Luís F. Teixeira

Cristiano Patrício, João C. Neves, Luís F. Teixeira

Early detection of melanoma is crucial for preventing severe complications and increasing the chances of successful treatment. Existing deep learning approaches for melanoma skin lesion diagnosis are deemed black-box models, as they omit the rationale behind the model prediction, compromising the trustworthiness and acceptability of these diagnostic methods. Attempts to provide concept-based explanations are based on post-hoc approaches, which depend on an additional model to derive interpretations. In this paper, we propose an inherently interpretable framework to improve the interpretability of concept-based models by incorporating a hard attention mechanism and a coherence loss term to assure the visual coherence of concept activations by the concept encoder, without requiring the supervision of additional annotations. The proposed framework explains its decision in terms of human-interpretable concepts and their respective contribution to the final prediction, as well as a visual interpretation of the locations where the concept is present in the image. Experiments on skin image datasets demonstrate that our method outperforms existing black-box and concept-based models for skin lesion classification.

Tiago Gonçalves, Isabel Rio-Torto, Luís F. Teixeira et al.

The increasing popularity of attention mechanisms in deep learning algorithms for computer vision and natural language processing made these models attractive to other research domains. In healthcare, there is a strong need for tools that may improve the routines of the clinicians and the patients. Naturally, the use of attention-based algorithms for medical applications occurred smoothly. However, being healthcare a domain that depends on high-stake decisions, the scientific community must ponder if these high-performing algorithms fit the needs of medical applications. With this motto, this paper extensively reviews the use of attention mechanisms in machine learning (including Transformers) for several medical applications. This work distinguishes itself from its predecessors by proposing a critical analysis of the claims and potentialities of attention mechanisms presented in the literature through an experimental case study on medical image classification with three different use cases. These experiments focus on the integrating process of attention mechanisms into established deep learning architectures, the analysis of their predictive power, and a visual assessment of their saliency maps generated by post-hoc explanation methods. This paper concludes with a critical analysis of the claims and potentialities presented in the literature about attention mechanisms and proposes future research lines in medical applications that may benefit from these frameworks.

Isabel Rio-Torto, Jaime S. Cardoso, Luís F. Teixeira

Natural language explanations provide an inherently human-understandable way to explain black-box models, closely reflecting how radiologists convey their diagnoses in textual reports. Most works explicitly supervise the explanation generation process using datasets annotated with explanations. Thus, though plausible, the generated explanations are not faithful to the model's reasoning. In this work, we propose WeNLEX, a weakly supervised model for the generation of natural language explanations for multilabel chest X-ray classification. Faithfulness is ensured by matching images generated from their corresponding natural language explanations with original images, in the black-box model's feature space. Plausibility is maintained via distribution alignment with a small database of clinician-annotated explanations. We empirically demonstrate, through extensive validation on multiple metrics to assess faithfulness, simulatability, diversity, and plausibility, that WeNLEX is able to produce faithful and plausible explanations, using as little as 5 ground-truth explanations per diagnosis. Furthermore, WeNLEX can operate in both post-hoc and in-model settings. In the latter, i.e., when the multilabel classifier is trained together with the rest of the network, WeNLEX improves the classification AUC of the standalone classifier by 2.21%, thus showing that adding interpretability to the training process can actually increase the downstream task performance. Additionally, simply by changing the database, WeNLEX explanations are adaptable to any target audience, and we showcase this flexibility by training a layman version of WeNLEX, where explanations are simplified for non-medical users.

Inês Gomes, Luís F. Teixeira, Jan N. van Rijn et al.

The increasing use of deep learning across various domains highlights the importance of understanding the decision-making processes of these black-box models. Recent research focusing on the decision boundaries of deep classifiers, relies on generated synthetic instances in areas of low confidence, uncovering samples that challenge both models and humans. We propose a novel approach to enhance the interpretability of deep binary classifiers by selecting representative samples from the decision boundary - prototypes - and applying post-model explanation algorithms. We evaluate the effectiveness of our approach through 2D visualizations and GradientSHAP analysis. Our experiments demonstrate the potential of the proposed method, revealing distinct and compact clusters and diverse prototypes that capture essential features that lead to low-confidence decisions. By offering a more aggregated view of deep classifiers' decision boundaries, our work contributes to the responsible development and deployment of reliable machine learning systems.

Cristiano Patrício, João C. Neves, Luís F. Teixeira

The remarkable success of deep learning has prompted interest in its application to medical imaging diagnosis. Even though state-of-the-art deep learning models have achieved human-level accuracy on the classification of different types of medical data, these models are hardly adopted in clinical workflows, mainly due to their lack of interpretability. The black-box-ness of deep learning models has raised the need for devising strategies to explain the decision process of these models, leading to the creation of the topic of eXplainable Artificial Intelligence (XAI). In this context, we provide a thorough survey of XAI applied to medical imaging diagnosis, including visual, textual, example-based and concept-based explanation methods. Moreover, this work reviews the existing medical imaging datasets and the existing metrics for evaluating the quality of the explanations. In addition, we include a performance comparison among a set of report generation-based methods. Finally, the major challenges in applying XAI to medical imaging and the future research directions on the topic are also discussed.

Cristiano Patrício, Luís F. Teixeira, João C. Neves

Concept-based models naturally lend themselves to the development of inherently interpretable skin lesion diagnosis, as medical experts make decisions based on a set of visual patterns of the lesion. Nevertheless, the development of these models depends on the existence of concept-annotated datasets, whose availability is scarce due to the specialized knowledge and expertise required in the annotation process. In this work, we show that vision-language models can be used to alleviate the dependence on a large number of concept-annotated samples. In particular, we propose an embedding learning strategy to adapt CLIP to the downstream task of skin lesion classification using concept-based descriptions as textual embeddings. Our experiments reveal that vision-language models not only attain better accuracy when using concepts as textual embeddings, but also require a smaller number of concept-annotated samples to attain comparable performance to approaches specifically devised for automatic concept generation.

Martin Aubard, László Antal, Ana Madureira et al.

This paper introduces ROSAR, a novel framework enhancing the robustness of deep learning object detection models tailored for side-scan sonar (SSS) images, generated by autonomous underwater vehicles using sonar sensors. By extending our prior work on knowledge distillation (KD), this framework integrates KD with adversarial retraining to address the dual challenges of model efficiency and robustness against SSS noises. We introduce three novel, publicly available SSS datasets, capturing different sonar setups and noise conditions. We propose and formalize two SSS safety properties and utilize them to generate adversarial datasets for retraining. Through a comparative analysis of projected gradient descent (PGD) and patch-based adversarial attacks, ROSAR demonstrates significant improvements in model robustness and detection accuracy under SSS-specific conditions, enhancing the model's robustness by up to 1.85%. ROSAR is available at https://github.com/remaro-network/ROSAR-framework.

Cristiano Patrício, Luís F. Teixeira, João C. Neves

The main challenges hindering the adoption of deep learning-based systems in clinical settings are the scarcity of annotated data and the lack of interpretability and trust in these systems. Concept Bottleneck Models (CBMs) offer inherent interpretability by constraining the final disease prediction on a set of human-understandable concepts. However, this inherent interpretability comes at the cost of greater annotation burden. Additionally, adding new concepts requires retraining the entire system. In this work, we introduce a novel two-step methodology that addresses both of these challenges. By simulating the two stages of a CBM, we utilize a pretrained Vision Language Model (VLM) to automatically predict clinical concepts, and an off-the-shelf Large Language Model (LLM) to generate disease diagnoses based on the predicted concepts. Furthermore, our approach supports test-time human intervention, enabling corrections to predicted concepts, which improves final diagnoses and enhances transparency in decision-making. We validate our approach on three skin lesion datasets, demonstrating that it outperforms traditional CBMs and state-of-the-art explainable methods, all without requiring any training and utilizing only a few annotated examples. The code is available at https://github.com/CristianoPatricio/2-step-concept-based-skin-diagnosis.

Martin Aubard, Ana Madureira, Luís Teixeira et al.

With the growing interest in underwater exploration and monitoring, Autonomous Underwater Vehicles (AUVs) have become essential. The recent interest in onboard Deep Learning (DL) has advanced real-time environmental interaction capabilities relying on efficient and accurate vision-based DL models. However, the predominant use of sonar in underwater environments, characterized by limited training data and inherent noise, poses challenges to model robustness. This autonomy improvement raises safety concerns for deploying such models during underwater operations, potentially leading to hazardous situations. This paper aims to provide the first comprehensive overview of sonar-based DL under the scope of robustness. It studies sonar-based DL perception task models, such as classification, object detection, segmentation, and SLAM. Furthermore, the paper systematizes sonar-based state-of-the-art datasets, simulators, and robustness methods such as neural network verification, out-of-distribution, and adversarial attacks. This paper highlights the lack of robustness in sonar-based DL research and suggests future research pathways, notably establishing a baseline sonar-based dataset and bridging the simulation-to-reality gap.

Cristiano Patrício, Isabel Rio-Torto, Jaime S. Cardoso et al.

The main challenges limiting the adoption of deep learning-based solutions in medical workflows are the availability of annotated data and the lack of interpretability of such systems. Concept Bottleneck Models (CBMs) tackle the latter by constraining the model output on a set of predefined and human-interpretable concepts. However, the increased interpretability achieved through these concept-based explanations implies a higher annotation burden. Moreover, if a new concept needs to be added, the whole system needs to be retrained. Inspired by the remarkable performance shown by Large Vision-Language Models (LVLMs) in few-shot settings, we propose a simple, yet effective, methodology, CBVLM, which tackles both of the aforementioned challenges. First, for each concept, we prompt the LVLM to answer if the concept is present in the input image. Then, we ask the LVLM to classify the image based on the previous concept predictions. Moreover, in both stages, we incorporate a retrieval module responsible for selecting the best examples for in-context learning. By grounding the final diagnosis on the predicted concepts, we ensure explainability, and by leveraging the few-shot capabilities of LVLMs, we drastically lower the annotation cost. We validate our approach with extensive experiments across four medical datasets and twelve LVLMs (both generic and medical) and show that CBVLM consistently outperforms CBMs and task-specific supervised methods without requiring any training and using just a few annotated examples. More information on our project page: https://cristianopatricio.github.io/CBVLM/.

Carla Monteiro, Valentina Corbetta, Regina Beets-Tan et al.

Automatic polyp segmentation is crucial for improving the clinical identification of colorectal cancer (CRC). While Deep Learning (DL) techniques have been extensively researched for this problem, current methods frequently struggle with generalization, particularly in data-constrained or challenging settings. Moreover, many existing polyp segmentation methods rely on complex, task-specific architectures. To address these limitations, we present a framework that leverages the intrinsic robustness of DINO self-attention "key" features for robust segmentation. Unlike traditional methods that extract tokens from the deepest layers of the Vision Transformer (ViT), our approach leverages the key features of the self-attention module with a simple convolutional decoder to predict polyp masks, resulting in enhanced performance and better generalizability. We validate our approach using a multi-center dataset under two rigorous protocols: Domain Generalization (DG) and Extreme Single Domain Generalization (ESDG). Our results, supported by a comprehensive statistical analysis, demonstrate that this pipeline achieves state-of-the-art (SOTA) performance, significantly enhancing generalization, particularly in data-scarce and challenging scenarios. While avoiding a polyp-specific architecture, we surpass well-established models like nnU-Net and UM-Net. Additionally, we provide a systematic benchmark of the DINO framework's evolution, quantifying the specific impact of architectural advancements on downstream polyp segmentation performance.

Cristiano Patrício, Carlo Alberto Barbano, Attilio Fiandrotti et al.

Contrastive Analysis (CA) detects anomalies by contrasting patterns unique to a target group (e.g., unhealthy subjects) from those in a background group (e.g., healthy subjects). In the context of brain MRIs, existing CA approaches rely on supervised contrastive learning or variational autoencoders (VAEs) using both healthy and unhealthy data, but such reliance on target samples is challenging in clinical settings. Unsupervised Anomaly Detection (UAD) offers an alternative by learning a reference representation of healthy anatomy without the need for target samples. Deviations from this reference distribution can indicate potential anomalies. In this context, diffusion models have been increasingly adopted in UAD due to their superior performance in image generation compared to VAEs. Nonetheless, precisely reconstructing the anatomy of the brain remains a challenge. In this work, we propose an unsupervised framework to improve the reconstruction quality by training a self-supervised contrastive encoder on healthy images to extract meaningful anatomical features. These features are used to condition a diffusion model to reconstruct the healthy appearance of a given image, enabling interpretable anomaly localization via pixel-wise comparison. We validate our approach through a proof-of-concept on a facial image dataset and further demonstrate its effectiveness on four brain MRI datasets, achieving state-of-the-art anomaly localization performance on the NOVA benchmark.

Mafalda Falcao Ferreira, Rui Camacho, Luis F. Teixeira

Cancer is still one of the most devastating diseases of our time. One way of automatically classifying tumor samples is by analyzing its derived molecular information (i.e., its genes expression signatures). In this work, we aim to distinguish three different types of cancer: thyroid, skin, and stomach. For that, we compare the performance of a Denoising Autoencoder (DAE) used as weight initialization of a deep neural network. Although we address a different domain problem in this work, we have adopted the same methodology of Ferreira et al.. In our experiments, we assess two different approaches when training the classification model: (a) fixing the weights, after pre-training the DAE, and (b) allowing fine-tuning of the entire classification network. Additionally, we apply two different strategies for embedding the DAE into the classification network: (1) by only importing the encoding layers, and (2) by inserting the complete autoencoder. Our best result was the combination of unsupervised feature learning through a DAE, followed by its full import into the classification network, and subsequent fine-tuning through supervised training, achieving an F1 score of 98.04% +/- 1.09 when identifying cancerous thyroid samples.

Daniel Fernandes Gomes, Shan Luo, Luis F. Teixeira

Developing autonomous assistants to help with domestic tasks is a vital topic in robotics research. Among these tasks, garment folding is one of them that is still far from being achieved mainly due to the large number of possible configurations that a crumpled piece of clothing may exhibit. Research has been done on either estimating the pose of the garment as a whole or detecting the landmarks for grasping separately. However, such works constrain the capability of the robots to perceive the states of the garment by limiting the representations for one single task. In this paper, we propose a novel end-to-end deep learning model named GarmNet that is able to simultaneously localize the garment and detect landmarks for grasping. The localization of the garment represents the global information for recognising the category of the garment, whereas the detection of landmarks can facilitate subsequent grasping actions. We train and evaluate our proposed GarmNet model using the CloPeMa Garment dataset that contains 3,330 images of different garment types in different poses. The experiments show that the inclusion of landmark detection (GarmNet-B) can largely improve the garment localization, with an error rate of 24.7% lower. Solutions as ours are important for robotics applications, as these offer scalable to many classes, memory and processing efficient solutions.

João Bernardino, Luís Filipe Teixeira, Hugo Sereno Ferreira

Knee injuries are frequent, varied and often require the patient to undergo intensive rehabilitation for several months. Treatment protocols usually contemplate some recurrent measurements in order to assess progress, such as goniometry. The need for specific equipment or the complexity and duration of these tasks cause them to often be neglected. A novel deep learning based solution is presented, supported by the generation of a synthetic image dataset. A 3D human-body model was used for this purpose, simulating a recovering patient. For each image, the coordinates of three key points were registered: the centers of the thigh, the knee and the lower leg. These values are sufficient to estimate the flexion angle. Convolutional neural networks were then trained for predicting these six coordinates. Transfer learning was used with the VGG16 and InceptionV3 models pre-trained on the ImageNet dataset, being an additional custom model trained from scratch. All models were tested with different combinations of data augmentation techniques applied on the training sets. InceptionV3 achieved the best overall results, producing considerably good predictions even on real unedited pictures.

Samaneh Khoshrou, Jaime S. Cardoso, Luis F. Teixeira

The practicality of a video surveillance system is adversely limited by the amount of queries that can be placed on human resources and their vigilance in response. To transcend this limitation, a major effort under way is to include software that (fully or at least semi) automatically mines video footage, reducing the burden imposed to the system. Herein, we propose a semi-supervised incremental learning framework for evolving visual streams in order to develop a robust and flexible track classification system. Our proposed method learns from consecutive batches by updating an ensemble in each time. It tries to strike a balance between performance of the system and amount of data which needs to be labelled. As no restriction is considered, the system can address many practical problems in an evolving multi-camera scenario, such as concept drift, class evolution and various length of video streams which have not been addressed before. Experiments were performed on synthetic as well as real-world visual data in non-stationary environments, showing high accuracy with fairly little human collaboration.