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Publications

Publications by Miguel Coimbra

2022

Identifying the determinants and understanding their effect on the perception of safety, security, and comfort by pedestrians and cyclists: A systematic review

Authors
Ferreira, MC; Costa, PD; Abrantes, D; Hora, J; Felicio, S; Coimbra, M; Dias, TG;

Publication
TRANSPORTATION RESEARCH PART F-TRAFFIC PSYCHOLOGY AND BEHAVIOUR

Abstract
The continuous growth of the world population and its agglomeration in urban cities, demand an increasing need for mobility, which in turn contributes to the worsening of traffic congestion and pollution in cities. Therefore, it is necessary to promote active travel, such as walking and cycling. However, this is not an easy task, as pedestrians and cyclists are the most vulnerable link in the system, and low levels of safety, security and comfort can contribute to choosing private cars over active travel. Hence, it is essential to understand the determinants that affect the perceptions of pedestrians and cyclists, in order to support the definition of policies that promote the use of active modes of transport. Thus, this article fills an important gap in the literature by identifying and discussing the objective and subjective determinants that affect the perceptions of safety, security and comfort of pedestrians and cyclists, through a systematic review of the literature published in the last ten years. It followed the PRISMA statement guidelines and checklist, resulting in 68 relevant articles that were carefully analyzed. The results show that the perception of safety is negatively affected by fear of traffic-related injuries, fear of falling related to infra-structure and infrastructure maintenance, and negative behavior of drivers. Regarding security, crime was the major concern of pedestrians and cyclists, either with emphasis on the person or on personal property. With regard to comfort, high levels of air and noise pollution, lack of vege-tation, bad weather conditions, slopes and long commuting distances negatively affected the users' perception. The results also suggest that poor lighting affects all domains, providing a negative perception of safety, security and comfort. Similarly, the presence of people is seen as negatively influencing the perception of safety and comfort, while the absence of people nega-tively impacts the perception of security. Therefore, the findings achieved by this study are key to assist in the definition of transport policies and infrastructure creation in large smart cities. Additionally, new transport policies are proposed and discussed.

2022

Supervised and semi-supervised training of deep convolutional neural networks for gastric landmark detection

Authors
Lopes, I; Silva, A; Coimbra, MT; Ribeiro, MD; Libânio, D; Renna, F;

Publication
EMBC

Abstract
This work focuses on detection of upper gas-trointestinal (GI) landmarks, which are important anatomical areas of the upper GI tract digestive system that should be photodocumented during endoscopy to guarantee a complete examination. The aim of this work consisted in testing new automatic algorithms, specifically based on convolutional neural network (CNN) systems, able to detect upper GI landmarks, that can help to avoid the presence of blind spots during esophagogastroduodenoscopy. We tested pre-trained CNN architectures, such as the ResNet-50 and VGG-16, in conjunction with different training approaches, including the use of class weights, batch normalization, dropout, and data augmentation. The ResNet-50 model trained with class weights was the best performing CNN, achieving an accuracy of 71.79% and a Mathews Correlation Coefficient (MCC) of 65.06%. The combination of supervised and unsupervised learning was also explored to increase classification performance. In particular, convolutional autoencoder architectures trained with unlabeled GI images were used to extract representative features. Such features were then concatenated with those extracted by the pre-trained ResNet-50 architecture. This approach achieved a classification accuracy of 72.45% and an MCC of 65.08%. Clinical relevance - Esophagogastroduodenoscopy (EGD) photodocumentation is essential to guarantee that all areas of the upper GI system are examined avoiding blind spots. This work has the objective to help the EGD photodocumentation monitorization by testing new CNN-based systems able to detect EGD landmarks.

2022

Detection of COVID-19 in Point of Care Lung Ultrasound

Authors
Maximino, J; Coimbra, MT; Pedrosa, J;

Publication
EMBC

Abstract
The coronavirus disease 2019 (COVID-19) evolved into a global pandemic, responsible for a significant number of infections and deaths. In this scenario, point-of-care ultrasound (POCUS) has emerged as a viable and safe imaging modality. Computer vision (CV) solutions have been proposed to aid clinicians in POCUS image interpretation, namely detection/segmentation of structures and image/patient classification but relevant challenges still remain. As such, the aim of this study is to develop CV algorithms, using Deep Learning techniques, to create tools that can aid doctors in the diagnosis of viral and bacterial pneumonia (VP and BP) through POCUS exams. To do so, convolutional neural networks were designed to perform in classification tasks. The architectures chosen to build these models were the VGG16, ResNet50, DenseNet169 e MobileNetV2. Patients images were divided in three classes: healthy (HE), BP and VP (which includes COVID-19). Through a comparative study, which was based on several performance metrics, the model based on the DenseNet169 architecture was designated as the best performing model, achieving 78% average accuracy value of the five iterations of 5- Fold Cross-Validation. Given that the currently available POCUS datasets for COVID-19 are still limited, the training of the models was negatively affected by such and the models were not tested in an independent dataset. Furthermore, it was also not possible to perform lesion detection tasks. Nonetheless, in order to provide explainability and understanding of the models, Gradient-weighted Class Activation Mapping (GradCAM) were used as a tool to highlight the most relevant classification regions. Clinical relevance - Reveals the potential of POCUS to support COVID-19 screening. The results are very promising although the dataset is limite

2023

Beyond Heart Murmur Detection: Automatic Murmur Grading From Phonocardiogram

Authors
Elola, A; Aramendi, E; Oliveira, J; Renna, F; Coimbra, MT; Reyna, MA; Sameni, R; Clifford, GD; Rad, AB;

Publication
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS

Abstract
Objective: Murmurs are abnormal heart sounds, identified by experts through cardiac auscultation. The murmur grade, a quantitative measure of the murmur intensity, is strongly correlated with the patient's clinical condition. This work aims to estimate each patient's murmur grade (i.e., absent, soft, loud) from multiple auscultation location phonocardiograms (PCGs) of a large population of pediatric patients from a low-resource rural area. Methods: The Mel spectrogram representation of each PCG recording is given to an ensemble of 15 convolutional residual neural networks with channel-wise attention mechanisms to classify each PCG recording. The final murmur grade for each patient is derived based on the proposed decision rule and considering all estimated labels for available recordings. The proposed method is cross-validated on a dataset consisting of 3456 PCG recordings from 1007 patients using a stratified ten-fold cross-validation. Additionally, the method was tested on a hidden test set comprised of 1538 PCG recordings from 442 patients. Results: The overall cross-validation performances for patient-level murmur gradings are 86.3% and 81.6% in terms of the unweighted average of sensitivities and F1-scores, respectively. The sensitivities (and F1-scores) for absent, soft, and loud murmurs are 90.7% (93.6%), 75.8% (66.8%), and 92.3% (84.2%), respectively. On the test set, the algorithm achieves an unweighted average of sensitivities of 80.4% and an F1-score of 75.8%. Conclusions: This study provides a potential approach for algorithmic pre-screening in low-resource settings with relatively high expert screening costs. Significance: The proposed method represents a significant step beyond detection of murmurs, providing characterization of intensity, which may provide an enhanced classification of clinical outcomes.

2022

Can Multi-channel Heart Sounds Analysis improve Murmur Detection?

Authors
Nogueira, M; Oliveira, J; Ferreira, CG; Coimbra, MT; Jorge, AM;

Publication
2022 IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS (BHI) JOINTLY ORGANISED WITH THE IEEE-EMBS INTERNATIONAL CONFERENCE ON WEARABLE AND IMPLANTABLE BODY SENSOR NETWORKS (BSN'22)

Abstract
Cardiac auscultation is still the most cost-effective screening procedure for cardiovascular diseases. The development of computer assisted methods can empower a large variety of health professionals and thus enable mass cardiac health low-cost screening. The procedure for correct cardiac auscultation includes listening to the heart sounds of the four main auscultation spots. Until recently, attempts to develop automatic heart sound analysis methods that explore the multi-channel richness of a real auscultation, were very difficult due to the lack of adequate public datasets. In this work, we use the CirCor Dataset which is characterized by the existence of more than one heart sound per patient (each patient has heart sounds collected at different auscultation spots). Using this dataset, we evaluate and quantify the comparative impact of using a single or a multichannel approach. A single channel approach uses the sound from a single auscultation spot, whereas a multi-channel approach uses four auscultation spots in an asynchronous way. From the different classifiers tested, models that use four auscultation spots achieved a higher overall performance than those that search for abnormalities in a single heart sound spot. Our best result is a multi-channel SVM that analyzes four auscultation spots, with an overall performance of 87,4 %. This opens the path to future research using a multi-channel approach.

2025

Understanding Squeeze-and-Excitation Layers for Medical Image Segmentation

Authors
Martins, ML; Coimbra, MT; Renna, F;

Publication
EUSIPCO

Abstract
The U-Net is one of the most fundamental architectural advancements in the deep learning era. It is a crucial tool for image segmentation, especially for biomedical modalities. The research community seems to interpret the effectiveness of neural architectural search (such as the nn-U-Net) as evidence that architectural enhancements proposed since its debut are mostly unnecessary. We argue that there are still network-in-network primitives that can be leveraged to further enhance its performance, focusing on the squeeze-and-excitation (SE) pathway specifically in this paper. Specifically, we study its use of global descriptors, since it should be at odds with the spatial resolution required for dense-prediction tasks. It is theorized in the literature that performance is probably gained from some implicit ability of the learned excitations to filter supposedly uninformative channels during training. We explain this almost unreasonable success through an analysis of the empirical estimates of the excitation covariance matrix. Our analysis also directly contradicts the above conjecture - the most effective SE approach actually displayed the less extreme filtering behaviour, weighing all channels much closer to the mean (0.5). Our experiments are conducted in three diverse, staple biomedical modalities: dermoscopy, colonoscopy, and ultrasound. © 2025 European Signal Processing Conference, EUSIPCO. All rights reserved.

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