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Publications

Publications by CTM

2024

Deep Learning Models to Predict Brain Cancer Grade Through MRI Analysis

Authors
Vale, P; Boer, J; Oliveira, HP; Pereira, T;

Publication
2024 IEEE 37TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS, CBMS 2024

Abstract
The early and accurate detection and the grading characterization of brain cancer will generate a positive impact on the treatment plan of those patients. AI-based models can help analyze the Magnetic Resonance Imaging (MRI) to make an initial assessment of the tumor grading. The objective of this work was to develop an Al-based model to classify the grading of the tumor using the MRI. Two regions of interest were explored, with several levels of complexity for the neural network architecture, and Iwo strategies to deal with Unbalanced data. The best results were obtained for the most complex architecture (Resnet50) with a combination of weighted random sampler and data augmentation achieving a balanced accuracy of 62.26%. This work confirmed that complex problems required a more dense neural network and strategies to deal with the unbalanced data.

2024

A review of machine learning methods for cancer characterization from microbiome data

Authors
Teixeira, M; Silva, F; Ferreira, RM; Pereira, T; Figueiredo, C; Oliveira, HP;

Publication
NPJ PRECISION ONCOLOGY

Abstract
Recent studies have shown that the microbiome can impact cancer development, progression, and response to therapies suggesting microbiome-based approaches for cancer characterization. As cancer-related signatures are complex and implicate many taxa, their discovery often requires Machine Learning approaches. This review discusses Machine Learning methods for cancer characterization from microbiome data. It focuses on the implications of choices undertaken during sample collection, feature selection and pre-processing. It also discusses ML model selection, guiding how to choose an ML model, and model validation. Finally, it enumerates current limitations and how these may be surpassed. Proposed methods, often based on Random Forests, show promising results, however insufficient for widespread clinical usage. Studies often report conflicting results mainly due to ML models with poor generalizability. We expect that evaluating models with expanded, hold-out datasets, removing technical artifacts, exploring representations of the microbiome other than taxonomical profiles, leveraging advances in deep learning, and developing ML models better adapted to the characteristics of microbiome data will improve the performance and generalizability of models and enable their usage in the clinic.

2024

CNN-based Methods for Survival Prediction using CT images for Lung Cancer Patients

Authors
Amaro, M; Oliveira, HP; Pereira, T;

Publication
2024 IEEE 37TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS, CBMS 2024

Abstract
Lung Cancer (LC) is still among the top main causes of death worldwide, and it is the leading death number among other cancers. Several AI-based methods have been developed for the early detection of LC, trying to use Computed Tomography (CT) images to identify the initial signs of the disease. The survival prediction could help the clinicians to adequate the treatment plan and all the proceedings, by the identification of the most severe cases that need more attention. In this study, several deep learning models were compared to predict the survival of LC patients using CT images. The best performing model, a CNN with 3 layers, achieved an AUC value of 0.80, a Precision value of 0.56 and a Recall of 0.64. The obtained results showed that CT images carry information that can be used to assess the survival of LC.

2024

Exploring the differences between Multi-task and Single-task with the use of hxplainable AI for lung nodule classification

Authors
Fernandes, L; Pereira, T; Oliveira, HP;

Publication
2024 IEEE 37TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS, CBMS 2024

Abstract
Currently, lung cancer is one of the deadliest diseases that affects millions of people globally. However, Artificial Intelligence is being increasingly integrated with healthcare practices, with the goal to aid in the early diagnosis of lung cancer. Although such methods have shown very promising results, they still lack transparency to the user, which consequently could make their generalised adoption a challenging task. Therefore, in this work we explore the use of post-hoc explainable methods, to better understand the inner-workings of an already established multitasking framework that executes the segmentation and the classification task of lung nodules simultaneously. The idea behind such study is to understand how a multitasking approach impacts the model's performance in the lung nodule classification task when compared to single-task models. Our results show that the multitasking approach works as an attention mechanism by aiding the model to learn more meaningful features. Furthermore, the multitasking framework was able to achieve a better performance in regard to the explainability metric, with an increase of 7% when compared to our baseline, and also during the classification and segmentation task, with an increase of 4.84% and 15.03%; for each task respectively, when also compared to the studied baselines.

2024

Tutorial on the Use of the Photon Diffusion Approximation for Fast Calculation of Tissue Optical Properties

Authors
Pinheiro, MR; Carvalho, MI; Oliveira, LM;

Publication
JOURNAL OF BIOPHOTONICS

Abstract
Computer simulations, which are performed at a single wavelength at a time, have been traditionally used to estimate the optical properties of tissues. The results of these simulations need to be interpolated. For a broadband estimation of tissue optical properties, the use of computer simulations becomes time consuming and computer demanding. When spectral measurements are available for a tissue, the use of the photon diffusion approximation can be done to perform simple and direct calculations to obtain the broadband spectra of some optical properties. The additional estimation of the reduced scattering coefficient at a small number of discrete wavelengths allows to perform further calculations to obtain the spectra of other optical properties. This study used spectral measurements from the heart muscle to explain the calculation pipeline to obtain a complete set of the spectral optical properties and to show its versatility for use with other tissues for various biophotonics applications.

2024

On the Use of VGs for Feature Selection in Supervised Machine Learning - A Use Case to Detect Distributed DoS Attacks

Authors
Lopes, J; Partida, A; Pinto, P; Pinto, A;

Publication
OPTIMIZATION, LEARNING ALGORITHMS AND APPLICATIONS, PT I, OL2A 2023

Abstract
Information systems depend on security mechanisms to detect and respond to cyber-attacks. One of the most frequent attacks is the Distributed Denial of Service (DDoS): it impairs the performance of systems and, in the worst case, leads to prolonged periods of downtime that prevent business processes from running normally. To detect this attack, several supervised Machine Learning (ML) algorithms have been developed and companies use them to protect their servers. A key stage in these algorithms is feature pre-processing, in which, input data features are assessed and selected to obtain the best results in the subsequent stages that are required to implement supervised ML algorithms. In this article, an innovative approach for feature selection is proposed: the use of Visibility Graphs (VGs) to select features for supervised machine learning algorithms used to detect distributed DoS attacks. The results show that VG can be quickly implemented and can compete with other methods to select ML features, as they require low computational resources and they offer satisfactory results, at least in our example based on the early detection of distributed DoS. The size of the processed data appears as the main implementation constraint for this novel feature selection method.

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