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: 26
2023
- , Exact and Approximate Determination of the Pareto Front Using Minimal Correction Subsets, article in Computers and Operations Research, to appear on 2023 [bibTex]
- , Base editing screens map mutations affecting interferon-γ signaling in cancer, article in Cancer Cell, Jan. 2023 [Article] [DOI Article link] [bibTex]
- , YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis, article in Nucleic Acids Research vol. 51 pp. D785–D791, Jan. 2023, Oxford University Press [DOI Article link] [bibTex]
2022
- , Integrating an academic management system with blockchain: A case study, article in Blockchain: Research and Applications vol. 3 (4), Dec. 2022, Elsevier [bibTex]
- , 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]
- , Wasmati: An Efficient Static Vulnerability Scanner for WebAssembly, article in Computers & Security, to appear on 2022 [bibTex]
- , Multiple-Input Neural Networks for Time Series Forecasting Incorporating Historical and Prospective Context, article in Data Mining and Knowledge Discovery, Nov. 2022 [bibTex]
- , bGSL: An Imperative Language for Specification and Refinement of Backtracking Programs, article in Journal of Logical and Algebraic Methods in Programming vol. 130, Sep. 2022 [DOI Article link] [Supplementary Material] [bibTex]
- , Pan-cancer proteomic map of 949 human cell lines, article in Cancer Cell vol. 40 pp. 835-849, Aug. 2022 [DOI Article link] [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: 30
2023
- , RuleKeeper: GDPR-Aware Personal Data Compliance for Web Frameworks, presented at Proceedings of 44th IEEE Symposium on Security and Privacy (S&P), to appear on 2023 [bibTex]
- , Community structure in transcriptional regulatory networks of yeast species, presented at International Conference on Complex Networks (CompleNet), Apr. 2023 [bibTex]
- , New Core-Guided and Hitting Set Algorithms for Multi-Objective Combinatorial Optimization, presented at Tools and Algorithms for Construction and Analysis of Systems (TACAS), Apr. 2023 [bibTex]
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]
- , Concolic Execution for WebAssembly, presented at Proceedings of European Conference on Object-Oriented Programming (ECOOP), to appear on 2022 [bibTex]
- , 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]
- , TestSelector: Automatic Test Suite Selection for Student Projects, presented at Runtime Verification, Sep. 2022 [DOI Article link] [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: 2
2022
- , Community detection for the characterization of transcriptional regulatory networks of yeast species, presented at INForum, Sep. 2022 [bibTex]
- , Predicting blood donor return in Portugal: the role of demographics, presented at 13th INForum - Simpósio de Informática (INForum'22), 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: 19
2022
- advised by Pedro T. Monteiro and Rui Miguel Carrasqueiro Henriques, Descriptive and predictive modelling of blood activity in Portugal, MSc Thesis, Dec. 2022 [bibTex]
- advised by João F. Ferreira and Martin Monperrus, KTH Royal Institute of Technology, A Comparative Study of Self-Supervised Learning Techniques for Functional Program Repair, MSc Thesis at Instituto Superior Técnico, Universidade de Lisboa, Nov. 2022 [bibTex]
- advised by João F. Ferreira and Rui Abreu, A Study on Generating Q# Quantum Programs using a Sequence-To-Sequence Machine Learning model, MSc Thesis, Nov. 2022 [bibTex]
- advised by Inês Lynce and Miguel Ângelo da Terra Neves, Data Formatting Synthesis by Example, MSc Thesis at Instituto Superior Técnico, Nov. 2022 [bibTex]
- advised by João F. Ferreira, Formal Specification and Verification of the Lazy JellyFish Skip List: A Case Study in Iris on the Verification of Concurrent Maps with Version Control, MSc Thesis at Instituto Superior Técnico, Universidade de Lisboa, Nov. 2022 [bibTex]
- advised by João F. Ferreira, GLITCH: Polyglot Code Smell Detection for Infrastructure as Code, MSc Thesis at Instituto Superior Técnico, Universidade de Lisboa, Nov. 2022 [bibTex]
- advised by Inês Lynce and Alexandre Duarte de Almeida Lemos, Incremental Synthesis of OutSystems Logic, MSc Thesis at Instituto Superior Técnico, Nov. 2022 [bibTex]
- advised by Pedro T. Monteiro and Inês Lynce, Optimization models for IPST blood collection, MSc Thesis at Instituto Superior Técnico, Nov. 2022 [bibTex]
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]
Internships: 1
2022
- advised by Rui Miguel Carrasqueiro Henriques and Vasco Manquinho, Descriptive and predictive analysis of spatiotemporal data in urban domain, short term traineeship, Jun. 2022 [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]