2025
Authors
Oliveira Coelho, BF; Cardoso, JS;
Publication
Neurocomputing
Abstract
In order to facilitate the adoption of deep learning in areas where decisions are of critical importance, understanding the model's internal workings is paramount. Nevertheless, since most models are considered black boxes, this task is usually not trivial, especially when the user does not have access to the network's intermediate outputs. In this paper, we propose IBISA, a model-agnostic attribution method that reaches state-of-the-art performance by optimizing sampling masks using the Information Bottleneck Principle. Our method improves on the previously known RISE and IBA techniques by placing the bottleneck right after the image input without complex formulations to estimate the mutual information. The method also requires only twenty forward passes and ten backward passes through the network, which is significantly faster than RISE, which needs at least 4000 forward passes. We evaluated IBISA using a VGG-16 and a ResNET-50 model, showing that our method produces explanations comparable or superior to IBA, RISE, and Grad-CAM but much more efficiently. © 2025 The Authors
2025
Authors
Nunes, JD; Montezuma, D; Oliveira, D; Pereira, T; Zlobec, I; Pinto, IM; Cardoso, JS;
Publication
SENSORS
Abstract
Due to the high variability in Hematoxylin and Eosin (H&E)-stained Whole Slide Images (WSIs), hidden stratification, and batch effects, generalizing beyond the training distribution is one of the main challenges in Deep Learning (DL) for Computational Pathology (CPath). But although DL depends on large volumes of diverse and annotated data, it is common to have a significant number of annotated samples from one or multiple source distributions, and another partially annotated or unlabeled dataset representing a target distribution for which we want to generalize, the so-called Domain Adaptation (DA). In this work, we focus on the task of generalizing from a single source distribution to a target domain. As it is still not clear which domain adaptation strategy is best suited for CPath, we evaluate three different DA strategies, namely FixMatch, CycleGAN, and a self-supervised feature extractor, and show that DA is still a challenge in CPath.
2025
Authors
Nogueira, AFR; Oliveira, HP; Teixeira, LF;
Publication
IMAGE AND VISION COMPUTING
Abstract
3D human pose estimation aims to reconstruct the human skeleton of all the individuals in a scene by detecting several body joints. The creation of accurate and efficient methods is required for several real-world applications including animation, human-robot interaction, surveillance systems or sports, among many others. However, several obstacles such as occlusions, random camera perspectives, or the scarcity of 3D labelled data, have been hampering the models' performance and limiting their deployment in real-world scenarios. The higher availability of cameras has led researchers to explore multi-view solutions due to the advantage of being able to exploit different perspectives to reconstruct the pose. Most existing reviews focus mainly on monocular 3D human pose estimation and a comprehensive survey only on multi-view approaches to determine the 3D pose has been missing since 2012. Thus, the goal of this survey is to fill that gap and present an overview of the methodologies related to 3D pose estimation in multi-view settings, understand what were the strategies found to address the various challenges and also, identify their limitations. According to the reviewed articles, it was possible to find that most methods are fully-supervised approaches based on geometric constraints. Nonetheless, most of the methods suffer from 2D pose mismatches, to which the incorporation of temporal consistency and depth information have been suggested to reduce the impact of this limitation, besides working directly with 3D features can completely surpass this problem but at the expense of higher computational complexity. Models with lower supervision levels were identified to overcome some of the issues related to 3D pose, particularly the scarcity of labelled datasets. Therefore, no method is yet capable of solving all the challenges associated with the reconstruction of the 3D pose. Due to the existing trade-off between complexity and performance, the best method depends on the application scenario. Therefore, further research is still required to develop an approach capable of quickly inferring a highly accurate 3D pose with bearable computation cost. To this goal, techniques such as active learning, methods that learn with a low level of supervision, the incorporation of temporal consistency, view selection, estimation of depth information and multi-modal approaches might be interesting strategies to keep in mind when developing a new methodology to solve this task.
2025
Authors
Patrício, C; Teixeira, LF; Neves, JC;
Publication
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
Abstract
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 grounded 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/2step-concept-based-skin-diagnosis.
2025
Authors
Silva, F; Oliveira, HP; Pereira, T;
Publication
ACM COMPUTING SURVEYS
Abstract
The large gap between the generalization level of state-of-the-art machine learning and human learning systems calls for the development of artificial intelligence (AI) models that are truly inspired by human cognition. In tasks related to image analysis, searching for pixel-level regularities has reached a power of information extraction still far from what humans capture with image-based observations. This leads to poor generalization when even small shifts occur at the level of the observations. We explore a perspective on this problem that is directed to learning the generative process with causality-related foundations, using models capable of combining symbolic manipulation, probabilistic reasoning, and pattern recognition abilities. We briefly review and explore connections of research from machine learning, cognitive science, and related fields of human behavior to support our perspective for the direction to more robust and human-like artificial learning systems.
2025
Authors
Ribeiro, R; Neves, I; Oliveira, HP; Pereira, T;
Publication
Comput. Biol. Medicine
Abstract
Traumatic Brain Injury (TBI) is a form of brain injury caused by external forces, resulting in temporary or permanent impairment of brain function. Despite advancements in healthcare, TBI mortality rates can reach 30%–40% in severe cases. This study aims to assist clinical decision-making and enhance patient care for TBI-related complications by employing Artificial Intelligence (AI) methods and data-driven approaches to predict decompensation. This study uses learning models based on sequential data from Electronic Health Records (EHR). Decompensation prediction was performed based on 24-h in-mortality prediction at each hour of the patient's stay in the Intensive Care Unit (ICU). A cohort of 2261 TBI patients was selected from the MIMIC-III dataset based on age and ICD-9 disease codes. Logistic Regressor (LR), Long-short term memory (LSTM), and Transformers architectures were used. Two sets of features were also explored combined with missing data strategies by imputing the normal value, data imbalance techniques with class weights, and oversampling. The best performance results were obtained using LSTMs with the original features with no unbalancing techniques and with the added features and class weight technique, with AUROC scores of 0.918 and 0.929, respectively. For this study, using EHR time series data with LSTM proved viable in predicting patient decompensation, providing a helpful indicator of the need for clinical interventions. © 2025 Elsevier Ltd
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