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About

About

Tomé Albuquerque received a B.Sc. degree in biochemistry from University of Aveiro and a M.S. degree in biomedical engineering from University of Porto. He is currently pursuing the Ph.D. degree with the University of Porto. He is also a Researcher at INESC TEC since 2019. His main research interests include machine learning, computer vision, and medical imaging diagnosis.

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Publications

2023

Rethinking low-cost microscopy workflow: Image enhancement using deep based Extended Depth of Field methods

Authors
Albuquerque, T; Rosado, L; Cruz, R; Vasconcelos, MJM; Oliveira, T; Cardoso, JS;

Publication
Intelligent Systems with Applications

Abstract
Microscopic techniques in low-to-middle income countries are constrained by the lack of adequate equipment and trained operators. Since light microscopy delivers crucial methods for the diagnosis and screening of numerous diseases, several efforts have been made by the scientific community to develop low-cost devices such as 3D-printed portable microscopes. Nevertheless, these devices present some drawbacks that directly affect image quality: the capture of the samples is done via mobile phones; more affordable lenses are usually used, leading to poorer physical properties and images with lower depth of field; misalignments in the microscopic set-up regarding optical, mechanical, and illumination components are frequent, causing image distortions such as chromatic aberrations. This work investigates several pre-processing methods to tackle the presented issues and proposed a new workflow for low-cost microscopy. Additionally, two new deep learning models based on Convolutional Neural Networks are also proposed (EDoF-CNN-Fast and EDoF-CNN-Pairwise) to generate Extended Depth of Field (EDoF) images, and compared against state-of-the-art approaches. The models were tested using two different datasets of cytology microscopic images: public Cervix93 and a new dataset that has been made publicly available containing images captured with µSmartScope. Experimental results demonstrate that the proposed workflow can achieve state-of-the-art performance when generating EDoF images from low-cost microscopes. © 2022 The Author(s)

2023

Fill in the blank for fashion complementary outfit product Retrieval: VISUM summer school competition

Authors
Castro, E; Ferreira, PM; Rebelo, A; Rio-Torto, I; Capozzi, L; Ferreira, MF; Goncalves, T; Albuquerque, T; Silva, W; Afonso, C; Sousa, RG; Cimarelli, C; Daoudi, N; Moreira, G; Yang, HY; Hrga, I; Ahmad, J; Keswani, M; Beco, S;

Publication
MACHINE VISION AND APPLICATIONS

Abstract
Every year, the VISion Understanding and Machine intelligence (VISUM) summer school runs a competition where participants can learn and share knowledge about Computer Vision and Machine Learning in a vibrant environment. 2021 VISUM's focused on applying those methodologies in fashion. Recently, there has been an increase of interest within the scientific community in applying computer vision methodologies to the fashion domain. That is highly motivated by fashion being one of the world's largest industries presenting a rapid development in e-commerce mainly since the COVID-19 pandemic. Computer Vision for Fashion enables a wide range of innovations, from personalized recommendations to outfit matching. The competition enabled students to apply the knowledge acquired in the summer school to a real-world problem. The ambition was to foster research and development in fashion outfit complementary product retrieval by leveraging vast visual and textual data with domain knowledge. For this, a new fashion outfit dataset (acquired and curated by FARFETCH) for research and benchmark purposes is introduced. Additionally, a competitive baseline with an original negative sampling process for triplet mining was implemented and served as a starting point for participants. The top 3 performing methods are described in this paper since they constitute the reference state-of-the-art for this particular problem. To our knowledge, this is the first challenge in fashion outfit complementary product retrieval. Moreover, this joint project between academia and industry brings several relevant contributions to disseminating science and technology, promoting economic and social development, and helping to connect early-career researchers to real-world industry challenges.

2022

Quasi-Unimodal Distributions for Ordinal Classification

Authors
Albuquerque, T; Cruz, R; Cardoso, JS;

Publication
MATHEMATICS

Abstract
Ordinal classification tasks are present in a large number of different domains. However, common losses for deep neural networks, such as cross-entropy, do not properly weight the relative ordering between classes. For that reason, many losses have been proposed in the literature, which model the output probabilities as following a unimodal distribution. This manuscript reviews many of these losses on three different datasets and suggests a potential improvement that focuses the unimodal constraint on the neighborhood around the true class, allowing for a more flexible distribution, aptly called quasi-unimodal loss. For this purpose, two constraints are proposed: A first constraint concerns the relative order of the top-three probabilities, and a second constraint ensures that the remaining output probabilities are not higher than the top three. Therefore, gradient descent focuses on improving the decision boundary around the true class in detriment to the more distant classes. The proposed loss is found to be competitive in several cases.

2022

Quality Control in Digital Pathology: Automatic Fragment Detection and Counting

Authors
Albuquerque, T; Moreira, A; Barros, B; Montezuma, D; Oliveira, SP; Neto, PC; Monteiro, JC; Ribeiro, L; Gonçalves, S; Monteiro, A; Pinto, IM; Cardoso, JS;

Publication
44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society, EMBC 2022, Glasgow, Scotland, United Kingdom, July 11-15, 2022

Abstract

2021

Ordinal losses for classification of cervical cancer risk

Authors
Albuquerque, T; Cruz, R; Cardoso, JS;

Publication
PEERJ COMPUTER SCIENCE

Abstract
Cervical cancer is the fourth leading cause of cancer-related deaths in women, especially in low to middle-income countries. Despite the outburst of recent scientific advances, there is no totally effective treatment, especially when diagnosed in an advanced stage. Screening tests, such as cytology or colposcopy, have been responsible for a substantial decrease in cervical cancer deaths. Cervical cancer automatic screening via Pap smear is a highly valuable cell imaging-based detection tool, where cells must be classified as being within one of a multitude of ordinal classes, ranging from abnormal to normal. Current approaches to ordinal inference for neural networks are found to not sufficiently take advantage of the ordinal problem or to be too uncompromising. A non-parametric ordinal loss for neuronal networks is proposed that promotes the output probabilities to follow a unimodal distribution. This is done by imposing a set of different constraints over all pairs of consecutive labels which allows for a more flexible decision boundary relative to approaches from the literature. Our proposed loss is contrasted against other methods from the literature by using a plethora of deep architectures. A first conclusion is the benefit of using non-parametric ordinal losses against parametric losses in cervical cancer risk prediction. Additionally, the proposed loss is found to be the top-performer in several cases. The best performing model scores an accuracy of 75.6% for seven classes and 81.3% for four classes.