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Publicações

Publicações por Hélder Filipe Oliveira

2021

Embedding Anatomical Characteristics in 3D Models of Lower-limb Sockets through Statistical Shape Modelling

Autores
Costa, A; Rodrigues, D; Castro, M; Assis, S; Oliveira, HP;

Publicação
VISAPP: PROCEEDINGS OF THE 16TH INTERNATIONAL JOINT CONFERENCE ON COMPUTER VISION, IMAGING AND COMPUTER GRAPHICS THEORY AND APPLICATIONS - VOL. 4: VISAPP

Abstract
Lower limb amputation is a condition affecting millions of people worldwide. Patients are often prescribed with lower limb prostheses to aid their mobility, but these prostheses require frequent adjustments through an iterative and manual process, which heavily depends on patient feedback and on the prosthetist's experience. New computer-aided design and manufacturing technologies have been emerging as a way to improve the fitting process by creating virtual socket models. Statistical Shape modelling was used to create 3D models of transtibial (TT) and transfemoral (TF) sockets. Their generalization errors were, respectively, 6.8 +/- 1.8 mm and 10.5 +/- 1.6 mm, while specificity errors were 9.7 +/- 0.6 mm and 9.8 +/- 0.2 mm. In both models, a visual analysis showed that biomechanically meaningful features were captured: the largest variations found for both types were in the length of the residual limb and in the perimeter variation along the limb. The results obtained proved that statistical shape modelling methods can be applied to TF and TT sockets, with several potential applications in the orthoprosthetic field: generation of new plausible shapes and on-demand socket design adjustments.

2021

Machine Learning and Feature Selection Methods for EGFR Mutation Status Prediction in Lung Cancer

Autores
Morgado, J; Pereira, T; Silva, F; Freitas, C; Negrao, E; de Lima, BF; da Silva, MC; Madureira, AJ; Ramos, I; Hespanhol, V; Costa, JL; Cunha, A; Oliveira, HP;

Publicação
APPLIED SCIENCES-BASEL

Abstract
The evolution of personalized medicine has changed the therapeutic strategy from classical chemotherapy and radiotherapy to a genetic modification targeted therapy, and although biopsy is the traditional method to genetically characterize lung cancer tumor, it is an invasive and painful procedure for the patient. Nodule image features extracted from computed tomography (CT) scans have been used to create machine learning models that predict gene mutation status in a noninvasive, fast, and easy-to-use manner. However, recent studies have shown that radiomic features extracted from an extended region of interest (ROI) beyond the tumor, might be more relevant to predict the mutation status in lung cancer, and consequently may be used to significantly decrease the mortality rate of patients battling this condition. In this work, we investigated the relation between image phenotypes and the mutation status of Epidermal Growth Factor Receptor (EGFR), the most frequently mutated gene in lung cancer with several approved targeted-therapies, using radiomic features extracted from the lung containing the nodule. A variety of linear, nonlinear, and ensemble predictive classification models, along with several feature selection methods, were used to classify the binary outcome of wild-type or mutant EGFR mutation status. The results show that a comprehensive approach using a ROI that included the lung with nodule can capture relevant information and successfully predict the EGFR mutation status with increased performance compared to local nodule analyses. Linear Support Vector Machine, Elastic Net, and Logistic Regression, combined with the Principal Component Analysis feature selection method implemented with 70% of variance in the feature set, were the best-performing classifiers, reaching Area Under the Curve (AUC) values ranging from 0.725 to 0.737. This approach that exploits a holistic analysis indicates that information from more extensive regions of the lung containing the nodule allows a more complete lung cancer characterization and should be considered in future radiogenomic studies.

2021

EGFR Assessment in Lung Cancer CT Images: Analysis of Local and Holistic Regions of Interest Using Deep Unsupervised Transfer Learning

Autores
Silva, F; Pereira, T; Morgado, J; Frade, J; Mendes, J; Freitas, C; Negrao, E; De Lima, BF; Da Silva, MC; Madureira, AJ; Ramos, I; Hespanhol, V; Costa, JL; Cunha, A; Oliveira, HP;

Publicação
IEEE ACCESS

Abstract
Statistics have demonstrated that one of the main factors responsible for the high mortality rate related to lung cancer is the late diagnosis. Precision medicine practices have shown advances in the individualized treatment according to the genetic profile of each patient, providing better control on cancer response. Medical imaging offers valuable information with an extensive perspective of the cancer, opening opportunities to explore the imaging manifestations associated with the tumor genotype in a non-invasive way. This work aims to study the relevance of physiological features captured from Computed Tomography images, using three different 2D regions of interest to assess the Epidermal growth factor receptor (EGFR) mutation status: nodule, lung containing the main nodule, and both lungs. A Convolutional Autoencoder was developed for the reconstruction of the input image. Thereafter, the encoder block was used as a feature extractor, stacking a classifier on top to assess the EGFR mutation status. Results showed that extending the analysis beyond the local nodule allowed the capture of more relevant information, suggesting the presence of useful biomarkers using the lung with nodule region of interest, which allowed to obtain the best prediction ability. This comparative study represents an innovative approach for gene mutations status assessment, contributing to the discussion on the extent of pathological phenomena associated with cancer development, and its contribution to more accurate Artificial Intelligence-based solutions, and constituting, to the best of our knowledge, the first deep learning approach that explores a comprehensive analysis for the EGFR mutation status classification.

2021

The Role of Liquid Biopsy in Early Diagnosis of Lung Cancer

Autores
Freitas, C; Sousa, C; Machado, F; Serino, M; Santos, V; Cruz Martins, N; Teixeira, A; Cunha, A; Pereira, T; Oliveira, HP; Costa, JL; Hespanhol, V;

Publicação
FRONTIERS IN ONCOLOGY

Abstract
Liquid biopsy is an emerging technology with a potential role in the screening and early detection of lung cancer. Several liquid biopsy-derived biomarkers have been identified and are currently under ongoing investigation. In this article, we review the available data on the use of circulating biomarkers for the early detection of lung cancer, focusing on the circulating tumor cells, circulating cell-free DNA, circulating micro-RNAs, tumor-derived exosomes, and tumor-educated platelets, providing an overview of future potential applicability in the clinical practice. While several biomarkers have shown exciting results, diagnostic performance and clinical applicability is still limited. The combination of different biomarkers, as well as their combination with other diagnostic tools show great promise, although further research is still required to define and validate the role of liquid biopsies in clinical practice.

2021

Sharing Biomedical Data: Strengthening AI Development in Healthcare

Autores
Pereira, T; Morgado, J; Silva, F; Pelter, MM; Dias, VR; Barros, R; Freitas, C; Negrao, E; de Lima, BF; da Silva, MC; Madureira, AJ; Ramos, I; Hespanhol, V; Costa, JL; Cunha, A; Oliveira, HP;

Publicação
HEALTHCARE

Abstract
Artificial intelligence (AI)-based solutions have revolutionized our world, using extensive datasets and computational resources to create automatic tools for complex tasks that, until now, have been performed by humans. Massive data is a fundamental aspect of the most powerful AI-based algorithms. However, for AI-based healthcare solutions, there are several socioeconomic, technical/infrastructural, and most importantly, legal restrictions, which limit the large collection and access of biomedical data, especially medical imaging. To overcome this important limitation, several alternative solutions have been suggested, including transfer learning approaches, generation of artificial data, adoption of blockchain technology, and creation of an infrastructure composed of anonymous and abstract data. However, none of these strategies is currently able to completely solve this challenge. The need to build large datasets that can be used to develop healthcare solutions deserves special attention from the scientific community, clinicians, all the healthcare players, engineers, ethicists, legislators, and society in general. This paper offers an overview of the data limitation in medical predictive models; its impact on the development of healthcare solutions; benefits and barriers of sharing data; and finally, suggests future directions to overcome data limitations in the medical field and enable AI to enhance healthcare. This perspective is dedicated to the technical requirements of the learning models, and it explains the limitation that comes from poor and small datasets in the medical domain and the technical options that try or can solve the problem related to the lack of massive healthcare data.

2021

Adversarial Data Augmentation on Breast MRI Segmentation

Autores
Teixeira, JF; Dias, M; Batista, E; Costa, J; Teixeira, LF; Oliveira, HP;

Publicação
APPLIED SCIENCES-BASEL

Abstract
The scarcity of balanced and annotated datasets has been a recurring problem in medical image analysis. Several researchers have tried to fill this gap employing dataset synthesis with adversarial networks (GANs). Breast magnetic resonance imaging (MRI) provides complex, texture-rich medical images, with the same annotation shortage issues, for which, to the best of our knowledge, no previous work tried synthesizing data. Within this context, our work addresses the problem of synthesizing breast MRI images from corresponding annotations and evaluate the impact of this data augmentation strategy on a semantic segmentation task. We explored variations of image-to-image translation using conditional GANs, namely fitting the generator's architecture with residual blocks and experimenting with cycle consistency approaches. We studied the impact of these changes on visual verisimilarity and how an U-Net segmentation model is affected by the usage of synthetic data. We achieved sufficiently realistic-looking breast MRI images and maintained a stable segmentation score even when completely replacing the dataset with the synthetic set. Our results were promising, especially when concerning to Pix2PixHD and Residual CycleGAN architectures.

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