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Publications

2023

The effectiveness of deep learning vs. traditional methods for lung disease diagnosis using chest X-ray images: A systematic review

Authors
Sajed, S; Sanati, A; Garcia, JE; Rostami, H; Keshavarz, A; Teixeira, A;

Publication
APPLIED SOFT COMPUTING

Abstract
Recently, deep learning has proven to be a successful technique especially in medical image analysis. This paper aims to highlight the importance of deep learning architectures in lung disease diagnosis using CXR images. Related articles were identified through searches of electronic resources, including IEEE, Springer, Elsevier, PubMed, Nature and, Hindawi digital library. The inclusion of articles was based on high-performance artificial intelligence models, developed for the classification of possible findings in CXR images published from 2018 to 2023.After the quality assessment of papers, 129 articles were included according to PRISMA guidelines. Papers were studied by types of lung disease, data source, algorithm type, and outcome metrics. Three main categories of computer-aided lung disease detection were covered: traditional machine learning, deep learning-based methods, and combination of aforementioned methods for all lung diseases.The results showed that various pre-trained networks including ResNet, VGG, and DenseNet, are the most frequently used CNN architectures and would result in a notable increase in sensitivity and accuracy. Recent research suggests that utilizing a combination of deep networks with a robust machine learning classifier can outperform deep learning approaches that rely solely on fully connected neural networks as their classifier. Finally, the limitations of the existing literature and potential future research opportunities in possible findings in CXR images using deep learning architectures are discussed in this systematic review.

2023

The role of regular asymptomatic testing in reducing the impact of a COVID-19 wave

Authors
Silva, MEP; Fyles, M; Pi, L; Panovska Griffiths, J; House, T; Jay, C; Fearon, E;

Publication
EPIDEMICS

Abstract
Testing for infection with SARS-CoV-2 is an important intervention in reducing onwards transmission of COVID-19, particularly when combined with the isolation and contact-tracing of positive cases. Many countries with the capacity to do so have made use of lab-processed Polymerase Chain Reaction (PCR) testing targeted at individuals with symptoms and the contacts of confirmed cases. Alternatively, Lateral Flow Tests (LFTs) are able to deliver a result quickly, without lab-processing and at a relatively low cost. Their adoption can support regular mass asymptomatic testing, allowing earlier detection of infection and isolation of infectious individuals. In this paper we extend and apply the agent-based epidemic modelling framework Covasim to explore the impact of regular asymptomatic testing on the peak and total number of infections in an emerging COVID-19 wave. We explore testing with LFTs at different frequency levels within a population with high levels of immunity and with background symptomatic PCR testing, case isolation and contact tracing for testing. The effectiveness of regular asymptomatic testing was compared with ‘lockdown’ interventions seeking to reduce the number of non-household contacts across the whole population through measures such as mandating working from home and restrictions on gatherings. Since regular asymptomatic testing requires only those with a positive result to reduce contact, while lockdown measures require the whole population to reduce contact, any policy decision that seeks to trade off harms from infection against other harms will not automatically favour one over the other. Our results demonstrate that, where such a trade off is being made, at moderate rates of early exponential growth regular asymptomatic testing has the potential to achieve significant infection control without the wider harms associated with additional lockdown measures.

2023

Idioblasts accumulating anticancer alkaloids in Catharanthus roseus leaves are a unique cell type

Authors
Guedes, JG; Ribeiro, R; Carqueijeiro, I; Guimaraes, AL; Bispo, C; Archer, J; Azevedo, H; Fonseca, NA; Sottomayor, M;

Publication

Abstract
Catharanthus roseus leaves produce a range of monoterpenoid indole alkaloids (MIAs) that include low levels of the anticancer drugs vinblastine and vincristine. The MIA pathway displays a complex architecture spanning different subcellular and cell-type localizations and is under complex regulation. As a result, the development of strategies to increase the levels of the anticancer MIAs has remained elusive. The pathway involves mesophyll specialised idioblasts where the late unsolved biosynthetic steps are thought to occur. Here, protoplasts of C. roseus leaf idioblasts were isolated by fluorescence-activated cell sorting, and their differential alkaloid and transcriptomic profiles were characterised. This involved the assembly of an improved C. roseus transcriptome from short- and long-read data, IDIO+. It was observed that C. roseus mesophyll idioblasts possess a distinctive transcriptomic profile associated with protection against biotic and abiotic stresses, and indicative that this cell type is a carbon sink, in contrast with surrounding mesophyll cells. Moreover, it is shown that idioblasts are a hotspot of alkaloid accumulation, suggesting that their transcriptome may hold the keys to the in-depth understanding of the MIA pathway and the success of strategies leading to higher levels of the anticancer drugs.

2023

Position-Based Machine Learning Propagation Loss Model Enabling Fast Digital Twins of Wireless Networks in ns-3

Authors
Almeida, EN; Fontes, H; Campos, R; Ricardo, M;

Publication
PROCEEDINGS OF THE 2023 WORKSHOP ON NS-3, WNS3 2023

Abstract
Digital twins have been emerging as a hybrid approach that combines the benefits of simulators with the realism of experimental testbeds. The accurate and repeatable set-ups replicating the dynamic conditions of physical environments, enable digital twins of wireless networks to be used to evaluate the performance of next-generation networks. In this paper, we propose the Position-based Machine Learning Propagation Loss Model (P-MLPL), enabling the creation of fast and more precise digital twins of wireless networks in ns-3. Based on network traces collected in an experimental testbed, the P-MLPL model estimates the propagation loss suffered by packets exchanged between a transmitter and a receiver, considering the absolute node's positions and the traffic direction. The P-MLPL model is validated with a test suite. The results show that the P-MLPL model can predict the propagation loss with a median error of 2.5 dB, which corresponds to 0.5x the error of existing models in ns-3. Moreover, ns-3 simulations with the P-MLPL model estimated the throughput with an error up to 2.5 Mbit/s, when compared to the real values measured in the testbed.

2023

Zero-shot face recognition: Improving the discriminability of visual face features using a Semantic-Guided Attention Model

Authors
Patrício, C; Neves, JC;

Publication
Expert Systems with Applications

Abstract
Zero-shot learning enables the recognition of classes not seen during training through the use of semantic information comprising a visual description of the class either in textual or attribute form. Despite the advances in the performance of zero-shot learning methods, most of the works do not explicitly exploit the correlation between the visual attributes of the image and their corresponding semantic attributes for learning discriminative visual features. In this paper, we introduce an attention-based strategy for deriving features from the image regions regarding the most prominent attributes of the image class. In particular, we train a Convolutional Neural Network (CNN) for image attribute prediction and use a gradient-weighted method for deriving the attention activation maps of the most salient image attributes. These maps are then incorporated into the feature extraction process of Zero-Shot Learning (ZSL) approaches for improving the discriminability of the features produced through the implicit inclusion of semantic information. For experimental validation, the performance of state-of-the-art ZSL methods was determined using features with and without the proposed attention model. Surprisingly, we discover that the proposed strategy degrades the performance of ZSL methods in classical ZSL datasets (AWA2), but it can significantly improve performance when using face datasets. Our experiments show that these results are a consequence of the interpretability of the dataset attributes, suggesting that existing ZSL datasets attributes are, in most cases, difficult to be identifiable in the image. Source code is available at https://github.com/CristianoPatricio/SGAM. © 2022 The Author(s)

2023

Online Anomaly Explanation: A Case Study on Predictive Maintenance

Authors
Ribeiro, RP; Mastelini, SM; Davari, N; Aminian, E; Veloso, B; Gama, J;

Publication
MACHINE LEARNING AND PRINCIPLES AND PRACTICE OF KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2022, PT II

Abstract
Predictive Maintenance applications are increasingly complex, with interactions between many components. Black-box models are popular approaches due to their predictive accuracy and are based on deep-learning techniques. This paper presents an architecture that uses an online rule learning algorithm to explain when the black-box model predicts rare events. The system can present global explanations that model the black-box model and local explanations that describe why the black-box model predicts a failure. We evaluate the proposed system using four real-world public transport data sets, presenting illustrative examples of explanations.

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