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Publications

Publications by Francesco Renna

2020

Deep Convolutional Neural Network Ensembles For Multi-Classification of Skin Lesions From Dermoscopic and Clinical Images

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

Publication
42ND ANNUAL INTERNATIONAL CONFERENCES OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY: ENABLING INNOVATIVE TECHNOLOGIES FOR GLOBAL HEALTHCARE EMBC'20

Abstract
In this paper, we consider the problem of classifying skin lesions into multiple classes using both dermoscopic and clinical images. Different convolutional neural network architectures are considered for this task and a novel ensemble scheme is proposed, which makes use of a progressive transfer learning strategy. The proposed approach is tested over a dataset of 4000 images containing both dermoscopic and clinical examples and it is shown to achieve an average specificity of 93.3% and an average sensitivity of 79.9% in discriminating skin lesions belonging to four different classes.

2021

Standalone performance of artificial intelligence for upper GI neoplasia: a meta-analysis

Authors
Arribas, J; Antonelli, G; Frazzoni, L; Fuccio, L; Ebigbo, A; van der Sommen, F; Ghatwary, N; Palm, C; Coimbra, M; Renna, F; Bergman, JJGHM; Sharma, P; Messmann, H; Hassan, C; Dinis Ribeiro, MJ;

Publication
GUT

Abstract
Objective Artificial intelligence (AI) may reduce underdiagnosed or overlooked upper GI (UGI) neoplastic and preneoplastic conditions, due to subtle appearance and low disease prevalence. Only disease-specific AI performances have been reported, generating uncertainty on its clinical value. Design We searched PubMed, Embase and Scopus until July 2020, for studies on the diagnostic performance of AI in detection and characterisation of UGI lesions. Primary outcomes were pooled diagnostic accuracy, sensitivity and specificity of AI. Secondary outcomes were pooled positive (PPV) and negative (NPV) predictive values. We calculated pooled proportion rates (%), designed summary receiving operating characteristic curves with respective area under the curves (AUCs) and performed metaregression and sensitivity analysis. Results Overall, 19 studies on detection of oesophageal squamous cell neoplasia (ESCN) or Barrett's esophagus-related neoplasia (BERN) or gastric adenocarcinoma (GCA) were included with 218, 445, 453 patients and 7976, 2340, 13 562 images, respectively. AI-sensitivity/specificity/PPV/NPV/positive likelihood ratio/negative likelihood ratio for UGI neoplasia detection were 90% (CI 85% to 94%)/89% (CI 85% to 92%)/87% (CI 83% to 91%)/91% (CI 87% to 94%)/8.2 (CI 5.7 to 11.7)/0.111 (CI 0.071 to 0.175), respectively, with an overall AUC of 0.95 (CI 0.93 to 0.97). No difference in AI performance across ESCN, BERN and GCA was found, AUC being 0.94 (CI 0.52 to 0.99), 0.96 (CI 0.95 to 0.98), 0.93 (CI 0.83 to 0.99), respectively. Overall, study quality was low, with high risk of selection bias. No significant publication bias was found. Conclusion We found a high overall AI accuracy for the diagnosis of any neoplastic lesion of the UGI tract that was independent of the underlying condition. This may be expected to substantially reduce the miss rate of precancerous lesions and early cancer when implemented in clinical practice.

2021

Joint Training of Hidden Markov Model and Neural Network for Heart Sound Segmentation

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

Publication
2021 COMPUTING IN CARDIOLOGY (CINC)

Abstract
In this work, we propose a novel algorithm for heart sound segmentation. The proposed approach is based on the combination of two families of state-of-the-art solutions for such problem, hidden Markov models and deep neural networks, in a single training framework. The proposed approach is tested with heart sounds from the PhysioNet dataset and it is shown to achieve an average sensitivity of 93.9% and an average positive predictive value of 94.2% in detecting the boundaries of fundamental heart sounds.

2021

Source Separation of the Second Heart Sound via Alternating Optimization

Authors
Renna, F; Plumbley, MD; Coimbra, M;

Publication
2021 COMPUTING IN CARDIOLOGY (CINC)

Abstract
A novel algorithm to separate S2 heart sounds into their aortic and pulmonary components is proposed. This approach is based on the assumption that, in different heartbeats of a given recording, aortic and pulmonary components maintain the same waveform but with different relative delays, which are induced by the variation of the thoracic pressure at different respiration phases. The proposed algorithm then retrieves the aortic and pulmonary components as the solution of an optimization problem which is approximated via alternating optimization. The proposed approach is shown to provide reconstructions of aortic and pulmonary components with normalized root mean-squared error consistently below 10% in various operational regimes.

2021

Do we really need a segmentation step in heart sound classification algorithms?

Authors
Oliveira, J; Nogueira, D; Renna, F; Ferreira, C; Jorge, AM; Coimbra, M;

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

Abstract
Cardiac auscultation is the key screening procedure to detect and identify cardiovascular diseases (CVDs). One of many steps to automatically detect CVDs using auscultation, concerns the detection and delimitation of the heart sound boundaries, a process known as segmentation. Whether to include or not a segmentation step in the signal classification pipeline is nowadays a topic of discussion. Up to our knowledge, the outcome of a segmentation algorithm has been used almost exclusively to align the different signal segments according to the heartbeat. In this paper, the need for a heartbeat alignment step is tested and evaluated over different machine learning algorithms, including deep learning solutions. From the different classifiers tested, Gate Recurrent Unit (GRU) Network and Convolutional Neural Network (CNN) algorithms are shown to be the most robust. Namely, these algorithms can detect the presence of heart murmurs even without a heartbeat alignment step. Furthermore, Support Vector Machine (SVM) and Random Forest (RF) algorithms require an explicit segmentation step to effectively detect heart sounds and murmurs, the overall performance is expected drop approximately 5% on both cases.

2022

The CirCor DigiScope Dataset: From Murmur Detection to Murmur Classification

Authors
Oliveira, J; Renna, F; Costa, PD; Nogueira, M; Oliveira, C; Ferreira, C; Jorge, A; Mattos, S; Hatem, T; Tavares, T; Elola, A; Rad, AB; Sameni, R; Clifford, GD; Coimbra, MT;

Publication
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS

Abstract
Cardiac auscultation is one of the most cost-effective techniques used to detect and identify many heart conditions. Computer-assisted decision systems based on auscultation can support physicians in their decisions. Unfortunately, the application of such systems in clinical trials is still minimal since most of them only aim to detect the presence of extra or abnormal waves in the phonocardiogram signal, i.e., only a binary ground truth variable (normal vs abnormal) is provided. This is mainly due to the lack of large publicly available datasets, where a more detailed description of such abnormal waves (e.g., cardiac murmurs) exists. To pave the way to more effective research on healthcare recommendation systems based on auscultation, our team has prepared the currently largest pediatric heart sound dataset. A total of 5282 recordings have been collected from the four main auscultation locations of 1568 patients, in the process, 215780 heart sounds have been manually annotated. Furthermore, and for the first time, each cardiac murmur has been manually annotated by an expert annotator according to its timing, shape, pitch, grading, and quality. In addition, the auscultation locations where the murmur is present were identified as well as the auscultation location where the murmur is detected more intensively. Such detailed description for a relatively large number of heart sounds may pave the way for new machine learning algorithms with a real-world application for the detection and analysis of murmur waves for diagnostic purposes.

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