Publications

Articles

International Journal Articles: 17

2021

- Andreia Guerreiro and Carlos M. Fonseca and Luís Paquete, The Hypervolume Indicator: Computational Problems and Algorithms, article in Computing Surveys, to appear on 2021, ACM [bibTex]
- Andreia Guerreiro and Vasco Manquinho and José Rui Figueira, Exact Hypervolume Subset Selection Through Incremental Computations, article in Computers & Operations Research, Jul. 2021, Elsevier [bibTex]

2020

- Abubakar Zakari and Sai Peck Lee and Rui Abreu and Babiker Hussien Ahmed, Multiple fault localization of software programs: A systematic literature review, article in Information and Software Technology vol. 124, to appear on 2020, Elsevier BV [DOI Article link] [bibTex] [PDF]
- Ana Salta and Rui Prada and Francisco S. Melo, A Game AI Competition to foster Collaborative AI research and development, article in IEEE Transactions on Games pp. 1-12, Sep. 2020, IEEE [DOI Article link] [bibTex]
- Pedro T. Monteiro and Tiago Godinho de Ornelas Pedreira and Monica Galocha and Miguel C. Teixeira and Claudine Chaouiya, Assessing regulatory features of the current transcriptional network of Saccharomyces cerevisiae, article in Scientific Reports, Sep. 2020, Nature [DOI Article link] [bibTex]
- Alexandre Lemos and Pedro T. Monteiro and Inês Lynce, Disruptions in Timetables: A Case Study at Universidade de Lisboa, article in Journal of Scheduling, Jun. 2020 [bibTex]
- Gianluca Selvaggio and Sara Canato and Archana Pawar and Pedro T. Monteiro and Patrícia S. Guerreiro and M. Manuela Brás and Florence Janody and Claudine Chaouiya, Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors, article in Cancer Research vol. 80 (11), Jun. 2020 [DOI Article link] [bibTex]
- Praveen Kumar Guttula and Pedro T. Monteiro and Mukesh Kumar Gupta, A Boolean Logical model for Reprogramming of Testes-derived male Germline Stem Cells into Germline pluripotent stem cells, article in Computer Methods and Programs in Biomedicine vol. 192, Mar. 2020 [DOI Article link] [bibTex]
- Filipe Gouveia and Inês Lynce and Pedro T. Monteiro, Revision of Boolean models of regulatory networks using stable state observations, article in Journal of Computational Biology vol. 27 (2) pp. 144-155, Feb. 2020, Mary Ann Liebert, Inc. [DOI Article link] [bibTex]
- Pedro T. Monteiro and Jorge dos Santos Oliveira and Pedro Pais and Miguel Antunes and Margarida Palma and Mafalda Cavalheiro and Mónica Galocha and Cláudia P Godinho and Luís C Martins and Nuno Bourbon and Marta N Mota and Ricardo A Ribeiro and Romeu Viana and Isabel Sá-Correia and Miguel C Teixeira, YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts, article in Nucleic Acids Research vol. 48 pp. D642-D649, Jan. 2020, Oxford University Press [DOI Article link] [bibTex]

2019

- Alexey Ignatiev and António José dos Reis Morgado and Joao Marques-Silva, {RC2:} an Efficient MaxSAT Solver, article in Journal on Satisfiability, Boolean Modeling and Computation vol. 11 (1) pp. 53--64, to appear on 2019 [DOI Article link] [bibTex]
- Pedro Varela and Pedro T. Monteiro and Claudine Chaouiya, Impact of Changing Cell-Cell Communication Network in Models of Epithelial Pattern Formation, article in IFAC-PapersOnLine vol. 52 (26) pp. 38-44, Oct. 2019 [DOI Article link] [bibTex]
- Miguel Neves and Inês Lynce and Vasco Manquinho, Virtual machine consolidation using constraint-based multi-objective optimization, article in Journal of Heuristics vol. 25 (3) pp. 339-375, Jun. 2019 [DOI Article link] [bibTex]
- Alexandre Lemos and Francisco S. Melo and Pedro T. Monteiro and Inês Lynce, Room Usage Optimization in Timetabling: A Case Study at Universidade de Lisboa, article in Operations Research Perspectives vol. 6 pp. 100092, May. 2019 [DOI Article link] [bibTex]
- Wassim Abou-Jaoudé and Pedro T. Monteiro, On Logical Bifurcation Diagrams, article in Journal of Theoretical Biology vol. 466 pp. 39-63, Apr. 2019 [DOI Article link] [bibTex]
- Pedro Varela and Camila Ramos and Pedro T. Monteiro and Claudine Chaouiya, EpiLog: A software for the logical modelling of epithelial dynamics, article in F1000Research vol. 7 pp. 1145, Mar. 2019, F1000 Research, Ltd. [DOI Article link] [bibTex]
- Alexandre Lemos and Inês Lynce and Pedro T. Monteiro, Repairing Boolean logical models from time-series data using Answer Set Programming, article in Algorithms for Molecular Biology vol. 14 pp. 9, Mar. 2019 [DOI Article link] [bibTex]

International Conferences: 31

2021

- Changjian Zhang and Ryan Wagner and Pedro Miguel Orvalho and David Garlan and Vasco Manquinho and Ruben Martins and Eunsuk Kang, AlloyMax: Bringing Maximum Satisfaction toRelational Specifications, presented at ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering (ESEC/FSE), Jun. 2021 [bibTex]
- Miguel Cabral and Mikolas Janota and Vasco Manquinho, How to Approximate Leximax-optimal Solutions, presented at Pragmatics of SAT 2021, Jun. 2021 [bibTex]
- Ansong Ni and Daniel Rosa Ramos and Aidan Yang and Inês Lynce and Vasco Manquinho and Ruben Martins and Claire Le Goues, SOAR: A Synthesis Approach for Data Science API Refactoring, presented at International Conference on Software Engineering (ICSE), May. 2021 [bibTex] [Video]
- Leonor Pimenta de Oliveira e Silva and Helena Galhardas and Vasco Manquinho and Rui Miguel Carrasqueiro Henriques, UNIANO: robust and efficient anomaly consensus in time series sensitive to cross-correlated anomaly profiles, presented at SIAM International Conference on Data Mining, Apr. 2021 [bibTex]

2020

- Daniel Rosa Ramos and Jorge Pereira and Inês Lynce and Vasco Manquinho and Ruben Carlos Gonçalves Martins, UnchartIt: An Interactive Framework for Program Recovery from Charts, presented at IEEE/ACM International Conference on Automated Software Engineering, Oct. 2020 [bibTex]
- Alexandre Lemos and Pedro T. Monteiro and Inês Lynce, Minimal Perturbation in University Timetabling with Maximum Satisfiability, presented at 17th Intl. Conf. on Constraint Programming, Artificial Intelligence, and Operations Research (CPAIOR'20), Sep. 2020 [DOI Article link] [bibTex]
- Filipe Gouveia and Inês Lynce and Pedro T. Monteiro, ModRev - Model Revision tool for Boolean logical models of biological regulatory networks, presented at 18th Intl. Conf. on Computational Methods in Systems Biology (CMSB'20), Sep. 2020 [DOI Article link] [bibTex]
- David Filipe Borges Perreira and João F. Ferreira and Alexandra Mendes, Evaluating the Accuracy of Password Strength Meters using Off-The-Shelf Guessing Attacks, presented at 2020 IEEE International Symposium on Software Reliability Engineering Workshops (ISSREW) – 5th International Workshop on Reliability and Security Data Analysis (RSDA), Aug. 2020 [bibTex] [PDF]
- Inês Lynce and Pedro T. Monteiro, ITC 2019: University Course Timetabling with MaxSAT, presented at Proceedings of the 13th International Conference on the Practice and Theory of Automated Timetabling - PATAT 2021:, Aug. 2020 [bibTex]
- Mikolas Janota and António José dos Reis Morgado, SAT-Based Encodings for Optimal Decision Trees with Explicit Paths., presented at Theory and Applications of Satisfiability Testing - {SAT} 2020, Jul. 2020 [DOI Article link] [bibTex]
- Saul Johnson and João F. Ferreira and Alexandra Mendes and Julien Cordry, Skeptic: Automatic, Justified and Privacy-Preserving Password Composition Policy Selection, presented at 15th ACM ASIA Conference on Computer and Communications Security, Jul. 2020 [bibTex] [PDF]
- João F. Ferreira and António Pedro Cruz Monteiro and Thomas Durieux and Rui Abreu, SmartBugs: A Framework to Analyze Solidity Smart Contracts, presented at 35th IEEE/ACM International Conference on Automated Software Engineering, Tool Demo Track, Jul. 2020 [bibTex] [PDF]
- Pedro Miguel Orvalho and Miguel Neves and Miguel Ventura and Ruben Carlos Gonçalves Martins and Vasco Manquinho, SQUARES : A SQL Synthesizer Using Query Reverse Engineering, presented at International Conference on Very Large Databases, Jul. 2020 [bibTex] [Video]
- Gabriela Sampaio and José Santos and Petar Maksimovic and Philippa Gardner, A Trusted Infrastructure for Symbolic Analysis of Event-Driven Web Applications, presented at European Conference on Object-Oriented Programming (ECOOP 2020), Jun. 2020 [bibTex] [PDF]
- José Fragoso Santos and Petar Maksimovic and Sacha-Elie Ayoun and Philippa Gardner, Gillian, Part I: A Multi-language Platform for Symbolic Execution, presented at ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI), Apr. 2020 [DOI Article link] [bibTex] [PDF]
- Julie Porteous and João F. Ferreira and Alan Lindsay and Marc Cavazza, Extending Narrative Planning Domains with Linguistic Resources, presented at International Conference on Autonomous Agents and Multi-Agent Systems (AAMAS 2020), Jan. 2020 [bibTex] [PDF]
- Rui Abreu and Marcelo D'Amorim and Carlos Mello, Visual Sketching: From Image Sketches to Code, presented at The 42th International Conference on Software Engineering (ICSE'20), Jan. 2020 [bibTex] [PDF]

2019

- Thomas Durieux and João F. Ferreira and Rui Abreu and António Pedro Cruz Monteiro, Empirical Review of Automated Analysis Tools on 47,587 Ethereum Smart Contracts, presented at 42nd International Conference on Software Engineering (ICSE 2020), Dec. 2019 [bibTex] [PDF]
- Thomas Hayton and Julie Porteous and João F. Ferreira and Alan Lindsay, Narrative Planning Model Acquisition from Text Summaries and Descriptions, presented at AAAI Conference on Artificial Intelligence (AAAI-20), Nov. 2019 [bibTex] [PDF]
- Andreia Guerreiro and Miguel Neves and Inês Lynce and José Rui Figueira and Vasco Manquinho, Constraint-Based Techniques in Stochastic Local Search MaxSAT Solving, presented at 25th International Conference Principles and Practice of Constraint Programming, CP 2019, Oct. 2019 [DOI Article link] [bibTex]
- Pedro Miguel Orvalho and Miguel Neves and Miguel Ventura and Ruben Carlos Gonçalves Martins and Vasco Manquinho, Encodings for Enumeration-Based Program Synthesis, presented at 25th International Conference on Principles and Practice of Constraint Programming, CP 2019, Oct. 2019 [DOI Article link] [bibTex]
- Tony Hoare and Alexandra Mendes and João F. Ferreira, Logic, Algebra, and Geometry at the Foundation of Computer Science, presented at Formal Methods Teaching Workshop (FMTea), Aug. 2019 [bibTex] [PDF]
- Alexey Ignatiev and António José dos Reis Morgado and Georg Weissenbacher and Joao Marques-Silva, Model-Based Diagnosis with Multiple Observations, presented at International Joint Conference on Artificial Intelligence, {IJCAI} 2019, Aug. 2019 [DOI Article link] [bibTex]
- João F. Ferreira and Alexandra Mendes, Open and Interactive Learning Resources for Algorithmic Problem Solving, presented at 9th International Workshop on Open Community approaches to Education, Research and Technology (OpenCert), Aug. 2019 [bibTex] [PDF]
- António José dos Reis Morgado and Alexey Ignatiev and Maria Luisa Bonet and Joao Marques-Silva and Sam Buss, DRMaxSAT with MaxHS: First Contact, presented at Theory and Applications of Satisfiability Testing, Jul. 2019 [DOI Article link] [bibTex]
- António José dos Reis Morgado and Alexey Ignatiev and Maria Luisa Bonet and Joao Marques-Silva and Sam Buss, DRMaxSAT with MaxHS: First Contact, presented at Theory and Applications of Satisfiability Testing, Jul. 2019 [DOI Article link] [bibTex]
- Rui Abreu and Sofia Oliveira Reis and Marcelo D'Amorim, Demystifying the Combination of Dynamic Slicing and Spectrum-based Fault Localization, presented at 28th International Joint Conference on Artificial Intelligence (IJCAI19), May. 2019 [bibTex] [PDF]
- Miguel Neves and Inês Lynce and Vasco Manquinho, Integrating Constraint Reasoning in Multi-Objective Evolutionary Algorithms, presented at 28th International Joint Conference on Artificial Intelligence, IJCAI 2019, May. 2019 [bibTex]
- Filipe Gouveia and Inês Lynce and Pedro T. Monteiro, Model revision of Boolean regulatory networks at stable state, presented at International Symposium on Bioinformatics Research and Applications, May. 2019 [DOI Article link] [bibTex]
- Ilya Zakirzyanov and António José dos Reis Morgado and Alexey Ignatiev and Vladimir Ulyantsev and Joao Marques-Silva, Efficient Symmetry Breaking for SAT-Based Minimum {DFA} Inference, presented at International Conference Language and Automata Theory and Applications, Mar. 2019 [DOI Article link] [bibTex]
- Miguel Neves and Nuno Machado and Inês Lynce and Vasco Manquinho, Concurrency Debugging with MaxSMT, presented at Thirty-Third AAAI Conference on Artificial Intelligence, AAAI 19, Jan. 2019 [bibTex]

National Conferences: 1

2019

- Ana Salta and Rui Prada and Francisco S. Melo, Solving Motion and Action Planning for a Cooperative Agent Problem Using Geometry Friends, presented at EPIA Conference on Artificial Intelligence, Sep. 2019 [DOI Article link] [bibTex]

Dissertations

PhD Theses: 1

2019

- Miguel Neves advised by Vasco Manquinho and Inês Lynce, Constraint-Based Multi-Objective Combinatorial Optimization, PhD Thesis at IST - Universidade de Lisboa, Jun. 2019 [bibTex]

MSc Theses: 13

2021

- Marcos António Pires Ferreira dos Santos advised by Mikolas Janota and Vasco Manquinho, Automated Computational Complexity Estimation, MSc Thesis at IST - Universidade de Lisboa, Jan. 2021 [bibTex]
- Tiago Miguel Correia de Almeida advised by Vasco Manquinho, Evaluating Redistricting of Electoral Areas, MSc Thesis at IST - U. Lisboa, Jan. 2021 [bibTex]
- Catarina Pina de Almeida Coelho advised by Inês Lynce and Miguel Neves, Pure Function Synthesis in the OutSystems Plataform, MSc Thesis at Instituto Superior Técnico, Jan. 2021 [bibTex]
- Miguel António dos Santos Machado Tavares advised by Vasco Manquinho and Miguel Angelo Terra Neves, Stochastic Multi-Objective Combinatorial Optimization Algorithms, MSc Thesis, Jan. 2021 [bibTex]

2020

- Ricardo Brancas advised by Vasco Manquinho and Miguel Neves, CUBES: A New Dimension in Query Synthesis From Examples, MSc Thesis at IST - Universidade de Lisboa, Nov. 2020 [bibTex]
- Margarida Ferreira advised by Inês Lynce and Miguel Neves, FOREST: An interactive multi-tree synthesizer for regular expressions, MSc Thesis at Instituto Superior Técnico, Nov. 2020 [bibTex]

2019

- Guilherme António Trindade Quintino advised by Vasco Manquinho and Luis Guerra e Silva, Data Center Optimization using vitual machine profiles, MSc Thesis, Nov. 2019 [bibTex]
- Francisco Madaleno Ferreira dos Santos advised by Vasco Manquinho and Nuno Roma, Flying Tourist Problem An Integer Linear Programming Approach, MSc Thesis, Nov. 2019 [bibTex]
- Ricardo António Moreira Pereira advised by Mikolas Janota and Vasco Manquinho, New Language for Program Test Generation, MSc Thesis, Nov. 2019 [bibTex]
- Pedro Miguel Orvalho advised by Vasco Manquinho and Miguel Neves, SQUARES : A SQL Synthesizer Using Query Reverse Engineering, MSc Thesis, Nov. 2019 [bibTex]
- Leonor Pimenta de Oliveira e Silva advised by Inês Lynce and Vasco Manquinho, DeepData: Machine Learning in the Marine Ecosystems, MSc Thesis at Instituto Superior Técnico, Oct. 2019 [bibTex]
- Daniel Rosa Ramos advised by Inês Lynce and Vasco Manquinho, Program Synthesis from Noisy Tabular Data, MSc Thesis, Oct. 2019 [bibTex]
- Rodrigo André Moreira Bernardo advised by Inês Lynce and Miguel Ventura, Program Synthesis with Formal Methods for outsystems language, MSc Thesis at Instituto Superior Técnico, May. 2019 [bibTex]

as Editors

Other Publications: 1

2020

- Andreia Guerreiro and Carlos M. Fonseca, editors, Evolutionary Multiobjective Optimization, EURO Working Group Multicriteria Decision Aiding 3, Nov. 2020 [bibTex]