Enzo Ferrante

Anatomically Constrained Neural Networks (ACNNs): Application to Cardiac Image Enhancement and Segmentation

Incorporation of prior knowledge about organ shape and location is key to improve performance of image analysis approaches. In particular, priors can be useful in cases where images are corrupted and contain artefacts due to limitations in image acquisition. The highly constrained nature of anatomical objects can be well captured with learning-based techniques. However, in most recent and promising techniques such as CNN-based segmentation it is not obvious how to incorporate such prior knowledge. State-of-the-art methods operate as pixel-wise classifiers where the training objectives do not incorporate the structure and inter-dependencies of the output. To overcome this limitation, we propose a generic training strategy that incorporates anatomical prior knowledge into CNNs through a new regularisation model, which is trained end-to-end. The new framework encourages models to follow the global anatomical properties of the underlying anatomy (e.g. shape, label structure) via learnt non-linear representations of the shape. We show that the proposed approach can be easily adapted to different analysis tasks (e.g. image enhancement, segmentation) and improve the prediction accuracy of the state-of-the-art models. The applicability of our approach is shown on multi-modal cardiac data sets and public benchmarks. In addition, we demonstrate how the learnt deep models of 3-D shapes can be interpreted and used as biomarkers for classification of cardiac pathologies.

Slice-to-volume medical image registration: A survey

During the last decades, the research community of medical imaging has witnessed continuous advances in image registration methods, which pushed the limits of the state-of-the-art and enabled the development of novel medical procedures. A particular type of image registration problem, known as slice-to-volume registration, played a fundamental role in areas like image guided surgeries and volumetric image reconstruction. However, to date, and despite the extensive literature available on this topic, no survey has been written to discuss this challenging problem. This paper introduces the first comprehensive survey of the literature about slice-to-volume registration, presenting a categorical study of the algorithms according to an ad-hoc taxonomy and analyzing advantages and disadvantages of every category. We draw some general conclusions from this analysis and present our perspectives on the future of the field.

DeepMedic for Brain Tumor Segmentation

Accurate automatic algorithms for the segmentation of brain tumours have the potential of improving disease diagnosis, treatment planning, as well as enabling large-scale studies of the pathology. In this work we employ DeepMedic [1], a 3D CNN architecture previously presented for lesion segmentation, which we further improve by adding residual connections. We also present a series of experiments on the BRATS 2015 training database for evaluating the robustness of the network when less training data are available or less filters are used, aiming to shed some light on requirements for employing such a system. Our method was further benchmarked on the BRATS 2016 Challenge, where it achieved very good performance despite the simplicity of the pipeline.

Spectral Graph Convolutions for Population-Based Disease Prediction

Exploiting the wealth of imaging and non-imaging information for disease prediction tasks requires models capable of representing, at the same time, individual features as well as data associations between subjects from potentially large populations. Graphs provide a natural framework for such tasks, yet previous graph-based approaches focus on pairwise similarities without modelling the subjects’ individual characteristics and features. On the other hand, relying solely on subject-specific imaging feature vectors fails to model the interaction and similarity between subjects, which can reduce performance. In this paper, we introduce the novel concept of Graph Convolutional Networks (GCN) for brain analysis in populations, combining imaging and non-imaging data. We represent populations as a sparse graph where its vertices are associated with image-based feature vectors and the edges encode phenotypic information. This structure was used to train a GCN model on partially labelled graphs, aiming to infer the classes of unlabelled nodes from the node features and pairwise associations between subjects. We demonstrate the potential of the method on the challenging ADNI and ABIDE databases, as a proof of concept of the benefit from integrating contextual information in classification tasks. This has a clear impact on the quality of the predictions, leading to 69.5% accuracy for ABIDE (outperforming the current state of the art of 66.8%) and 77% for ADNI for prediction of MCI conversion, significantly outperforming standard linear classifiers where only individual features are considered.

Distance Metric Learning Using Graph Convolutional Networks: Application to Functional Brain Networks

Evaluating similarity between graphs is of major importance in several computer vision and pattern recognition problems, where graph representations are often used to model objects or interactions between elements. The choice of a distance or similarity metric is, however, not trivial and can be highly dependent on the application at hand. In this work, we propose a novel metric learning method to evaluate distance between graphs that leverages the power of convolutional neural networks, while exploiting concepts from spectral graph theory to allow these operations on irregular graphs. We demonstrate the potential of our method in the field of connectomics, where neuronal pathways or functional connections between brain regions are commonly modelled as graphs. In this problem, the definition of an appropriate graph similarity function is critical to unveil patterns of disruptions associated with certain brain disorders. Experimental results on the ABIDE dataset show that our method can learn a graph similarity metric tailored for a clinical application, improving the performance of a simple k-nn classifier by 11.9% compared to a traditional distance metric.

Ensembles of Multiple Models and Architectures for Robust Brain Tumour Segmentation

Deep learning approaches such as convolutional neural nets have consistently outperformed previous methods on challenging tasks such as dense, semantic segmentation. However, the various proposed networks perform differently, with behaviour largely influenced by architectural choices and training settings. This paper explores Ensembles of Multiple Models and Architectures (EMMA) for robust performance through aggregation of predictions from a wide range of methods. The approach reduces the influence of the meta-parameters of individual models and the risk of overfitting the configuration to a particular database. EMMA can be seen as an unbiased, generic deep learning model which is shown to yield excellent performance, winning the first position in the BRATS 2017 competition among 50+ participating teams.

(Hyper)-graphical models in biomedical image analysis.

Computational vision, visual computing and biomedical image analysis have made tremendous progress over the past two decades. This is mostly due the development of efficient learning and inference algorithms which allow better and richer modeling of image and visual understanding tasks. Hyper-graph representations are among the most prominent tools to address such perception through the casting of perception as a graph optimization problem. In this paper, we briefly introduce the importance of such representations, discuss their strength and limitations, provide appropriate strategies for their inference and present their application to address a variety of problems in biomedical image analysis.

Metric learning with spectral graph convolutions on brain connectivity networks.

ABSTRACT Graph representations are often used to model structured data at an individual or population level and have numerous applications in pattern recognition problems. In the field of neuroscience, where such representations are commonly used to model structural or functional connectivity between a set of brain regions, graphs have proven to be of great importance. This is mainly due to the capability of revealing patterns related to brain development and disease, which were previously unknown. Evaluating similarity between these brain connectivity networks in a manner that accounts for the graph structure and is tailored for a particular application is, however, non‐trivial. Most existing methods fail to accommodate the graph structure, discarding information that could be beneficial for further classification or regression analyses based on these similarities. We propose to learn a graph similarity metric using a siamese graph convolutional neural network (s‐GCN) in a supervised setting. The proposed framework takes into consideration the graph structure for the evaluation of similarity between a pair of graphs, by employing spectral graph convolutions that allow the generalisation of traditional convolutions to irregular graphs and operates in the graph spectral domain. We apply the proposed model on two datasets: the challenging ABIDE database, which comprises functional MRI data of 403 patients with autism spectrum disorder (ASD) and 468 healthy controls aggregated from multiple acquisition sites, and a set of 2500 subjects from UK Biobank. We demonstrate the performance of the method for the tasks of classification between matching and non‐matching graphs, as well as individual subject classification and manifold learning, showing that it leads to significantly improved results compared to traditional methods. HighlightsMetric learning approach for similarity estimation between brain connectivity graphs.The method employs spectral graph convolutions to learn localised feature maps.Quantitative and qualitative evaluation on ABIDE and UK Biobank databases.Global loss function leads to improved results on heterogeneous datasets.

Deformable Registration Through Learning of Context-Specific Metric Aggregation

We propose a novel weakly supervised discriminative algorithm for learning context specific registration metrics as a linear combination of conventional similarity measures. Conventional metrics have been extensively used over the past two decades and therefore both their strengths and limitations are known. The challenge is to find the optimal relative weighting (or parameters) of different metrics forming the similarity measure of the registration algorithm. Hand-tuning these parameters would result in sub optimal solutions and quickly become infeasible as the number of metrics increases. Furthermore, such hand-crafted combination can only happen at global scale (entire volume) and therefore will not be able to account for the different tissue properties. We propose a learning algorithm for estimating these parameters locally, conditioned to the data semantic classes. The objective function of our formulation is a special case of non-convex function, difference of convex function, which we optimize using the concave convex procedure. As a proof of concept, we show the impact of our approach on three challenging datasets for different anatomical structures and modalities.

Graph-Based Slice-to-Volume Deformable Registration

Deformable image registration is a fundamental problem in computer vision and medical image computing. In this paper we investigate the use of graphical models in the context of a particular type of image registration problem, known as slice-to-volume registration. We introduce a scalable, modular and flexible formulation that can accommodate low-rank and high order terms, that simultaneously selects the plane and estimates the in-plane deformation through a single shot optimization approach. The proposed framework is instantiated into different variants seeking either a compromise between computational efficiency (soft plane selection constraints and approximate definition of the data similarity terms through pair-wise components) or exact definition of the data terms and the constraints on the plane selection. Simulated and real-data in the context of ultrasound and magnetic resonance registration (where both framework instantiations as well as different optimization strategies are considered) demonstrate the potentials of our method.