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Publications

Publications by CRIIS

2025

Data Augmentation with Generative Methods for Inherited Retinal Diseases: A Systematic Review

Authors
Machado, J; Marta, A; Mestre, P; Beirao, JM; Cunha, A;

Publication
APPLIED SCIENCES-BASEL

Abstract
Inherited retinal diseases (IRDs) are rare and genetically diverse disorders that cause progressive vision loss and affect 1 in 3000 individuals worldwide. Their rarity and genetic variability pose a challenge for deep learning models due to the limited amount of data. Generative models offer a promising solution by creating synthetic data to improve training datasets. This study carried out a systematic literature review to investigate the use of generative models to augment data in IRDs and assess their impact on the performance of classifiers for these diseases. Following PRISMA 2020 guidelines, searches in four databases identified 32 relevant studies, 2 focused on IRD and the rest on other retinal diseases. The results indicate that generative models effectively augment small datasets. Among the techniques identified, Deep Convolutional Adversarial Generative Networks (DCGAN) and the Style-Based Generator Architecture of Generative Adversarial Networks 2 (StyleGAN2) were the most widely used. These architectures generated highly realistic and diverse synthetic data, often indistinguishable from real data, even for experts. The results highlight the need for more research into data generation in IRD to develop robust diagnostic tools and improve genetic studies by creating more comprehensive genetic repositories.

2025

Progress in applications of self-supervised learning to computer vision in agriculture: A systematic review

Authors
Carneiro, GA; Aubry, TJ; Cunha, A; Radeva, P; Sousa, JJ;

Publication
COMPUTERS AND ELECTRONICS IN AGRICULTURE

Abstract
Precision Agriculture (PA) has emerged as an approach to optimize production, comprise different technology and principles focusing on how to improve agricultural production. Currently, one of the main foundations of PA is the use of artificial intelligence, through deep learning (DL) algorithms. By processing large volumes of complex data, DL enhances decision-making and boosts farming efficiency. However, these methods are hungry for annotated data, which contrasts with the scarce availability of annotated agricultural data and the costs of annotation. Self-supervised learning (SSL) has emerged as a solution to tackle the lack of annotated agricultural data. This study presents a review of the application of SSL methods to computer vision tasks in the agricultural context. The aim is to create a starting point for professionals and scientists who intend to apply these methods using agricultural data. The results of 33 studies found in the literature are discussed, highlighting their pros and cons. In most of the studies, SSL outperformed its supervised counterpart, using datasets from 4000 to 60,000 samples. Potential directions for improving future research are suggested.

2025

Retinitis Pigmentosa Classification with Deep Learning and Integrated Gradients Analysis

Authors
Ferreira, H; Marta, A; Machado, J; Couto, I; Marques, JP; Beirao, JM; Cunha, A;

Publication
APPLIED SCIENCES-BASEL

Abstract
Inherited retinal diseases (IRDs) are genetic disorders affecting photoreceptors and the retinal pigment epithelium, leading to progressive vision loss. Retinitis pigmentosa (RP), the most common IRD, manifests as night blindness, peripheral vision loss, and eventually central vision decline. RP is genetically diverse and can be categorized into non-syndromic and syndromic. Advanced imaging technologies such as fundus autofluorescence (FAF) and spectral-domain optical coherence tomography (SD-OCT) facilitate diagnosing and managing these conditions. The integration of artificial intelligence in analyzing retinal images has shown promise in identifying genes associated with RP. This study used a dataset from Portuguese public hospitals, comprising 2798 FAF images labeled for syndromic and non-syndromic RP across 66 genes. Three pre-trained models, Inception-v3, ResNet-50, and VGG-19, were used to classify these images, obtaining an accuracy of over 80% in the training data and 54%, 56%, and 54% in the test data for all models. Data preprocessing included class balancing and boosting to address variability in gene representation. Model performance was evaluated using some main metrics. The findings demonstrate the effectiveness of deep learning in automatically classifying retinal images for different RP-associated genes, marking a significant advancement in the diagnostic capabilities of artificial intelligence and advanced imaging techniques in IRD.

2025

CTCovid19: Automatic Covid-19 model for Computed Tomography Scans Using Deep Learning

Authors
Antunes, C; Rodrigues, J; Cunha, A;

Publication
Intelligence-Based Medicine

Abstract
COVID-19 is an extremely contagious respiratory sickness instigated by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Common symptoms encompass fever, cough, fatigue, and breathing difficulties, often leading to hospitalization and fatalities in severe cases. CTCovid19 is a novel model tailored for COVID-19 detection, specifically honing in on a distinct deep learning structure, ResNet-50 trained with ImageNet serves as the foundational framework for our model. To enhance its capability to capture pertinent features related to COVID-19 patterns in Computed Tomography scans, the network underwent fine-tuning through layer adjustments and the addition of new ones. The model achieved accuracy rates that went from 97.0 % to 99.8 % across three widely recognized and documented datasets dedicated to COVID-19 detection. © 2024 The Authors

2025

MT-InSAR and Dam Modeling for the Comprehensive Monitoring of an Earth-Fill Dam: The Case of the Beninar Dam (Almeria, Spain) (vol 15, 2802, 2023)

Authors
Marchamalo-Sacristán, M; Ruiz-Armenteros, AM; Lamas-Fernández, F; González-Rodrigo, B; Martínez-Marín, R; Delgado-Blasco, JM; Bakon, M; Lazecky, M; Perissin, D; Papco, J; Sousa, JJ;

Publication
REMOTE SENSING

Abstract
The authors wish to make the following corrections to this manuscript [...]

2025

Improvement associated with mesh geometry for the decomposition of InSAR results

Authors
Alonso Diaz, A; Solla, M; Bakon, M; Sousa, J;

Publication
GEO-SPATIAL INFORMATION SCIENCE

Abstract
This paper presents a novel approach to improve the conversion of interferometric synthetic aperture radar (InSAR) ascending and descending orbit measurements into horizontal and vertical deformation components, explicitly considering SAR product characteristics (acquisition geometry, resolution, and positional accuracy). Conventional decomposition methods use square grids, inadequately addressing directional biases associated with satellite images characteristics, reducing measurement accuracy. It is proposed optimized alternative geometries - rectangle, hexagon, and double inverted isosceles trapezoid (diIT) - derived from theoretical analysis of scatterer influence areas for Sentinel-1 imagery and calibrated data from the European ground motion service (EGMS). Validation was conducted comparing results against global navigation satellite system (GNSS) ground-truth data. Accuracy was quantitatively evaluated using deformation velocity (DV) and average Euclidean distance (ED) metrics. Results demonstrated an average 25% improvement in DV detection over traditional square grids, with only minor trade-offs, such as lower scatterer density and sub-millimetric increases in error for hexagon and diIT geometries.

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