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Publications

Publications by CTM

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.

2021

An Interpretable Approach for Lung Cancer Prediction and Subtype Classification using Gene Expression

Authors
Ramos, B; Pereira, T; Moranguinho, J; Morgado, J; Costa, JL; Oliveira, HP;

Publication
2021 43RD ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY (EMBC)

Abstract
Lung cancer is the deadliest form of cancer, accounting for 20% of total cancer deaths. It represents a group of histologically and molecularly heterogeneous diseases even within the same histological subtype. Moreover, accurate histological subtype diagnosis influences the specific subtype's target genes, which will help define the treatment plan to target those genes in therapy. Deep learning (DL) models seem to set the benchmarks for the tasks of cancer prediction and subtype classification when using gene expression data; however, these methods do not provide interpretability, which is great concern from the perspective of cancer biology since the identification of the cancer driver genes in an individual provides essential information for treatment and prognosis. In this work, we identify some limitations of previous work that showed efforts to build algorithms to extract feature weights from DL models, and we propose using tree-based learning algorithms that address these limitations. Preliminary results show that our methods outperform those of related research while providing model interpretability.

2021

Attention Based Deep Multiple Instance Learning Approach for Lung Cancer Prediction using Histopathological Images

Authors
Moranguinho, J; Pereira, T; Ramos, B; Morgado, J; Costa, JL; Oliveira, HP;

Publication
2021 43RD ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY (EMBC)

Abstract
Deep Neural Networks using histopathological images as an input currently embody one of the gold standards in automated lung cancer diagnostic solutions, with Deep Convolutional Neural Networks achieving the state of the art values for tissue type classification. One of the main reasons for such results is the increasing availability of voluminous amounts of data, acquired through the efforts employed by extensive projects like The Cancer Genome Atlas. Nonetheless, whole slide images remain weakly annotated, as most common pathologist annotations refer to the entirety of the image and not to individual regions of interest in the patient's tissue sample. Recent works have demonstrated Multiple Instance Learning as a successful approach in classification tasks entangled with this lack of annotation, by representing images as a bag of instances where a single label is available for the whole bag. Thus, we propose a bag/embedding-level lung tissue type classifier using Multiple Instance Learning, where the automated inspection of lung biopsy whole slide images determines the presence of cancer in a given patient. Furthermore, we use a post-model interpretability algorithm to validate our model's predictions and highlight the regions of interest for such predictions.

2021

A Review of Attacks, Vulnerabilities, and Defenses in Industry 4.0 with New Challenges on Data Sovereignty Ahead

Authors
Pedreira, V; Barros, D; Pinto, P;

Publication
SENSORS

Abstract
The concepts brought by Industry 4.0 have been explored and gradually applied.The cybersecurity impacts on the progress of Industry 4.0 implementations and their interactions with other technologies require constant surveillance, and it is important to forecast cybersecurity-related challenges and trends to prevent and mitigate these impacts. The contributions of this paper are as follows: (1) it presents the results of a systematic review of industry 4.0 regarding attacks, vulnerabilities and defense strategies, (2) it details and classifies the attacks, vulnerabilities and defenses mechanisms, and (3) it presents a discussion of recent challenges and trends regarding cybersecurity-related areas for Industry 4.0. From the systematic review, regarding the attacks, the results show that most attacks are carried out on the network layer, where dos-related and mitm attacks are the most prevalent ones. Regarding vulnerabilities, security flaws in services and source code, and incorrect validations in authentication procedures are highlighted. These are vulnerabilities that can be exploited by dos attacks and buffer overflows in industrial devices and networks. Regarding defense strategies, Blockchain is presented as one of the most relevant technologies under study in terms of defense mechanisms, thanks to its ability to be used in a variety of solutions, from Intrusion Detection Systems to the prevention of Distributed dos attacks, and most defense strategies are presented as an after-attack solution or prevention, in the sense that the defense mechanisms are only placed or thought, only after the harm has been done, and not as a mitigation strategy to prevent the cyberattack. Concerning challenges and trends, the review shows that digital sovereignty, cyber sovereignty, and data sovereignty are recent topics being explored by researchers within the Industry 4.0 scope, and GAIA-X and International Data Spaces are recent initiatives regarding data sovereignty. A discussion of trends is provided, and future challenges are pointed out.

2021

A Performance Assessment of Free-to-Use Vulnerability Scanners - Revisited

Authors
Araújo, R; Pinto, A; Pinto, P;

Publication
ICT Systems Security and Privacy Protection - 36th IFIP TC 11 International Conference, SEC 2021, Oslo, Norway, June 22-24, 2021, Proceedings

Abstract
Vulnerability scanning tools can help secure the computer networks of organisations. Triggered by the release of the Tsunami vulnerability scanner by Google, the authors analysed and compared the commonly used, free-to-use vulnerability scanners. The performance, accuracy and precision of these scanners are quite disparate and vary accordingly to the target systems. The computational, memory and network resources required be these scanners also differ. We present a recent and detailed comparison of such tools that are available for use by organisations with lower resources such as small and medium-sized enterprises. © 2021, IFIP International Federation for Information Processing.

2021

Security Vulnerabilities in LPWANs-An Attack Vector Analysis for the IoT Ecosystem

Authors
Torres, N; Pinto, P; Lopes, SI;

Publication
APPLIED SCIENCES-BASEL

Abstract
Due to its pervasive nature, the Internet of Things (IoT) is demanding for Low Power Wide Area Networks (LPWAN) since wirelessly connected devices need battery-efficient and long-range communications. Due to its low-cost and high availability (regional/city level scale), this type of network has been widely used in several IoT applications, such as Smart Metering, Smart Grids, Smart Buildings, Intelligent Transportation Systems (ITS), SCADA Systems. By using LPWAN technologies, the IoT devices are less dependent on common and existing infrastructure, can operate using small, inexpensive, and long-lasting batteries (up to 10 years), and can be easily deployed within wide areas, typically above 2 km in urban zones. The starting point of this work was an overview of the security vulnerabilities that exist in LPWANs, followed by a literature review with the main goal of substantiating an attack vector analysis specifically designed for the IoT ecosystem. This methodological approach resulted in three main contributions: (i) a systematic review regarding cybersecurity in LPWANs with a focus on vulnerabilities, threats, and typical defense strategies; (ii) a state-of-the-art review on the most prominent results that have been found in the systematic review, with focus on the last three years; (iii) a security analysis on the recent attack vectors regarding IoT applications using LPWANs. Results have shown that LPWANs communication technologies contain security vulnerabilities that can lead to irreversible harm in critical and non-critical IoT application domains. Also, the conception and implementation of up-to-date defenses are relevant to protect systems, networks, and data.

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