João Mendes

Mr. João Mendes

Instituto de Biofísica e Engenharia Biomédica, Faculdade de Ciências da Universidade de Lisboa
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Research Focus & Metrics

Academic Career Length

6Years (2021-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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26 August 2022 in Journal of Imaging
Verified
Journal Article
Open access
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João MendesJoão Mendes
João Mendes
José David DominguesJosé David Domingues
José David Domingues
HAHelena Aidos
Helena Aidos
Nuno M. GarciaNuno M. Garcia
Nuno M. Garcia
Nuno MatelaNuno Matela
Nuno Matela
Breast cancer was the most diagnosed cancer in 2020. Several thousand women continue to die from this disease. A better and earlier diagnosis may be of great importance to improving prognosis, and that is where Artificial Intelligence (AI) could play a major role. This paper surveys different applications of AI in Breast Imaging. First, traditional Machine Learning and Deep Learning methods that can detect the presence of a lesion and classify it into benign/malignant—which could be important to diminish reading time and improve accuracy—are analyzed. Following that, researches in the field of breast cancer risk prediction using mammograms—which may be able to allow screening programs customization both on periodicity and modality—are reviewed. The subsequent section analyzes different applications of augmentation techniques that allow to surpass the lack of labeled data. Finally, still concerning the absence of big datasets with labeled data, the last section studies Self-Supervised learning, where AI models are able to learn a representation of the input by themselves. This review gives a general view of what AI can give in the field of Breast Imaging, discussing not only its potential but also the challenges that still have to be overcome.

20 June 2024 in Biomedicines
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Ana M. MotaAna M. Mota
Ana M. Mota
João MendesJoão Mendes
João Mendes
Nuno MatelaNuno Matela
Nuno Matela
Breast cancer remains a leading cause of mortality among women, with molecular subtypes significantly influencing prognosis and treatment strategies. Currently, identifying the molecular subtype of cancer requires a biopsy—a specialized, expensive, and time-consuming procedure, often yielding to results that must be supported with additional biopsies due to technique errors or tumor heterogeneity. This study introduces a novel approach for predicting breast cancer molecular subtypes using mammography images and advanced artificial intelligence (AI) methodologies. Using the OPTIMAM imaging database, 1397 images from 660 patients were selected. The pretrained deep learning model ResNet-101 was employed to classify tumors into five subtypes: Luminal A, Luminal B1, Luminal B2, HER2, and Triple Negative. Various classification strategies were studied: binary classifications (one vs. all others, specific combinations) and multi-class classification (evaluating all subtypes simultaneously). To address imbalanced data, strategies like oversampling, undersampling, and data augmentation were explored. Performance was evaluated using accuracy and area under the receiver operating characteristic curve (AUC). Binary classification results showed a maximum average accuracy and AUC of 79.02% and 64.69%, respectively, while multi-class classification achieved an average AUC of 60.62% with oversampling and data augmentation. The most notable binary classification was HER2 vs. non-HER2, with an accuracy of 89.79% and an AUC of 73.31%. Binary classification for specific combinations of subtypes revealed an accuracy of 76.42% for HER2 vs. Luminal A and an AUC of 73.04% for HER2 vs. Luminal B1. These findings highlight the potential of mammography-based AI for non-invasive breast cancer subtype prediction, offering a promising alternative to biopsies and paving the way for personalized treatment plans.

12 June 2021 in Journal of Imaging
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Journal Article
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João MendesJoão Mendes
João Mendes
Nuno MatelaNuno Matela
Nuno Matela
Breast cancer affects thousands of women across the world, every year. Methods to predict risk of breast cancer, or to stratify women in different risk levels, could help to achieve an early diagnosis, and consequently a reduction of mortality. This paper aims to review articles that extracted texture features from mammograms and used those features along with machine learning algorithms to assess breast cancer risk. Besides that, deep learning methodologies that aimed for the same goal were also reviewed. In this work, first, a brief introduction to breast cancer statistics and screening programs is presented; after that, research done in the field of breast cancer risk assessment are analyzed, in terms of both methodologies used and results obtained. Finally, considerations about the analyzed papers are conducted. The results of this review allow to conclude that both machine and deep learning methodologies provide promising results in the field of risk analysis, either in a stratification in risk groups, or in a prediction of a risk score. Although promising, future endeavors in this field should consider the possibility of the implementation of the methodology in clinical practice.

10 October 2023 in Journal of Imaging
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Journal Article
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DSDuarte Saraiva
Duarte Saraiva
João MendesJoão Mendes
João Mendes
JLJoao Leote
Joao Leote
Filipe André GonzalezFilipe André Gonzalez
Filipe André Gonzalez
Nuno M. GarciaNuno M. Garcia
Nuno M. Garcia
Nuno MatelaNuno Matela
Nuno Matela
Ultrasound (US) imaging is used in the diagnosis and monitoring of COVID-19 and breast cancer. The presence of Speckle Noise (SN) is a downside to its usage since it decreases lesion conspicuity. Filters can be used to remove SN, but they involve time-consuming computation and parameter tuning. Several researchers have been developing complex Deep Learning (DL) models (150,000–500,000 parameters) for the removal of simulated added SN, without focusing on the real-world application of removing naturally occurring SN from original US images. Here, a simpler (<30,000 parameters) Convolutional Neural Network Autoencoder (CNN-AE) to remove SN from US images of the breast and lung is proposed. In order to do so, simulated SN was added to such US images, considering four different noise levels (σ = 0.05, 0.1, 0.2, 0.5). The original US images (N = 1227, breast + lung) were given as targets, while the noised US images served as the input. The Structural Similarity Index Measure (SSIM) and Peak Signal-to-Noise Ratio (PSNR) were used to compare the output of the CNN-AE and of the Median and Lee filters with the original US images. The CNN-AE outperformed the use of these classic filters for every noise level. To see how well the model removed naturally occurring SN from the original US images and to test its real-world applicability, a CNN model that differentiates malignant from benign breast lesions was developed. Several inputs were used to train the model (original, CNN-AE denoised, filter denoised, and noised US images). The use of the original US images resulted in the highest Matthews Correlation Coefficient (MCC) and accuracy values, while for sensitivity and negative predicted values, the CNN-AE-denoised US images (for higher σ values) achieved the best results. Our results demonstrate that the application of a simpler DL model for SN removal results in fewer misclassifications of malignant breast lesions in comparison to the use of original US images and the application of the Median filter. This shows that the use of a less-complex model and the focus on clinical practice applicability are relevant and should be considered in future studies.

14 February 2023 in Tomography
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João MendesJoão Mendes
João Mendes
Nuno MatelaNuno Matela
Nuno Matela
Nuno M. GarciaNuno M. Garcia
Nuno M. Garcia
Breast cancer was the most diagnosed cancer around the world in 2020. Screening programs, based on mammography, aim to achieve early diagnosis which is of extreme importance when it comes to cancer. There are several flaws associated with mammography, with one of the most important being tissue overlapping that can result in both lesion masking and fake-lesion appearance. To overcome this, digital breast tomosynthesis takes images (slices) at different angles that are later reconstructed into a 3D image. Having in mind that the slices are planar images where tissue overlapping does not occur, the goal of the work done here was to develop a deep learning model that could, based on the said slices, classify lesions as benign or malignant. The developed model was based on the work done by Muduli et. al, with a slight change in the fully connected layers and in the regularization done. In total, 77 DBT volumes—39 benign and 38 malignant—were available. From each volume, nine slices were taken, one where the lesion was most visible and four above/below. To increase the quantity and the variability of the data, common data augmentation techniques (rotation, translation, mirroring) were applied to the original images three times. Therefore, 2772 images were used for training. Data augmentation techniques were then applied two more times—one set used for validation and one set used for testing. Our model achieved, on the testing set, an accuracy of 93.2% while the values of sensitivity, specificity, precision, F1-score, and Cohen’s kappa were 92%, 94%, 94%, 94%, and 0.86, respectively. Given these results, the work done here suggests that the use of single-slice DBT can compare to state-of-the-art studies and gives a hint that with more data, better augmentation techniques and the use of transfer learning might overcome the use of mammograms in this type of studies.

11 June 2023 in Journal of Imaging
Verified
Journal Article
Open access
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Ana M. MotaAna M. Mota
Ana M. Mota
João MendesJoão Mendes
João Mendes
Nuno MatelaNuno Matela
Nuno Matela
Currently, breast cancer is the most commonly diagnosed type of cancer worldwide. Digital Breast Tomosynthesis (DBT) has been widely accepted as a stand-alone modality to replace Digital Mammography, particularly in denser breasts. However, the image quality improvement provided by DBT is accompanied by an increase in the radiation dose for the patient. Here, a method based on 2D Total Variation (2D TV) minimization to improve image quality without the need to increase the dose was proposed. Two phantoms were used to acquire data at different dose ranges (0.88–2.19 mGy for Gammex 156 and 0.65–1.71 mGy for our phantom). A 2D TV minimization filter was applied to the data, and the image quality was assessed through contrast-to-noise ratio (CNR) and the detectability index of lesions before and after filtering. The results showed a decrease in 2D TV values after filtering, with variations of up to 31%, increasing image quality. The increase in CNR values after filtering showed that it is possible to use lower doses (−26%, on average) without compromising on image quality. The detectability index had substantial increases (up to 14%), especially in smaller lesions. So, not only did the proposed approach allow for the enhancement of image quality without increasing the dose, but it also improved the chances of detecting small lesions that could be overlooked.