2023
Authors
Reyna, A; Kiarashi, Y; Elola, A; Oliveira, J; Renna, F; Gu, A; Perez Alday, A; Sadr, N; Sharma, A; Kpodonu, J; Mattos, S; Coimbra, T; Sameni, R; Rad, AB; Clifford, D;
Publication
PLOS Digital Health
Abstract
Cardiac auscultation is an accessible diagnostic screening tool that can help to identify patients with heart murmurs, who may need follow-up diagnostic screening and treatment for abnormal cardiac function. However, experts are needed to interpret the heart sounds, limiting the accessibility of cardiac auscultation in resource-constrained environments. Therefore, the George B. Moody PhysioNet Challenge 2022 invited teams to develop algorithmic approaches for detecting heart murmurs and abnormal cardiac function from phonocardiogram (PCG) recordings of heart sounds. For the Challenge, we sourced 5272 PCG recordings from 1452 primarily pediatric patients in rural Brazil, and we invited teams to implement diagnostic screening algorithms for detecting heart murmurs and abnormal cardiac function from the recordings. We required the participants to submit the complete training and inference code for their algorithms, improving the transparency, reproducibility, and utility of their work. We also devised an evaluation metric that considered the costs of screening, diagnosis, misdiagnosis, and treatment, allowing us to investigate the benefits of algorithmic diagnostic screening and facilitate the development of more clinically relevant algorithms. We received 779 algorithms from 87 teams during the Challenge, resulting in 53 working codebases for detecting heart murmurs and abnormal cardiac function from PCG recordings. These algorithms represent a diversity of approaches from both academia and industry, including methods that use more traditional machine learning techniques with engineered clinical and statistical features as well as methods that rely primarily on deep learning models to discover informative features. The use of heart sound recordings for identifying heart murmurs and abnormal cardiac function allowed us to explore the potential of algorithmic approaches for providing more accessible diagnostic screening in resourceconstrained environments. The submission of working, open-source algorithms and the use of novel evaluation metrics supported the reproducibility, generalizability, and clinical relevance of the research from the Challenge. © 2023 Reyna et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
2024
Authors
Martins, ML; Coimbra, MT; Renna, F;
Publication
32ND EUROPEAN SIGNAL PROCESSING CONFERENCE, EUSIPCO 2024
Abstract
This paper is concerned with the semantic segmentation within domain-specific contexts, such as those pertaining to biology, physics, or material science. Under these circumstances, the objects of interest are often irregular and have fine structure, i.e., detail at arbitrarily small scales. Empirically, they are often understood as self-similar processes, a concept grounded in Multifractal Analysis. We find that this multifractal behaviour is carried out through a convolutional neural network (CNN), if we view its channel-wise responses as self-similar measures. A function of the local singularities of each measure we call Singularity Stregth Recalibration (SSR) is set forth to modulate the response at each layer of the CNN. SSR is a lightweight, plug-in module for CNNs. We observe that it improves a baseline U-Net in two biomedical tasks: skin lesion and colonic polyp segmentation, by an average of 1.36% and 1.12% Dice score, respectively. To the best of our knowledge, this is the first time multifractal-analysis is conducted end-to-end for semantic segmentation.
2025
Authors
Antonelli, G; Libanio, D; De Groof, AJ; van der Sommen, F; Mascagni, P; Sinonquel, P; Abdelrahim, M; Ahmad, O; Berzin, T; Bhandari, P; Bretthauer, M; Coimbra, M; Dekker, E; Ebigbo, A; Eelbode, T; Frazzoni, L; Gross, SA; Ishihara, R; Kaminski, MF; Messmann, H; Mori, Y; Padoy, N; Parasa, S; Pilonis, ND; Renna, F; Repici, A; Simsek, C; Spadaccini, M; Bisschops, R; Bergman, JJGHM; Hassan, C; Ribeiro, MD;
Publication
GUT
Abstract
Artificial intelligence (AI) holds significant potential for enhancing quality of gastrointestinal (GI) endoscopy, but the adoption of AI in clinical practice is hampered by the lack of rigorous standardisation and development methodology ensuring generalisability. The aim of the Quality Assessment of pre-clinical AI studies in Diagnostic Endoscopy (QUAIDE) Explanation and Checklist was to develop recommendations for standardised design and reporting of preclinical AI studies in GI endoscopy. The recommendations were developed based on a formal consensus approach with an international multidisciplinary panel of 32 experts among endoscopists and computer scientists. The Delphi methodology was employed to achieve consensus on statements, with a predetermined threshold of 80% agreement. A maximum three rounds of voting were permitted. Consensus was reached on 18 key recommendations, covering 6 key domains: data acquisition and annotation (6 statements), outcome reporting (3 statements), experimental setup and algorithm architecture (4 statements) and result presentation and interpretation (5 statements). QUAIDE provides recommendations on how to properly design (1. Methods, statements 1-14), present results (2. Results, statements 15-16) and integrate and interpret the obtained results (3. Discussion, statements 17-18). The QUAIDE framework offers practical guidance for authors, readers, editors and reviewers involved in AI preclinical studies in GI endoscopy, aiming at improving design and reporting, thereby promoting research standardisation and accelerating the translation of AI innovations into clinical practice.
2024
Authors
Ferraz, S; Coimbra, MT; Pedrosa, J;
Publication
46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2024, Orlando, FL, USA, July 15-19, 2024
Abstract
Motion estimation in echocardiography is critical when assessing heart function and calculating myocardial deformation indices. Nevertheless, there are limitations in clinical practice, particularly with regard to the accuracy and reliability of measurements retrieved from images. In this study, deep learning-based motion estimation architectures were used to determine the left ventricular longitudinal strain in echocardiography. Three motion estimation approaches, pretrained on popular optical flow datasets, were applied to a simulated echocardiographic dataset. Results show that PWC-Net, RAFT and FlowFormer achieved an average end point error of 0.20, 0.11 and 0.09 mm per frame, respectively. Additionally, global longitudinal strain was calculated from the FlowFormer outputs to assess strain correlation. Notably, there is variability in strain accuracy among different vendors. Thus, optical flow-based motion estimation has the potential to facilitate the use of strain imaging in clinical practice.
2024
Authors
Oliveira, B; Lobo, A; Botelho Costa, CIA; Carvalho, RF; Coimbra, MT; Renna, F;
Publication
46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2024, Orlando, FL, USA, July 15-19, 2024
Abstract
We introduce a Gradient-weighted Class Activation Mapping (Grad-CAM) methodology to assess the performance of five distinct models for binary classification (normal/abnormal) of synchronized heart sounds and electrocardiograms. The applied models comprise a one-dimensional convolutional neural network (1D-CNN) using solely ECG signals, a two-dimensional convolutional neural network (2D-CNN) applied separately to PCG and ECG signals, and two multimodal models that employ both signals. In the multimodal models, we implement two fusion approaches: an early fusion and a late fusion. The results indicate a performance improvement in using an early fusion model for the joint classification of both signals, as opposed to using a PCG 2D-CNN or ECG 1D-CNN alone (e.g., ROC-AUC score of 0.81 vs. 0.79 and 0.79, respectively). Although the ECG 2D-CNN demonstrates a higher ROC-AUC score (0.82) compared to the early fusion model, it exhibits a lower F1-score (0.85 vs. 0.86). Grad-CAM unveils that the models tend to yield higher gradients in the QRS complex and T/P-wave of the ECG signal, as well as between the two PCG fundamental sounds (S1 and S2), for discerning normalcy or abnormality, thus showcasing that the models focus on clinically relevant features of the recorded data.
2024
Authors
Lopes, I; Vakalopoulou, M; Ferrante, E; Libânio, D; Ribeiro, MD; Coimbra, MT; Renna, F;
Publication
46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2024, Orlando, FL, USA, July 15-19, 2024
Abstract
In this work, we assess the impact of self-supervised learning (SSL) approaches on the detection of gastritis atrophy (GA) and intestinal metaplasia (IM) conditions. GA and IM are precancerous gastric lesions. Detecting these lesions is crucial to intervene early and prevent their progression to cancer. A set of experiments is conducted over the Chengdu dataset, by considering different amounts of annotated data in the training phase. Our results reveal that, when all available data is used for training, SSL approaches achieve a classification accuracy on par with a supervised learning baseline, (81.52% vs 81.76%). Interestingly, we observe that in low-data regimes (here represented as retaining only 12.5% of annotated data for training), the SSL model guarantees an accuracy gain with respect to the supervised learning baseline of approximately 1.5% (73.00% vs 71.52%). This observation hints at the potential of SSL models in leveraging unlabeled data, thus showcasing more robust performance improvements and generalization. Experimental results also show that SSL performance is significantly dependent on the specific data augmentation techniques and parameters adopted for contrastive learning, thus advocating for further investigations into the definition of optimal data augmentation frameworks specifically tailored for gastric lesion detection applications.
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