Publications
Filter Publications: 2021 - 2023
Books
Book Chapters: 2
2022
- , Prediction of Gene and Genomic Regulation in Candida Species, Using the PathoYeastract Database: A Comparative Genomics Approach, chapter of Yeast Functional Genomics. Methods in Molecular Biology, May. 2022, Humana [bibTex]
2021
- , Pseudo-Boolean and Cardinality Constraints, chapter of Handbook of Satisfiability - Second Edition, to appear on 2021, IOS Press [bibTex]
Articles
International Journal Articles: 19
2022
- , Introducing UniCorT: A University Course Timetabling Tool, article in Journal of Scheduling, to appear on 2022, Springer [DOI Article link] [bibTex]
- , Wasmati: An Efficient Static Vulnerability Scanner for WebAssembly, article in Computers & Security pp. 102745, to appear on 2022, Elsevier [Article] [DOI Article link] [bibTex]
- , Multiple-Input Neural Networks for Time Series Forecasting Incorporating Historical and Prospective Context, article in Data Mining and Knowledge Discovery, Nov. 2022 [bibTex]
- , DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies, article in Scientific Reports, Jul. 2022 [DOI Article link] [bibTex]
- , Associative Analysis of Inefficiencies and Station Activity Levels in Emergency Response, article in International Journal of Geo-Information, Jun. 2022 [bibTex]
- , DeepData: Machine Learning in the Marine Ecosystems, article in Expert Systems With Applications, Jun. 2022 [bibTex]
- , Route choice estimation in rail transit systems using smart card data: handling vehicle schedule and walking time uncertainties, article in European Transport and Research Review (ETRR), Jun. 2022 [bibTex]
- , Constraint-based Electoral Districting Using a New Compactness Measure: an application to Portugal, article in Computers and Operations Research, May. 2022, Elsevier [bibTex]
- , A suspension technique for efficient large-scale cancer organoid culturing and perturbation screens, article in Scientific Reports vol. 12, Apr. 2022 [Article] [DOI Article link] [bibTex]
- , Boolean function metrics can assist modelers to check and choose logical rules, article in Journal of Theoretical Biology vol. 538 pp. 111025, Apr. 2022, Elsevier [DOI Article link] [bibTex]
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]
- , 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]
- , Disruptions in Timetables: A Case Study at Universidade de Lisboa, article in Journal of Scheduling vol. 24 (1) pp. 35-48, Feb. 2021 [bibTex]
International Conferences: 25
2022
- , A Preliminary Study on Generating Well-Formed Q# Quantum Programs for Fuzz Testing, presented at 2nd International Workshop on Artificial Intelligence in Software Testing (AIST'22), to appear on 2022 [bibTex] [PDF]
- , Extending EcoAndroid with Automated Detection of Resource Leaks, presented at 9th IEEE/ACM International Conference on Mobile Software Engineering and Systems 2022, to appear on 2022 [bibTex]
- , SAT-based Leximax Optimisation Algorithms, presented at International Conference on Theory and Applications of Satisfiability Testing (SAT), to appear on 2022 [bibTex]
- , Verified Password Generation from Password Composition Policies, presented at 17th International Conference on integrated Formal Methods (iFM), to appear on 2022 [bibTex] [PDF]
- , Leveraging Practitioners’ Feedback to Improve a Security Linter, presented at 37th IEEE/ACM International Conference on Automated Software Engineering, Nov. 2022 [bibTex] [PDF]
- , MultIPAs : Applying Program Transformations to Introductory Programming Assignments for Data Augmentation, presented at 30th Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering (ESEC/FSE) (ESEC/FSE 2022), Nov. 2022 [bibTex]
- , GLITCH: Automated Polyglot Security Smell Detection in Infrastructure as Code, presented at 37th IEEE/ACM International Conference on Automated Software Engineering (ASE), Jul. 2022 [bibTex] [PDF]
- , Studying Users' Willingness to Use a Formally Verified Password Manager, presented at PhD Symposium at the 17th International Conference on integrated Formal Methods (iFM), Jun. 2022 [bibTex] [PDF]
- , Consolidation of massive medical emergency events with heterogeneous situational context data sources, presented at 6th International workshop on Data Analytics solutions for Real-LIfe APplications @ EDBT/ICDT 2022, Mar. 2022 [bibTex] [PDF]
- , Automatic Generation of Neural Architecture Search Spaces, presented at AAAI-2022 Workshop on Combining Learning and Reasoning: Programming Languages, Formalisms, and Representations (CLeaR), Feb. 2022 [bibTex]
- , Functional characterization of transcriptional regulatory networks of yeast species, presented at International School and Conference on Network Science (NetSciX'22), Feb. 2022 [DOI Article link] [bibTex]
2021
- , EcoAndroid: An Android Studio Plugin for Developing Energy-Efficient Java Mobile Applications, presented at 2021 IEEE 21st International Conference on Software Quality, Reliability and Security (QRS), Dec. 2021 [DOI Article link] [bibTex] [PDF]
- , Hybrid Information Flow Control for Low-Level Code, presented at Software Engineering and Formal Methods, Dec. 2021 [DOI Article link] [bibTex] [PDF]
- , Supervised Learning for Test Suit Selection in Continuous Integration, presented at 2021 IEEE International Conference on Software Testing, Verification and Validation Workshops (ICSTW), to appear on 2021 [DOI Article link] [bibTex]
- , Automatic Repair of Java Code with Timing Side-Channel Vulnerabilities, presented at International Workshop on Refactoring (IWoR 21), Nov. 2021 [bibTex]
- , Counterfeiting Congestion Control Algorithms, presented at HotNets '21: The 20th ACM Workshop on Hot Topics in Networks, Nov. 2021 [DOI Article link] [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]
- , The Seesaw Algorithm: Function Optimization Using Implicit Hitting Sets, presented at 27th International Conference on Principles and Practice of Constraint Programming, Oct. 2021 [DOI Article link] [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]
- , Gillian, Part II: Real-World Verification for JavaScript and C, presented at Computer Aided Verification, Jul. 2021 [DOI Article link] [bibTex] [PDF]
- , 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]
- , FOREST: An Interactive Multi-tree Synthesizer for Regular Expressions, presented at 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2021, Mar. 2021 [DOI Article link] [bibTex]
National Conferences: 1
2022
- , Community detection for the characterization of transcriptional regulatory networks of yeast species, presented at INForum, Sep. 2022 [bibTex]
Dissertations
PhD Theses: 2
2021
- advised by Pedro T. Monteiro and Inês Lynce, Model Revision of Boolean Logical Models of Biological Regulatory Networks, PhD Thesis at Instituto Superior Técnico, Sep. 2021 [bibTex]
- advised by Inês Lynce and Pedro T. Monteiro, Solving Scheduling Problems under Disruptions, PhD Thesis at Instituto Superior Técnico, Jul. 2021 [bibTex]
MSc Theses: 11
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 Instituto Superior Técnico, 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 Inês Lynce and Miguel Neves, Next-Gen Pure Function Synthesis in OutSystems, MSc Thesis, Nov. 2021 [bibTex]
- advised by João F. Ferreira and Alexandra Mendes, On Usable Security and Verified Password Managers, MSc Thesis at Instituto Superior Técnico, University of Lisbon, Nov. 2021 [bibTex]
- advised by Inês Lynce and Miguel Neves, Sketch-Driven SQL Synthesis, MSc Thesis, 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]
as Editors
Edited Proceedings: 1
2021
- , editors, Formal Methods Teaching: 4th International Workshop and Tutorial, FMTea 2021, Virtual Event, November 21, 2021, Proceedings, LNCS 13122, Nov. 2021, Springer [bibTex]