2023
Authors
Pereira, T; Cunha, A; Oliveira, HP;
Publication
APPLIED SCIENCES-BASEL
Abstract
2023
Authors
Ribeiro, G; Pereira, T; Silva, F; Sousa, J; Carvalho, DC; Dias, SC; Oliveira, HP;
Publication
APPLIED SCIENCES-BASEL
Abstract
Bone marrow edema (BME) is the term given to the abnormal fluid signal seen within the bone marrow on magnetic resonance imaging (MRI). It usually indicates the presence of underlying pathology and is associated with a myriad of conditions/causes. However, it can be misleading, as in some cases, it may be associated with normal changes in the bone, especially during the growth period of childhood, and objective methods for assessment are lacking. In this work, learning models for BME detection were developed. Transfer learning was used to overcome the size limitations of the dataset, and two different regions of interest (ROI) were defined and compared to evaluate their impact on the performance of the model: bone segmention and intensity mask. The best model was obtained for the high intensity masking technique, which achieved a balanced accuracy of 0.792 +/- 0.034. This study represents a comparison of different models and data regularization techniques for BME detection and showed promising results, even in the most difficult range of ages: children and adolescents. The application of machine learning methods will help to decrease the dependence on the clinicians, providing an initial stratification of the patients based on the probability of edema presence and supporting their decisions on the diagnosis.
2023
Authors
Mendes, J; Pereira, T; Silva, F; Frade, J; Morgado, J; Freitas, C; Negrao, E; de Lima, BF; da Silva, MC; Madureira, AJ; Ramos, I; Costa, JL; Hespanhol, V; Cunha, A; Oliveira, HP;
Publication
EXPERT SYSTEMS WITH APPLICATIONS
Abstract
Biomedical engineering has been targeted as a potential research candidate for machine learning applications, with the purpose of detecting or diagnosing pathologies. However, acquiring relevant, high-quality, and heterogeneous medical datasets is challenging due to privacy and security issues and the effort required to annotate the data. Generative models have recently gained a growing interest in the computer vision field due to their ability to increase dataset size by generating new high-quality samples from the initial set, which can be used as data augmentation of a training dataset. This study aimed to synthesize artificial lung images from corresponding positional and semantic annotations using two generative adversarial networks and databases of real computed tomography scans: the Pix2Pix approach that generates lung images from the lung segmentation maps; and the conditional generative adversarial network (cCGAN) approach that was implemented with additional semantic labels in the generation process. To evaluate the quality of the generated images, two quantitative measures were used: the domain-specific Frechet Inception Distance and Structural Similarity Index. Additionally, an expert assessment was performed to measure the capability to distinguish between real and generated images. The assessment performed shows the high quality of synthesized images, which was confirmed by the expert evaluation. This work represents an innovative application of GAN approaches for medical application taking into consideration the pathological findings in the CT images and the clinical evaluation to assess the realism of these features in the generated images.
2025
Authors
Gonçalves, S; Sousa, JV; Gouveia, M; Amaro, M; Oliveira, HP; Pereira, T;
Publication
BIBM
Abstract
Lung cancer remains the leading cause of cancer related deaths globally, responsible for approximately 1.8 million deaths each year. A key contributor to this high mortality rate is the late-stage diagnosis of the disease, underscoring the urgent need for effective early detection strategies. Low-dose computed tomography (CT) has shown great value in early screening, particularly when paired with clinical information. Clinical data, while valuable, lacks spatial and morphological insights essential for comprehensive evaluation. Combining both modalities offers a more holistic approach for lung cancer classification. This study presents AI-based methods for lung cancer classification using unimodal approaches - structured clinical data and chest CT imaging - alongside a novel multimodal deep learning framework that integrates both data types to classify lung nodules as malignant or benign. For the clinical modality, machine learning models including logistic regression, random forests, LightGBM, XGBoost, and multilayer perceptrons were evaluated with extensive hyperparameter tuning. In the imaging modality, ResNet18 and ResNet34 convolutional neural networks were used, with and without data augmentation. The study explored both intermediate and late fusion strategies to combine modality-specific representations. Results show that multimodal models consistently outperformed their unimodal counterparts, achieving a best-case area under the ROC curve (AUC) of 0.9138, with an accuracy of 0.8424 and an F1-score of 0.8422. These findings highlight the complementary strengths of imaging and clinical data and support the growing potential of multimodal deep learning in improving diagnostic accuracy in lung cancer classification. © 2025 IEEE.
2025
Authors
Saraiva, A; Gouveia, M; Lopes, C; Marinho, J; Pereira, T; Mendes, J;
Publication
BIBM
Abstract
Accurate surgical planning is critical in mandibular reconstruction to restore the oncology patient's function and aesthetics. However, the use of physical three-dimensional (3D) models is often limited by time-consuming manual segmentation procedures or the high cost of commercial solutions. This work addresses the need for an accessible, quick, and low-cost pipeline to obtain a 3D printed model of the segmented mandible from a Computed Tomography (CT) scan. The automatic segmentation stage relied on the two-dimensional U-Net architecture, which was trained and validated with slices across two public datasets (PDDCA, HaN-Seg) and tested with the other two public datasets (TCIA RT, Austrian). The best model achieved an average dice similarity coefficient (DSC) of 0.912 ± 0.077 across all test sets. The segmentation output was reconstructed into a 3D volume, improved through a post-processing method (with morphological closing, upsample, smoothing, and mesh reduction), and 3D printed through fused deposition modelling. The assessment of a stomatologist confirmed overall high anatomical fidelity to the CT and clinical utility, even though further improvements in important fine anatomical elements were suggested. This solution contributes to a promising alternative to producing 3D personalised mandibles for surgical planning, reducing time and manual effort while improving the quality and accessibility. Future work may explore the use of 3D DL architectures and a broader evaluation of the 3D mandible models.
2025
Authors
Nunes, JD; Montezuma, D; Oliveira, D; Pereira, T; Zlobec, I; Cardoso, JS;
Publication
2025 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS, IJCNN
Abstract
Deep learning in computational pathology (CPath) has rapidly advanced in recent years. Research has primarily focused on enhancing accuracy and interpretability across various histology image analysis tasks, from tile-level to slide-level foundation models and novel multiple instance learning (MIL) strategies. However, it is equally important for models to provide well-calibrated confidence estimates. Due to factors such as dataset bias, overfitting, and limited training data, existing models tend to be overly confident on test sets. Promising solutions to address this issue include temperature scaling, a post-hoc method that adjusts logits using a single scalar value. However, the role of calibration in CPath is yet to be clarified. In this study, we evaluate temperature scaling and linear temperature scaling for CPath tasks, analyzing their impact on recalibration in both in-domain and out-of-domain distributions. The results show the limitations of current probability calibration techniques and motivate future work.
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