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Daniel Gonçalves completed his master's degree in Computer Science and Engineering in November of 2020 at Instituto Superior Técnico and has since authored four publications, three of which as a first author, published in high impact journals. He holds a BSc in Informatics Engineering, completed in June 2018 at the University of Aveiro and, since September 2021, he is pursuing a PhD in Computer Science and Engineering. Simultaneously, he is working as an invited teaching assistant at Instituto Superior Técnico, teaching four Computer Science courses: Information Processing and Retrieval (MSc course), Information Systems and Databases (MSc course), Data Administration and Information Systems (MSc course), and Databases (BSc course). Daniel is also a Research Fellow at IDMEC-IST since 2019. As such, he participated in a project collaboration with IPO-Porto to predict postoperative complications in cancer patients using machine learning models, developing his master's thesis in this context, leading him to publish two articles in 2021. Furthermore, together with other colleagues, he contributed to the creation of an online platform for oncologists, aiming to help in perioperative care. These results have been published in a recent article from 2022. More recently, Daniel has been working with glycoproteomics data employing pattern mining and deep learning to find potential targets for cancer immunology research. He has recently been accepted in a conference with a paper holding early contributions from his latest research. In parallel to all his work, he is also an assiduous speaker at seminars and tutor of young people (7th to 12th grade) on Artificial Intelligence in an after-school volunteer program.
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Identification

Personal identification

Full name
Daniel Gonçalves
Gender
Male

Citation names

  • Gonçalves, Daniel

Author identifiers

Ciência ID
9D14-B66F-A1CF
ORCID iD
0000-0001-5388-870X

Email addresses

  • dmateusgoncalves@tecnico.ulisboa.pt (Professional)
  • danielmateusgoncalves@gmail.com (Personal)

Telephones

Mobile phone
  • 932283938 (Personal)

Addresses

  • Rua Luis Pastor de Macedo, 7, 3F, 1750-156, Lisboa, Lisboa, Portugal (Personal)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Computer and Information Sciences - Information Science
  • Exact Sciences - Computer and Information Sciences - Computer Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Spanish; Castilian Intermediate (B1) Intermediate (B1) Elementary (A2) Intermediate (B1) Elementary (A2)
Portuguese (Mother tongue)
Education
Degree Classification
2021/09/10 - 2025
Ongoing
 Engenharia Informática e de Computadores (Doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Glycoproteogenomics Characterization in Colorectal Cancer using Deep Learning Approaches " (THESIS/DISSERTATION)
2018/09/12 - 2020/11/20
Concluded
 Engenharia Informática e de Computadores (Mestrado)
Major in Sistemas Inteligentes
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Clinical prognosis and risk prediction of postoperative complications in cancer patients" (THESIS/DISSERTATION)
 16
2015/09/14 - 2018/06/21
Concluded
 Engenharia Informática (Licenciatura)
Universidade de Aveiro, Portugal
"Catch Me If You Can - Geolocalização entre conhecidos com garantias de privacidade " (THESIS/DISSERTATION)
 14
Affiliation

Teaching in Higher Education

Category
Host institution 		Employer
2022/09/19 - 2023/08/19 Invited Assistant (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/10/01 - 2022/08/31 Invited Assistant (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
Universidade de Lisboa Instituto Superior Técnico, Portugal

Others

Category
Host institution 		Employer
2022/07/15 - 2022/11/15 Bolseiro de Investigação Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2019/10/20 - 2022/07/17 Bolseiro de Investigação Instituto de Engenharia Mecânica, Portugal
Universidade de Lisboa Instituto Superior Técnico, Portugal
Projects

Grant

Designation Funders
2022/06/15 - 2022/11/15 LAIfeBlood - Inteligência Artificial para a Gestão do Sangue
DSAIPA/AI/0033/2019
Research Fellow
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2019/10/20 - 2022/06/14 IPOscore - Predicting the risk of complications of surgical treatment and define prognosis of cancer patients through clinical and biopathological data integration
DSAIPA/DS/0042/2018
Research Fellow
Instituto de Engenharia Mecânica, Portugal

Instituto Português de Oncologia do Porto Francisco Gentil EPE, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Conference paper
  1. Gonçalves, Daniel; Costa, Rafael S.; Henriques, Rui. "Context-situated visualization of biclusters to aid decisions: going beyond subspaces with parallel coordinates". Paper presented in AVI 2022: International Conference on Advanced Visual Interfaces, Roma, 2022.
    Published • 10.1145/3531073.3531124
Conference poster
  1. Gonçalves, Daniel. "Glycoproteogenomics Characterization in Colorrectal Cancer using Deep Learning Approaches". Paper presented in 19th International Symposium on Intelligent Data Analysis, 2021.
Journal article
  1. Daniel M. Gonçalves; Rui Henriques; Rafael S. Costa. "Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven approaches". Computational and Structural Biotechnology Journal (2023): https://doi.org/10.1016/j.csbj.2023.10.002.
    Accepted • 10.1016/j.csbj.2023.10.002
  2. Mochão, Hugo; Gonçalves, Daniel; Alexandre, Leonardo; Castro, Carolina; Valério, Duarte; Barahona, Pedro; Moreira-Gonçalves, Daniel; et al. "IPOscore: an interactive web-based platform for postoperative surgical complications analysis and prediction in the oncology domain". Computer Methods and Programs in Biomedicine (2022): 106754. http://dx.doi.org/10.1016/j.cmpb.2022.106754.
    Published • 10.1016/j.cmpb.2022.106754
  3. Gonçalves, Daniel M.; Henriques, Rui; Costa, Rafael S.. "Predicting Postoperative Complications in Cancer Patients: A Survey Bridging Classical and Machine Learning Contributions to Postsurgical Risk Analysis". Cancers 13 13 (2021): 3217. http://dx.doi.org/10.3390/cancers13133217.
    Open access • Published • 10.3390/cancers13133217
  4. Gonçalves, Daniel; Henriques, Rui; Santos, Lúcio Lara; Costa, Rafael S.. "On the predictability of postoperative complications for cancer patients: a Portuguese cohort study". BMC Medical Informatics and Decision Making 21 1 (2021): http://dx.doi.org/10.1186/s12911-021-01562-2.
    Open access • Published • 10.1186/s12911-021-01562-2
Thesis / Dissertation
  1. Gonçalves, Daniel. "Clinical prognosis and risk prediction of postoperative complications in cancer patients". Master, Universidade de Lisboa Instituto Superior Técnico, 2020. https://github.com/danielmg97/master-thesis-iposcore.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/11/28 IPOscore Platform Workshop Inteligência Artificial - IPO Porto
IPO Porto (Porto, Portugal)
2022/03/02 Context-situated visualization of biclusters to aid decisions: going beyond subspaces with parallel coordinates Research Topics Seminars
Professor Francisco Correia dos Santos (Lisbon, Portugal)
2021/05/11 Glycoproteogenomics Characterization in Colorectal Cancer Using Deep Learning (Proposal Presentation) Systems Biology and Engineering Lab Seminars
NOVA School of Science and Technology | FCT NOVA (Almada, Portugal)
2021/04/28 Glycoproteogenomics Characterization in Colorectal Cancer using Deep Learning Approaches 19th International Symposium on Intelligent Data Analysis
IDA Society (Porto, Portugal)
2020/12/04 Clinical prognosis and risk prediction of postoperative complications in cancer patients (IPO - Update 2)
Instituto Português e Oncologia do Porto (Porto, Portugal)
2020/09/30 Clinical prognosis and risk prediction of postoperative complications in cancer patients (SBE - Update) Systems Biology and Engineering Lab Seminars
NOVA School of Science and Technology | FCT NOVA (Lisboa, Portugal)
2020/05/01 Clinical prognosis and risk prediction of postoperative complications in cancer patients (IPO - Update)
Instituto Português e Oncologia do Porto (Porto, Portugal)
2020/04/08 Clinical prognosis and risk prediction of postoperative complications in cancer patients (SBE) Systems Biology and Engineering Lab Seminars
NOVA School of Science and Technology | FCT NOVA (Lisboa, Portugal)
2019/11/20 Clinical prognosis and risk prediction of postoperative complications in cancer patients (IPO)
Intituto Português de Oncologia do Porto (Porto, Portugal)

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2023/02/02 - Current PhD Weekly Meetings - Informal weekly one-hour meetings with peer PhD candidates, divided in two parts: weekly task review, and rotating presentation + discussion. (2023/02/02)
Other (Co-organisor)
2023/11/06 - 2023/11/09 ER 2023 - The 42nd International Conference On Conceptual Modeling (2023/11/06 - 2023/11/09)
Conference (Other)
 Universidade de Lisboa Instituto Superior Técnico, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2023/04/27 - 2023/04/27 Workshop on the use of Deep Learning to leverage the study of Genomics presented by Bernardo Almeida, from iMP and University of Vienna, at INESC-ID, Lisbon.
Workshop
 Decoding the Genome with Deep Learning
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2022/07/11 - 2022/07/15 Monitor at the "Verão na ULisboa" Summer School, representing INESC-ID as a research unit.
Other
 Summer at ULisboa
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/06/14 - 2021/06/16 This event gathered senior and junior researchers from INESC-ID, ETH Zürich, Inria, and EMBL; in order to share their work in the context of Project OLISSIPO. This project is funded by the European Commission within its H2020 Research and Innovation programme “Spreading Excellence and Widening Participation|Twinning”, OLISSIPO aims to enhance the competences in Computational Biology at INESC-ID in Lisbon, towards the creation of an international pole of excellence in multi-disciplinary science in Portugal.
Meeting
 OLISSIPO Week
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Conference scientific committee

Conference name Conference host
2023/02/15 - 2023/02/15 ISMB ECCB 2023 - Intelligent Systems for Molecular Biology, European Conference on Molecular Biology 2023 Lyon, France

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2021 - 2022 Processamento e Recuperação de Informação (Information Retrieval and Processing) (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022 Sistemas de Informação e Bases de Dados (Information Systems and Databases) (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022 Administração de Dados e Sistemas de Informação (Data Administration in Information Systems) (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022 Bases de Dados (Databases) (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal

Mentoring / Tutoring

Topic Student name
2022/01/08 - 2022/02/26 AfterSchool by TreeTree2 - Inteligência Artificial 2022 Turma: "Alan Turing"
2021/02/15 - 2021/02/19 Lab Rotation - Integrated Laboratory Practicals II (Data Science Week) Rodrigo Barriga Alves
2021/02/15 - 2021/02/19 Lab Rotation - Integrated Laboratory Practicals II (Data Science Week) Joana Pimenta