Tiago Gonçalves

Porto, Portugal tiago.f.goncalves@inesctec.pt

PhD Student at FEUP | Research Assistant at INESC TEC | Machine Learning and Deep Learning Enthusiast

I received my MSc in Bioengineering (Biomedical Engineering) from Faculdade de Engenharia da Universidade do Porto (FEUP) in 2019. Currently, I am a PhD Candidate in Electrical and Computer Engineering at FEUP and a research assistant at the Centre for Telecommunications and Multimedia of INESC TEC with the Visual Computing & Machine Intelligence (VCMI) Research Group.
My research interests include machine learning, explainable artificial intelligence (in-model approaches), computer vision, medical decision support systems, and machine learning deployment.

Besides working, I enjoy practising Karate-Do Shotokai or reading about life, philosophy, economy, politics or fundamental science.
Moreover, I do not refuse a good TV series or a good film (preferably at the cinema).

Experience

Visiting Researcher / PhD Student

Netherlands Cancer Institute

Visiting PhD student at the Department of Radiology, under the supervision of Wilson Silva.

April 2024 - Present

Visiting Researcher / PhD Student

University of Utrecht

Visiting PhD student with AI Technology for Life research group of the Department of Information and Computing Sciences, under the supervision of Wilson Silva.

April 2024 - Present

External Researcher / PhD Student

Athinoula A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital

External PhD student with The Quantitative Translational Imaging in Medicine Lab (QTIM), under the supervision of Albert Kim and Christopher P. Bridge.

February 2024 - Present

Visiting Researcher / PhD Student

Athinoula A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital

Visiting PhD student with The Quantitative Translational Imaging in Medicine Lab (QTIM), under the supervision of Albert Kim and Christopher P. Bridge.

September 2023 - February 2024

Invited Teaching Assistant

Faculty of Engineering | University of Porto

Invited Teaching Assistant during the 1st Semester of 2022-2023 on the course PRO - Programming (L.EEC004)

Invited Teaching Assistant during the 1st Semester of 2021-2022 on the course TAIA - Advanced Topics on Artificial Intelligence

September 2021 - Present

Research Assistant

INESC TEC | Centre for Telecommunications and Multimedia

January 2020 - Present

Research Assistant

Faculty of Engineering | University of Porto

September 2019 - December 2019

Junior Researcher

Fraunhofer Portugal AICOS

March 2018 - September 2018

Education

Faculty of Engineering | University of Porto

Doctor of Philosophy

Electrical and Computer Engineering

September 2020 - Present

Faculty of Engineering | University of Porto

Bachelor of Science & Master of Science

Bioengineering - Biomedical Engineering

September 2016 - July 2019

University of Twente

Bachelor of Science

Bioengineering - Biomedical Engineering

Internship and Bachelor's Thesis as an Erasmus+ Student.

February 2016 - June 2016

Faculty of Biotechnology | Universidade Católica Portuguesa

Bachelor of Science

Bioengineering - Biomedical Engineering

September 2013 - July 2016

Skills

Programming Languages & Tools

News & Awards

News

[2024/05/01] I presented my research on interpretable machine learning to the AI Technology for Life research group of the Department of Information and Computing Sciences of the Utrecht University. Thank you for discussing science with me! You can get the slides here.
[2023/10/27] I presented my research on interpretable machine learning to the AI for Multi-center Data research group of the Department of Radiology of the Netherlands Cancer Institute. Thank you, Wilson Silva (and colleagues), for inviting and listening to me! You can get the slides here.
[2023/10/26] INESC TEC's BIP Magazine highlighted two of my recent achievements! The first is the victory at the "Image CLEF Medical GANs" of the ImageCLEF Challenge 2023, alongside Helena Montenegro, Pedro Neto, Cristiano Patrício, Isabel Rio-Torto, Tiago Gonçalves and Luís F. Teixeira. The second is the victory at the Discover Datathon 2023, promoted by the Society of Critical Care Medicine (SCCM) alongside João Matos. Thank you!
[2023/05/31] The Centre of Telecommunications and Multimedia (CTM) coordinators recognised me as one of INESC TEC's "Incredibles" of May 2023. Thank you for this positive appreciation of my work, leading to this nomination. Last but not least, this nomination is only possible thanks to the incredible people with whom I have the privilege of interacting and collaborating: this nomination is also yours. Thank you!
[2023/03/18] I gave a talk titled "Interpretable Artificial Intelligence in Medicine: What Else?" for the XIV Symposium on Bioengineering. You can get the slides here. I want to thank Bioengineering Students Association from the Faculty of Engineering of the University of Porto / School of Medicine and Biomedical Sciences (NEB-FEUP/ICBAS) for the invitation!
[2023/03/15] I gave a talk titled "Attention Mechanisms for Medical Applications: Claims, Potentialities and Future Challenges" for Deep Learning Sessions Portugal. You can get the slides or watch the video. I want to thank Deep Learning Sessions Portugal for the invite and Startup Lisboa and Neuraspace for supporting the event!

Awards

MICCAI Hackathon 2021 Best Contribution Award - Member of the winning team "HIT" (Helena Montenegro, Isabel Rio-Torto, João Nunes and Tiago Gonçalves) with the work titled "Show Me Consistency! Increasing the quality and consistency of annotations"
2^nd Place World Data League - Member of the team "Tech Moguls" (Joana Morgado, Paulo Maia, Tiago Gonçalves and Tomé Albuquerque) that achieved 2^nd place at the World Data League competition on data science

Publications

International Conference and Journal Articles

Caldeira, Eduarda, Pedro C. Neto, Tiago Gonçalves, Naser Damer, Ana F. Sequeira, and Jaime S. Cardoso. "Disentangling morphed identities for face morphing detection." Science Talks 10 (2024): 100331.
[link][bib]

Gonçalves, Tiago, Dagoberto Pulido-Arias, Julian Willett, Katharina V. Hoebel, Mason Cleveland, Syed Rakin Ahmed, Elizabeth Gerstner et al. "Deep Learning-based Prediction of Breast Cancer Tumor and Immune Phenotypes from Histopathology." arXiv preprint arXiv:2404.16397 (2024).
[link][bib][pdf][poster][presentation][code]

Neto, Pedro C., Rafael M. Mamede, Carolina Albuquerque, Tiago Gonçalves, and Ana F. Sequeira. "Massively Annotated Datasets for Assessment of Synthetic and Real Data in Face Recognition." arXiv preprint arXiv:2404.15234 (2024).
[link][bib][pdf]

Caldeira, Eduarda, Pedro C. Neto, Tiago Gonçalves, Naser Damer, Ana F. Sequeira, and Jaime S. Cardoso. "Unveiling the two-faced truth: Disentangling morphed identities for face morphing detection." In 2023 31st European Signal Processing Conference (EUSIPCO), pp. 955-959. IEEE, 2023.
[link][bib][pdf][code]

Kaidar-Person, Orit, Marilia Antunes, Jaime S. Cardoso, Oriana Ciani, Helena Cruz, Rosa Di Micco, Oreste D. Gentilini et al. "Evaluating the ability of an artificial-intelligence cloud-based platform designed to provide information prior to locoregional therapy for breast cancer in improving patient's satisfaction with therapy: The CINDERELLA trial." PLoS One 18, no. 8 (2023): e0289365.
[link][bib][pdf]

Serrano e Silva, Pedro, Ricardo Cruz, A. S. M. Shihavuddin, and Tiago Gonçalves. "Interpretability-Guided Human Feedback During Neural Network Training." In Iberian Conference on Pattern Recognition and Image Analysis, pp. 276-287. Cham: Springer Nature Switzerland, 2023.
[link][bib][pdf][poster][code]

e Silva, Diana Teixeira, Ricardo Cruz, Tiago Gonçalves, and Diogo Carneiro. "Two-stage semantic segmentation in neural networks." In Fifteenth International Conference on Machine Vision (ICMV 2022), vol. 12701, pp. 122-131. SPIE, 2023.
[link][bib][pdf][presentation][code]

Cruz, Ricardo, Diana Teixeira E. Silva, Tiago Gonçalves, Diogo Carneiro, and Jaime S. Cardoso. "Two-Stage Framework for Faster Semantic Segmentation." Sensors 23, no. 6 (2023): 3092.
[link][bib][pdf][code]

Montenegro, Helena, Pedro Neto, Cristiano Patrício, Isabel Rio-Torto, Tiago Gonçalves, and Luís F. Teixeira. "Evaluating privacy on synthetic images generated using gans: Contributions of the vcmi team to imageclefmedical gans 2023." Challenge (2023): 8.
[link][bib][pdf][code]

Rio-Torto, Isabel, Cristiano Patrício, Helena Montenegro, Tiago Gonçalves, and Jaime S. Cardoso. "Detecting concepts and generating captions from medical images: Contributions of the VCMI team to Image-CLEFmedical caption 2023." In CLEF2023 Working Notes, CEUR Workshop Proceedings, CEUR-WS. org, Thessaloniki, Greece. 2023.
[link][bib][pdf][code]

Silva, Wilson, Tiago Gonçalves, Kirsi Härmä, Erich Schröder, Verena Carola Obmann, María Cecilia Barroso, Alexander Poellinger, Mauricio Reyes, and Jaime S. Cardoso. "Computer-aided diagnosis through medical image retrieval in radiology." Scientific reports 12, no. 1 (2022): 20732.
[link][bib][pdf]

Huber, Marco, Fadi Boutros, Anh Thi Luu, Kiran Raja, Raghavendra Ramachandra, Naser Damer, Pedro C. Neto et al. "SYN-MAD 2022: Competition on face morphing attack detection based on privacy-aware synthetic training data." In 2022 IEEE International Joint Conference on Biometrics (IJCB), pp. 1-10. IEEE, 2022.
[link][bib][pdf]

Neto, Pedro C., Tiago Gonçalves, Marco Huber, Naser Damer, Ana F. Sequeira, and Jaime S. Cardoso. "Orthomad: Morphing attack detection through orthogonal identity disentanglement." In 2022 International Conference of the Biometrics Special Interest Group (BIOSIG), pp. 1-5. IEEE, 2022.
[link][bib][pdf][code]

Gonçalves, Tiago, Isabel Rio-Torto, Luís F. Teixeira, and Jaime S. Cardoso. "A survey on attention mechanisms for medical applications: are we moving toward better Algorithms?." IEEE Access 10 (2022): 98909-98935.
[link][bib][pdf][code]

Neto, Pedro C., Tiago Gonçalves, João Ribeiro Pinto, Wilson Silva, Ana F. Sequeira, Arun Ross, and Jaime S. Cardoso. "Explainable biometrics in the age of deep learning." arXiv preprint arXiv:2208.09500 (2022).
[link][bib][pdf]

Rio-Torto, Isabel, Cristiano Patrício, Helena Montenegro, and Tiago Gonçalves. "Detecting Concepts and Generating Captions from Medical Images: Contributions of the VCMI Team to ImageCLEFmedical 2022 Caption." (2022).
[link][bib][pdf][poster][presentation][code]

Sequeira, Ana F., Tiago Gonçalves, Wilson Silva, João Ribeiro Pinto, and Jaime S. Cardoso. "An exploratory study of interpretability for face presentation attack detection." IET Biometrics 10, no. 4 (2021): 441-455.
[link][bib][pdf]

Pinto, João Ribeiro, Tiago Gonçalves, Carolina Pinto, Luís Sanhudo, Joaquim Fonseca, Filipe Gonçalves, Pedro Carvalho, and Jaime S. Cardoso. "Audiovisual classification of group emotion valence using activity recognition networks." In 2020 IEEE 4th International Conference on Image Processing, Applications and Systems (IPAS), pp. 114-119. IEEE, 2020.
[link][bib][pdf]

Gonçalves, Tiago, Wilson Silva, Maria J. Cardoso, and Jaime S. Cardoso. "Deep image segmentation for breast keypoint detection." In Proceedings, vol. 54, no. 1, p. 35. MDPI, 2020.
[link][bib][pdf]

Oliveira, Sara P., João Ribeiro Pinto, Tiago Gonçalves, Rita Canas-Marques, Maria-João Cardoso, Hélder P. Oliveira, and Jaime S. Cardoso. "Weakly-supervised classification of HER2 expression in breast cancer haematoxylin and eosin stained slides." Applied Sciences 10, no. 14 (2020): 4728.
[link][bib][pdf][code]

Gonçalves, Tiago, Wilson Silva, Maria J. Cardoso, and Jaime S. Cardoso. "A novel approach to keypoint detection for the aesthetic evaluation of breast cancer surgery outcomes." Health and Technology 10 (2020): 891-903.
[link][bib][pdf][code]

Sequeira, Ana F., Wilson Silva, Joao Ribeiro Pinto, Tiago Gonçalves, and Jaime S. Cardoso. "Interpretable biometrics: Should we rethink how presentation attack detection is evaluated?." In 2020 8th International Workshop on Biometrics and Forensics (IWBF), pp. 1-6. IEEE, 2020.
[link][bib][pdf]

Gonçalves, Tiago, Wilson Silva, and Jaime Cardoso. "Deep aesthetic assessment of breast cancer surgery outcomes." In XV Mediterranean Conference on Medical and Biological Engineering and Computing-MEDICON 2019: Proceedings of MEDICON 2019, September 26-28, 2019, Coimbra, Portugal, pp. 1967-1983. Springer International Publishing, 2020.
[link][bib][pdf]

National Conference and Journal Articles

Diana Teixeira e Silva, Ricardo Cruz and Tiago Gonçalves. "Preliminary Study on Deep Iterative Semantic Segmentation" 28th Portuguese Conference in Pattern Recognition (RECPAD), 2022.
[bib][pdf][poster][code]

Tiago Gonçalves and Jaime S. Cardoso. "Preliminary Study on the Impact of Attention Mechanisms for Medical Image Classification" 27th Portuguese Conference in Pattern Recognition (RECPAD), 2021.
[bib][pdf][poster][code]

Tiago Gonçalves, Wilson Silva and Jaime S. Cardoso. "A Deep Image Segmentation Approach to Breast Keypoint Detection" 26th Portuguese Conference in Pattern Recognition (RECPAD), 2020.
[bib][pdf][poster]

Sara P. Oliveira, João R. Pinto, Tiago Gonçalves, Hélder P. Oliveira and Jaime S. Cardoso. "IHC Classification in Breast Cancer H&E Slides with a Weakly-Supervised Approach" 26th Portuguese Conference in Pattern Recognition (RECPAD), 2020.
[bib][pdf][poster]

Wilson Silva, João R. Pinto, Tiago Gonçalves, Ana F. Sequeira and Jaime S. Cardoso. "Explainable Artificial Intelligence for Face Presentation Attack Detection" 26th Portuguese Conference in Pattern Recognition (RECPAD), 2020.
[bib][pdf][poster]

Tiago Gonçalves, Wilson Silva, and Jaime Cardoso. "Towards a Deep Keypoint Detection Algorithm for the Aesthetic Assessment of Breast Cancer Surgery Outcomes" 25th Portuguese Conference in Pattern Recognition (RECPAD), 2019.
[bib][pdf]

Rybarczyk, Yves, Clément Cointe, Tiago Gonçalves, Vitor Minhoto, Jan Kleine Deters, Santiago Villarreal, Arián Aladro Gonzalo, Jonathan Baldeón, and Danilo Esparza. "On the use of natural user interfaces in physical rehabilitation: A web-based application for patients with hip prosthesis." Journal of Science and Technology of the Arts 10, no. 2 (2018): 15-24.
[link][bib][pdf]

Theses

Tiago Filipe Sousa Gonçalves "Deep Aesthetic Assessment of Breast Cancer Surgery Outcomes"
Master in Bioengineering - Biomedical Engineering, Faculty of Engineering of the University of Porto, 2019.
[link][bib]

Activity

Supervised MSc Students

Co-supervisor of Pedro João Cruz Serrano e Silva (2021-2022)
"Human Feedback during Neural Networks Training"
Master in Bioengineering - Biomedical Engineering, Faculty of Engineering of the University of Porto
Co-supervisor of José Pedro Moreira de Almeida Baptista (2021-2022)
"Website Development for the VCMI Research Group"
Master in Informatics and Computing Engineering, Faculty of Engineering of the University of Porto
Co-supervisor of João Gonçalves Rodrigues (2019-2020)
"WebBCCT.core - A Web Application for the Assessment of Breast Cancer Conservative Treatment Cosmetic Results"
Master in Network and Informatic Systems Engineering, Faculty of Sciences of the University of Porto

Supervised BSc Students

Co-supervisor of David Ferreira Sá Machado (2021-2022)
"Classification of Breast Masses using a Multiple-feature Regularisation Approach"
Bachelor in Bioengineering - Biomedical Engineering, Faculty of Engineering of the University of Porto
Co-supervisor of Diana Raquel Teixeira e Silva (2021-2022)
"Semantic Segmentation in Neural Networks using Iterative Visual Attention"
Bachelor in Bioengineering - Biomedical Engineering, Faculty of Engineering of the University of Porto
Co-supervisor of Érica Ferreira Gomes (2021-2022)
"Classification of Breast Lesion Features using a Concept-learning Algorithm"
Bachelor in Bioengineering - Biomedical Engineering, Faculty of Engineering of the University of Porto
Co-supervisor of Manuel Leão Fortunato (2021-2022)
"Identification of Breast Cancer Features: A Classification Algorithm based on Concept Learning"
Bachelor in Bioengineering - Biomedical Engineering, Faculty of Engineering of the University of Porto
Co-supervisor of Maria Eduarda Loureiro Caldeira (2021-2022)
"From Easy to Hard: a Curriculum Learning Approach for Breast Lesion Classification"
Bachelor in Bioengineering - Biomedical Engineering, Faculty of Engineering of the University of Porto

Supervised Internships

Co-supervisor of Ana Cristina da Silva Gomes (2022)
"Classify and Protect"
ANEEB Summer Internships 2022, Portuguese Biomedical Engineering Students' Association (ANEEB)
Co-supervisor of Margarida Duarte da Conceição (2022)
"Towards a unified framework to assess Deep Learning medical explanations"
ANEEB Summer Internships 2022, Portuguese Biomedical Engineering Students' Association (ANEEB)
Co-supervisor of Beatriz Arcipreste, Cláudia Ribeiro and José Macedo (2022)
"Classification of human activity in videos"
CTM Summer Internships 2022, Institute for Systems and Computer Engineering, Technology and Science (INESC TEC)
Co-supervisor of André Soares (2021)
"xAI for COVID-19 Classification: Using explainable artificial intelligence to assess deep neural networks"
CTM Summer Internships 2021, Institute for Systems and Computer Engineering, Technology and Science (INESC TEC)
Co-supervisor of Daniel Silva and Raquel Belo (2021)
"Interpretable Machine Learning for Mammography Screening"
NEB Outclass Internship, Faculty of Engineering of the University of Porto
Co-supervisor of João Abelha, João Ribeiro and José Matias (2020)
"WebBCCT.core - A Web Application for the Assessment of Breast Cancer Conservative Treatment Cosmetic Results"
CTM Summer Internships 2020, Institute for Systems and Computer Engineering, Technology and Science (INESC TEC)