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Publications

Publications by CTM

2023

Symmetry-based regularization in deep breast cancer screening

Authors
Castro, E; Pereira, JC; Cardoso, JS;

Publication
MEDICAL IMAGE ANALYSIS

Abstract
Breast cancer is the most common and lethal form of cancer in women. Recent efforts have focused on developing accurate neural network-based computer-aided diagnosis systems for screening to help anticipate this disease. The ultimate goal is to reduce mortality and improve quality of life after treatment. Due to the difficulty in collecting and annotating data in this domain, data scarcity is - and will continue to be - a limiting factor. In this work, we present a unified view of different regularization methods that incorporate domain-known symmetries in the model. Three general strategies were followed: (i) data augmentation, (ii) invariance promotion in the loss function, and (iii) the use of equivariant architectures. Each of these strategies encodes different priors on the functions learned by the model and can be readily introduced in most settings. Empirically we show that the proposed symmetry-based regularization procedures improve generalization to unseen examples. This advantage is verified in different scenarios, datasets and model architectures. We hope that both the principle of symmetry-based regularization and the concrete methods presented can guide development towards more data-efficient methods for breast cancer screening as well as other medical imaging domains.

2023

Two-Stage Framework for Faster Semantic Segmentation

Authors
Cruz, R; Silva, DTE; Goncalves, T; Carneiro, D; Cardoso, JS;

Publication
SENSORS

Abstract
Semantic segmentation consists of classifying each pixel according to a set of classes. Conventional models spend as much effort classifying easy-to-segment pixels as they do classifying hard-to-segment pixels. This is inefficient, especially when deploying to situations with computational constraints. In this work, we propose a framework wherein the model first produces a rough segmentation of the image, and then patches of the image estimated as hard to segment are refined. The framework is evaluated in four datasets (autonomous driving and biomedical), across four state-of-the-art architectures. Our method accelerates inference time by four, with additional gains for training time, at the cost of some output quality.

2023

Deep Minutiae Fingerprint Extraction Using Equivariance Priors

Authors
Gouveia, M; Castro, E; Rebelo, A; Cardoso, JS; Patrão, B;

Publication
Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2023, Volume 4: BIOSIGNALS, Lisbon, Portugal, February 16-18, 2023.

Abstract

2023

Annotating for Artificial Intelligence Applications in Digital Pathology: A Practical Guide for Pathologists and Researchers

Authors
Montezuma, D; Oliveira, SP; Neto, PC; Oliveira, D; Monteiro, A; Cardoso, JS; Macedo-Pinto, I;

Publication
MODERN PATHOLOGY

Abstract
Training machine learning models for artificial intelligence (AI) applications in pathology often requires extensive annotation by human experts, but there is little guidance on the subject. In this work, we aimed to describe our experience and provide a simple, useful, and practical guide addressing annotation strategies for AI development in computational pathology. Annotation methodology will vary significantly depending on the specific study's objectives, but common difficulties will be present across different settings. We summarize key aspects and issue guiding principles regarding team interaction, ground-truth quality assessment, different annotation types, and available software and hardware options and address common difficulties while annotating. This guide was specifically designed for pathology annotation, intending to help pathologists, other researchers, and AI developers with this process.(c) 2022 THE AUTHORS. Published by Elsevier Inc. on behalf of the United States & Canadian Academy of Pathology. This is an open access article under the CC BY-NC-ND license (http://creativecommons. org/licenses/by-nc-nd/4.0/).

2023

Author Correction: Computer-aided diagnosis through medical image retrieval in radiology (Scientific Reports, (2022), 12, 1, (20732), 10.1038/s41598-022-25027-2)

Authors
Silva, W; Gonçalves, T; Härmä, K; Schröder, E; Obmann, VC; Barroso, MC; Poellinger, A; Reyes, M; Cardoso, JS;

Publication
Scientific Reports

Abstract
The original version of this Article contained an error in the Acknowledgements section. “This work was partially funded by the Project TAMI—Transparent Artificial Medical Intelligence (NORTE- 01-0247-FEDER-045905) financed by ERDF—European Regional Fund through the North Portugal Regional Operational Program—NORTE 2020 and by the Portuguese Foundation for Science and Technology—FCT under the CMU—Portugal International Partnership, and also by the Portuguese Foundation for Science and Technology—FCT within PhD grants SFRH/BD/139468/2018 and 2020.06434.BD. The authors thank the Swiss National Science Foundation grant number 198388, as well as the Lindenhof foundation for their grant support.” now reads: “This work was supported by National Funds through the Portuguese Funding Agency, FCT–Foundation for Science and Technology Portugal, under Project LA/P/0063/2020, and also by the Portuguese Foundation for Science and Technology - FCT within PhD grants SFRH/BD/139468/2018 and 2020.06434.BD. The authors thank the Swiss National Science Foundation grant number 198388, as well as the Lindenhof foundation for their grant support.” The original Article has been corrected. © The Author(s) 2023.

2023

Deep Edge Detection Methods for the Automatic Calculation of the Breast Contour

Authors
Freitas, N; Silva, D; Mavioso, C; Cardoso, MJ; Cardoso, JS;

Publication
BIOENGINEERING-BASEL

Abstract
Breast cancer conservative treatment (BCCT) is a form of treatment commonly used for patients with early breast cancer. This procedure consists of removing the cancer and a small margin of surrounding tissue, while leaving the healthy tissue intact. In recent years, this procedure has become increasingly common due to identical survival rates and better cosmetic outcomes than other alternatives. Although significant research has been conducted on BCCT, there is no gold-standard for evaluating the aesthetic results of the treatment. Recent works have proposed the automatic classification of cosmetic results based on breast features extracted from digital photographs. The computation of most of these features requires the representation of the breast contour, which becomes key to the aesthetic evaluation of BCCT. State-of-the-art methods use conventional image processing tools that automatically detect breast contours based on the shortest path applied to the Sobel filter result in a 2D digital photograph of the patient. However, because the Sobel filter is a general edge detector, it treats edges indistinguishably, i.e., it detects too many edges that are not relevant to breast contour detection and too few weak breast contours. In this paper, we propose an improvement to this method that replaces the Sobel filter with a novel neural network solution to improve breast contour detection based on the shortest path. The proposed solution learns effective representations for the edges between the breasts and the torso wall. We obtain state of the art results on a dataset that was used for developing previous models. Furthermore, we tested these models on a new dataset that contains more variable photographs and show that this new approach shows better generalization capabilities as the previously developed deep models do not perform so well when faced with a different dataset for testing. The main contribution of this paper is to further improve the capabilities of models that perform the objective classification of BCCT aesthetic results automatically by improving upon the current standard technique for detecting breast contours in digital photographs. To that end, the models introduced are simple to train and test on new datasets which makes this approach easily reproducible.

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