Jose Dolz

Sina Hajimiri, Malik Boudiaf, Ismail Ben Ayed et al.

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 predictions is maximized. In addition, the terms derived from our MI-based formulation are coupled with a knowledge distillation term to retain the knowledge on base classes. With a simple training process, our inference model can be applied on top of any segmentation network trained on base classes. The proposed inference yields substantial improvements on the popular few-shot segmentation benchmarks, PASCAL-$5^i$ and COCO-$20^i$. Particularly, for novel classes, the improvement gains range from 7% to 26% (PASCAL-$5^i$) and from 3% to 12% (COCO-$20^i$) in the 1-shot and 5-shot scenarios, respectively. Furthermore, we propose a more challenging setting, where performance gaps are further exacerbated. Our code is publicly available at https://github.com/sinahmr/DIaM.

Balamurali Murugesan, Julio Silva-Rodriguez, Ismail Ben Ayed et al.

This paper addresses the critical issue of miscalibration in CLIP-based model adaptation, particularly in the challenging scenario of out-of-distribution (OOD) samples, which has been overlooked in the existing literature on CLIP adaptation. We empirically demonstrate that popular CLIP adaptation approaches, such as Adapters, Prompt Learning, and Test-Time Adaptation, substantially degrade the calibration capabilities of the zero-shot baseline in the presence of distributional drift. We identify the increase in logit ranges as the underlying cause of miscalibration of CLIP adaptation methods, contrasting with previous work on calibrating fully-supervised models. Motivated by these observations, we present a simple and model-agnostic solution to mitigate miscalibration, by scaling the logit range of each sample to its zero-shot prediction logits. We explore three different alternatives to achieve this, which can be either integrated during adaptation or directly used at inference time. Comprehensive experiments on popular OOD classification benchmarks demonstrate the effectiveness of the proposed approaches in mitigating miscalibration while maintaining discriminative performance, whose improvements are consistent across the three families of these increasingly popular approaches. The code is publicly available at: https://github.com/Bala93/CLIPCalib

Fereshteh Shakeri, Yunshi Huang, Julio Silva-Rodríguez et al.

Integrating image and text data through multi-modal learning has emerged as a new approach in medical imaging research, following its successful deployment in computer vision. While considerable efforts have been dedicated to establishing medical foundation models and their zero-shot transfer to downstream tasks, the popular few-shot setting remains relatively unexplored. Following on from the currently strong emergence of this setting in computer vision, we introduce the first structured benchmark for adapting medical vision-language models (VLMs) in a strict few-shot regime and investigate various adaptation strategies commonly used in the context of natural images. Furthermore, we evaluate a simple generalization of the linear-probe adaptation baseline, which seeks an optimal blending of the visual prototypes and text embeddings via learnable class-wise multipliers. Surprisingly, such a text-informed linear probe yields competitive performances in comparison to convoluted prompt-learning and adapter-based strategies, while running considerably faster and accommodating the black-box setting. Our extensive experiments span three different medical modalities and specialized foundation models, nine downstream tasks, and several state-of-the-art few-shot adaptation methods. We made our benchmark and code publicly available to trigger further developments in this emergent subject: \url{https://github.com/FereshteShakeri/few-shot-MedVLMs}.

Bingyuan Liu, Jérôme Rony, Adrian Galdran et al.

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 controlling the relative contribution of each term. Nevertheless, these methods share two major drawbacks: 1) the scalar balancing weight is the same for all classes, hindering the ability to address different intrinsic difficulties or imbalance among classes; and 2) the balancing weight is usually fixed without an adaptive strategy, which may prevent from reaching the best compromise between accuracy and calibration, and requires hyper-parameter search for each application. We propose Class Adaptive Label Smoothing (CALS) for calibrating deep networks, which allows to learn class-wise multipliers during training, yielding a powerful alternative to common label smoothing penalties. Our method builds on a general Augmented Lagrangian approach, a well-established technique in constrained optimization, but we introduce several modifications to tailor it for large-scale, class-adaptive training. Comprehensive evaluation and multiple comparisons on a variety of benchmarks, including standard and long-tailed image classification, semantic segmentation, and text classification, demonstrate the superiority of the proposed method. The code is available at https://github.com/by-liu/CALS.

Balamurali Murugesan, Rukhshanda Hussain, Rajarshi Bhattacharya et al.

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 tokens. Motivated by this progress, in this work we question whether other fundamental problems, such as weakly supervised semantic segmentation (WSSS), can benefit from prompt tuning. Our findings reveal two interesting observations that shed light on the impact of prompt tuning on WSSS. First, modifying only the class token of the text prompt results in a greater impact on the Class Activation Map (CAM), compared to arguably more complex strategies that optimize the context. And second, the class token associated with the image ground truth does not necessarily correspond to the category that yields the best CAM. Motivated by these observations, we introduce a novel approach based on a PrOmpt cLass lEarning (POLE) strategy. Through extensive experiments we demonstrate that our simple, yet efficient approach achieves SOTA performance in a well-known WSSS benchmark. These results highlight not only the benefits of language-vision models in WSSS but also the potential of prompt learning for this problem. The code is available at https://github.com/rB080/WSS_POLE.

Farzad Beizaee, Gregory A. Lodygensky, Chris L. Adamson et al.

Lack of standardization and various intrinsic parameters for magnetic resonance (MR) image acquisition results in heterogeneous images across different sites and devices, which adversely affects the generalization of deep neural networks. To alleviate this issue, this work proposes a novel unsupervised harmonization framework that leverages normalizing flows to align MR images, thereby emulating the distribution of a source domain. The proposed strategy comprises three key steps. Initially, a normalizing flow network is trained to capture the distribution characteristics of the source domain. Then, we train a shallow harmonizer network to reconstruct images from the source domain via their augmented counterparts. Finally, during inference, the harmonizer network is updated to ensure that the output images conform to the learned source domain distribution, as modeled by the normalizing flow network. Our approach, which is unsupervised, source-free, and task-agnostic is assessed in the context of both adults and neonatal cross-domain brain MRI segmentation, as well as neonatal brain age estimation, demonstrating its generalizability across tasks and population demographics. The results underscore its superior performance compared to existing methodologies. The code is available at https://github.com/farzad-bz/Harmonizing-Flows

Julio Silva-Rodríguez, Hadi Chakor, Riadh Kobbi et al.

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 significant domain shift and the complex, expert domain knowledge inherent to medical-imaging tasks. Motivated by the need for domain-expert foundation models, we present FLAIR, a pre-trained vision-language model for universal retinal fundus image understanding. To this end, we compiled 38 open-access, mostly categorical fundus imaging datasets from various sources, with up to 101 different target conditions and 288,307 images. We integrate the expert's domain knowledge in the form of descriptive textual prompts, during both pre-training and zero-shot inference, enhancing the less-informative categorical supervision of the data. Such a textual expert's knowledge, which we compiled from the relevant clinical literature and community standards, describes the fine-grained features of the pathologies as well as the hierarchies and dependencies between them. We report comprehensive evaluations, which illustrate the benefit of integrating expert knowledge and the strong generalization capabilities of FLAIR under difficult scenarios with domain shifts or unseen categories. When adapted with a lightweight linear probe, FLAIR outperforms fully-trained, dataset-focused models, more so in the few-shot regimes. Interestingly, FLAIR outperforms by a wide margin larger-scale generalist image-language models and retina domain-specific self-supervised networks, which emphasizes the potential of embedding experts' domain knowledge and the limitations of generalist models in medical imaging.

Florent Chiaroni, Jose Dolz, Ziko Imtiaz Masud et al.

We introduce a Parametric Information Maximization (PIM) model for the Generalized Category Discovery (GCD) problem. Specifically, we propose a bi-level optimization formulation, which explores a parameterized family of objective functions, each evaluating a weighted mutual information between the features and the latent labels, subject to supervision constraints from the labeled samples. Our formulation mitigates the class-balance bias encoded in standard information maximization approaches, thereby handling effectively both short-tailed and long-tailed data sets. We report extensive experiments and comparisons demonstrating that our PIM model consistently sets new state-of-the-art performances in GCD across six different datasets, more so when dealing with challenging fine-grained problems.

Sukesh Adiga, Jose Dolz, Herve Lombaert

Semi-supervised learning relaxes the need of large pixel-wise labeled datasets for image segmentation by leveraging unlabeled data. A prominent way to exploit unlabeled data is to regularize model predictions. Since the predictions of unlabeled data can be unreliable, uncertainty-aware schemes are typically employed to gradually learn from meaningful and reliable predictions. Uncertainty estimation methods, however, rely on multiple inferences from the model predictions that must be computed for each training step, which is computationally expensive. Moreover, these uncertainty maps capture pixel-wise disparities and do not consider global information. This work proposes a novel method to estimate segmentation uncertainty by leveraging global information from the segmentation masks. More precisely, an anatomically-aware representation is first learnt to model the available segmentation masks. The learnt representation thereupon maps the prediction of a new segmentation into an anatomically-plausible segmentation. The deviation from the plausible segmentation aids in estimating the underlying pixel-level uncertainty in order to further guide the segmentation network. The proposed method consequently estimates the uncertainty using a single inference from our representation, thereby reducing the total computation. We evaluate our method on two publicly available segmentation datasets of left atria in cardiac MRIs and of multiple organs in abdominal CTs. Our anatomically-aware method improves the segmentation accuracy over the state-of-the-art semi-supervised methods in terms of two commonly used evaluation metrics.

Julio Silva-Rodríguez, Jose Dolz, Ismail Ben Ayed

The recent popularity of foundation models and the pre-train-and-adapt paradigm, where a large-scale model is transferred to downstream tasks, is gaining attention for volumetric medical image segmentation. However, current transfer learning strategies devoted to full fine-tuning for transfer learning may require significant resources and yield sub-optimal results when the labeled data of the target task is scarce. This makes its applicability in real clinical settings challenging since these institutions are usually constrained on data and computational resources to develop proprietary solutions. To address this challenge, we formalize Few-Shot Efficient Fine-Tuning (FSEFT), a novel and realistic scenario for adapting medical image segmentation foundation models. This setting considers the key role of both data- and parameter-efficiency during adaptation. Building on a foundation model pre-trained on open-access CT organ segmentation sources, we propose leveraging Parameter-Efficient Fine-Tuning and black-box Adapters to address such challenges. Furthermore, novel efficient adaptation methodologies are introduced in this work, which include Spatial black-box Adapters that are more appropriate for dense prediction tasks and constrained transductive inference, leveraging task-specific prior knowledge. Our comprehensive transfer learning experiments confirm the suitability of foundation models in medical image segmentation and unveil the limitations of popular fine-tuning strategies in few-shot scenarios.

Julio Silva-Rodríguez, Valery Naranjo, Jose Dolz

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-specific threshold to locate the anomalies. This limits their usability in realistic scenarios, where only normal data is typically accessible. Despite this major drawback, only a handful of works have addressed this limitation, by integrating supervision on attention maps during training. In this work, we propose a novel formulation that does not require accessing images with abnormalities to define the threshold. Furthermore, and in contrast to very recent work, the proposed constraint is formulated in a more principled manner, leveraging well-known knowledge in constrained optimization. In particular, the equality constraint on the attention maps in prior work is replaced by an inequality constraint, which allows more flexibility. In addition, to address the limitations of penalty-based functions we employ an extension of the popular log-barrier methods to handle the constraint. Last, we propose an alternative regularization term that maximizes the Shannon entropy of the attention maps, reducing the amount of hyperparameters of the proposed model. Comprehensive experiments on two publicly available datasets on brain lesion segmentation demonstrate that the proposed approach substantially outperforms relevant literature, establishing new state-of-the-art results for unsupervised lesion segmentation, and without the need to access anomalous images.

Balamurali Murugesan, Sukesh Adiga, Bingyuan Liu et al.

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 disregards the local structure of the object of interest. In particular, only the recent Spatially Varying Label Smoothing (SVLS) approach addresses this issue by softening the pixel label assignments with a discrete spatial Gaussian kernel. In this work, we first present a constrained optimization perspective of SVLS and demonstrate that it enforces an implicit constraint on soft class proportions of surrounding pixels. Furthermore, our analysis shows that SVLS lacks a mechanism to balance the contribution of the constraint with the primary objective, potentially hindering the optimization process. Based on these observations, we propose a principled and simple solution based on equality constraints on the logit values, which enables to control explicitly both the enforced constraint and the weight of the penalty, offering more flexibility. Comprehensive experiments on a variety of well-known segmentation benchmarks demonstrate the superior performance of the proposed approach.

Sukesh Adiga, Jose Dolz, Herve Lombaert

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, therefore, uncertainty-aware methods have been proposed to gradually learn from meaningful and reliable predictions. Uncertainty estimation, however, relies on multiple inferences from model predictions that need to be computed for each training step, which is computationally expensive. This work proposes a novel method to estimate the pixel-level uncertainty by leveraging the labeling representation of segmentation masks. On the one hand, a labeling representation is learnt to represent the available segmentation masks. The learnt labeling representation is used to map the prediction of the segmentation into a set of plausible masks. Such a reconstructed segmentation mask aids in estimating the pixel-level uncertainty guiding the segmentation network. The proposed method estimates the uncertainty with a single inference from the labeling representation, thereby reducing the total computation. We evaluate our method on the 3D segmentation of left atrium in MRI, and we show that our uncertainty estimates from our labeling representation improve the segmentation accuracy over state-of-the-art methods.

Farzad Beizaee, Christian Desrosiers, Gregory A. Lodygensky et al.

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 then trained to learn the distribution of the source domain. Finally, at test time, a harmonizer network is modified so that the output images match the source domain's distribution learned by the normalizing flow model. Our unsupervised, source-free and task-independent approach is evaluated on cross-domain brain MRI segmentation using data from four different sites. Results demonstrate its superior performance compared to existing methods.

Julien Nicolas, Florent Chiaroni, Imtiaz Ziko et al.

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 limitation hampers their generalizability, and restricts their scalability to more realistic settings where train and test data are drawn from different distributions. To address these limitations, we present a novel DIL approach based on a mixture of prompt-tuned CLIP models (MoP-CLIP), which generalizes the paradigm of S-Prompting to handle both in-distribution and out-of-distribution data at inference. In particular, at the training stage we model the features distribution of every class in each domain, learning individual text and visual prompts to adapt to a given domain. At inference, the learned distributions allow us to identify whether a given test sample belongs to a known domain, selecting the correct prompt for the classification task, or from an unseen domain, leveraging a mixture of the prompt-tuned CLIP models. Our empirical evaluation reveals the poor performance of existing DIL methods under domain shift, and suggests that the proposed MoP-CLIP performs competitively in the standard DIL settings while outperforming state-of-the-art methods in OOD scenarios. These results demonstrate the superiority of MoP-CLIP, offering a robust and general solution to the problem of domain incremental learning.

Balamurali Murugesan, Bingyuan Liu, Adrian Galdran et al.

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-hot label assignments. Nevertheless, this yields a pre-softmax activation of the correct class that is significantly larger than the remaining activations, which exacerbates the miscalibration problem. Recent observations from the classification literature suggest that loss functions that embed implicit or explicit maximization of the entropy of predictions yield state-of-the-art calibration performances. Despite these findings, the impact of these losses in the relevant task of calibrating medical image segmentation networks remains unexplored. In this work, we provide a unifying constrained-optimization perspective of current state-of-the-art calibration losses. Specifically, these losses could be viewed as approximations of a linear penalty (or a Lagrangian term) imposing equality constraints on logit distances. This points to an important limitation of such underlying equality constraints, whose ensuing gradients constantly push towards a non-informative solution, which might prevent from reaching the best compromise between the discriminative performance and calibration of the model during gradient-based optimization. Following our observations, we propose a simple and flexible generalization based on inequality constraints, which imposes a controllable margin on logit distances. Comprehensive experiments on a variety of public medical image segmentation benchmarks demonstrate that our method sets novel state-of-the-art results on these tasks in terms of network calibration, whereas the discriminative performance is also improved.

Martin Van Waerebeke, Gregory Lodygensky, Jose Dolz

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 the entropy of the predictions. While this has shown to work well in a binary scenario, we demonstrate in this work that this strategy leads to suboptimal results in a multi-class context, a more realistic and challenging setting. We argue, indeed, that these approaches underperform due to the erroneous uncertainty approximations in the presence of inter-class overlap. Furthermore, we propose an alternative solution to compute the uncertainty in a multi-class setting, based on divergence distances and which account for inter-class overlap. We evaluate the proposed solution on a challenging multi-class segmentation dataset and in two well-known uncertainty-based segmentation methods. The reported results demonstrate that by simply replacing the mechanism used to compute the uncertainty, our proposed solution brings substantial improvement on tested setups.

Badr-Eddine Marani, Julio Silva-Rodriguez, Ismail Ben Ayed et al.

Deep neural networks have achieved remarkable success across a variety of tasks, yet they often suffer from unreliable probability estimates. As a result, they can be overconfident in their predictions. Conformal Prediction (CP) offers a principled framework for uncertainty quantification, yielding prediction sets with rigorous coverage guarantees. Existing conformal training methods optimize for overall set size, but shaping the prediction sets in a class-conditional manner is not straightforward and typically requires prior knowledge of the data distribution. In this work, we introduce Class Adaptive Conformal Training (CaCT), which formulates conformal training as an augmented Lagrangian optimization problem that adaptively learns to shape prediction sets class-conditionally without making any distributional assumptions. Experiments on multiple benchmark datasets, including standard and long-tailed image recognition as well as text classification, demonstrate that CaCT consistently outperforms prior conformal training methods, producing significantly smaller and more informative prediction sets while maintaining the desired coverage guarantees.

Leo Fillioux, Omprakash Chakraborty, Ismail Ben Ayed et al.

With the increasing adoption of vision-language models (VLMs) in critical decision-making systems such as healthcare or autonomous driving, the calibration of their uncertainty estimates becomes paramount. Yet, this dimension has been largely underexplored in the VLM test-time prompt-tuning (TPT) literature, which has predominantly focused on improving their discriminative performance. Recent state-of-the-art advocates for enforcing full orthogonality over pairs of text prompt embeddings to enhance separability, and therefore calibration. Nevertheless, as we theoretically show in this work, the inherent gradients from fully orthogonal constraints will strongly push semantically related classes away, ultimately making the model overconfident. Based on our findings, we propose Semantic Orthogonal Calibration (SoC), a Huber-based regularizer that enforces smooth prototype separation while preserving semantic proximity, thereby improving calibration compared to prior orthogonality-based approaches. Across a comprehensive empirical validation, we demonstrate that SoC consistently improves calibration performance, while also maintaining competitive discriminative capabilities.

Sukesh Adiga, Jose Dolz, Herve Lombaert

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, shape, or artifacts. Encoding such attributes using a single metric learner is inadequate and may fail to generalize. Instead, multiple learners could focus on separate aspects of these attributes in subspaces of an overarching embedding. This, however, implies the number of learners to be found empirically for each new dataset. This work, Dynamic Subspace Learners, proposes to dynamically exploit multiple learners by removing the need of knowing apriori the number of learners and aggregating new subspace learners during training. Furthermore, the visual interpretability of such subspace learning is enforced by integrating an attention module into our method. This integrated attention mechanism provides a visual insight of discriminative image features that contribute to the clustering of image sets and a visual explanation of the embedding features. The benefits of our attention-based dynamic subspace learners are evaluated in the application of image clustering, image retrieval, and weakly supervised segmentation. Our method achieves competitive results with the performances of multiple learners baselines and significantly outperforms the classification network in terms of clustering and retrieval scores on three different public benchmark datasets. Moreover, our attention maps offer a proxy-labels, which improves the segmentation accuracy up to 15% in Dice scores when compared to state-of-the-art interpretation techniques.

Soufiane Belharbi, Jérôme Rony, Jose Dolz et al.

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 lack mechanisms for modeling explicitly non-discriminative regions which raises false-positive rates. We propose novel regularization terms, which enable the model to seek both non-discriminative and discriminative regions, while discouraging unbalanced segmentations and using only image class label. Our method is composed of two networks: a localizer that yields segmentation mask, followed by a classifier. The training loss pushes the localizer to build a segmentation mask that holds most discrimiantive regions while simultaneously modeling background regions. Comprehensive experiments over two histology datasets showed the merits of our method in reducing false positives and accurately segmenting ROI.

Omprakash Chakraborty, Jose Dolz, Ismail Ben Ayed

Vision language models (VLMs) have demonstrated remarkable generalization across diverse tasks, yet their performance remains constrained by the quality and geometry of the textual prototypes used to represent classes. Standard zero shot classifiers, derived from frozen text encoders and handcrafted prompts, may yield correlated or weakly separated embeddings that limit task specific discriminability. We introduce ORION, a text encoder fine tuning framework that improves pretrained VLMs using only class names. Our method optimizes, via low rank adaptation, a novel loss integrating two terms, one promoting pairwise orthogonality between the textual representations of the classes of a given task and the other penalizing deviations from the initial class prototypes. Furthermore, we provide a probabilistic interpretation of our orthogonality penalty, connecting it to the general maximum likelihood estimation (MLE) principle via Huygens theorem. We report extensive experiments on 11 benchmarks and three large VLM backbones, showing that the refined textual embeddings yield powerful replacements for the standard CLIP prototypes. Added as plug and play module on top of various state of the art methods, and across different prediction settings (zero shot, few shot and test time adaptation), ORION improves the performance consistently and significantly.

Kunal Mahatha, Jose Dolz, Christian Desrosiers

Despite recent advances in Open-Vocabulary Semantic Segmentation (OVSS), existing training-free methods face several limitations: use of computationally expensive affinity refinement strategies, ineffective fusion of transformer attention maps due to equal weighting or reliance on fixed-size Gaussian kernels to reinforce local spatial smoothness, enforcing isotropic neighborhoods. We propose a strong baseline for training-free OVSS termed as NERVE (Neighbourhood \& Entropy-guided Random-walk for open-Vocabulary sEgmentation), which uniquely integrates global and fine-grained local information, exploiting the neighbourhood structure from the self-attention layer of a stable diffusion model. We also introduce a stochastic random walk for refining the affinity rather than relying on fixed-size Gaussian kernels for local context. This spatial diffusion process encourages propagation across connected and semantically related areas, enabling it to effectively delineate objects with arbitrary shapes. Whereas most existing approaches treat self-attention maps from different transformer heads or layers equally, our method uses entropy-based uncertainty to select the most relevant maps. Notably, our method does not require any conventional post-processing techniques like Conditional Random Fields (CRF) or Pixel-Adaptive Mask Refinement (PAMR). Experiments are performed on 7 popular semantic segmentation benchmarks, yielding an overall state-of-the-art zero-shot segmentation performance, providing an effective approach to open-vocabulary semantic segmentation.

Yunshi Huang, Fereshteh Shakeri, Jose Dolz et al.

In a recent, strongly emergent literature on few-shot CLIP adaptation, Linear Probe (LP) has been often reported as a weak baseline. This has motivated intensive research building convoluted prompt learning or feature adaptation strategies. In this work, we propose and examine from convex-optimization perspectives a generalization of the standard LP baseline, in which the linear classifier weights are learnable functions of the text embedding, with class-wise multipliers blending image and text knowledge. As our objective function depends on two types of variables, i.e., the class visual prototypes and the learnable blending parameters, we propose a computationally efficient block coordinate Majorize-Minimize (MM) descent algorithm. In our full-batch MM optimizer, which we coin LP++, step sizes are implicit, unlike standard gradient descent practices where learning rates are intensively searched over validation sets. By examining the mathematical properties of our loss (e.g., Lipschitz gradient continuity), we build majorizing functions yielding data-driven learning rates and derive approximations of the loss's minima, which provide data-informed initialization of the variables. Our image-language objective function, along with these non-trivial optimization insights and ingredients, yields, surprisingly, highly competitive few-shot CLIP performances. Furthermore, LP++ operates in black-box, relaxes intensive validation searches for the optimization hyper-parameters, and runs orders-of-magnitudes faster than state-of-the-art few-shot CLIP adaptation methods. Our code is available at: \url{https://github.com/FereshteShakeri/FewShot-CLIP-Strong-Baseline.git}.

Sina Hajimiri, Ismail Ben Ayed, Jose Dolz

Despite the significant progress in deep learning for dense visual recognition problems, such as semantic segmentation, traditional methods are constrained by fixed class sets. Meanwhile, vision-language foundation models, such as CLIP, have showcased remarkable effectiveness in numerous zero-shot image-level tasks, owing to their robust generalizability. Recently, a body of work has investigated utilizing these models in open-vocabulary semantic segmentation (OVSS). However, existing approaches often rely on impractical supervised pre-training or access to additional pre-trained networks. In this work, we propose a strong baseline for training-free OVSS, termed Neighbour-Aware CLIP (NACLIP), representing a straightforward adaptation of CLIP tailored for this scenario. Our method enforces localization of patches in the self-attention of CLIP's vision transformer which, despite being crucial for dense prediction tasks, has been overlooked in the OVSS literature. By incorporating design choices favouring segmentation, our approach significantly improves performance without requiring additional data, auxiliary pre-trained networks, or extensive hyperparameter tuning, making it highly practical for real-world applications. Experiments are performed on 8 popular semantic segmentation benchmarks, yielding state-of-the-art performance on most scenarios. Our code is publicly available at https://github.com/sinahmr/NACLIP.

Farzad Beizaee, Gregory A. Lodygensky, Christian Desrosiers et al.

Recent advances in diffusion models have spurred research into their application for Reconstruction-based unsupervised anomaly detection. However, these methods may struggle with maintaining structural integrity and recovering the anomaly-free content of abnormal regions, especially in multi-class scenarios. Furthermore, diffusion models are inherently designed to generate images from pure noise and struggle to selectively alter anomalous regions of an image while preserving normal ones. This leads to potential degradation of normal regions during reconstruction, hampering the effectiveness of anomaly detection. This paper introduces a reformulation of the standard diffusion model geared toward selective region alteration, allowing the accurate identification of anomalies. By modeling anomalies as noise in the latent space, our proposed Deviation correction diffusion (DeCo-Diff) model preserves the normal regions and encourages transformations exclusively on anomalous areas. This selective approach enhances the reconstruction quality, facilitating effective unsupervised detection and localization of anomaly regions. Comprehensive evaluations demonstrate the superiority of our method in accurately identifying and localizing anomalies in complex images, with pixel-level AUPRC improvements of 11-14% over state-of-the-art models on well known anomaly detection datasets. The code is available at https://github.com/farzad-bz/DeCo-Diff

Pablo Morales-Álvarez, Stergios Christodoulidis, Maria Vakalopoulou et al.

The emergence of large pre-trained vision-language models (VLMs) represents a paradigm shift in machine learning, with unprecedented results in a broad span of visual recognition tasks. CLIP, one of the most popular VLMs, has exhibited remarkable zero-shot and transfer learning capabilities in classification. To transfer CLIP to downstream tasks, adapters constitute a parameter-efficient approach that avoids backpropagation through the large model (unlike related prompt learning methods). However, CLIP adapters have been developed to target discriminative performance, and the quality of their uncertainty estimates has been overlooked. In this work we show that the discriminative performance of state-of-the-art CLIP adapters does not always correlate with their uncertainty estimation capabilities, which are essential for a safe deployment in real-world scenarios. We also demonstrate that one of such adapters is obtained through MAP inference from a more general probabilistic framework. Based on this observation we introduce BayesAdapter, which leverages Bayesian inference to estimate a full probability distribution instead of a single point, better capturing the variability inherent in the parameter space. In a comprehensive empirical evaluation we show that our approach obtains high quality uncertainty estimates in the predictions, standing out in calibration and selective classification. Our code will be publicly available upon acceptance of the paper.

Marc Lafon, Yannis Karmim, Julio Silva-Rodríguez et al.

Reliable Uncertainty Quantification (UQ) and failure prediction remain open challenges for Vision-Language Models (VLMs). We introduce ViLU, a new Vision-Language Uncertainty quantification framework that contextualizes uncertainty estimates by leveraging all task-relevant textual representations. ViLU constructs an uncertainty-aware multi-modal representation by integrating the visual embedding, the predicted textual embedding, and an image-conditioned textual representation via cross-attention. Unlike traditional UQ methods based on loss prediction, ViLU trains an uncertainty predictor as a binary classifier to distinguish correct from incorrect predictions using a weighted binary cross-entropy loss, making it loss-agnostic. In particular, our proposed approach is well-suited for post-hoc settings, where only vision and text embeddings are available without direct access to the model itself. Extensive experiments on diverse datasets show the significant gains of our method compared to state-of-the-art failure prediction methods. We apply our method to standard classification datasets, such as ImageNet-1k, as well as large-scale image-caption datasets like CC12M and LAION-400M. Ablation studies highlight the critical role of our architecture and training in achieving effective uncertainty quantification. Our code is publicly available and can be found here: https://github.com/ykrmm/ViLU.

Farzad Beizaee, Gregory Lodygensky, Christian Desrosiers et al.

Unsupervised anomaly detection in brain images is crucial for identifying injuries and pathologies without access to labels. However, the accurate localization of anomalies in medical images remains challenging due to the inherent complexity and variability of brain structures and the scarcity of annotated abnormal data. To address this challenge, we propose a novel approach that incorporates masking within diffusion models, leveraging their generative capabilities to learn robust representations of normal brain anatomy. During training, our model processes only normal brain MRI scans and performs a forward diffusion process in the latent space that adds noise to the features of randomly-selected patches. Following a dual objective, the model learns to identify which patches are noisy and recover their original features. This strategy ensures that the model captures intricate patterns of normal brain structures while isolating potential anomalies as noise in the latent space. At inference, the model identifies noisy patches corresponding to anomalies and generates a normal counterpart for these patches by applying a reverse diffusion process. Our method surpasses existing unsupervised anomaly detection techniques, demonstrating superior performance in generating accurate normal counterparts and localizing anomalies. The code is available at hhttps://github.com/farzad-bz/MAD-AD.

Farzad Beizaee, Sina Hajimiri, Ismail Ben Ayed et al.

Unsupervised anomaly detection (UAD) in brain imaging is crucial for identifying pathologies without the need for labeled data. However, accurately localizing anomalies remains challenging due to the intricate structure of brain anatomy and the scarcity of abnormal examples. In this work, we introduce REFLECT, a novel framework that leverages rectified flows to establish a direct, linear trajectory for correcting abnormal MR images toward a normal distribution. By learning a straight, one-step correction transport map, our method efficiently corrects brain anomalies and can precisely localize anomalies by detecting discrepancies between anomalous input and corrected counterpart. In contrast to the diffusion-based UAD models, which require iterative stochastic sampling, rectified flows provide a direct transport map, enabling single-step inference. Extensive experiments on popular UAD brain segmentation benchmarks demonstrate that REFLECT significantly outperforms state-of-the-art unsupervised anomaly detection methods. The code is available at https://github.com/farzad-bz/REFLECT.

Pierre Marza, Leo Fillioux, Sofiène Boutaj et al.

Progress in a research field can be hard to assess, in particular when many concurrent methods are proposed in a short period of time. This is the case in digital pathology, where many foundation models have been released recently to serve as feature extractors for tile-level images, being used in a variety of downstream tasks, both for tile- and slide-level problems. Benchmarking available methods then becomes paramount to get a clearer view of the research landscape. In particular, in critical domains such as healthcare, a benchmark should not only focus on evaluating downstream performance, but also provide insights about the main differences between methods, and importantly, further consider uncertainty and robustness to ensure a reliable usage of proposed models. For these reasons, we introduce THUNDER, a tile-level benchmark for digital pathology foundation models, allowing for efficient comparison of many models on diverse datasets with a series of downstream tasks, studying their feature spaces and assessing the robustness and uncertainty of predictions informed by their embeddings. THUNDER is a fast, easy-to-use, dynamic benchmark that can already support a large variety of state-of-the-art foundation, as well as local user-defined models for direct tile-based comparison. In this paper, we provide a comprehensive comparison of 23 foundation models on 16 different datasets covering diverse tasks, feature analysis, and robustness. The code for THUNDER is publicly available at https://github.com/MICS-Lab/thunder.

Sina Hajimiri, Farzad Beizaee, Fereshteh Shakeri et al.

Vision transformers have demonstrated remarkable success in classification by leveraging global self-attention to capture long-range dependencies. However, this same mechanism can obscure fine-grained spatial details crucial for tasks such as segmentation. In this work, we seek to enhance segmentation performance of vision transformers after standard image-level classification training. More specifically, we present a simple yet effective add-on that improves performance on segmentation tasks while retaining vision transformers' image-level recognition capabilities. In our approach, we modulate the self-attention with a learnable Gaussian kernel that biases the attention toward neighboring patches. We further refine the patch representations to learn better embeddings at patch positions. These modifications encourage tokens to focus on local surroundings and ensure meaningful representations at spatial positions, while still preserving the model's ability to incorporate global information. Experiments demonstrate the effectiveness of our modifications, evidenced by substantial segmentation gains on three benchmarks (e.g., over 6% and 4% on ADE20K for ViT Tiny and Base), without changing the training regime or sacrificing classification performance. The code is available at https://github.com/sinahmr/LocAtViT/.

Ghassen Baklouti, Julio Silva-Rodríguez, Jose Dolz et al.

Parameter-efficient fine-tuning (PEFT) of pre-trained foundation models is increasingly attracting interest in medical imaging due to its effectiveness and computational efficiency. Among these methods, Low-Rank Adaptation (LoRA) is a notable approach based on the assumption that the adaptation inherently occurs in a low-dimensional subspace. While it has shown good performance, its implementation requires a fixed and unalterable rank, which might be challenging to select given the unique complexities and requirements of each medical imaging downstream task. Inspired by advancements in natural image processing, we introduce a novel approach for medical image segmentation that dynamically adjusts the intrinsic rank during adaptation. Viewing the low-rank representation of the trainable weight matrices as a singular value decomposition, we introduce an l_1 sparsity regularizer to the loss function, and tackle it with a proximal optimizer. The regularizer could be viewed as a penalty on the decomposition rank. Hence, its minimization enables to find task-adapted ranks automatically. Our method is evaluated in a realistic few-shot fine-tuning setting, where we compare it first to the standard LoRA and then to several other PEFT methods across two distinguishable tasks: base organs and novel organs. Our extensive experiments demonstrate the significant performance improvements driven by our method, highlighting its efficiency and robustness against suboptimal rank initialization. Our code is publicly available: https://github.com/ghassenbaklouti/ARENA

Andreas Lolos, Stergios Christodoulidis, Maria Vakalopoulou et al.

Multiple Instance Learning (MIL) offers a natural solution for settings where only coarse, bag-level labels are available, without having access to instance-level annotations. This is usually the case in digital pathology, which consists of gigapixel sized images. While deterministic attention-based MIL approaches achieve strong bag-level performance, they often overlook the uncertainty inherent in instance relevance. In this paper, we address the lack of uncertainty quantification in instance-level attention scores by introducing \textbf{SGPMIL}, a new probabilistic attention-based MIL framework grounded in Sparse Gaussian Processes (SGP). By learning a posterior distribution over attention scores, SGPMIL enables principled uncertainty estimation, resulting in more reliable and calibrated instance relevance maps. Our approach not only preserves competitive bag-level performance but also significantly improves the quality and interpretability of instance-level predictions under uncertainty. SGPMIL extends prior work by introducing feature scaling in the SGP predictive mean function, leading to faster training, improved efficiency, and enhanced instance-level performance. Extensive experiments on multiple well-established digital pathology datasets highlight the effectiveness of our approach across both bag- and instance-level evaluations. Our code will be made publicly available.

Balamurali Murugesan, Julio Silva-Rodriguez, Ismail Ben Ayed et al.

In this work, we present a novel approach to calibrate segmentation networks that considers the inherent challenges posed by different categories and object regions. In particular, we present a formulation that integrates class and region-wise constraints into the learning objective, with multiple penalty weights to account for class and region differences. Finding the optimal penalty weights manually, however, might be unfeasible, and potentially hinder the optimization process. To overcome this limitation, we propose an approach based on Class and Region-Adaptive constraints (CRaC), which allows to learn the class and region-wise penalty weights during training. CRaC is based on a general Augmented Lagrangian method, a well-established technique in constrained optimization. Experimental results on two popular segmentation benchmarks, and two well-known segmentation networks, demonstrate the superiority of CRaC compared to existing approaches. The code is available at: https://github.com/Bala93/CRac/

Bingyuan Liu, Ismail Ben Ayed, Adrian Galdran et al.

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 assignments. This yields a pre-softmax activation of the correct class that is significantly larger than the remaining activations. Recent evidence from the literature suggests that loss functions that embed implicit or explicit maximization of the entropy of predictions yield state-of-the-art calibration performances. We provide a unifying constrained-optimization perspective of current state-of-the-art calibration losses. Specifically, these losses could be viewed as approximations of a linear penalty (or a Lagrangian) imposing equality constraints on logit distances. This points to an important limitation of such underlying equality constraints, whose ensuing gradients constantly push towards a non-informative solution, which might prevent from reaching the best compromise between the discriminative performance and calibration of the model during gradient-based optimization. Following our observations, we propose a simple and flexible generalization based on inequality constraints, which imposes a controllable margin on logit distances. Comprehensive experiments on a variety of image classification, semantic segmentation and NLP benchmarks demonstrate that our method sets novel state-of-the-art results on these tasks in terms of network calibration, without affecting the discriminative performance. The code is available at https://github.com/by-liu/MbLS .

Bingyuan Liu, Christian Desrosiers, Ismail Ben Ayed et al.

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 applicability in scenarios. Mixed supervision is an appealing alternative for mitigating this obstacle. In this work, we propose a dual-branch architecture, where the upper branch (teacher) receives strong annotations, while the bottom one (student) is driven by limited supervision and guided by the upper branch. Combined with a standard cross-entropy loss over the labeled pixels, our novel formulation integrates two important terms: (i) a Shannon entropy loss defined over the less-supervised images, which encourages confident student predictions in the bottom branch; and (ii) a KL divergence term, which transfers the knowledge (i.e., predictions) of the strongly supervised branch to the less-supervised branch and guides the entropy (student-confidence) term to avoid trivial solutions. We show that the synergy between the entropy and KL divergence yields substantial improvements in performance. We also discuss an interesting link between Shannon-entropy minimization and standard pseudo-mask generation, and argue that the former should be preferred over the latter for leveraging information from unlabeled pixels. We evaluate the effectiveness of the proposed formulation through a series of quantitative and qualitative experiments using two publicly available datasets. Results demonstrate that our method significantly outperforms other strategies for semantic segmentation within a mixed-supervision framework, as well as recent semi-supervised approaches. Our code is publicly available: https://github.com/by-liu/ConfKD.

Mathilde Bateson, Hoel Kervadec, Jose Dolz et al.

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 often impede the availability of source images in the adaptation phase. This is a very frequent DA scenario in medical imaging, where, for instance, the source and target images could come from different clinical sites. We introduce a source-free domain adaptation for image segmentation. Our formulation is based on minimizing a label-free entropy loss defined over target-domain data, which we further guide with a domain-invariant prior on the segmentation regions. Many priors can be derived from anatomical information. Here, a class ratio prior is estimated from anatomical knowledge and integrated in the form of a Kullback Leibler (KL) divergence in our overall loss function. Furthermore, we motivate our overall loss with an interesting link to maximizing the mutual information between the target images and their label predictions. We show the effectiveness of our prior aware entropy minimization in a variety of domain-adaptation scenarios, with different modalities and applications, including spine, prostate, and cardiac segmentation. Our method yields comparable results to several state of the art adaptation techniques, despite having access to much less information, as the source images are entirely absent in our adaptation phase. Our straightforward adaptation strategy uses only one network, contrary to popular adversarial techniques, which are not applicable to a source-free DA setting. Our framework can be readily used in a breadth of segmentation problems, and our code is publicly available: https://github.com/mathilde-b/SFDA

Malik Boudiaf, Ziko Imtiaz Masud, Jérôme Rony et al.

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 classification accuracy and mutual-information maximization. Furthermore, we propose a new alternating-direction solver, which substantially speeds up transductive inference over gradient-based optimization, while yielding competitive accuracy. We also provide a convergence analysis of our solver based on Zangwill's theory and bound-optimization arguments. TIM inference is modular: it can be used on top of any base-training feature extractor. Following standard transductive few-shot settings, our comprehensive experiments demonstrate that TIM outperforms state-of-the-art methods significantly across various datasets and networks, while used on top of a fixed feature extractor trained with simple cross-entropy on the base classes, without resorting to complex meta-learning schemes. It consistently brings between 2 % and 5 % improvement in accuracy over the best performing method, not only on all the well-established few-shot benchmarks but also on more challenging scenarios, with random tasks, domain shift and larger numbers of classes, as in the recently introduced META-DATASET. Our code is publicly available at https://github.com/mboudiaf/TIM. We also publicly release a standalone PyTorch implementation of META-DATASET, along with additional benchmarking results, at https://github.com/mboudiaf/pytorch-meta-dataset.

Hoel Kervadec, Houda Bahig, Laurent Letourneau-Guillon et al.

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, when used on their own as segmentation losses for training deep networks. Not only interesting theoretically, there exist deeper motivations to posing segmentation problems as a reconstruction of shape descriptors: Annotations to obtain approximations of low-order shape moments could be much less cumbersome than their full-mask counterparts, and anatomical priors could be readily encoded into invariant shape descriptions, which might alleviate the annotation burden. Also, and most importantly, we hypothesize that, given a task, certain shape descriptions might be invariant across image acquisition protocols/modalities and subject populations, which might open interesting research avenues for generalization in medical image segmentation. We introduce and formulate a few shape descriptors in the context of deep segmentation, and evaluate their potential as standalone losses on two different challenging tasks. Inspired by recent works in constrained optimization for deep networks, we propose a way to use those descriptors to supervise segmentation, without any pixel-level label. Very surprisingly, as little as 4 descriptors values per class can approach the performance of a segmentation mask with 65k individual discrete labels. We also found that shape descriptors can be a valid way to encode anatomical priors about the task, enabling to leverage expert knowledge without additional annotations. Our implementation is publicly available and can be easily extended to other tasks and descriptors: https://github.com/hkervadec/shape_descriptors

Malik Boudiaf, Hoel Kervadec, Ziko Imtiaz Masud et al.

We show that the way inference is performed in few-shot segmentation tasks has a substantial effect on performances -- an aspect often overlooked in the literature in favor of the meta-learning paradigm. We introduce a transductive inference for a given query image, leveraging the statistics of its unlabeled pixels, by optimizing a new loss containing three complementary terms: i) the cross-entropy on the labeled support pixels; ii) the Shannon entropy of the posteriors on the unlabeled query-image pixels; and iii) a global KL-divergence regularizer based on the proportion of the predicted foreground. As our inference uses a simple linear classifier of the extracted features, its computational load is comparable to inductive inference and can be used on top of any base training. Foregoing episodic training and using only standard cross-entropy training on the base classes, our inference yields competitive performances on standard benchmarks in the 1-shot scenarios. As the number of available shots increases, the gap in performances widens: on PASCAL-5i, our method brings about 5% and 6% improvements over the state-of-the-art, in the 5- and 10-shot scenarios, respectively. Furthermore, we introduce a new setting that includes domain shifts, where the base and novel classes are drawn from different datasets. Our method achieves the best performances in this more realistic setting. Our code is freely available online: https://github.com/mboudiaf/RePRI-for-Few-Shot-Segmentation.

Le Thanh Nguyen-Meidine, Atif Belal, Madhu Kiran et al.

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 practical importance, e.g., in multi-camera video-surveillance applications. The MTDA problem can be addressed by adapting one specialized model per target domain, although this solution is too costly in many real-world applications. Blending multiple targets for MTDA has been proposed, yet this solution may lead to a reduction in model specificity and accuracy. In this paper, we propose a novel unsupervised MTDA approach to train a CNN that can generalize well across multiple target domains. Our Multi-Teacher MTDA (MT-MTDA) method relies on multi-teacher knowledge distillation (KD) to iteratively distill target domain knowledge from multiple teachers to a common student. The KD process is performed in a progressive manner, where the student is trained by each teacher on how to perform UDA for a specific target, instead of directly learning domain adapted features. Finally, instead of combining the knowledge from each teacher, MT-MTDA alternates between teachers that distill knowledge, thereby preserving the specificity of each target (teacher) when learning to adapt to the student. MT-MTDA is compared against state-of-the-art methods on several challenging UDA benchmarks, and empirical results show that our proposed model can provide a considerably higher level of accuracy across multiple target domains. Our code is available at: https://github.com/LIVIAETS/MT-MTDA

Reza Azad, Abdur R Fayjie, Claude Kauffman et al.

Despite the initial belief that Convolutional Neural Networks (CNNs) are driven by shapes to perform visual recognition tasks, recent evidence suggests that texture bias in CNNs provides higher performing models when learning on large labeled training datasets. This contrasts with the perceptual bias in the human visual cortex, which has a stronger preference towards shape components. Perceptual differences may explain why CNNs achieve human-level performance when large labeled datasets are available, but their performance significantly degrades in lowlabeled data scenarios, such as few-shot semantic segmentation. To remove the texture bias in the context of few-shot learning, we propose a novel architecture that integrates a set of Difference of Gaussians (DoG) to attenuate high-frequency local components in the feature space. This produces a set of modified feature maps, whose high-frequency components are diminished at different standard deviation values of the Gaussian distribution in the spatial domain. As this results in multiple feature maps for a single image, we employ a bi-directional convolutional long-short-term-memory to efficiently merge the multi scale-space representations. We perform extensive experiments on three well-known few-shot segmentation benchmarks -- Pascal i5, COCO-20i and FSS-1000 -- and demonstrate that our method outperforms state-of-the-art approaches in two datasets under the same conditions. The code is available at: https://github.com/rezazad68/fewshot-segmentation

Soufiane Belharbi, Jérôme Rony, Jose Dolz et al.

Pointwise localization allows more precise localization and accurate interpretability, compared to bounding box, in applications where objects are highly unstructured such as in medical domain. In this work, we focus on weakly supervised localization (WSL) where a model is trained to classify an image and localize regions of interest at pixel-level using only global image annotation. Typical convolutional attentions maps are prune to high false positive regions. To alleviate this issue, we propose a new deep learning method for WSL, composed of a localizer and a classifier, where the localizer is constrained to determine relevant and irrelevant regions using conditional entropy (CE) with the aim to reduce false positive regions. Experimental results on a public medical dataset and two natural datasets, using Dice index, show that, compared to state of the art WSL methods, our proposal can provide significant improvements in terms of image-level classification and pixel-level localization (low false positive) with robustness to overfitting. A public reproducible PyTorch implementation is provided in: https://github.com/sbelharbi/wsol-min-max-entropy-interpretability .

Ashish Sinha, Jose Dolz

Even though convolutional neural networks (CNNs) are driving progress in medical image segmentation, standard models still have some drawbacks. First, the use of multi-scale approaches, i.e., encoder-decoder architectures, leads to a redundant use of information, where similar low-level features are extracted multiple times at multiple scales. Second, long-range feature dependencies are not efficiently modeled, resulting in non-optimal discriminative feature representations associated with each semantic class. In this paper we attempt to overcome these limitations with the proposed architecture, by capturing richer contextual dependencies based on the use of guided self-attention mechanisms. This approach is able to integrate local features with their corresponding global dependencies, as well as highlight interdependent channel maps in an adaptive manner. Further, the additional loss between different modules guides the attention mechanisms to neglect irrelevant information and focus on more discriminant regions of the image by emphasizing relevant feature associations. We evaluate the proposed model in the context of semantic segmentation on three different datasets: abdominal organs, cardiovascular structures and brain tumors. A series of ablation experiments support the importance of these attention modules in the proposed architecture. In addition, compared to other state-of-the-art segmentation networks our model yields better segmentation performance, increasing the accuracy of the predictions while reducing the standard deviation. This demonstrates the efficiency of our approach to generate precise and reliable automatic segmentations of medical images. Our code is made publicly available at https://github.com/sinAshish/Multi-Scale-Attention

Hoel Kervadec, Jihene Bouchtiba, Christian Desrosiers et al.

Widely used loss functions for CNN segmentation, e.g., Dice or cross-entropy, are based on integrals over the segmentation regions. Unfortunately, for highly unbalanced segmentations, such regional summations have values that differ by several orders of magnitude across classes, which affects training performance and stability. We propose a boundary loss, which takes the form of a distance metric on the space of contours, not regions. This can mitigate the difficulties of highly unbalanced problems because it uses integrals over the interface between regions instead of unbalanced integrals over the regions. Furthermore, a boundary loss complements regional information. Inspired by graph-based optimization techniques for computing active-contour flows, we express a non-symmetric $L_2$ distance on the space of contours as a regional integral, which avoids completely local differential computations involving contour points. This yields a boundary loss expressed with the regional softmax probability outputs of the network, which can be easily combined with standard regional losses and implemented with any existing deep network architecture for N-D segmentation. We report comprehensive evaluations and comparisons on different unbalanced problems, showing that our boundary loss can yield significant increases in performances while improving training stability. Our code is publicly available: https://github.com/LIVIAETS/surface-loss .

Arnab Kumar Mondal, Jose Dolz, Christian Desrosiers

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 and unlabeled images. The proposed method prevents over-fitting by learning to discriminate between true and fake patches obtained by a generator network. Our work extends current adversarial learning approaches, which focus on 2D single-modality images, to the more challenging context of 3D volumes of multiple modalities. The proposed method is evaluated on the problem of segmenting brain MRI from the iSEG-2017 and MRBrainS 2013 datasets. Significant performance improvement is reported, compared to state-of-art segmentation networks trained in a fully-supervised manner. In addition, our work presents a comprehensive analysis of different GAN architectures for semi-supervised segmentation, showing recent techniques like feature matching to yield a higher performance than conventional adversarial training approaches. Our code is publicly available at https://github.com/arnab39/FewShot_GAN-Unet3D

Jose Dolz, Karthik Gopinath, Jing Yuan et al.

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 HyperDenseNet, a 3D fully convolutional neural network that extends the definition of dense connectivity to multi-modal segmentation problems. Each imaging modality has a path, and dense connections occur not only between the pairs of layers within the same path, but also between those across different paths. This contrasts with the existing multi-modal CNN approaches, in which modeling several modalities relies entirely on a single joint layer (or level of abstraction) for fusion, typically either at the input or at the output of the network. Therefore, the proposed network has total freedom to learn more complex combinations between the modalities, within and in-between all the levels of abstraction, which increases significantly the learning representation. We report extensive evaluations over two different and highly competitive multi-modal brain tissue segmentation challenges, iSEG 2017 and MRBrainS 2013, with the former focusing on 6-month infant data and the latter on adult images. HyperDenseNet yielded significant improvements over many state-of-the-art segmentation networks, ranking at the top on both benchmarks. We further provide a comprehensive experimental analysis of features re-use, which confirms the importance of hyper-dense connections in multi-modal representation learning. Our code is publicly available at https://www.github.com/josedolz/HyperDenseNet.

Julio Silva-Rodríguez, Sina Hajimiri, Ismail Ben Ayed et al.

Efficient transfer learning (ETL) is receiving increasing attention to adapt large pre-trained language-vision models on downstream tasks with a few labeled samples. While significant progress has been made, we reveal that state-of-the-art ETL approaches exhibit strong performance only in narrowly-defined experimental setups, and with a careful adjustment of hyperparameters based on a large corpus of labeled samples. In particular, we make two interesting, and surprising empirical observations. First, to outperform a simple Linear Probing baseline, these methods require to optimize their hyper-parameters on each target task. And second, they typically underperform -- sometimes dramatically -- standard zero-shot predictions in the presence of distributional drifts. Motivated by the unrealistic assumptions made in the existing literature, i.e., access to a large validation set and case-specific grid-search for optimal hyperparameters, we propose a novel approach that meets the requirements of real-world scenarios. More concretely, we introduce a CLass-Adaptive linear Probe (CLAP) objective, whose balancing term is optimized via an adaptation of the general Augmented Lagrangian method tailored to this context. We comprehensively evaluate CLAP on a broad span of datasets and scenarios, demonstrating that it consistently outperforms SoTA approaches, while yet being a much more efficient alternative.

Leo Fillioux, Julio Silva-Rodríguez, Ismail Ben Ayed et al.

Recent advances in self-supervision and contrastive learning have brought the performance of foundation models to unprecedented levels in a variety of tasks. Fueled by this progress, these models are becoming the prevailing approach for a wide array of real-world vision problems, including risk-sensitive and high-stakes applications. However, ensuring safe deployment in these scenarios requires a more comprehensive understanding of their uncertainty modeling capabilities, which has been barely explored. In this work, we delve into the behaviour of vision and vision-language foundation models under Conformal Prediction (CP), a statistical framework that provides theoretical guarantees of marginal coverage of the true class. Across extensive experiments including popular vision classification benchmarks, well-known foundation vision models, and three CP methods, our findings reveal that foundation models are well-suited for conformalization procedures, particularly those integrating Vision Transformers. We also show that calibrating the confidence predictions of these models, a popular strategy to improve their uncertainty quantification, actually leads to efficiency degradation of the conformal set on adaptive CP methods. Furthermore, few-shot adaptation of Vision-Language Models (VLMs) to downstream tasks, whose popularity is surging, enhances conformal scores compared to zero-shot predictions. Last, our empirical study exposes APS as particularly promising in the context of vision foundation models, as it does not violate the marginal coverage guarantees across multiple challenging, yet realistic scenarios.