Research

Research Interests

Main research interests:

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

Other research interests:

Computer Science Education and Programming Contests.
Artificial Intelligence, Agents, Machine Learning and Robotics.

Students

Current Students:

PhD Students

(since 2014) David Aparício (MAPi - Doctoral Programme in Computer Science)
Co-advisor: Fernando Silva
PhD Topic: Discovering Patterns in Complex Networks
(since 2016) Jorge Silva (MAPi - Doctoral Programme in Computer Science)
Main advisor: Fernando Silva
PhD Topic: Network Analysis for Research Interests Discovery
(Starting in 18/19) - Vanessa Silva (awarded a PhD grant from FCT 2018 Call for PhD Scholarships)
(Starting in 18/19) - Alberto Barbosa (awarded a PhD grant from FCT 2018 Call for PhD Scholarships)

MSc Students

(2018 - 2019) Luciano Grácio (towards the detection of larger network motifs)
(2018 - 2019) André Meira (discovering patterns in multilayer networks)
(2018 - 2019) Miguel Martins (improving subgraph counts with graph summarizations)
(2018 - 2019) Miguel Amaral (patterns in evolving networks)
(2018 - 2019) Pedro Abranches [EPFL, Switzerland]
(2018 - 2019) Luis Alves (discovering pseudogenes) [with Filipe Castro, from CiiMAR]

Alumni:

PhD Students

(2012 - 2017) Miguel Araújo (CMU|Portugal and MAPi computer science doctoral programmes)
CMU advisor: Christos Faloutsos
PhD Thesis Title: Communities and Anomaly Detection in Large Edge-Labeled Graphs
(2010 - 2015) Sarvenaz Choobdar (PhD in Computer Science)
Main advisor: Fernando Silva
PhD Thesis Title: On the Characterization and Comparison of Complex Networks

MSc Students

(2017 - 2018) Rui Fonseca
MSc Thesis Title: Motif Based Community Discovery
(2017 - 2018) Pedro Belém (main advisor: Fernando Silva)
MSc Thesis Title: Temporal Research Interests Discovery Using Co-Occurrence Keywords Networks
(2017 - 2018) André Diegues (co-advisor: José Pinto)
MSc Thesis Title: Automatic Habitat Mapping using Machine Learning
(2017 - 2018) André Cascais
MSc Thesis Title: Adaptive Parallel Subgraph Sampling in Large Complex Networks
(2017 - 2018) Vanessa Silva (main advisor: Fernando Silva, co-advisor: Maria Eduarda Silva)
MSc Thesis Title: Time Series Analysis based on Complex Networks
(2016 - 2017) Pedro Paredes (currently a PhD student at CMU)
MSc Thesis Title: Counting subgraphs: from static to dynamic networks
(2016 - 2017) Augusto Bilabila
MSc Thesis Title: CompAlg - A Tool for Teaching and Learning the Logic of Programming
(2016 - 2017) Alberto Barbosa (main advisor: Inês Dutra)
MSc Thesis Title: Improving the search for multi-relational concepts in ILP
(2016 - 2017) Miguel Duarte (@IST main advisor: Alexandre Francisco) (currently a software eng. at MemSQL)
MSc Thesis Title: Fast Hierarchical Graph Clustering
(2015 - 2016) Ahmad Naser Eddin (currently a Data Warehouse Analyst at BNP Paribas)
MSc Thesis Title: Large Scale Parallel Subgraph Search
(2015 - 2016) Manuel Lopes (currently a C++ software developer at Euronext)
MSc Thesis Title: Bomberman as an Artificial Intelligence Platform
(2013 - 2014) David Aparício (co-advisor: Fernando Silva)
MSc Thesis Title: Pattern Discovery in Complex Network using Parallelism

Projects

Among others, I have been involved in the following research projects:

2015-2017

REMINDS - RElevance MINing and Detection System
Project Total Funding: 182.443,00 euros Funding Entity: FCT (UT Austin|Portugal Programme)
My role:Graph Algorithms

2013-2015

SIBILA - Towards Smart Interacting Blocks that Improve Learned Advice
Project Total Funding: 688.048,91 euros Funding Entity: PIDAC & ERDF
My role:WP2 - Data Mining and Decision Support

2010-2012

Breadcrumbs
Project Total Funding: 160,000 euros Funding Entity: (UT Austin|Portugal Programme)
My role: Graph Algorithms

2008-2010

Callas - Calculi and Languages for Sensor Networks
Project Total Funding: 190.000 euros Funding Entity: FCT
My role: parallel algorithms

2008

CARMEN: Code Analysis Repository & Modelling for e-Neuroscience
e-Science Pilot Project funded by the Eng. and Phys. Sciences Research Council (UK) with £5M
My role: WP0 - Virtual laboratory infrastructure

2002-2004

APRIL: Applications using Parallelism in Induction and Logic
Project Total Funding: 66.000 euros Funding Entity: FCT
My role: ILP applications

Publications

Please see the publications page.

Talks

In Scientific Meetings

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

Biological Networks

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 Gonçalvez 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

(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

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 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)