2023
Authors
Pereira, SC; Rocha, J; Campilho, A; Sousa, P; Mendonca, AM;
Publication
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
Abstract
Background and Objective: Convolutional neural networks are widely used to detect radiological findings in chest radiographs. Standard architectures are optimized for images of relatively small size (for exam-ple, 224 x 224 pixels), which suffices for most application domains. However, in medical imaging, larger inputs are often necessary to analyze disease patterns. A single scan can display multiple types of radi-ological findings varying greatly in size, and most models do not explicitly account for this. For a given network, whose layers have fixed-size receptive fields, smaller input images result in coarser features, which better characterize larger objects in an image. In contrast, larger inputs result in finer grained features, beneficial for the analysis of smaller objects. By compromising to a single resolution, existing frameworks fail to acknowledge that the ideal input size will not necessarily be the same for classifying every pathology of a scan. The goal of our work is to address this shortcoming by proposing a lightweight framework for multi-scale classification of chest radiographs, where finer and coarser features are com-bined in a parameter-efficient fashion. Methods: We experiment on CheXpert, a large chest X-ray database. A lightweight multi-resolution (224 x 224, 4 48 x 4 48 and 896 x 896 pixels) network is developed based on a Densenet-121 model where batch normalization layers are replaced with the proposed size-specific batch normalization. Each input size undergoes batch normalization with dedicated scale and shift parameters, while the remaining parameters are shared across sizes. Additional external validation of the proposed approach is performed on the VinDr-CXR data set. Results: The proposed approach (AUC 83 . 27 +/- 0 . 17 , 7.1M parameters) outperforms standard single-scale models (AUC 81 . 76 +/- 0 . 18 , 82 . 62 +/- 0 . 11 and 82 . 39 +/- 0 . 13 for input sizes 224 x 224, 4 48 x 4 48 and 896 x 896, respectively, 6.9M parameters). It also achieves a performance similar to an ensemble of one individual model per scale (AUC 83 . 27 +/- 0 . 11 , 20.9M parameters), while relying on significantly fewer parameters. The model leverages features of different granularities, resulting in a more accurate classifi-cation of all findings, regardless of their size, highlighting the advantages of this approach. Conclusions: Different chest X-ray findings are better classified at different scales. Our study shows that multi-scale features can be obtained with nearly no additional parameters, boosting performance. (c) 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )
2023
Authors
Melo, T; Carneiro, A; Campilho, A; Mendonca, AM;
Publication
JOURNAL OF MEDICAL IMAGING
Abstract
Purpose: The development of accurate methods for retinal layer and fluid segmentation in optical coherence tomography images can help the ophthalmologists in the diagnosis and follow-up of retinal diseases. Recent works based on joint segmentation presented good results for the segmentation of most retinal layers, but the fluid segmentation results are still not satisfactory. We report a hierarchical framework that starts by distinguishing the retinal zone from the background, then separates the fluid-filled regions from the rest, and finally, discriminates the several retinal layers.Approach: Three fully convolutional networks were trained sequentially. The weighting scheme used for computing the loss function during training is derived from the outputs of the networks trained previously. To reinforce the relative position between retinal layers, the mutex Dice loss (included for optimizing the last network) was further modified so that errors between more distant layers are more penalized. The method's performance was evaluated using a public dataset.Results: The proposed hierarchical approach outperforms previous works in the segmentation of the inner segment ellipsoid layer and fluid (Dice coefficient = 0.95 and 0.82, respectively). The results achieved for the remaining layers are at a state-of-the-art level.Conclusions: The proposed framework led to significant improvements in fluid segmentation, without compromising the results in the retinal layers. Thus, its output can be used by ophthalmologists as a second opinion or as input for automatic extraction of relevant quantitative biomarkers.
2022
Authors
Sousa, J; Pereira, T; Silva, F; Silva, MC; Vilares, AT; Cunha, A; Oliveira, HP;
Publication
APPLIED SCIENCES-BASEL
Abstract
Lung cancer is one of the most common causes of cancer-related mortality, and since the majority of cases are diagnosed when the tumor is in an advanced stage, the 5-year survival rate is dismally low. Nevertheless, the chances of survival can increase if the tumor is identified early on, which can be achieved through screening with computed tomography (CT). The clinical evaluation of CT images is a very time-consuming task and computed-aided diagnosis systems can help reduce this burden. The segmentation of the lungs is usually the first step taken in image analysis automatic models of the thorax. However, this task is very challenging since the lungs present high variability in shape and size. Moreover, the co-occurrence of other respiratory comorbidities alongside lung cancer is frequent, and each pathology can present its own scope of CT imaging appearances. This work investigated the development of a deep learning model, whose architecture consists of the combination of two structures, a U-Net and a ResNet34. The proposed model was designed on a cross-cohort dataset and it achieved a mean dice similarity coefficient (DSC) higher than 0.93 for the 4 different cohorts tested. The segmentation masks were qualitatively evaluated by two experienced radiologists to identify the main limitations of the developed model, despite the good overall performance obtained. The performance per pathology was assessed, and the results confirmed a small degradation for consolidation and pneumocystis pneumonia cases, with a DSC of 0.9015 +/- 0.2140 and 0.8750 +/- 0.1290, respectively. This work represents a relevant assessment of the lung segmentation model, taking into consideration the pathological cases that can be found in the clinical routine, since a global assessment could not detail the fragilities of the model.
2022
Authors
Vilas-Boas, MD; Rocha, AP; Cardoso, MN; Fernandes, JM; Coelho, T; Cunha, JPS;
Publication
FRONTIERS IN NEUROLOGY
Abstract
In the published article, there was an error in Table 2 as published. The units of the Total body center of mass sway in x-axis (TBCMx) and y-axis (TBCMy) were shown in mm when they should be in cm. The corrected Table 2 and its caption appear below. In the published article, there was an error in Table 3 as published. The units of the Total body center of mass sway in x-axis (TBCMx) and y-axis (TBCMy) were shown in mm. The correct unit is cm. The corrected Table 3 and its caption appear below. In the published article, there was an error in Figure 3 as published. The units of the Total body center of mass sway in x-axis were shown in mm in the vertical axis of the plot. The correct unit is cm. The corrected Figure 3 and its caption appear below. In the published article, there was an error in Supplementary Table S.I. The units of the Total body center of mass sway in x-axis (TBCMx) and y-axis (TBCMy) were shown in mm. The correct unit is cm. The correct material statement appears below. In the published article, there was a mistake on the computation description of one of the assessed parameters (total body center of mass). A correction has been made to “Data Processing,” Paragraph 3: “For each gait cycle, we computed the 24 spatiotemporal and kinematic gait parameters listed in Table 2 and defined in (15). The total body center of mass (TBCM) sway was computed as the standard deviation of the distance (in the x/y-axis, i.e., medial-lateral and vertical directions) of the total body center of mass (TBCM), in relation to the RGBD sensor’s coordinate system, for all gait cycle frames. For each frame, TBCM’s position is the mean position of all body segments’ CM, which was obtained according to (21).” The authors apologize for these errors and state that this does not change the scientific conclusions of the article in any way. The original article has been updated. © 2022 Vilas-Boas, Rocha, Cardoso, Fernandes, Coelho and Cunha.
2022
Authors
Neto, PC; Sequeira, AF; Cardoso, JS;
Publication
2022 IEEE/CVF WINTER CONFERENCE ON APPLICATIONS OF COMPUTER VISION WORKSHOPS (WACVW 2022)
Abstract
Presentation attacks are recurrent threats to biometric systems, where impostors attempt to bypass these systems. Humans often use background information as contextual cues for their visual system. Yet, regarding face-based systems, the background is often discarded, since face presentation attack detection (PAD) models are mostly trained with face crops. This work presents a comparative study of face PAD models (including multi-task learning, adversarial training and dynamic frame selection) in two settings: with and without crops. The results show that the performance is consistently better when the background is present in the images. The proposed multi-task methodology beats the state-of-the-art results on the ROSE-Youtu dataset by a large margin with an equal error rate of 0.2%. Furthermore, we analyze the models' predictions with Grad-CAM++ with the aim to investigate to what extent the models focus on background elements that are known to be useful for human inspection. From this analysis we can conclude that the background cues are not relevant across all the attacks. Thus, showing the capability of the model to leverage the background information only when necessary.
2022
Authors
Domingues, I; Sequeira, AF;
Publication
COMPUTATIONAL AND MATHEMATICAL ORGANIZATION THEORY
Abstract
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