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Publications

Publications by António Cunha

2021

Stacking Approach for Lung Cancer EGFR Mutation Status Prediction from CT Scans

Authors
Ventura, A; Pereira, T; Silva, F; Freitas, C; Cunha, A; Oliveira, HP;

Publication
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021, Houston, TX, USA, December 9-12, 2021

Abstract
Due to the huge mortality rate of lung cancer, there is a strong need for developing solutions that help with the early diagnosis and the definition of the most appropriate treatment. In the particular case of target therapy, effective genotyping of the tumor is fundamental since this treatment uses targeted drugs that can induce death in cancer cells. The biopsy is the traditional method to assess the genotype information but it is extremely invasive and painful. Medical imaging is a valuable alternative to biopsies, considering the potential to extract imaging features correlated with specific genomic alterations. Regarding the limitations of single model approaches for gene mutation status predictions, ensemble strategies might bring valuable benefits by combining the strengths and weaknesses of the aggregated methods. This preliminary work aims to provide further advances in the radiogenomics field by studying the use of ensemble methods to predict the Epidermal Growth Factor Receptor (EGFR) mutation status in lung cancer. The best result obtained for the proposed ensemble approach was an AUC of 0.706 (± 0.122). However, the ensemble did not outperform the single models with AUC values of 0.712 (± 0.119) for Logistic Regression, 0.711 (± 0.119) for Support Vector Machine and 0.712 (± 0.120) for Elastic Net. The high correlation found on the decisions of each single model might be a plausible explanation for this behavior, which caused the ensemble to misclassify the same examples as the single models.

2022

Literature Review on Artificial Intelligence Methods for Glaucoma Screening, Segmentation, and Classification

Authors
Camara, J; Neto, A; Pires, IM; Villasana, MV; Zdravevski, E; Cunha, A;

Publication
JOURNAL OF IMAGING

Abstract
Artificial intelligence techniques are now being applied in different medical solutions ranging from disease screening to activity recognition and computer-aided diagnosis. The combination of computer science methods and medical knowledge facilitates and improves the accuracy of the different processes and tools. Inspired by these advances, this paper performs a literature review focused on state-of-the-art glaucoma screening, segmentation, and classification based on images of the papilla and excavation using deep learning techniques. These techniques have been shown to have high sensitivity and specificity in glaucoma screening based on papilla and excavation images. The automatic segmentation of the contours of the optic disc and the excavation then allows the identification and assessment of the glaucomatous disease's progression. As a result, we verified whether deep learning techniques may be helpful in performing accurate and low-cost measurements related to glaucoma, which may promote patient empowerment and help medical doctors better monitor patients.

2022

Lung Segmentation in CT Images: A Residual U-Net Approach on a Cross-Cohort Dataset

Authors
Sousa, J; Pereira, T; Silva, F; Silva, MC; Vilares, AT; Cunha, A; Oliveira, HP;

Publication
APPLIED SCIENCES-BASEL

Abstract
Lung cancer is one of the most common causes of cancer-related mortality, and since the majority of cases are diagnosed when the tumor is in an advanced stage, the 5-year survival rate is dismally low. Nevertheless, the chances of survival can increase if the tumor is identified early on, which can be achieved through screening with computed tomography (CT). The clinical evaluation of CT images is a very time-consuming task and computed-aided diagnosis systems can help reduce this burden. The segmentation of the lungs is usually the first step taken in image analysis automatic models of the thorax. However, this task is very challenging since the lungs present high variability in shape and size. Moreover, the co-occurrence of other respiratory comorbidities alongside lung cancer is frequent, and each pathology can present its own scope of CT imaging appearances. This work investigated the development of a deep learning model, whose architecture consists of the combination of two structures, a U-Net and a ResNet34. The proposed model was designed on a cross-cohort dataset and it achieved a mean dice similarity coefficient (DSC) higher than 0.93 for the 4 different cohorts tested. The segmentation masks were qualitatively evaluated by two experienced radiologists to identify the main limitations of the developed model, despite the good overall performance obtained. The performance per pathology was assessed, and the results confirmed a small degradation for consolidation and pneumocystis pneumonia cases, with a DSC of 0.9015 +/- 0.2140 and 0.8750 +/- 0.1290, respectively. This work represents a relevant assessment of the lung segmentation model, taking into consideration the pathological cases that can be found in the clinical routine, since a global assessment could not detail the fragilities of the model.

2022

Evaluations of Deep Learning Approaches for Glaucoma Screening Using Retinal Images from Mobile Device

Authors
Neto, A; Camara, J; Cunha, A;

Publication
SENSORS

Abstract
Glaucoma is a silent disease that leads to vision loss or irreversible blindness. Current deep learning methods can help glaucoma screening by extending it to larger populations using retinal images. Low-cost lenses attached to mobile devices can increase the frequency of screening and alert patients earlier for a more thorough evaluation. This work explored and compared the performance of classification and segmentation methods for glaucoma screening with retinal images acquired by both retinography and mobile devices. The goal was to verify the results of these methods and see if similar results could be achieved using images captured by mobile devices. The used classification methods were the Xception, ResNet152 V2 and the Inception ResNet V2 models. The models' activation maps were produced and analysed to support glaucoma classifier predictions. In clinical practice, glaucoma assessment is commonly based on the cup-to-disc ratio (CDR) criterion, a frequent indicator used by specialists. For this reason, additionally, the U-Net architecture was used with the Inception ResNet V2 and Inception V3 models as the backbone to segment and estimate CDR. For both tasks, the performance of the models reached close to that of state-of-the-art methods, and the classification method applied to a low-quality private dataset illustrates the advantage of using cheaper lenses.

2021

Optic disc and cup segmentations for glaucoma assessment using cup-to-disc ratio

Authors
Neto, A; Camera, J; Oliveira, S; Cláudia, A; Cunha, A;

Publication
Procedia Computer Science

Abstract
Glaucoma is a silent disease that shows symptoms when severe, leading to partial vision loss or irreversible blindness. Early screening permits treating patients in time. For glaucoma screening, retinal images are very important since they enable the observation of initial glaucoma lesions, which typically begins with the cupping formation in the optic disc (OD). In clinical settings, practical indicators such as Cup-to-Disc Ratio (CDR) are frequently used to evaluate the presence and stage of glaucoma. The ratio between the cup and the optic disc can be measured using the vertical or horizontal diameter, or the area of the two. Mass screening programs are limited by the high costs of specialised teams and equipment. Current deep learning (DL) methods can assist the glaucoma mass screening, lower the cost and allow it to be extended to larger populations. With DL methods in the OD and optic cup (OC) segmentation, is possible to evaluate the presence of glaucoma in the patient more quickly based on cupping formation in the OD, using CDR. In this work, is assessed the contribution of Multi-Class and Single-Class segmentation methods for glaucoma screening using the 3 types of CDR. U-Net architecture is trained using transfer learning models (Inception V3 and Inception ResNet V2) to segment the OD and OC and then evaluate glaucoma prediction based on different types of CDRs indicators. The models were trained and evaluated on main public known databases (REFUGE, RIM-ONE r3 and DRISHTI-GS). The segmentation of both OD and OC reach Dice over 0.8 and IoU above 0.7. The CDRs were computed to glaucoma assessment where was reach sensitivity above 0.8, specificity of 0.7, F1-Score around 0.7 and AUC above 0.85. Finally, conclusions of segmentation methods showing adequate performance to be used in practical glaucoma screening.

2021

Machine Learning automatic assessment for glaucoma and myopia based on Corvis ST data

Authors
Leite, D; Campelos, M; Fernandes, A; Batista, P; Beirão, J; Menéres, P; Cunha, A;

Publication
Procedia Computer Science

Abstract
Glaucoma is a silent disease characterized by progressive degeneration of retinal ganglion cells and, when not detected or treated early, can lead to blindness. Computer systems have demonstrated their efficiency in the medical decision-making process and Artificial Intelligence (AI) techniques have helped advances in ophthalmology, allowing for faster and more effective detection of glaucoma. Machine learning is a very promising subfield of AI that supports research in understanding the development, progression and treatment of glaucoma, identifying new risk factors and assessing the importance of existing ones. This study aims to test and analyze the results of different models of supervised machine learning in the detection and classification of ophthalmic diseases (Glaucoma, high myopia and low myopia) based on data from Corvis ST. The most important characteristics were selected based on a variance greater than 0.02. In terms of accuracy, the models that obtained the best results were Random Forrest 0.73, Stochastic Gradient Descent (SGD) 0.75, Gradient Boosting Classifier (GBC) 0.76 and K-Nearest Neighbors 0.71. The GBC model achieved the best results in accuracy, AUC, Recall and F1Score 76.00, 52.5, 78.00, 70.2 respectively.

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