Research

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Research Interests

Main research interests:

• Complex Network Analysis, Network Science, Graph Mining.
• Algorithms and Data Structures, Complexity.
• Parallel and Distributed Computing.
• Bioinformatics Applications; Biological Networks; Social Networks; Sports Analytics.

Other research interests:

• Computer Science Education and Programming Contests.
• Artificial Intelligence, Machine Learning, Knowledge Discovery and Data Mining.

Students

Current Students:

PhD Students

• (since 2018) - Alberto Barbosa (PhD in Computer Science, FCUP)
  Co-advisor: Inês Dutra
• (since 2020) Luciano Grácio (PhD in Computer Science, FCUP)
• (since 2021) André Meira (PhD in Computer Science, FCUP)
• (since 2021) Hugo Oliveira (PhD in Computer Science, FCUP)
  Co-advisor: Hélder Oliveira
• (since 2022) Cláudio Villar (PhD in Informatics Engineering, FEUP)
• (since 2023) Ricardo Pereira (PhD in Computer Science, FCUP)
  Co-advisor: Carlos Soares

Alumni:

PhD Students

• (2019 - 2024) Ahmad Naser eddin (PhD in Computer Science, FCUP)
  Co-advisors: David Aparício and Jacopo Bono
  PhD Thesis: Anti-money Laundering using Graph Techniques
• (2018 - 2023) Vanessa Silva (MAPi - Doctoral Programme in Computer Science)
  Co-advisor: Maria Eduarda Silva
  PhD Thesis: Multidimensional Time Series Analysis: A Complex Networks Approach
• (2016 - 2021) Jorge Silva (MAPi - Doctoral Programme in Computer Science)
  Main advisor: Fernando Silva
  PhD Thesis: Towards Measuring Scientific Impact Using Network Science
• (2014 - 2020) David Aparício (MAPi - Doctoral Programme in Computer Science)
  Co-advisor: Fernando Silva
  PhD Thesis: Network Comparison and Node Ranking in Complex Networks
• (2012 - 2017) Miguel Araújo (CMU|Portugal and MAPi computer science doctoral programmes)
  CMU advisor: Christos Faloutsos
  PhD Thesis: Communities and Anomaly Detection in Large Edge-Labeled Graphs
• (2010 - 2015) Sarvenaz Choobdar (PhD in Computer Science, FCUP)
  Main advisor: Fernando Silva
  PhD Thesis: On the Characterization and Comparison of Complex Networks

MSc Students

• (2023 - 2024) Pedro Vieira (co-advisor: Miguel Silva)
  MSc Thesis: Studying GNNs and their Capabilities for Finding Motifs
• (2023 - 2024) Diogo Ferreira (co-advisor: Miguel Silva)
  MSc Thesis: Football passing sequences and networks for goal prediction
• (2022 - 2023) Darmit Kumar (main advisor: Pedro Ferreira)
  MSc Thesis: Unravelling the Complexity of Human Disease: Transcriptomic Networks of Phenotype - Gene Expression Data
• (2021 - 2022) José Ferreira (co-advisor: Alberto Barbosa)
  MSc Thesis: Subgraph Patterns in Spatial Networks
• (2021 - 2022) Filipe Justiça (co-advisor: Maria Eduarda Silva and Vanessa Silva)
  MSc Thesis: Time series forecasting via Network Science
• (2021 - 2022) Manuel Lamas
  MSc Thesis: Characterizing Music through Complex Networks
• (2021 - 2022) Isac Novo
  MSc Thesis: On the Summarization of Complex Networks
• (2021 - 2022) Joana Cortez Trindade (main advisor: Pedro Campos, FEP)
  MSc Thesis: Spotting fraud: detecting patterns and red flags in financial networks
• (2020 - 2021) Ricardo Pereira   (co-advisors: David Aparício and Jacopo Bono)
  MSc Thesis: A machine learning approach to money laundering detection inspired by GANs
• (2020 - 2021) Beatriz Pinto (co-advisor: Luciano Grácio)
  MSc Thesis: Subgraph Patterns in Colored Networks
• (2019 - 2020) Henrique Branquinho (co-advisor: Luciano Grácio)
  MSc Thesis: Counting Subgraphs in Streaming Networks
• (2019 - 2020) Francisco Bento (co-advisor: Alberto Barbosa)
  MSc Thesis: Characterizing the Passing Networks of Football Teams
• (2018 - 2019) Luciano Grácio
  MSc Thesis: From Supergraph Counting to Subgraph Generation
• (2018 - 2019) André Meira
  MSc Thesis: Subgraph Patterns in Multiplex Networks
• (2018 - 2019) Miguel Martins
  MSc Thesis: Condensed Graphs: Towards a General Approach for Faster Subgraph Census
• (2018 - 2019) Miguel Amaral
  MSc Thesis: Time-memory trade-off in graphlet counting & Orbit vertex frequency vs. degree in the expected degree model
• (2018 - 2019) Pedro Abranches   (co-advisor: Prof. Grégoire Courtine)
  MSc Thesis: Gaussian Processes for Automatic Optimization of Spinal Electrical Stimulation
• (2018 - 2019) Luis Alves   (co-advisor: Filipe Castro)
  MSc Thesis: PseudoChecker: An integrated online platform for automatised gene loss inference in mammals
• (2017 - 2018) Rui Fonseca
  MSc Thesis: Motif Based Community Discovery
• (2017 - 2018) Pedro Belém   (main advisor: Fernando Silva)
  MSc Thesis: Temporal Research Interests Discovery Using Co-Occurrence Keywords Networks
• (2017 - 2018) André Diegues (co-advisor: José Pinto)
  MSc Thesis: Automatic Habitat Mapping using Machine Learning
• (2017 - 2018) André Cascais
  MSc Thesis: Adaptive Parallel Subgraph Sampling in Large Complex Networks
• (2017 - 2018) Vanessa Silva (main advisor: Fernando Silva, co-advisor: Maria Eduarda Silva)
  MSc Thesis: Time Series Analysis based on Complex Networks
• (2016 - 2017) Pedro Paredes
  MSc Thesis: Counting subgraphs: from static to dynamic networks
• (2016 - 2017) Augusto Bilabila
  MSc Thesis: CompAlg - A Tool for Teaching and Learning the Logic of Programming
• (2016 - 2017) Alberto Barbosa (main advisor: Inês Dutra)
  MSc Thesis: Improving the search for multi-relational concepts in ILP
• (2016 - 2017) Miguel Duarte (@IST main advisor: Alexandre Francisco)
  MSc Thesis: Fast Hierarchical Graph Clustering
• (2015 - 2016) Ahmad Naser eddin
  MSc Thesis: Large Scale Parallel Subgraph Search
• (2015 - 2016) Manuel Lopes
  MSc Thesis: Bomberman as an Artificial Intelligence Platform
• (2013 - 2014) David Aparício (co-advisor: Fernando Silva)
  MSc Thesis: Pattern Discovery in Complex Network using Parallelism

Publications

Please see the publications page.

Talks

In Scientific Meetings

• Towards the Concept of Spatial Network Motifs
  11th International Conference on Complex Networks and their Applications, Palermo, Italy, November, 2022.
• Improving the characterization and comparison of football players with spatial flow motifs
  11th International Conference on Complex Networks and their Applications, Palermo, Italy, November, 2022.
• TensorCast: Forecasting Time-Evolving Networks with Contextual Information.
  27th International Joint Conference on Artificial Intelligence (IJCAI), Stockholm, Sweden, July, 2018.
• Fast streaming small graph canonization.
  9th International Conference on Complex Networks (CompleNet), Boston, USA, March, 2018.
• Evolutionary role mining in complex networks by ensemble clustering
  32nd ACM SIGAPP Symposium On Applied Computing (ACM-SAC), Marrakech, Morocco, April, 2017.
• Scalable subgraph counting using MapReduce
  32nd ACM SIGAPP Symposium On Applied Computing (ACM-SAC), Marrakech, Morocco, April, 2017.
• Dynamic inference of social roles in information cascades
  26th European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Porto, Portugal, September, 2015.
• Discovering Colored Network Motifs
  5th Workshop on Complex Networks (CompleNet), Bologna, Italy, March, 2014.
• Towards a Faster Network-Centric Subgraph Census
  IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), Niagara Falls, Canada, August, 2013.
• Motif Mining in Weighted Networks
  IEEE ICDM Workshop on Data Mining in Networks (DaMNet), Brussels, Belgium, November, 2012.
• Event Detection in Evolving Networks
  Int. Conference on Computational Aspects of Social Networks (CASoN), São Carlos, Brazil, November, 2012.
• Querying Subgraph Sets with G-Tries
  ACM SIGMOD Workshop on Databases and Social Networks (DBSocial), Scottsdale, USA, May, 2012.
• Efficient Parallel Subgraph Counting using G-Tries
  IEEE International Conference on Cluster Computing (CLUSTER), Crete, Greece, September, 2010
• Efficient Subgraph Frequency Estimation with G-Tries
  International Workshop on Algorithms in Bioinformatics (WABI), Liverpool, UK, September, 2010
• G-Tries: an efficient data structure for discovering network motifs
  ACM Symposium On Applied Computing (ACM-SAC), Sierre, Switzerland, March, 2010
• Parallel Calculation of Subgraph Census in Biological Networks
  International Conference on Bioinformatics (BIOINFORMATICS), Valencia, Spain, January, 2010
• Strategies for Network Motifs Discovery
  IEEE International Conference on e-Science (ESCIENCE), Oxford, UK, December, 2009
• Improving the Automatic Evaluation of Problem Solutions in Programming Contests
  3rd Olympiads in Informatics Conference, Plovdiv, Bulgaria, August, 2009
• Early Introduction of Competitive Programming
  2nd Olympiads in Informatics Conference,Cair, Egypt, August, 2008.
• Increasing the Appeal of Programming Contests with Tasks Involving Graphical User Interfaces and Computer Graphics
  1st Olympiads in Informatics Conference, Zagreb, Croatia, August, 2007
• An autonomous hybrid robot system to navigate through unknown maze environments
  Int. Conference on Artificial Intelligence and Soft Computing (ASC), Palma de Mallorca, Spain, August, 2007

Invited Talks and Seminars

• Network Science and Subgraphs (or how Kevin Bacon cured cancer)
  Invited Talk, Western-European Olympiad in Informatics, London, June, 2024
• Six Degrees of Separation: the world as a network [Announcement]
  Invited Talk, Escola Profissional de Espinho, Tech Week, March, 2024
• Subgraphs for Network Analysis
  Keynote at Learning on Graphs Meetup (MidNorth) [online], Univ. Notre Dame, Indiana, USA, January, 2024
• Creative Teaching and Learning
  Keynote at the P.Pic (Porto Pedagogical Innovation Conference), IPP, Porto, July, 2023
• Computational Thinking and its Importance
  Round table at PictoCiência, Centro de Ciência Viva, Guimarães, July, 2023
• Six degrees of separation [Announcement]
  Invited Talk, iNIGMA, FCUP, December, 2022
• Problem Solving and Creative Thinking
  Invited Talk, online, ANPRI, November, 2022
• Introduction to the Analysis and Visualisation of Complex Networks
  Mini-Course (6h), CLAD, online, November, 2022 [see announcement]
• Competitive Programming and Programming Contests
  Invited Talk, SINF, FEUP, November, 2022 [see announcement]
• Gamification on Education
  FCA Webinar, Invited Panel, online, March, 2022 [see video]
• Six Degrees of Separation: the world as a network
  Invited Talk, Marques de Castilho High School, Águeda, online, February, 2022
• 007, License to Randomize [Announcement]
  Invited Talk, iNIGMA, FCUP, Online, May, 2021
• Programming Challenges and Creative Thinking [Announcement]
  Invited Talk, UPDATE, NUCC, FCUP, Online, February, 2021
• Subgraphs as Fundamental Ingredients of Complex Networks: Concepts, Methods and Applications
  Statistics and Risk Management Seminar, Dep. of Mathematics, CMA/FCT NOVA, Online, November, 2020
• Biological Networks (an introduction to Network Science)
  Invited Talk, 2020 Summer School in Computational Biology, Univ. Coimbra, Online, October, 2020
• A gentle introduction to the world of Network Science [video] [Announcement]
  Invited Talk, Data Science and Statistics Webinar (DaSSWeb), FEP, Online, September, 2020
• Problem Solving and the Road to Creative Thinking [video]
  Keynote at the 1st International Computer Programming Education Conference (ICPEC), Online, June, 2020
• Six Degrees of Separation: the world as a network [Announcement]
  Invited Talk, UPDATE, NUCC, FCUP, February, 2020
• Six degrees of separation (or how Kevin Bacon cured cancer) [Announcement]
  Invited Talk on National Math Students Meeting (ENEMath), University of Porto, April, 2019
• Biological Networks
  Seminar on the 10th National Biomedical Sciences Meeting, University of Aveiro, March, 2019
• Six Degrees of Separation: the world as a network
  Invited Talk, D. Sancho I High School, V. N. Famalicão, March, 2019
• An Introduction to Network Science
  (a gentle introduction to the the world of complex networks and graph visualization)
  Tutorial, Porto Winter School on Network Science, December, 2018
• Subgraphs as Fundamental Ingredients of Complex Networks
  (concepts, methods and applications)
  Tutorial, Porto Winter School on Network Science, December, 2018
• An Exploratory Journey Into Network Analysis
  Invited Talk, Advanced School on Data Science for Big Data, Porto, July, 2018
• On the analysis of biological networks
  Invited Talk, Bioinformatics and Computational Biology Workshop, FCUP, Porto, January, 2018
• Problem Solving and Teaching Computational Thinking
  Invited Talk, Masters Degree in Informatics Teaching Seminars, Minho University, Braga, January, 2018
• Six Degrees of Separation: the world as a network
  Invited Talk, João Gonçalves Zarco High School, Matosinhos, November, 2017
• Competitive Programming
  Student Talk, DCC/FCUP, University of Porto, October, 2017
• Olympiads in Informatics: what they are and how to prepare [Announcement]
  Invited Talk, Summer Academy on Learning and Scientific Olympiads, IST, July, 2017
• Subgraphs: the building blocks of complex networks [Announcement]
  Invited Talk, Carnegie Mellon University (CMU), USA, May, 2017
• Subgraphs: the fundamental structural units of complex networks
  Invited Talk, IST Técnico Lisboa, November, 2016
• Six Degrees of Separation: the world as a network [Announcement]
  Invited Talk, Camilo Castelo Branco High School, V. N. Famalicão, April, 2016
• An Exploratory Journey Into Network Analysis
  (A Gentle Introduction to Network Science and Graph Visualization)
  Tutorial, Porto Winter School on Graph Analytics and Applications, December, 2015
• Subgraphs as Fundamental Ingredients of Complex Networks
  (Concepts, Methods and Applications)
  Tutorial, Porto Winter School on Graph Analytics and Applications, December, 2015
• Discovering Subgraph Patterns in Complex Networks [Announcement]
  Invited Talk, MAPi Doctoral Symposium, University of Aveiro, September, 2015
• Discovering Subgraph Patterns in Complex Networks [Announcement]
  Invited Talk, DCC Talks, University of Porto, April, 2015
• Competitive Programming [Announcement]
  Invited Talk, National Informatics Students Meeting (ENEI), University of Coimbra, March, 2015
• A journey through the world of Bioinformatics [poster]
  Invited Talk, AEFCUP, University of Porto, October, 2014
• Artificial Intelligence and Intelligent Agents [poster]
  Invited Talk, Camilo Castelo Branco High School, V. N. Famalicão, April, 2013
• G-Tries: an efficient data-structure for counting subgraphs [Announcement]
  Invited Talk, Knowledge Discovery and Bioinformatics (KDBIO) group, INESC-ID, Lisbon, December, 2011
• G-Tries: an efficient data-structure for subgraph counting [Announcement]
  Invited Talk, Computer Science Department, University of Texas, Austin, USA, July, 2011
• Artificial Intelligence and Intelligent Agents [Announcement]
  Invited Talk, Viana do Castelo Polytechnic Institute, Valença, April, 2010
• Dynamic Programming - A methodology for solving problems [PDF] [Announcement]
  Invited Talk, National Informatics Students Meeting (ENEI), University of Coimbra, April, 2010
• G-Tries: a specialized data-structure for Network Motif Discovery
  Invited Talk, CS-Bioinformatics Meeting, Newcastle University, UK, December, 2009
• Improving Network Motifs Detection
  Invited Talk, e-Therapeutics PLC, Newcastle, UK, December, 2009
• Efficient Algorithms for Network Motifs Discovery
  CRACS Seminar, DCC-FCUP, April, 2008
• Virtualization Techniques for Grid Computing
  CRACS Seminar, DCC-FCUP, May, 2007
• Computing Laboratories Setup for Grid Computing: a hands on report
  CRACS Seminar, DCC-FCUP, March, 2007
• How to prepare the participation on a programming contest
  Invited Talk, CPUP Awards Cerimony, FEUP, Porto, May, 2005
• Symmetries in Space: exploration using a computer
  Invited Talk, José Régio High School, Vila do Conde, June, 2003
• Artificial Intelligence and Intelligent Agents
  Invited Talk with demonstration of physical agents.
  Given in several schools and sites during the year:
  • Valongo High School, Valongo
  • Avelar Brotero High School, Coimbra
  • José Régio High School, Vila do Conde
  • DCC-FCUP, Porto

Programming Contests Problem Discussion Sessions

• MIUP'2016 Problems Discussion Session (PDF)
  Invited Talk, DI/FCT, New University of Lisbon, October, 2016
• MIUP'2015 Problems Discussion Session
  DCC/FCUP, University of Porto, October, 2015
• MIUP'2014 Problems Discussion Session
  Invited Talk, FEUP, University of Porto, October, 2014
• MIUP'2013 Problems Discussion Session [HTML]
  Invited Talk, FCUL, University of Lisbon, October, 2013
• MIUP'2012 Problems Discussion Session [HTML]
  DCC/FCUP, University of Porto, October, 2012
• MIUP'2011 Problems Discussion Session [HTML]
  Invited Talk, University of Algarve, October, 2011
• MIUP'2009 Problems Discussion Session [HTML]
  Invited Talk, ESTGA - University of Aveiro, October, 2009
• MIUP'2008 Problems Discussion Session [HTML]
  Invited Talk, University of Coimbra, October, 2008
• MIUP'2007 Problems Discussion Session [HTML]
  Invited Talk, IST Tagus Park, Technical University of Lisbon, October, 2007
• MIUP'2006 Problems Discussion Session [HTML]
  Invited Talk, University of Beira Interior, Covilhã, October, 2006
• MIUP'2005 Problems Discussion Session [HTML]
  Invited Talk, University of Aveiro, 2005

Organization of Events and Reviewing

Service as PC member

• (CompleNet'2023) 14th International Conference on Complex Networks
• (FRCCS'2023) 3rd French Regional Conference on Complex Systems
• (CN'2022) 11th International Conference on Complex Networks and Their Applications
• (AAAI'2022) 35th AAAI Conference on Artificial Intelligence
• (SAC'2022) 36th ACM/SIGAPP Symposium On Applied Computing (SONAMA track)
• (CN'2021) 10th International Conference on Complex Networks and Their Applications
• (CompleNet'2021) 12th International Conference on Complex Networks
• (ICPEC'2021) 2nd International Computer Programming Education Conference
• (AAAI'2021) 35th AAAI Conference on Artificial Intelligence
• (SAC'2021) 36th ACM/SIGAPP Symposium On Applied Computing (SONAMA track)
• (CN'2020) 9th International Conference on Complex Networks and Their Applications
• (AAAI'2020) 34th AAAI Conference on Artificial Intelligence
• (SAC'2020) 35th ACM/SIGAPP Symposium On Applied Computing (SONAMA track)
• (CN'2019) 8th International Conference on Complex Networks and Their Applications
• (AAAI'2019) 33rd AAAI Conference on Artificial Intelligence
• (SAC'2019) 34th ACM/SIGAPP Symposium On Applied Computing (SONAMA track)
• (ICCS'2019) 19th International Conference on Computational Science
• (CN'2018) 7th International Conference on Complex Networks and Their Applications
• (VECPAR'2018) 13th International Meeting on High Performance Computing for Computational Science
• (SAC'2018) 33rd ACM/SIGAPP Symposium On Applied Computing (SONAMA track)
• (ICCS'2018) 18th International Conference on Computational Science
• (CN'2017) 6th International Conference on Complex Networks and Their Applications
• (DSAA'2017) 4th IEEE International Conference on Data Science and Advanced Analytics - Special Session on Evolving Networks (Track Chair)
• (IJCAI'2017) 26th International Joint Conference on Artificial Intelligence (Senior PC)
• (Euro-Par'2017) 23rd International Conference on Parallel Processing (Local Topic Chair)
• (VECPAR'2016) 12th International Meeting on High Performance Computing for Computational Science
• (CSE'2015) 18th IEEE International Conference on Computational Science and Engineering
• (FSKD'2015) 12th International Conference on Fuzzy Systems and Knowledge Discovery
• (Euro-Par'2014) 20th International Conference on Parallel Processing (Local Topic Chair)
• (INForum'2014) 6º INForum - Simpósio de Informática (CPDLA track)
• (KDIR'2013) 5th International Conference on Knowledge Discovery and Information Retrieval (SNAM session)

External or Invited Reviewer

Journals

• Machine Learning (Springer)
• Data Mining and Knowledge Discovery (Springer)
• BMC Bioinformatics (BioMed Central)
• BMC Research Notes (BioMed Central)
• PLOS ONE (Public Library of Science)
• TKDE - Transactions on Knowledge and Data Engineering (IEEE)
• TCBB - Transactions on Computational Biology and Bioinformatics (IEEE/ACM)
• Data & Knowledge Engineering (Elsevier)
• Advances in Engineering Software (Elsevier)
• Parallel Computing: Systems & Applications (Elsevier)
• Concurrency and Computation: Practice and Experience (Wiley)
• New Generation Computing (Springer)
• Journal of the Brazilian Computer Society (Springer)
• Olympiads in Informatics
• Inteligencia Artificial (Iberamia)

Conferences/Workshops/Book Chapters

• EPIA - EPIA Conference on Artificial Intelligence
• NIPS - Advances in Neural Information Processing Systems
• Euro-Par - International Conference on Parallel Processing
• WSCAD - Simpósio em Sistemas Computacionais de Alto Desempenho
• ICNC - International Conference on Natural Computation
• AIECM - Artificial Intelligence, Evolutionary Computation and Metaheuristics

Other Organization Duties

• (NetSci-X 2022) International School and Conference on Network Science (Organization, Program Chair)
• (NetSci Porto'2018) Porto Winter School on Network Science (Organization)
• (Graph'2015) Porto Winter School on Graph Analytics and Applications (Organization)
• (Euro-Par'2014) 20th International Conference on Parallel Processing (Local Organization)
• (ICLP'2007) 23rd International Conference on Logic Programming (Local Organization)
• (ACM-SAC 2010) 25th ACM Symposium On Applied Computing (Session Chair)