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End-to-end training of graph neural networks (GNN) on large graphs presents several memory and computational challenges, and limits the application to shallow architectures as depth exponentially increases the memory and space complexities. In this manuscript, we propose Layer-wise Regularized Graph Infomax, an algorithm to train GNNs layer by layer in a self-supervised manner. We decouple the feature propagation and feature transformation carried out by GNNs to learn node representations in order to derive a loss function based on the prediction of future inputs. We evaluate the algorithm in inductive large graphs and show similar performance to other end to end methods and a substantially increased efficiency, which enables the training of more sophisticated models in one single device. We also show that our algorithm avoids the oversmoothing of the representations, another common challenge of deep GNNs.

Self-supervised learning is gaining considerable attention as a solution to avoid the requirement of extensive annotations in representation learning on graphs. Current algorithms are based on contrastive learning, which is computation an memory expensive, and the assumption of invariance under certain graph augmentations. However, graph transformations such as edge sampling may modify the semantics of the data so that the iinvariance assumption may be incorrect. We introduce Regularized Graph Infomax (RGI), a simple yet effective framework for node level self-supervised learning that trains a graph neural network encoder by maximizing the mutual information between output node embeddings and their propagation through the graph, which encode the nodes' local and global context, respectively. RGI do not use graph data augmentations but instead generates self-supervision signals with feature propagation, is non-contrastive and does not depend on a two branch architecture. We run RGI on both transductive and inductive settings with popular graph benchmarks and show that it can achieve state-of-the-art performance regardless of its simplicity., Comment: 16 pages, 1 figure, preprint

In this paper we present SurvLIMEpy, an open-source Python package that implements the SurvLIME algorithm. This method allows to compute local feature importance for machine learning algorithms designed for modelling Survival Analysis data. Our implementation takes advantage of the parallelisation paradigm as all computations are performed in a matrix-wise fashion which speeds up execution time. Additionally, SurvLIMEpy assists the user with visualization tools to better understand the result of the algorithm. The package supports a wide variety of survival models, from the Cox Proportional Hazards Model to deep learning models such as DeepHit or DeepSurv. Two types of experiments are presented in this paper. First, by means of simulated data, we study the ability of the algorithm to capture the importance of the features. Second, we use three open source survival datasets together with a set of survival algorithms in order to demonstrate how SurvLIMEpy behaves when applied to different models.

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at: https://github.com/RagMeh11/QU-BraTS., Comment: Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA): https://www.melba-journal.org/papers/2022:026.html

Automation of brain tumor segmentation in 3D magnetic resonance images (MRIs) is key to assess the diagnostic and treatment of the disease. In recent years, convolutional neural networks (CNNs) have shown improved results in the task. However, high memory consumption is still a problem in 3D-CNNs. Moreover, most methods do not include uncertainty information, which is especially critical in medical diagnosis. This work studies 3D encoder-decoder architectures trained with patch-based techniques to reduce memory consumption and decrease the effect of unbalanced data. The different trained models are then used to create an ensemble that leverages the properties of each model, thus increasing the performance. We also introduce voxel-wise uncertainty information, both epistemic and aleatoric using test-time dropout (TTD) and data-augmentation (TTA) respectively. In addition, a hybrid approach is proposed that helps increase the accuracy of the segmentation. The model and uncertainty estimation measurements proposed in this work have been used in the BraTS'20 Challenge for task 1 and 3 regarding tumor segmentation and uncertainty estimation., Comment: Extended paper. BrainLes Workshop, MICCAI 2020. arXiv admin note: substantial text overlap with arXiv:2009.12188

Automation of brain tumors in 3D magnetic resonance images (MRIs) is key to assess the diagnostic and treatment of the disease. In recent years, convolutional neural networks (CNNs) have shown improved results in the task. However, high memory consumption is still a problem in 3D-CNNs. Moreover, most methods do not include uncertainty information, which is specially critical in medical diagnosis. This work proposes a 3D encoder-decoder architecture, based on V-Net \cite{vnet} which is trained with patching techniques to reduce memory consumption and decrease the effect of unbalanced data. We also introduce voxel-wise uncertainty, both epistemic and aleatoric using test-time dropout and data-augmentation respectively. Uncertainty maps can provide extra information to expert neurologists, useful for detecting when the model is not confident on the provided segmentation., Comment: Pre-conference paper. Brain Tumor Segmentation (BraTS) Challenge 2020

Active Learning techniques are used to tackle learning problems where obtaining training labels is costly. In this work we use Meta-Active Learning to learn to select a subset of samples from a pool of unsupervised input for further annotation. This scenario is called Static Pool-based Meta- Active Learning. We propose to extend existing approaches by performing the selection in a manner that, unlike previous works, can handle the selection of each sample based on the whole selected subset.

This article summarizes the BCN20000 dataset, composed of 19424 dermoscopic images of skin lesions captured from 2010 to 2016 in the facilities of the Hospital Cl\'inic in Barcelona. With this dataset, we aim to study the problem of unconstrained classification of dermoscopic images of skin cancer, including lesions found in hard-to-diagnose locations (nails and mucosa), large lesions which do not fit in the aperture of the dermoscopy device, and hypo-pigmented lesions. The BCN20000 will be provided to the participants of the ISIC Challenge 2019, where they will be asked to train algorithms to classify dermoscopic images of skin cancer automatically., Comment: Abstract for BCN20000

Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR images, which is a laborious procedure. Automatic WMH segmentation methods exist, but a standardized comparison of the performance of such methods is lacking. We organized a scientific challenge, in which developers could evaluate their method on a standardized multi-center/-scanner image dataset, giving an objective comparison: the WMH Segmentation Challenge (https://wmh.isi.uu.nl/). Sixty T1+FLAIR images from three MR scanners were released with manual WMH segmentations for training. A test set of 110 images from five MR scanners was used for evaluation. Segmentation methods had to be containerized and submitted to the challenge organizers. Five evaluation metrics were used to rank the methods: (1) Dice similarity coefficient, (2) modified Hausdorff distance (95th percentile), (3) absolute log-transformed volume difference, (4) sensitivity for detecting individual lesions, and (5) F1-score for individual lesions. Additionally, methods were ranked on their inter-scanner robustness. Twenty participants submitted their method for evaluation. This paper provides a detailed analysis of the results. In brief, there is a cluster of four methods that rank significantly better than the other methods, with one clear winner. The inter-scanner robustness ranking shows that not all methods generalize to unseen scanners. The challenge remains open for future submissions and provides a public platform for method evaluation., Comment: Accepted for publication in IEEE Transactions on Medical Imaging

In this work we approach the brain tumor segmentation problem with a cascade of two CNNs inspired in the V-Net architecture \cite{VNet}, reformulating residual connections and making use of ROI masks to constrain the networks to train only on relevant voxels. This architecture allows dense training on problems with highly skewed class distributions, such as brain tumor segmentation, by focusing training only on the vecinity of the tumor area. We report results on BraTS2017 Training and Validation sets., Comment: Third International Workshop, BrainLes 2017, Held in Conjunction with MICCAI 2017, Quebec City, QC, Canada, September 14, 2017, Revised Selected Papers

Leishmaniasis is considered a neglected disease that causes thousands of deaths annually in some tropical and subtropical countries. There are various techniques to diagnose leishmaniasis of which manual microscopy is considered to be the gold standard. There is a need for the development of automatic techniques that are able to detect parasites in a robust and unsupervised manner. In this paper we present a procedure for automatizing the detection process based on a deep learning approach. We train a U-net model that successfully segments leismania parasites and classifies them into promastigotes, amastigotes and adhered parasites., Comment: 10th International Conference, AMDO 2018, Palma de Mallorca, Spain, July 12-13, 2018, Proceedings

We propose a patch sampling strategy based on a sequential Monte-Carlo method for high resolution image classification in the context of Multiple Instance Learning. When compared with grid sampling and uniform sampling techniques, it achieves higher generalization performance. We validate the strategy on two artificial datasets and two histological datasets for breast cancer and sun exposure classification., Comment: accepted at 4th International Workshop on Deep Learning for Medical Image Analysis (DLMIA), MICCAI 2018, Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support, Springer International Publishing, 2018

In this work we propose an adversarial learning approach to generate high resolution MRI scans from low resolution images. The architecture, based on the SRGAN model, adopts 3D convolutions to exploit volumetric information. For the discriminator, the adversarial loss uses least squares in order to stabilize the training. For the generator, the loss function is a combination of a least squares adversarial loss and a content term based on mean square error and image gradients in order to improve the quality of the generated images. We explore different solutions for the upsampling phase. We present promising results that improve classical interpolation, showing the potential of the approach for 3D medical imaging super-resolution. Source code available at https://github.com/imatge-upc/3D-GAN-superresolution, Comment: First International Conference on Medical Imaging with Deep Learning, Amsterdam, 2018

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset., Comment: The International Multimodal Brain Tumor Segmentation (BraTS) Challenge

This paper analyzes the use of 3D Convolutional Neural Networks for brain tumor segmentation in MR images. We address the problem using three different architectures that combine fine and coarse features to obtain the final segmentation. We compare three different networks that use multi-resolution features in terms of both design and performance and we show that they improve their single-resolution counterparts.

This paper describes a new neuroimaging analysis toolbox that allows for the modeling of nonlinear effects at the voxel level, overcoming limitations of methods based on linear models like the GLM. We illustrate its features using a relevant example in which distinct nonlinear trajectories of Alzheimer's disease related brain atrophy patterns were found across the full biological spectrum of the disease. The open-source toolbox presented in this paper is available at https://github.com/imatge-upc/VNeAT., Comment: 4 pages + 1 page for acknowledgements and references. NIPS 2016 Workshop on Machine Learning for Health (NIPS ML4HC)

In this paper we propose two saliency models for salient object segmentation based on a hierarchical image segmentation, a tree-like structure that represents regions at different scales from the details to the whole image (e.g. gPb-UCM, BPT). The first model is based on a hierarchy of image partitions. The saliency at each level is computed on a region basis, taking into account the contrast between regions. The maps obtained for the different partitions are then integrated into a final saliency map. The second model directly works on the structure created by the segmentation algorithm, computing saliency at each node and integrating these cues in a straightforward manner into a single saliency map. We show that the proposed models produce high quality saliency maps. Objective evaluation demonstrates that the two methods achieve state-of-the-art performance in several benchmark datasets., Comment: Accepted for publication in Signal Processing: Image Communications, 2015

This paper explores novel approaches for improving the spatial codification for the pooling of local descriptors to solve the semantic segmentation problem. We propose to partition the image into three regions for each object to be described: Figure, Border and Ground. This partition aims at minimizing the influence of the image context on the object description and vice versa by introducing an intermediate zone around the object contour. Furthermore, we also propose a richer visual descriptor of the object by applying a Spatial Pyramid over the Figure region. Two novel Spatial Pyramid configurations are explored: Cartesian-based and crown-based Spatial Pyramids. We test these approaches with state-of-the-art techniques and show that they improve the Figure-Ground based pooling in the Pascal VOC 2011 and 2012 semantic segmentation challenges., Comment: Paper accepted at the IEEE International Conference on Image Processing, ICIP 2015. Quebec City, 27-30 September. Project page: https://imatge.upc.edu/web/publications/improving-spatial-codification-semantic-segmentation