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Publications

Publications by C-BER

2019

Using Soft Attention Mechanisms to Classify Heart Sounds

Authors
Oliveira, J; Nogueira, DM; Ramos, C; Renna, F; Ferreira, CA; Coimbra, MT;

Publication
2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

Abstract

2019

Active Contours Based Segmentation and Lesion Periphery Analysis for Characterization of Skin Lesions in Dermoscopy Images

Authors
Riaz, F; Naeem, S; Nawaz, R; Coimbra, M;

Publication
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS

Abstract
This paper proposes a computer assisted diagnostic system for the detection of melanoma in dermoscopy images. Clinical findings have concluded that in case of melanoma, the lesion borders exhibit differential structures such as pigment networks and streaks as opposed to normal skin spots, which have smoother borders. We aim at validating these findings by performing segmentation of the skin lesions followed by an extraction of the peripheral region of the lesion that is subjected to feature extraction and classification for detecting melanoma. For segmentation, we propose a novel active contours based method that takes an initial lesion contour followed by the usage of Kullback-Leibler divergence between the lesion and skin to fit a curve to the lesion boundaries. After segmentation of the lesion, its periphery is extracted to detect melanoma using image features that are based on local binary patterns. For validation of our algorithms, we have used the publicly available PH2 and ISIC dermoscopy datasets. An extensive experimental analysis reveals two important findings: 1) the proposed segmentation method mimics the ground truth data; and 2) the most significant melanoma characteristics in the lesion actually lie on the lesion periphery.

2019

Virtual M-Mode for Echocardiography: A New Approach for the Segmentation of the Anterior Mitral Leaflet

Authors
Sultan, MS; Martins, N; Costa, E; Veiga, D; Ferreira, MJ; Mattos, S; Coimbra, MT;

Publication
IEEE J. Biomedical and Health Informatics

Abstract

2019

A Subject-Driven Unsupervised Hidden Semi-Markov Model and Gaussian Mixture Model for Heart Sound Segmentation

Authors
Oliveira, J; Renna, F; Coimbra, M;

Publication
IEEE JOURNAL OF SELECTED TOPICS IN SIGNAL PROCESSING

Abstract
The analysis of heart sounds is a challenging task, due to the quick temporal onset between successive events and the fact that an important fraction of the information carried by phonocardiogram (PCG) signals lies in the inaudible part of the human spectrum. For these reasons, computer-aided analysis of the PCG can dramatically improve the quantity of information recovered from such signals. In this paper, a hidden semi-Markov model (HSMM) is used to automatically segment PCG signals. In the proposed models, the emission probability distributions are approximated via Gaussian mixture model (GMM) priors. The choice of GMM emission probability distributions allow to apply re-estimation routines to automatically adjust the HSMM emission probability distributions to each subject. Building on the proposed method for fine tuning emission distributions, a novel subject-driven unsupervised heart sound segmentation algorithm is proposed and validated over the publicly available PhysioNet dataset. Perhaps surprisingly, the proposed unsupervised method achieved results in line with state-of-the-art supervised approaches, when applied to long heart sounds.

2019

Adaptive Sojourn Time HSMM for Heart Sound Segmentation

Authors
Oliveira, J; Renna, F; Mantadelis, T; Coimbra, M;

Publication
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS

Abstract
Heart sounds are difficult to interpret due to events with very short temporal onset between them (tens of milliseconds) and dominant frequencies that are out of the human audible spectrum. Computer-assisted decision systems may help but they require robust signal processing algorithms. In this paper, we propose a new algorithm for heart sound segmentation using a hidden semi-Markov model. The proposed algorithm infers more suitable sojourn time parameters than those currently suggested by the state of the art, through a maximum likelihood approach. We test our approach over three different datasets, including the publicly available PhysioNet and Pascal datasets. We also release a pediatric dataset composed of 29 heart sounds. In contrast with any other dataset available online, the annotations of the heart sounds in the released dataset contain information about the beginning and the ending of each heart sound event. Annotations were made by two cardiopulmonologists. The proposed algorithm is compared with the current state of the art. The results show a significant increase in segmentation performance, regardless the dataset or the methodology presented. For example, when using the PhysioNet dataset to train and to evaluate the HSMMs, our algorithm achieved average an F-score of 92% compared to 89% achieved by the algorithm described in [D.B. Springer, L. Tarassenko, and G. D. Clifford, "Logistic regressionHSMM-based heart sound segmentation," IEEE Transactions on Biomedical Engineering, vol. 63, no. 4, pp. 822-832, 2016]. In this sense, the proposed approach to adapt sojourn time parameters represents an effective solution for heart sound segmentation problems, even when the training data does not perfectly express the variability of the testing data.

2019

Designing a software for qualitative and quantitative analysis of oropharyngeal swallowing by videofluoroscopy

Authors
Silva, A; Santos, R; Silva, R; Coimbra, M;

Publication
6th IEEE Portuguese Meeting on Bioengineering, ENBENG 2019 - Proceedings

Abstract
Swallowing is a dynamic, complex and synergistic process, composed of three phases with a refined neuromotor control. A malfunction of this process, denominated dysphasia, can occur in any age like a result of congenital, structural, functional and/or medical problems. The quantitative analysis of this process is crucial to understand the temporal relations between the mechanisms of the oropharyngeal deglutition. Designing a software to support the qualitative and quantitative analysis of the swallowing process through dynamic images obtained by videofluoroscopy is the main motivation and objective of this work. First, a survey of requirements for such a software was made, consisting in a research protocol for assessing dysphagia by videofluoroscopy. Secondly, best practices in humancomputer interaction were used to design a conceptual model for the proposed software. Two protocols were selected for the assessment of dysphagia by videofluoroscopy: the Protocol of Boston and the Protocol used in the Hospital Privado da Trofa. These protocols allowed the identification of several events that are evaluated in the swallowing process and that can be recorded, measured and quantified during ingestion of the bolus. The second phase resulted in a conceptual model for an interactive system embodying the evaluation protocol selected and contemplates the integration of automatic algorithms for qualitative and quantitative evaluation of the parameters of swallowing. The proposed software model has a high potential to be a useful tool for assessing parameters of swallowing.

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