Gemma Piella

Valentin Comte, Mireia Alenya, Andrea Urru et al.

Accurate segmentation of fetal brain magnetic resonance images is crucial for analyzing fetal brain development and detecting potential neurodevelopmental abnormalities. Traditional deep learning-based automatic segmentation, although effective, requires extensive training data with ground-truth labels, typically produced by clinicians through a time-consuming annotation process. To overcome this challenge, we propose a novel unsupervised segmentation method based on multi-atlas segmentation, that accurately segments multiple tissues without relying on labeled data for training. Our method employs a cascaded deep learning network for 3D image registration, which computes small, incremental deformations to the moving image to align it precisely with the fixed image. This cascaded network can then be used to register multiple annotated images with the image to be segmented, and combine the propagated labels to form a refined segmentation. Our experiments demonstrate that the proposed cascaded architecture outperforms the state-of-the-art registration methods that were tested. Furthermore, the derived segmentation method achieves similar performance and inference time to nnU-Net while only using a small subset of annotated data for the multi-atlas segmentation task and none for training the network. Our pipeline for registration and multi-atlas segmentation is publicly available at https://github.com/ValBcn/CasReg.

Andrea Urru, Ayako Nakaki, Oualid Benkarim et al.

The automatic segmentation of perinatal brain structures in magnetic resonance imaging (MRI) is of utmost importance for the study of brain growth and related complications. While different methods exist for adult and pediatric MRI data, there is a lack for automatic tools for the analysis of perinatal imaging. In this work, a new pipeline for fetal and neonatal segmentation has been developed. We also report the creation of two new fetal atlases, and their use within the pipeline for atlas-based segmentation, based on novel registration methods. The pipeline is also able to extract cortical and pial surfaces and compute features, such as curvature, thickness, sulcal depth, and local gyrification index. Results show that the introduction of the new templates together with our segmentation strategy leads to accurate results when compared to expert annotations, as well as better performances when compared to a reference pipeline (developing Human Connectome Project (dHCP)), for both early and late-onset fetal brains.

Araceli Morales, Antonio R. Porras, Marius George Linguraru et al.

We present a 3D face reconstruction system that aims at recovering the 3D facial geometry of babies from uncalibrated photographs, BabyNet. Since the 3D facial geometry of babies differs substantially from that of adults, baby-specific facial reconstruction systems are needed. BabyNet consists of two stages: 1) a 3D graph convolutional autoencoder learns a latent space of the baby 3D facial shape; and 2) a 2D encoder that maps photographs to the 3D latent space based on representative features extracted using transfer learning. In this way, using the pre-trained 3D decoder, we can recover a 3D face from 2D images. We evaluate BabyNet and show that 1) methods based on adult datasets cannot model the 3D facial geometry of babies, which proves the need for a baby-specific method, and 2) BabyNet outperforms classical model-fitting methods even when a baby-specific 3D morphable model, such as BabyFM, is used.

Antonia Alomar, Mireia Masias, Marius George Linguraru et al.

Early detection of developmental disorders can be aided by analyzing infant craniofacial morphology, but modeling infant faces is challenging due to limited data and frequent spontaneous expressions. We introduce BabyFlow, a generative AI model that disentangles facial identity and expression, enabling independent control over both. Using normalizing flows, BabyFlow learns flexible, probabilistic representations that capture the complex, non-linear variability of expressive infant faces without restrictive linear assumptions. To address scarce and uncontrolled expressive data, we perform cross-age expression transfer, adapting expressions from adult 3D scans to enrich infant datasets with realistic and systematic expressive variants. As a result, BabyFlow improves 3D reconstruction accuracy, particularly in highly expressive regions such as the mouth, eyes, and nose, and supports synthesis and modification of infant expressions while preserving identity. Additionally, by integrating with diffusion models, BabyFlow generates high-fidelity 2D infant images with consistent 3D geometry, providing powerful tools for data augmentation and early facial analysis.

Amelia Jiménez-Sánchez, Mickael Tardy, Miguel A. González Ballester et al.

For early breast cancer detection, regular screening with mammography imaging is recommended. Routinary examinations result in datasets with a predominant amount of negative samples. A potential solution to such class-imbalance is joining forces across multiple institutions. Developing a collaborative computer-aided diagnosis system is challenging in different ways. Patient privacy and regulations need to be carefully respected. Data across institutions may be acquired from different devices or imaging protocols, leading to heterogeneous non-IID data. Also, for learning-based methods, new optimization strategies working on distributed data are required. Recently, federated learning has emerged as an effective tool for collaborative learning. In this setting, local models perform computation on their private data to update the global model. The order and the frequency of local updates influence the final global model. Hence, the order in which samples are locally presented to the optimizers plays an important role. In this work, we define a memory-aware curriculum learning method for the federated setting. Our curriculum controls the order of the training samples paying special attention to those that are forgotten after the deployment of the global model. Our approach is combined with unsupervised domain adaptation to deal with domain shift while preserving data privacy. We evaluate our method with three clinical datasets from different vendors. Our results verify the effectiveness of federated adversarial learning for the multi-site breast cancer classification. Moreover, we show that our proposed memory-aware curriculum method is beneficial to further improve classification performance. Our code is publicly available at: https://github.com/ameliajimenez/curriculum-federated-learning.

Amelia Jiménez-Sánchez, Diana Mateus, Sonja Kirchhoff et al.

An adequate classification of proximal femur fractures from X-ray images is crucial for the treatment choice and the patients' clinical outcome. We rely on the commonly used AO system, which describes a hierarchical knowledge tree classifying the images into types and subtypes according to the fracture's location and complexity. In this paper, we propose a method for the automatic classification of proximal femur fractures into 3 and 7 AO classes based on a Convolutional Neural Network (CNN). As it is known, CNNs need large and representative datasets with reliable labels, which are hard to collect for the application at hand. In this paper, we design a curriculum learning (CL) approach that improves over the basic CNNs performance under such conditions. Our novel formulation reunites three curriculum strategies: individually weighting training samples, reordering the training set, and sampling subsets of data. The core of these strategies is a scoring function ranking the training samples. We define two novel scoring functions: one from domain-specific prior knowledge and an original self-paced uncertainty score. We perform experiments on a clinical dataset of proximal femur radiographs. The curriculum improves proximal femur fracture classification up to the performance of experienced trauma surgeons. The best curriculum method reorders the training set based on prior knowledge resulting into a classification improvement of 15%. Using the publicly available MNIST dataset, we further discuss and demonstrate the benefits of our unified CL formulation for three controlled and challenging digit recognition scenarios: with limited amounts of data, under class-imbalance, and in the presence of label noise. The code of our work is available at: https://github.com/ameliajimenez/curriculum-learning-prior-uncertainty.

Antonia Alomar, Ricardo Rubio, Laura Salort et al.

Craniofacial anomalies indicate early developmental disturbances and are usually linked to many genetic syndromes. Early diagnosis is critical, yet ultrasound (US) examinations often fail to identify these features. This study presents an AI-driven tool to assist clinicians in standardizing fetal facial axes/planes in 3D US, reducing sonographer workload and facilitating the facial evaluation. Our network, structured into three blocks-feature extractor, rotation and translation regression, and spatial transformer-processes three orthogonal 2D slices to estimate the necessary transformations for standardizing the facial planes in the 3D US. These transformations are applied to the original 3D US using a differentiable module (the spatial transformer block), yielding a standardized 3D US and the corresponding 2D facial standard planes. The dataset used consists of 1180 fetal facial 3D US images acquired between weeks 20 and 35 of gestation. Results show that our network considerably reduces inter-observer rotation variability in the test set, with a mean geodesic angle difference of 14.12$^{\circ}$ $\pm$ 18.27$^{\circ}$ and an Euclidean angle error of 7.45$^{\circ}$ $\pm$ 14.88$^{\circ}$. These findings demonstrate the network's ability to effectively standardize facial axes, crucial for consistent fetal facial assessments. In conclusion, the proposed network demonstrates potential for improving the consistency and accuracy of fetal facial assessments in clinical settings, facilitating early evaluation of craniofacial anomalies.

Sikha O K, Meritxell Riera-Marín, Adrian Galdran et al.

Image segmentation is a critical step in computational biomedical image analysis, typically evaluated using metrics like the Dice coefficient during training and validation. However, in clinical settings without manual annotations, assessing segmentation quality becomes challenging, and models lacking reliability indicators face adoption barriers. To address this gap, we propose a novel framework for predicting segmentation quality without requiring ground truth annotations during test time. Our approach introduces two complementary frameworks: one leveraging predicted segmentation and uncertainty maps, and another integrating the original input image, uncertainty maps, and predicted segmentation maps. We present Bayesian adaptations of two benchmark segmentation models-SwinUNet and Feature Pyramid Network with ResNet50-using Monte Carlo Dropout, Ensemble, and Test Time Augmentation to quantify uncertainty. We evaluate four uncertainty estimates: confidence map, entropy, mutual information, and expected pairwise Kullback-Leibler divergence on 2D skin lesion and 3D liver segmentation datasets, analyzing their correlation with segmentation quality metrics. Our framework achieves an R2 score of 93.25 and Pearson correlation of 96.58 on the HAM10000 dataset, outperforming previous segmentation quality assessment methods. For 3D liver segmentation, Test Time Augmentation with entropy achieves an R2 score of 85.03 and a Pearson correlation of 65.02, demonstrating cross-modality robustness. Additionally, we propose an aggregation strategy that combines multiple uncertainty estimates into a single score per image, offering a more robust and comprehensive assessment of segmentation quality. Finally, we use Grad-CAM and UMAP-based embedding analysis to interpret the model's behavior and reliability, highlighting the impact of uncertainty integration.

Comte Valentin, Gemma Piella, Mario Ceresa et al.

Cardiac diseases are among the leading causes of morbidity and mortality worldwide, which requires accurate and timely diagnostic strategies. In this study, we introduce an innovative approach that combines deep learning image registration with physics-informed regularization to predict the biomechanical properties of moving cardiac tissues and extract features for disease classification. We utilize the energy strain formulation of Neo-Hookean material to model cardiac tissue deformations, optimizing the deformation field while ensuring its physical and biomechanical coherence. This explainable approach not only improves image registration accuracy, but also provides insights into the underlying biomechanical processes of the cardiac tissues. Evaluation on the Automated Cardiac Diagnosis Challenge (ACDC) dataset achieved Dice scores of 0.945 for the left ventricular cavity, 0.908 for the right ventricular cavity, and 0.905 for the myocardium. Subsequently, we estimate the local strains within the moving heart and extract a detailed set of features used for cardiovascular disease classification. We evaluated five classification algorithms, Logistic Regression, Multi-Layer Perceptron, Support Vector Classifier, Random Forest, and Nearest Neighbour, and identified the most relevant features using a feature selection algorithm. The best performing classifier obtained a classification accuracy of 98% in the training set and 100% in the test set of the ACDC dataset. By integrating explainable artificial intelligence, this method empowers clinicians with a transparent understanding of the model's predictions based on cardiac mechanics, while also significantly improving the accuracy and reliability of cardiac disease diagnosis, paving the way for more personalized and effective patient care.

Xavier Rafael-Palou, Anton Aubanell, Mario Ceresa et al.

Early detection and quantification of tumour growth would help clinicians to prescribe more accurate treatments and provide better surgical planning. However, the multifactorial and heterogeneous nature of lung tumour progression hampers identification of growth patterns. In this study, we present a novel method based on a deep hierarchical generative and probabilistic framework that, according to radiological guidelines, predicts tumour growth, quantifies its size and provides a semantic appearance of the future nodule. Unlike previous deterministic solutions, the generative characteristic of our approach also allows us to estimate the uncertainty in the predictions, especially important for complex and doubtful cases. Results of evaluating this method on an independent test set reported a tumour growth balanced accuracy of 74%, a tumour growth size MAE of 1.77 mm and a tumour segmentation Dice score of 78%. These surpassed the performances of equivalent deterministic and alternative generative solutions (i.e. probabilistic U-Net, Bayesian test dropout and Pix2Pix GAN) confirming the suitability of our approach.

Xavier Rafael-Palou, Anton Aubanell, Mario Ceresa et al.

We address the problem of supporting radiologists in the longitudinal management of lung cancer. Therefore, we proposed a deep learning pipeline, composed of four stages that completely automatized from the detection of nodules to the classification of cancer, through the detection of growth in the nodules. In addition, the pipeline integrated a novel approach for nodule growth detection, which relied on a recent hierarchical probabilistic U-Net adapted to report uncertainty estimates. Also, a second novel method was introduced for lung cancer nodule classification, integrating into a two stream 3D-CNN network the estimated nodule malignancy probabilities derived from a pretrained nodule malignancy network. The pipeline was evaluated in a longitudinal cohort and reported comparable performances to the state of art.

Araceli Morales, Gemma Piella, Federico M. Sukno

Recently, a lot of attention has been focused on the incorporation of 3D data into face analysis and its applications. Despite providing a more accurate representation of the face, 3D facial images are more complex to acquire than 2D pictures. As a consequence, great effort has been invested in developing systems that reconstruct 3D faces from an uncalibrated 2D image. However, the 3D-from-2D face reconstruction problem is ill-posed, thus prior knowledge is needed to restrict the solutions space. In this work, we review 3D face reconstruction methods proposed in the last decade, focusing on those that only use 2D pictures captured under uncontrolled conditions. We present a classification of the proposed methods based on the technique used to add prior knowledge, considering three main strategies, namely, statistical model fitting, photometry, and deep learning, and reviewing each of them separately. In addition, given the relevance of statistical 3D facial models as prior knowledge, we explain the construction procedure and provide a list of the most popular publicly available 3D facial models. After the exhaustive study of 3D-from-2D face reconstruction approaches, we observe that the deep learning strategy is rapidly growing since the last few years, becoming the standard choice in replacement of the widespread statistical model fitting. Unlike the other two strategies, photometry-based methods have decreased in number due to the need for strong underlying assumptions that limit the quality of their reconstructions compared to statistical model fitting and deep learning methods. The review also identifies current challenges and suggests avenues for future research.

Xavier Rafael-Palou, Anton Aubanell, Ilaria Bonavita et al.

Nodule malignancy assessment is a complex, time-consuming and error-prone task. Current clinical practice requires measuring changes in size and density of the nodule at different time-points. State of the art solutions rely on 3D convolutional neural networks built on pulmonary nodules obtained from single CT scan per patient. In this work, we propose a two-stream 3D convolutional neural network that predicts malignancy by jointly analyzing two pulmonary nodule volumes from the same patient taken at different time-points. Best results achieve 77% of F1-score in test with an increment of 9% and 12% of F1-score with respect to the same network trained with images from a single time-point.

Amelia Jiménez-Sánchez, Diana Mateus, Sonja Kirchhoff et al.

Current deep-learning based methods do not easily integrate to clinical protocols, neither take full advantage of medical knowledge. In this work, we propose and compare several strategies relying on curriculum learning, to support the classification of proximal femur fracture from X-ray images, a challenging problem as reflected by existing intra- and inter-expert disagreement. Our strategies are derived from knowledge such as medical decision trees and inconsistencies in the annotations of multiple experts, which allows us to assign a degree of difficulty to each training sample. We demonstrate that if we start learning "easy" examples and move towards "hard", the model can reach a better performance, even with fewer data. The evaluation is performed on the classification of a clinical dataset of about 1000 X-ray images. Our results show that, compared to class-uniform and random strategies, the proposed medical knowledge-based curriculum, performs up to 15% better in terms of accuracy, achieving the performance of experienced trauma surgeons.

Xavier Rafael-Palou, Anton Aubanell, Ilaria Bonavita et al.

Lung cancer follow-up is a complex, error prone, and time consuming task for clinical radiologists. Several lung CT scan images taken at different time points of a given patient need to be individually inspected, looking for possible cancerogenous nodules. Radiologists mainly focus their attention in nodule size, density, and growth to assess the existence of malignancy. In this study, we present a novel method based on a 3D siamese neural network, for the re-identification of nodules in a pair of CT scans of the same patient without the need for image registration. The network was integrated into a two-stage automatic pipeline to detect, match, and predict nodule growth given pairs of CT scans. Results on an independent test set reported a nodule detection sensitivity of 94.7%, an accuracy for temporal nodule matching of 88.8%, and a sensitivity of 92.0% with a precision of 88.4% for nodule growth detection.

Ilaria Bonavita, Xavier Rafael-Palou, Mario Ceresa et al.

The early identification of malignant pulmonary nodules is critical for better lung cancer prognosis and less invasive chemo or radio therapies. Nodule malignancy assessment done by radiologists is extremely useful for planning a preventive intervention but is, unfortunately, a complex, time-consuming and error-prone task. This explains the lack of large datasets containing radiologists malignancy characterization of nodules. In this article, we propose to assess nodule malignancy through 3D convolutional neural networks and to integrate it in an automated end-to-end existing pipeline of lung cancer detection. For training and testing purposes we used independent subsets of the LIDC dataset. Adding the probabilities of nodules malignity in a baseline lung cancer pipeline improved its F1-weighted score by 14.7%, whereas integrating the malignancy model itself using transfer learning outperformed the baseline prediction by 11.8% of F1-weighted score. Despite the limited size of the lung cancer datasets, integrating predictive models of nodule malignancy improves prediction of lung cancer.

Santi Puch, Irina Sánchez, Aura Hernández et al.

In this work, we introduce the Global Planar Convolution module as a building-block for fully-convolutional networks that aggregates global information and, therefore, enhances the context perception capabilities of segmentation networks in the context of brain tumor segmentation. We implement two baseline architectures (3D UNet and a residual version of 3D UNet, ResUNet) and present a novel architecture based on these two architectures, ContextNet, that includes the proposed Global Planar Convolution module. We show that the addition of such module eliminates the need of building networks with several representation levels, which tend to be over-parametrized and to showcase slow rates of convergence. Furthermore, we provide a visual demonstration of the behavior of GPC modules via visualization of intermediate representations. We finally participate in the 2018 edition of the BraTS challenge with our best performing models, that are based on ContextNet, and report the evaluation scores on the validation and the test sets of the challenge.

Spyridon Bakas, Mauricio Reyes, Andras Jakab et al.

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.