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Publications

Publications by CTM

2022

The Influence of a Coherent Annotation and Synthetic Addition of Lung Nodules for Lung Segmentation in CT Scans

Authors
Sousa, J; Pereira, T; Neves, I; Silva, F; Oliveira, HP;

Publication
SENSORS

Abstract
Lung cancer is a highly prevalent pathology and a leading cause of cancer-related deaths. Most patients are diagnosed when the disease has manifested itself, which usually is a sign of lung cancer in an advanced stage and, as a consequence, the 5-year survival rates are low. To increase the chances of survival, improving the cancer early detection capacity is crucial, for which computed tomography (CT) scans represent a key role. The manual evaluation of the CTs is a time-consuming task and computer-aided diagnosis (CAD) systems can help relieve that burden. The segmentation of the lung is one of the first steps in these systems, yet it is very challenging given the heterogeneity of lung diseases usually present and associated with cancer development. In our previous work, a segmentation model based on a ResNet34 and U-Net combination was developed on a cross-cohort dataset that yielded good segmentation masks for multiple pathological conditions but misclassified some of the lung nodules. The multiple datasets used for the model development were originated from different annotation protocols, which generated inconsistencies for the learning process, and the annotations are usually not adequate for lung cancer studies since they did not comprise lung nodules. In addition, the initial datasets used for training presented a reduced number of nodules, which was showed not to be enough to allow the segmentation model to learn to include them as a lung part. In this work, an objective protocol for the lung mask's segmentation was defined and the previous annotations were carefully reviewed and corrected to create consistent and adequate ground-truth masks for the development of the segmentation model. Data augmentation with domain knowledge was used to create lung nodules in the cases used to train the model. The model developed achieved a Dice similarity coefficient (DSC) above 0.9350 for all test datasets and it showed an ability to cope, not only with a variety of lung patterns, but also with the presence of lung nodules as well. This study shows the importance of using consistent annotations for the supervised learning process, which is a very time-consuming task, but that has great importance to healthcare applications. Due to the lack of massive datasets in the medical field, which consequently brings a lack of wide representativity, data augmentation with domain knowledge could represent a promising help to overcome this limitation for learning models development.

2022

The effect of augmentation and transfer learning on the modelling of lower-limb sockets using 3D adversarial autoencoders

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

Publication
DISPLAYS

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 ways to improve the fitting process by creating virtual models of the prosthesis' interface component with the limb, the socket. Using Adversarial Autoencoders, a generative model describing both transtibial and transfemoral sockets was created. Two strategies were tested to counteract the small size of the dataset: transfer learning using the ModelNet dataset and data augmentation through a previously validated socket statistical shape model. The minimum reconstruction error was 0.00124 mm and was obtained for the model which combined the two approaches. A single-blind assessment conducted with prosthetists showed that, while generated and real shapes are distinguishable, most generated ones assume plausible shapes. Our results show that the use of transfer learning allowed for a correct training and regularization of the latent space, inducing in the model generative abilities with potential clinical applications.

2022

Learning Models for Traumatic Brain Injury Mortality Prediction on Pediatric Electronic Health Records

Authors
Fonseca, J; Liu, XY; Oliveira, HP; Pereira, T;

Publication
FRONTIERS IN NEUROLOGY

Abstract
BackgroundTraumatic Brain Injury (TBI) is one of the leading causes of injury related mortality in the world, with severe cases reaching mortality rates of 30-40%. It is highly heterogeneous both in causes and consequences, complicating medical interpretation and prognosis. Gathering clinical, demographic, and laboratory data to perform a prognosis requires time and skill in several clinical specialties. Machine learning (ML) methods can take advantage of the data and guide physicians toward a better prognosis and, consequently, better healthcare. The objective of this study was to develop and test a wide range of machine learning models and evaluate their capability of predicting mortality of TBI, at hospital discharge, while assessing the similarity between the predictive value of the data and clinical significance. MethodsThe used dataset is the Hackathon Pediatric Traumatic Brain Injury (HPTBI) dataset, composed of electronic health records containing clinical annotations and demographic data of 300 patients. Four different classification models were tested, either with or without feature selection. For each combination of the classification model and feature selection method, the area under the receiver operator curve (ROC-AUC), balanced accuracy, precision, and recall were calculated. ResultsMethods based on decision trees perform better when using all features (Random Forest, AUC = 0.86 and XGBoost, AUC = 0.91) but other models require prior feature selection to obtain the best results (k-Nearest Neighbors, AUC = 0.90 and Artificial Neural Networks, AUC = 0.84). Additionally, Random Forest and XGBoost allow assessing the feature's importance, which could give insights for future strategies on the clinical routine. ConclusionPredictive capability depends greatly on the combination of model and feature selection methods used but, overall, ML models showed a very good performance in mortality prediction for TBI. The feature importance results indicate that predictive value is not directly related to clinical significance.

2022

Invasive and minimally invasive optical detection of pigment accumulation in brain cortex

Authors
Oliveira, LR; Gonçalves, TM; Pinheiro, MR; Fernandes, LE; Martins, IS; Silva, HF; Oliveira, HP; Tuchin, VV;

Publication
Journal of Biomedical Photonics and Engineering

Abstract
The estimation of the spectral absorption coefficient of biological tissues provides valuable information that can be used in diagnostic procedures. Such estimation can be made using direct calculations from invasive spectral measurements or though machine learning algorithms based on noninvasive or minimally invasive spectral measurements. Since in a noninvasive approach, the number of measurements is limited, an exploratory study to investigate the use of artificial generated data in machine learning techniques was performed to evaluate the spectral absorption coefficient of the brain cortex. Considering the spectral absorption coefficient that was calculated directly from invasive measurements as reference, the similar spectra that were estimated through different machine learning approaches were able to provide comparable information in terms of pigment, DNA and blood contents in the cortex. The best estimated results were obtained based only on the experimental measurements, but it was also observed that artificially generated spectra can be used in the estimations to increase accuracy, provided that a significant number of experimental spectra are available both to generate the complementary artificial spectra and to estimate the resulting absorption spectrum of the tissue. © 2022 Journal of Biomedical Photonics & Engineering. © J-BPE.

2022

On the way for the best imaging features from CT images to predict <i>EGFR</i> Mutation Status in Lung Cancer

Authors
Silva, P; Pereira, T; Teixeira, M; Silva, F; Oliveira, HP;

Publication
2022 44TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY, EMBC

Abstract
Artificial Intelligence-based tools have shown promising results to help clinicians in diagnosis tasks. Radio-genomics would aid in the genotype characterization using information from radiologic images. The prediction of the mutations status of main oncogenes associated with lung cancer will help the clinicians to have a more accurate diagnosis and a personalized treatment plan, decreasing the need to use the biopsy. In this work, novel and objective features were extracted from the lung that contained the nodule, and several machine learning methods were combined with feature selection techniques to select the best approach to predict the EGFR mutation status in lung cancer CT images. An AUC of 0.756 ± 0.055 was obtained using a logistic regression and independent component analysis as feature selector, supporting the hypothesis that CT images can capture pathophysiological information with great value for clinical assessment and personalized medicine of lung cancer. Clinical Relevance-Radiogenomic approaches could be an interesting help for lung cancer characterization. This work represents a preliminary study for the development of computer-aided decision systems to provide a more accurate and fast characterization of lung cancer which is fundamental for an adequate treatment plan for lung cancer patients.

2022

A Random Forest-based Classifier for <i>MYCN</i> Status Prediction in Neuroblastoma using CT Images

Authors
Pereira, T; Silva, F; Claro, P; Carvalho, DC; Dias, SC; Torrao, H; Oliveira, HP;

Publication
2022 44TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY, EMBC

Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. Genomic amplification of MYCN is associated with poor outcomes and is detected in 16% of all NB cases. CT scans and MRI are the imaging techniques recommended for diagnosis and disease staging. The assessment of imaging features such as tumor volume, shape, and local extension represent relevant prognostic information. Radiogenomics have shown powerful results in the assessment of the genotype based on imaging findings automatically extracted from medical images. In this work, random forest was used to classify the MYCN amplification using radiomic features extracted from CT slices in a population of 46 NB patients. The learning model showed an area under the curve (AUC) of 0.85 ± 0.13, suggesting that radiomic-based methodologies might be helpful in the extraction of information that is not accessible by human naked eyes but could aid the clinicians on the diagnosis and treatment plan definition. Clinical relevance - This approach represents a random forest-based model to predict the MYCN amplification in NB patients that could give a faster, earlier, and repeatable analysis of the tumor along the time.

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