Jose Dolz

École de Technologie Supérieure · Software Engineering

This study investigates a 3D and fully convolutional neural network (CNN) for subcortical brain structure segmentation in MRI. 3D CNN architectures have been generally avoided due to their computational and memory requirements during inference. We address the problem via small kernels, allowing deeper architectures. We further model both local and...

Precise 3D segmentation of infant brain tissues is an essential step towards comprehensive vol-umetric studies and quantitative analysis of early brain developement. However, computing such segmentations is very challenging, especially for 6-month infant brain, due to the poor image quality, among other difficulties inherent to infant brain MRI, e....

Recently, dense connections have attracted substantial attention in computer vision because they facilitate gradient flow and implicit deep supervision during training. Particularly, DenseNet, which connects each layer to every other layer in a feed-forward fashion, has shown impressive performances in natural image classification tasks. We propose...

We address the problem of segmenting 3D multi-modal medical images in scenarios where very few labeled examples are available for training. Leveraging the recent success of adversarial learning for semi-supervised segmentation, we propose a novel method based on Generative Adversarial Networks (GANs) to train a segmentation model with both labeled...

Weakly-supervised learning based on, e.g., partially labelled images or image-tags, is currently attracting significant attention in CNN segmentation as it can mitigate the need for full and laborious pixel/voxel annotations. Enforcing high-order (global) inequality constraints on the network output (for instance, to constrain the size of the targe...

With the recent raise of foundation models in computer vision and NLP, the pretrain-and-adapt strategy, where a large-scale model is fine-tuned on downstream tasks, is gaining popularity. However, traditional fine-tuning approaches may still require significant resources and yield sub-optimal results when the labeled data of the target task is scar...

Modern deep neural networks achieved remarkable progress in medical image segmentation tasks. However, it has recently been observed that they tend to produce overconfident estimates, even in situations of high uncertainty, leading to poorly calibrated and unreliable models. In this work we introduce Maximum Entropy on Erroneous Predictions (MEEP),...

Ensuring reliable confidence scores from deep networks is of pivotal importance in critical decision-making systems, notably in the medical domain. While recent literature on calibrating deep segmentation networks has led to significant progress, their uncertainty is usually modeled by leveraging the information of individual pixels, which disregar...

Neonatal MRIs are used increasingly in preterm infants. However, it is not always feasible to analyze this data. Having a tool that assesses brain maturation during this period of extraordinary changes would be immensely helpful. Approaches based on deep learning approaches could solve this task since, once properly trained and validated, they can...

Foundation vision-language models are currently transforming computer vision, and are on the rise in medical imaging fueled by their very promising generalization capabilities. However, the initial attempts to transfer this new paradigm to medical imaging have shown less impressive performances than those observed in other domains, due to the signi...

Despite the recent progress in incremental learning, addressing catastrophic forgetting under distributional drift is still an open and important problem. Indeed, while state-of-the-art domain incremental learning (DIL) methods perform satisfactorily within known domains, their performance largely degrades in the presence of novel domains. This lim...

Recently, CLIP-based approaches have exhibited remarkable performance on generalization and few-shot learning tasks, fueled by the power of contrastive language-vision pre-training. In particular, prompt tuning has emerged as an effective strategy to adapt the pre-trained language-vision models to downstream tasks by employing task-related textual...

In this paper, we propose an unsupervised framework based on normalizing flows that harmonizes MR images to mimic the distribution of the source domain. The proposed framework consists of three steps. First, a shallow harmonizer network is trained to recover images of the source domain from their augmented versions. A normalizing flow network is th...

Privacy protection in medical data is a legitimate obstacle for centralized machine learning applications. Here, we propose a client-server image segmentation system which allows for the analysis of multi-centric medical images while preserving patient privacy. In this approach, the client protects the to-be-segmented patient image by mixing it to...

Privacy protection in medical data is a legitimate obstacle for centralized machine learning applications. Here, we propose a client-server image segmentation system which allows for the analysis of multi-centric medical images while preserving patient privacy. In this approach, the client protects the to-be-segmented patient image by mixing it to...

Despite the undeniable progress in visual recognition tasks fueled by deep neural networks, there exists recent evidence showing that these models are poorly calibrated, resulting in over-confident predictions. The standard practices of minimizing the cross-entropy loss during training promote the predicted softmax probabilities to match the one-ho...

With the recent raise of foundation models in computer vision and NLP, the pretrain-and-adapt strategy, where a large-scale model is fine-tuned on downstream tasks, is gaining popularity. However, traditional fine-tuning approaches may still require significant resources and yield sub-optimal results when the labeled data of the target task is scar...

Ensuring reliable confidence scores from deep networks is of pivotal importance in critical decision-making systems, notably in the medical domain. While recent literature on calibrating deep segmentation networks has led to significant progress, their uncertainty is usually modeled by leveraging the information of individual pixels, which disregar...

Using state-of-the-art deep learning (DL) models to diagnose cancer from histology data presents several challenges related to the nature and availability of labeled histology images, including image size, stain variations, and label ambiguity. In addition, cancer grading and the localization of regions of interest (ROIs) in such images normally re...

In this paper, we propose an unsupervised framework based on normalizing flows that harmonizes MR images to mimic the distribution of the source domain. The proposed framework consists of three steps. First, a shallow harmonizer network is trained to recover images of the source domain from their augmented versions. A normalizing flow network is th...

We introduce an information-maximization approach for the Generalized Category Discovery (GCD) problem. Specifically, we explore a parametric family of loss functions evaluating the mutual information between the features and the labels, and find automatically the one that maximizes the predictive performances. Furthermore, we introduce the Elbow M...

Recent studies have revealed that, beyond conventional accuracy, calibration should also be considered for training modern deep neural networks. To address miscalibration during learning, some methods have explored different penalty functions as part of the learning objective, alongside a standard classification loss, with a hyper-parameter control...

This paper introduces a generalized few-shot segmentation framework with a straightforward training process and an easy-to-optimize inference phase. In particular, we propose a simple yet effective model based on the well-known InfoMax principle, where the Mutual Information (MI) between the learned feature representations and their corresponding p...

Despite achieving promising results in a breadth of medical image segmentation tasks, deep neural networks (DNNs) require large training datasets with pixel-wise annotations. Obtaining these curated datasets is a cumbersome process which limits the applicability of DNNs in scenarios where annotated images are scarce. Mixed supervision is an appeali...

Semi-supervised segmentation tackles the scarcity of annotations by leveraging unlabeled data with a small amount of labeled data. A prominent way to utilize the unlabeled data is by consistency training which commonly uses a teacher-student network, where a teacher guides a student segmentation. The predictions of unlabeled data are not reliable,...

Estimating the prediction uncertainty of a deep segmentation network is very useful in multiple learning scenarios. For example, in the semi-supervised learning paradigm, the vast majority of recent methods rely on pseudo-label generation to leverage unlabeled data, whose training is guided by uncertainty estimates. While the commonly-used entropy-...

Despite the undeniable progress in visual recognition tasks fueled by deep neural networks, there exists recent evidence showing that these models are poorly calibrated, resulting in over-confident predictions. The standard practices of minimizing the cross entropy loss during training promote the predicted softmax probabilities to match the one-ho...

Domain adaptation (DA) has drawn high interest for its capacity to adapt a model trained on labeled source data to perform well on unlabeled or weakly labeled target data from a different domain. Most common DA techniques require concurrent access to the input images of both the source and target domains. However, in practice, privacy concerns ofte...

Learning similarity is a key aspect in medical image analysis, particularly in recommendation systems or in uncovering the interpretation of anatomical data in images. Most existing methods learn such similarities in the embedding space over image sets using a single metric learner. Images, however, have a variety of object attributes such as color...

Learning similarity is a key aspect in medical image analysis, particularly in recommendation systems or in uncovering the interpretation of anatomical data in images. Most existing methods learn such similarities in the embedding space over image sets using a single metric learner. Images, however, have a variety of object attributes such as color...

Current unsupervised anomaly localization approaches rely on generative models to learn the distribution of normal images, which is later used to identify potential anomalous regions derived from errors on the reconstructed images. To address the limitations of residual-based anomaly localization, very recent literature has focused on attention map...

Trained using only image class label, deep weakly supervised methods allow image classification and ROI segmentation for interpretability. Despite their success on natural images, they face several challenges over histology data where ROI are visually similar to background making models vulnerable to high pixel-wise false positives. These methods l...

Trained using only image class label, deep weakly supervised methods allow image classification and ROI segmentation for interpretability. Despite their success on natural images, they face several challenges over histology data where ROI are visually similar to background making models vulnerable to high pixel-wise false positives. These methods l...

Recent advances in unsupervised domain adaptation have significantly improved the recognition accuracy of CNNs by alleviating the domain shift between (labeled) source and (unlabeled) target data distributions. While the problem of single-target domain adaptation (STDA) for object detection has recently received much attention, multi-target domain...

The segmentation of retinal vasculature from eye fundus images is a fundamental task in retinal image analysis. Over recent years, increasingly complex approaches based on sophisticated Convolutional Neural Network architectures have been pushing performance on well-established benchmark datasets. In this paper, we take a step back and analyze the...

Semi-supervised segmentation tackles the scarcity of annotations by leveraging unlabeled data with a small amount of labeled data. A prominent way to utilize the unlabeled data is by consistency training which commonly uses a teacher-student network, where a teacher guides a student segmentation. The predictions of unlabeled data are not reliable,...

Semi-supervised learning has emerged as an appealing strategy to train deep models with limited supervision. Most prior literature under this learning paradigm resorts to dual-based architectures, typically composed of a teacher-student duple. To drive the learning of the student, many of these models leverage the aleatoric uncertainty derived from...

Current unsupervised anomaly localization approaches rely on generative models to learn the distribution of normal images, which is later used to identify potential anomalous regions derived from errors on the reconstructed images. However, a main limitation of nearly all prior literature is the need of employing anomalous images to set a class-spe...

Weakly supervised learning has emerged as an appealing alternative to alleviate the need for large labeled datasets in semantic segmentation. Most current approaches exploit class activation maps (CAMs), which can be generated from image-level annotations. Nevertheless, resulting maps have been demonstrated to be highly discriminant, failing to ser...

Modern deep neural networks have achieved remarkable progress in medical image segmentation tasks. However, it has recently been observed that they tend to produce overconfident estimates, even in situations of high uncertainty, leading to poorly calibrated and unreliable models. In this work we introduce Maximum Entropy on Erroneous Predictions (M...

In spite of the dominant performances of deep neural networks, recent works have shown that they are poorly calibrated, resulting in over-confident predictions. Miscalibration can be exacerbated by overfitting due to the minimization of the cross-entropy during training, as it promotes the predicted softmax probabilities to match the one-hot label...

In this paper, we present a self-training-based framework for glaucoma grading using OCT B-scans under the presence of domain shift. Particularly, the proposed two-step learning methodology resorts to pseudo-labels generated during the first step to augment the training dataset on the target domain, which is then used to train the final target mode...

Weakly-supervised learning (WSL) has recently triggered substantial interest as it mitigates the lack of pixel-wise annotations. Given global image labels, WSL methods yield pixel-level predictions (segmentations), which enable to interpret class predictions. Despite their recent success, mostly with natural images, such methods can face important...

Despite achieving promising results in a breadth of medical image segmentation tasks, deep neural networks require large training datasets with pixel-wise annotations. Obtaining these curated datasets is a cumbersome process which limits the application in scenarios where annotated images are scarce. Mixed supervision is an appealing alternative fo...

Despite the astonishing performance of deep-learning based approaches for visual tasks such as semantic segmentation, they are known to produce miscalibrated predictions, which could be harmful for critical decision-making processes. Ensemble learning has shown to not only boost the performance of individual models but also reduce their miscalibrat...

Current unsupervised anomaly localization approaches rely on generative models to learn the distribution of normal images, which is later used to identify potential anomalous regions derived from errors on the reconstructed images. However, a main limitation of nearly all prior literature is the need of employing anomalous images to set a class-spe...

Domain adaptation (DA) has drawn high interest for its capacity to adapt a model trained on labeled source data to perform well on unlabeled or weakly labeled target data from a different domain. Most common DA techniques require concurrent access to the input images of both the source and target domains. However, in practice, privacy concerns ofte...

We introduce Transductive Infomation Maximization (TIM) for few-shot learning. Our method maximizes the mutual information between the query features and their label predictions for a given few-shot task, in conjunction with a supervision loss based on the support set. We motivate our transductive loss by deriving a formal relation between the clas...

We investigate a general formulation for clustering and transductive few-shot learning, which integrates prototype-based objectives, Laplacian regularization and supervision constraints from a few labeled data points. We propose a concave-convex relaxation of the problem, and derive a computationally efficient block-coordinate bound optimizer, with...

Deep neural networks have achieved promising results in a breadth of medical image segmentation tasks. Nevertheless, they require large training datasets with pixel-wise segmentations, which are expensive to obtain in practice. Mixed supervision could mitigate this difficulty, with a small fraction of the data containing complete pixel-wise annotat...

Unsupervised domain adaptation (UDA) seeks to alleviate the problem of domain shift between the distribution of unlabeled data from the target domain w.r.t. labeled data from the source domain. While the single-target UDA scenario is well studied in the literature, Multi-Target Domain Adaptation (MTDA) remains largely unexplored despite its practic...

Despite the astonishing performance of deep-learning based approaches for visual tasks such as semantic segmentation, they are known to produce miscalibrated predictions, which could be harmful for critical decision-making processes. Ensemble learning has shown to not only boost the performance of individual models but also reduce their miscalibrat...

Prostate cancer is one of the main diseases affecting men worldwide. The gold standard for diagnosis and prognosis is the Gleason grading system. In this process, pathologists manually analyze prostate histology slides under microscope, in a high time-consuming and subjective task. In the last years, computer-aided-diagnosis (CAD) systems have emer...

Standard losses for training deep segmentation networks could be seen as individual classifications of pixels, instead of supervising the global shape of the predicted segmentations. While effective, they require exact knowledge of the label of each pixel in an image. This study investigates how effective global geometric shape descriptors could be...

Precise determination and assessment of bladder cancer (BC) extent of muscle invasion involvement guides proper risk stratification and personalized therapy selection. In this context, segmentation of both bladder walls and cancer are of pivotal importance, as it provides invaluable information to stage the primary tumor. Hence, multiregion segment...

Most segmentation losses are arguably variants of the Cross-Entropy (CE) or Dice loss. In the literature, there is no clear consensus as to which of these losses is a better choice, with varying performances for each across different benchmarks and applications. We develop a theoretical analysis that links these two types of losses, exposing their...

Techniques for multi-target domain adaptation (MTDA) seek to adapt a recognition model such that it can generalize well across multiple target domains. While several successful techniques have been proposed for unsupervised single-target domain adaptation (STDA) in object detection, adapting a model to multiple target domains using unlabeled image...

Weakly supervised learning has emerged as an appealing alternative to alleviate the need for large labeled datasets in semantic segmentation. Most current approaches exploit class activation maps (CAMs), which can be generated from image-level annotations. Nevertheless, resulting maps have been demonstrated to be highly discriminant, failing to ser...

Domain Adaption tasks have recently attracted substantial attention in computer vision as they improve the transferability of deep network models from a source to a target domain with different characteristics. A large body of state-of-the-art domain-adaptation methods was developed for image classification purposes, which may be inadequate for seg...