2024
Authors
Eduard-Alexandru Bonci; Orit Kaidar-Person; Marília Antunes; Oriana Ciani; Helena Cruz; Rosa Di Micco; Oreste Davide Gentilini; Nicole Rotmensz; Pedro Gouveia; Jörg Heil; Pawel Kabata; Nuno Freitas; Tiago Gonçalves; Miguel Romariz; Helena Montenegro; Hélder P. Oliveira; Jaime S. Cardoso; Henrique Martins; Daniela Lopes; Marta Martinho; Ludovica Borsoi; Elisabetta Listorti; Carlos Mavioso; Martin Mika; André Pfob; Timo Schinköthe; Giovani Silva; Maria-Joao Cardoso;
Publication
Cancer Research
Abstract
2024
Authors
Rio-Torto, I; Cardoso, JS; Teixeira, LF;
Publication
MEDICAL IMAGING WITH DEEP LEARNING
Abstract
The increased interest and importance of explaining neural networks' predictions, especially in the medical community, associated with the known unreliability of saliency maps, the most common explainability method, has sparked research into other types of explanations. Natural Language Explanations (NLEs) emerge as an alternative, with the advantage of being inherently understandable by humans and the standard way that radiologists explain their diagnoses. We extend upon previous work on NLE generation for multi-label chest X-ray diagnosis by replacing the traditional decoder-only NLE generator with an encoder-decoder architecture. This constitutes a first step towards Reinforcement Learning-free adversarial generation of NLEs when no (or few) ground-truth NLEs are available for training, since the generation is done in the continuous encoder latent space, instead of in the discrete decoder output space. However, in the current scenario, large amounts of annotated examples are still required, which are especially costly to obtain in the medical domain, given that they need to be provided by clinicians. Thus, we explore how the recent developments in Parameter-Efficient Fine-Tuning (PEFT) can be leveraged for this usecase. We compare different PEFT methods and find that integrating the visual information into the NLE generator layers instead of only at the input achieves the best results, even outperforming the fully fine-tuned encoder-decoder-based model, while only training 12% of the model parameters. Additionally, we empirically demonstrate the viability of supervising the NLE generation process on the encoder latent space, thus laying the foundation for RL-free adversarial training in low ground-truth NLE availability regimes. The code is publicly available at https://github.com/icrto/peft-nles.
2024
Authors
Patrício, C; Neves, C; Teixeira, F;
Publication
ACM COMPUTING SURVEYS
Abstract
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 nature 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 discussed.
2024
Authors
Patricio, C; Teixeira, LF; Neves, JC;
Publication
IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING, ISBI 2024
Abstract
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.
2024
Authors
Gomes, I; Teixeira, LF; van Rijn, JN; Soares, C; Restivo, A; Cunha, L; Santos, M;
Publication
CoRR
Abstract
2024
Authors
Patrício, C; Barbano, CA; Fiandrotti, A; Renzulli, R; Grangetto, M; Teixeira, LF; Neves, JC;
Publication
CoRR
Abstract
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