Publications
Filter Publications: 2020 - 2022
Articles
International Journal Articles: 17
2021
- , Exact Hypervolume Subset Selection Through Incremental Computations, article in Computers & Operations Research vol. 136 pp. 15, Dec. 2021, Elsevier [DOI Article link] [bibTex]
- , Genome and metabolome: chance and necessity, article in Genome Biology, Sep. 2021, Springer Nature [DOI Article link] [bibTex] [PDF]
- , Prediction and Boolean logical modelling of synergistic microRNA regulatory networks during reprogramming of male germline pluripotent stem cells, article in Biosystems vol. 207, Sep. 2021, Elsevier [DOI Article link] [bibTex]
- , The N.C.Yeastract and CommunityYeastract databases to study gene and genomic transcription regulation in non-conventional yeasts, article in FEMS Yeast Research, Aug. 2021 [DOI Article link] [bibTex]
- , From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon, article in BMC Bioinformatics, Jul. 2021, accepted [bibTex]
- , Introducing UniCorT: A University Course Timetabling Tool, article in Journal of Scheduling, Jul. 2021, Springer [DOI Article link] [bibTex]
- , The Hypervolume Indicator: Computational Problems and Algorithms, article in Computing Surveys vol. 54 (6) pp. 42, Jul. 2021, ACM [DOI Article link] [bibTex]
- , Automated narrative planning model extension, article in Autonomous Agents and Multi-Agent Systems vol. 35 (19) pp. 1-29, May. 2021, Springer [DOI Article link] [bibTex]
- , Transcriptome-wide differences between Saccharomyces cerevisiae and Saccharomyces cerevisiae var. boulardii: clues on host survival and probiotic activity based on promoter sequence variability, article in Genomics vol. 113 (2), Mar. 2021 [DOI Article link] [bibTex]
2020
- , 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]
- , 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]
- , Assessing regulatory features of the current transcriptional network of Saccharomyces cerevisiae, article in Scientific Reports, Sep. 2020, Nature [DOI Article link] [bibTex]
- , Disruptions in Timetables: A Case Study at Universidade de Lisboa, article in Journal of Scheduling, Jun. 2020 [bibTex]
- , Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors, article in Cancer Research vol. 80 (11), Jun. 2020 [DOI Article link] [bibTex]
- , 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]
- , 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]
- , 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]
International Conferences: 21
2021
- , Automatic Repair of Java Code with Timing Side-Channel Vulnerabilities, presented at International Workshop on Refactoring (IWoR 21), Nov. 2021 [bibTex]
- , Exploring Usable Security to Improve the Impact of Formal Verification: A Research Agenda, presented at 1st International Workshop on Applicable Formal Methods (appFM), Nov. 2021 [bibTex] [PDF]
- , Where are the Passengers? Individual Passenger Route Choice Estimation from Gate Information in Urban Rail Transit Systems, presented at European Transport Conference (ETC), Sep. 2021 [bibTex]
- , The Seesaw Algorithm: Function Optimization using Implicit Hitting Sets, presented at International Conference on Principles and Practice of Constraint Programming, Aug. 2021 [bibTex]
- , 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]
- , How to Approximate Leximax-optimal Solutions, presented at Pragmatics of SAT 2021, Jun. 2021 [bibTex]
- , SOAR: A Synthesis Approach for Data Science API Refactoring, presented at International Conference on Software Engineering (ICSE), May. 2021 [bibTex] [Video]
- , 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
- , UnchartIt: An Interactive Framework for Program Recovery from Charts, presented at IEEE/ACM International Conference on Automated Software Engineering, Oct. 2020 [bibTex]
- , 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]
- , 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]
- , 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]
- , 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]
- , 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]
- , 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]
- , 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]
- , SQUARES : A SQL Synthesizer Using Query Reverse Engineering, presented at International Conference on Very Large Databases, Jul. 2020 [bibTex] [Video]
- , 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]
- , 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]
- , Extending Narrative Planning Domains with Linguistic Resources, presented at International Conference on Autonomous Agents and Multi-Agent Systems (AAMAS 2020), Jan. 2020 [bibTex] [PDF]
- , Visual Sketching: From Image Sketches to Code, presented at The 42th International Conference on Software Engineering (ICSE'20), Jan. 2020 [bibTex] [PDF]
Dissertations
MSc Theses: 10
2021
- advised by Pedro T. Monteiro and Miguel C. Teixeira, A Metabolic-Regulatory Genome-Scale Integration forSaccharomyces cerevisiae: Predicting Targets forIncreased Ethanol Production, MSc Thesis at IST, Dec. 2021 [bibTex]
- advised by Pedro T. Monteiro and Sofia Teixeira, Network motifs in multi-graphs, MSc Thesis at IST, Dec. 2021 [bibTex]
- advised by Vasco Manquinho and Inês Lynce, Automatic Chart Interpretation, MSc Thesis at IST, Nov. 2021 [bibTex]
- advised by Mikolas Janota and Vasco Manquinho, Boolean Leximax Optimisation using Iterative SAT Solving, MSc Thesis at IST, U. Lisboa, Nov. 2021 [bibTex]
- advised by Mikolas Janota and Vasco Manquinho, Automated Computational Complexity Estimation, MSc Thesis at IST - Universidade de Lisboa, Jan. 2021 [bibTex]
- advised by Vasco Manquinho, Evaluating Redistricting of Electoral Areas, MSc Thesis at IST - U. Lisboa, Jan. 2021 [bibTex]
- advised by Inês Lynce and Miguel Neves, Pure Function Synthesis in the OutSystems Plataform, MSc Thesis at Instituto Superior Técnico, Jan. 2021 [bibTex]
- advised by Vasco Manquinho and Miguel Angelo Terra Neves, Stochastic Multi-Objective Combinatorial Optimization Algorithms, MSc Thesis, Jan. 2021 [bibTex]
2020
- 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]
- 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]
as Editors
Other Publications: 1
2020
- , editors, Evolutionary Multiobjective Optimization, EURO Working Group Multicriteria Decision Aiding 3, Nov. 2020 [bibTex]