benchmarking datasets for natural and medical images. We demonstrate that our technique reports state-of-the-art results for semi-supervised classification.

cs.LG↗

arXiv2021

Learning convex regularizers satisfying the variational source condition for inverse problems

Variational regularization has remained one of the most successful approaches for reconstruction in imaging inverse problems for several decades. With the emergence and astonishing success of deep learning in recent years, a considerable amount of research has gone into data-driven modeling of the regularizer in the variational setting. Our work extends a recently proposed method, referred to as adversarial convex regularization (ACR), that seeks to learn data-driven convex regularizers via adversarial training in an attempt to combine the power of data with the classical convex regularization theory. Specifically, we leverage the variational source condition (SC) during training to enforce that the ground-truth images minimize the variational loss corresponding to the learned convex regularizer. This is achieved by adding an appropriate penalty term to the ACR training objective. The resulting regularizer (abbreviated as ACR-SC) performs on par with the ACR, but unlike ACR, comes with a quantitative convergence rate estimate.

cs.LG↗

arXiv2021

StyleGAN-induced data-driven regularization for inverse problems

Recent advances in generative adversarial networks (GANs) have opened up the possibility of generating high-resolution photo-realistic images that were impossible to produce previously. The ability of GANs to sample from high-dimensional distributions has naturally motivated researchers to leverage their power for modeling the image prior in inverse problems. We extend this line of research by developing a Bayesian image reconstruction framework that utilizes the full potential of a pre-trained StyleGAN2 generator, which is the currently dominant GAN architecture, for constructing the prior distribution on the underlying image. Our proposed approach, which we refer to as learned Bayesian reconstruction with generative models (L-BRGM), entails joint optimization over the style-code and the input latent code, and enhances the expressive power of a pre-trained StyleGAN2 generator by allowing the style-codes to be different for different generator layers. Considering the inverse problems of image inpainting and super-resolution, we demonstrate that the proposed approach is competitive with, and sometimes superior to, state-of-the-art GAN-based image reconstruction methods.

cs.CV↗

arXiv2021

Wasserstein GANs Work Because They Fail (to Approximate the Wasserstein Distance)

Wasserstein GANs are based on the idea of minimising the Wasserstein distance between a real and a generated distribution. We provide an in-depth mathematical analysis of differences between the theoretical setup and the reality of training Wasserstein GANs. In this work, we gather both theoretical and empirical evidence that the WGAN loss is not a meaningful approximation of the Wasserstein distance. Moreover, we argue that the Wasserstein distance is not even a desirable loss function for deep generative models, and conclude that the success of Wasserstein GANs can in truth be attributed to a failure to approximate the Wasserstein distance.

stat.ML↗

arXiv2021

Bayesian optimization assisted unsupervised learning for efficient intra-tumor partitioning in MRI and survival prediction for glioblastoma patients

Glioblastoma is profoundly heterogeneous in microstructure and vasculature, which may lead to tumor regional diversity and distinct treatment response. Although successful in tumor sub-region segmentation and survival prediction, radiomics based on machine learning algorithms, is challenged by its robustness, due to the vague intermediate process and track changes. Also, the weak interpretability of the model poses challenges to clinical application. Here we proposed a machine learning framework to semi-automatically fine-tune the clustering algorithms and quantitatively identify stable sub-regions for reliable clinical survival prediction. Hyper-parameters are automatically determined by the global minimum of the trained Gaussian Process (GP) surrogate model through Bayesian optimization(BO) to alleviate the difficulty of tuning parameters for clinical researchers. To enhance the interpretability of the survival prediction model, we incorporated the prior knowledge of intra-tumoral heterogeneity, by segmenting tumor sub-regions and extracting sub-regional features. The results demonstrated that the global minimum of the trained GP surrogate can be used as sub-optimal hyper-parameter solutions for efficient. The sub-regions segmented based on physiological MRI can be applied to predict patient survival, which could enhance the clinical interpretability for the machine learning model.

eess.IV↗

arXiv2021

TFPnP: Tuning-free Plug-and-Play Proximal Algorithm with Applications to Inverse Imaging Problems

Plug-and-Play (PnP) is a non-convex optimization framework that combines proximal algorithms, for example, the alternating direction method of multipliers (ADMM), with advanced denoising priors. Over the past few years, great empirical success has been obtained by PnP algorithms, especially for the ones that integrate deep learning-based denoisers. However, a key challenge of PnP approaches is the need for manual parameter tweaking as it is essential to obtain high-quality results across the high discrepancy in imaging conditions and varying scene content. In this work, we present a class of tuning-free PnP proximal algorithms that can determine parameters such as denoising strength, termination time, and other optimization-specific parameters automatically. A core part of our approach is a policy network for automated parameter search which can be effectively learned via a mixture of model-free and model-based deep reinforcement learning strategies. We demonstrate, through rigorous numerical and visual experiments, that the learned policy can customize parameters to different settings, and is often more efficient and effective than existing handcrafted criteria. Moreover, we discuss several practical considerations of PnP denoisers, which together with our learned policy yield state-of-the-art results. This advanced performance is prevalent on both linear and nonlinear exemplar inverse imaging problems, and in particular shows promising results on compressed sensing MRI, sparse-view CT, single-photon imaging, and phase retrieval.

cs.CV↗

arXiv2021

Predicting isocitrate dehydrogenase mutation status in glioma using structural brain networks and graph neural networks

Glioma is a common malignant brain tumor with distinct survival among patients. The isocitrate dehydrogenase (IDH) gene mutation provides critical diagnostic and prognostic value for glioma. It is of crucial significance to non-invasively predict IDH mutation based on pre-treatment MRI. Machine learning/deep learning models show reasonable performance in predicting IDH mutation using MRI. However, most models neglect the systematic brain alterations caused by tumor invasion, where widespread infiltration along white matter tracts is a hallmark of glioma. Structural brain network provides an effective tool to characterize brain organisation, which could be captured by the graph neural networks (GNN) to more accurately predict IDH mutation. Here we propose a method to predict IDH mutation using GNN, based on the structural brain network of patients. Specifically, we firstly construct a network template of healthy subjects, consisting of atlases of edges (white matter tracts) and nodes (cortical/subcortical brain regions) to provide regions of interest (ROIs). Next, we employ autoencoders to extract the latent multi-modal MRI features from the ROIs of edges and nodes in patients, to train a GNN architecture for predicting IDH mutation. The results show that the proposed method outperforms the baseline models using the 3D-CNN and 3D-DenseNet. In addition, model interpretation suggests its ability to identify the tracts infiltrated by tumor, corresponding to clinical prior knowledge. In conclusion, integrating brain networks with GNN offers a new avenue to study brain lesions using computational neuroscience and computer vision approaches.

eess.IV↗

arXiv2021

Adaptive unsupervised learning with enhanced feature representation for intra-tumor partitioning and survival prediction for glioblastoma

Glioblastoma is profoundly heterogeneous in regional microstructure and vasculature. Characterizing the spatial heterogeneity of glioblastoma could lead to more precise treatment. With unsupervised learning techniques, glioblastoma MRI-derived radiomic features have been widely utilized for tumor sub-region segmentation and survival prediction. However, the reliability of algorithm outcomes is often challenged by both ambiguous intermediate process and instability introduced by the randomness of clustering algorithms, especially for data from heterogeneous patients. In this paper, we propose an adaptive unsupervised learning approach for efficient MRI intra-tumor partitioning and glioblastoma survival prediction. A novel and problem-specific Feature-enhanced Auto-Encoder (FAE) is developed to enhance the representation of pairwise clinical modalities and therefore improve clustering stability of unsupervised learning algorithms such as K-means. Moreover, the entire process is modelled by the Bayesian optimization (BO) technique with a custom loss function that the hyper-parameters can be adaptively optimized in a reasonably few steps. The results demonstrate that the proposed approach can produce robust and clinically relevant MRI sub-regions and statistically significant survival predictions.

cs.LG↗

arXiv2021

Expectation-Maximization Regularized Deep Learning for Weakly Supervised Tumor Segmentation for Glioblastoma

We present an Expectation-Maximization (EM) Regularized Deep Learning (EMReDL) model for weakly supervised tumor segmentation. The proposed framework is tailored to glioblastoma, a type of malignant tumor characterized by its diffuse infiltration into the surrounding brain tissue, which poses significant challenge to treatment target and tumor burden estimation using conventional structural MRI. Although physiological MRI provides more specific information regarding tumor infiltration, the relatively low resolution hinders a precise full annotation. This has motivated us to develop a weakly supervised deep learning solution that exploits the partial labelled tumor regions. EMReDL contains two components: a physiological prior prediction model and EM-regularized segmentation model. The physiological prior prediction model exploits the physiological MRI by training a classifier to generate a physiological prior map. This map is passed to the segmentation model for regularization using the EM algorithm. We evaluated the model on a glioblastoma dataset with the pre-operative multiparametric and recurrence MRI available. EMReDL showed to effectively segment the infiltrated tumor from the partially labelled region of potential infiltration. The segmented core tumor and infiltrated tumor demonstrated high consistency with the tumor burden labelled by experts. The performance comparisons showed that EMReDL achieved higher accuracy than published state-of-the-art models. On MR spectroscopy, the segmented region displayed more aggressive features than other partial labelled region. The proposed model can be generalized to other segmentation tasks that rely on partial labels, with the CNN architecture flexible in the framework.

eess.IV↗