

<!-- Since 2022, Integrated Member of the "Intelligent Systems" group of the research unit NOVALINCS.

Twelve articles published in international journals or conference proceedings (>= Core B and Q2).

Since 2011, author and co-author of nine computer programs and systems, available in public repositories, of academic or pedagogical content, available in public repositories. 

Since  1997, university professor, having taught more than twenty undergraduate or master's courses.

Since 2022, Supervisor of three doctoral students (in progress) and seven master's students (in progress and completed).

-->

# Narrative CV


  - Contributions to the generation of new ideas, tools, methodologies, or knowledge
  - Contributions to the development of individuals and/or research teams
  - Contributions to the research community and the broader society
  - Selected outputs and/or activities
  - Why would this grant be timely for me, at this point in my career path and/or in my research?

## Career profile (2000)

> a summary of the PI's education (specifying the year the PhD was completed), key qualifications, and employment history. If applicable, any period of leave from research, such as parental leaves, long-term absence due to illness, period of work in industry, secondments, volunteering, or other non-research activities may be specified. Explain how these interruption(s) or the unconventional path and/or gap(s) has/have impacted your activity.

1993, Degree in Mathematics, Faculdade de Ciências, Universidade de Lisboa.
1997, MSc in Mathematics (Algebra), Faculdade de Ciências, Universidade de Lisboa. On Hilbert's tenth problem and a computational model based on geometric constructions with ruler and compass.
1997, Teaching Assistant, Mathematics Department, Universidade de Évora.
2006, PhD in Informatics (Computer Science), Universidade de Lisboa. On deliberation by autonomous agents.
2006, Assistant Professor, Mathematics Department, Universidade de Évora.
2006, Assistant Professor, Computer Science Department, Universidade de Évora.
2008 -- 2021, Teaching and research and teaching activity on ideas about computing and geometry, started in the master's dissertation; the integration of logic and statistical AI; learning polynomial models using genetic algorithms, with several publications, e.g., articles and books; 
2021 -- present, Researcher at the chair "High Performance Computing" at Universidade de Évora; Integrated member of the NOVALINCS center; Preparation and lecturing of courses on the Julia language, aimed at the digital humanities and social sciences, under the HPC Chair and the european projects EuroCC and EuroCC2, funded by  the European Commission - EuroHPC Joint Undertaking: PI of the project CPCA/A0/427668/2021, FCT, Portugal, a small FCT founded project exploring the use of "high-level" languages (Julia, Python) in distributed computing and HPC systems; Work on the extension of ASP with probabilistic annotations, and respective induction by a set of data and background knowledge; Supervisor of a BII scholarship 

## Contributions to Science and Society

### Contributions to the generation of new ideas, tools, methodologies or knowledge (2000)

> description of how the PI has contributed to the generation of new ideas, tools,
methodologies, or knowledge, and
>
> the relevance and impact of your contributions.
>
> publications, key data sets, software, intellectual property (patents, licenses, trademarks, copyrights, novel assays, and reagents), conference presentations and proceedings, research, and policy publications, or other scientific, technological, cultural or artistic achievements; 
> 
> What + how + where

2021, Mentor of i-Days: Student competition to tackle health challenges, organized by EIT-Health and StartUB!C (Universidad de Barcelona), that took place in PACT, Évora. i-Days promote health innovation among university students through dozens of one-day and two-day programmes held in academic institutions around Europe.

2021, Co-author of "Lattice-Maker", a set of tools to present lattices of combinatorial games in LaTeX, used on the PhD thesis "Lattices related to Conway's construction", where I was member of the juri, and two papers where I'm co-author: DOI:10.1016/j.tcs.2014.01.025 and DOI:10.1007/s00182-020-00715-3

2017, Co-author of "Genetic Algorithms for Polynomial Regression", R code to find the best polynomial regression using genetic algorithms, used in the journal paper DOI:10.1016/j.asoc.2017.05.047.

2015, Author of "Galaxity", a Java system to assess the correction of perceptions of AgentSpeak(L) agents using probabilistic methods, and used in the conference paper DOI:10.1007/978-3-319-25524-8_44.

2014, Author of "TeseUE", a LaTeX class to MSc dissertations and PhD thesis in Universidade de Évora, is currently used by many students.

### Contributions to the development of individuals and/or research teams (3000)

> expertise provided by the PI which was relevant to the development of individuals and/or teams
> 
> project participation, leadership or management, collaborative contributions, and team support. Contributions to the development of individuals and/or research teams
> 
> Teaching activities, workshops, summer schools,  the supervision of students, mentoring or other contributions to the success of a team or advancement of colleagues.
> role: PI, team member, other; ongoing or past funded projects;


2024, Mentor of the mini-project "Automatic Differentiation", aimed at MSc and PhD students, at the Birla Institute of Technology and Science, Pilani, India, within the Asian and European Schools in Mathematics. Travel was supported by a CIMPA scholarship.

2024, Lecturer of the course "An Introduction to Julia for Scholars", aimed at MSc and PhD students and researchers, at the Birla Institute of Technology and Science, Pilani, India, within the Asian and European Schools in Mathematics. Travel was supported by a CIMPA scholarship.

2023, 2024, Coordinator and lecturer of the online course "Programming in Julia for Digital Humanities", aimed to digital humanities and social sciences researchers, part of the training and dissemination activities of the HPC Centre and the HPC Chair.

2023, 2024, Mentor of one BII Scholarship within the scope of the multi-annual financing of the R&D unit with reference UIDP/04516/2020, financed by national funds through the FCT/MCTES.

2022 -- present, Supervisor of three ongoing PhD thesis on computer science.

2016 -- present, Course director and lecturer of "Introdução ao LaTeX"  (Introduction to LaTeX), directed at students and researchers, at Universidade de Évora.

2016, Co-author of the book "Introdução à Matemática - Álgebra, Análise e Otimização"(LIDEL), ISBN:978-989-752-209-3, addressing core mathematical subjects (algebra, calculus and optimization) for social sciences university courses. Used in the course "Matemática Aplicada à Economia e Gestão", Universidade de Évora.

2010 -- present, Supervisor of six completed and three ongoing MSc dissertations about topics such as e-learning, virtual reality, serious games or game design.

2010 -- present, Member of the juri in 13 academic examinations, including three as examiner.

2010, co-author of the book "Teoria da Computação, Computabilidade e Complexidade", ISBN:978-972-592-281-1, where computation is explained starting with simple machines, addressing the computation limits such as the Halting Problem, polynomial equivalence and complexity. A draft version of this book was used in the course "Teoria da Computabilidade e Complexidade", Universidade de Évora.

2006 -- present, Assistant professor at Universidade de Évora. Within this role I coordinated more than 26 courses, including mathematics and computer science, for graduation or MSc grades.

### Contributions to the research community and the broader society (3000)

> activities the PI has participated in to progress the research community and engage with the broader society.
> 
> editing, reviewing, refereeing, evaluation of funding applications; and organization of events that have benefited the research community, or improved research culture


2024, An introduction course to the Julia language, for students on technical courses and researchers.
2024, A mini-project/introduction course to automatic derivation with Python, for students of technical courses.
2023, 2024, An introduction course to the Julia language, for researchers in the areas of digital humanities and social sciences.
2024, 2023, 2010, Visited higher education institutions in India, the Czech Republic and Timor-Lorosa'e to disseminate knowledge and to establish or reinforce cooperation between Universidade de Évora and local HEI.
2023, Invited Talk, "Fronteiras da Inteligência Artificial", Festival da Ciência'23,  Universidade de Évora, aimed at societal engagement with science.
2022 -- present, Reviewer for the "Applied Soft Computing" journal (Q1).
2021 -- present, Participation in the "High Performance Computing Chair" of Universidade de Évora, as member of the scientific team, technical-scientific board, coordinator of the "Programming in Digital Humanities" task and member of five work packages.
2016 -- present, Course director and lecturer of "Introdução ao LaTeX"  (Introduction to LaTeX), directed at students and researchers, at Universidade de Évora.
2016, 2010, Co-author of two pedagogical books, about Mathematics and Computer Science, aimed at higher education students, contributions to the dissemination of knowledge.
2011 -- present, Member of several organizing and scientific committees of international scientific events. In the most recent, the international conference "Programming and Data Infrastructure in Digital Humanities", I was member of both the scientific and organizing committee.
1997 -- present, Fifteen communications at scientific dissemination events, either at international conferences or invited to scientific lectures.

### Selected outputs and/or activities (2500)

> provide additional and detailed information on a maximum of five scientific outputs and/or activities that **best describes the PI's research career and experience**. For each one, the PI should indicate his/her role and how it has impacted the advancement of knowledge in the respective scientific area. Any type of contribution from the three previous sections can be also included. Whenever the outputs have a DOI, please include it.

Activity "Combinatorial Games Theory" and results

    Contributed to the development of "Lattice-Maker", a set of tools to present lattices of combinatorial games in LaTeX, available in the public repository <https://github.com/fmgc/Lattice-Maker>.
    Lattice-Maker was used by Cátia Dias on her PhD thesis "Lattices related to Conway's construction" where I was member of the juri, and in two international, indexed, jornal papers:
        2021, Carvalho, Dias, Coelho, Neto, Nowakowski, Vinagre, "On lattices from combinatorial game theory: infinite case", DOI:10.1007/s00182-020-00715-3
        2014, Carvalho, Santos, Dias, Coelho, Neto, Nowakowski, Vinagre, "On lattices from combinatorial game theory. Modularity and a representation theorem: Finite case", DOI:10.1016/j.tcs.2014.01.025

Activity "Polynomial Regression" and results

    Contributed to "Genetic Algorithms for Polynomial Regression", R code to find the best polynomial regression using genetic algorithms, available in the public repository <https://github.com/jpneto/GenAlgPoly>.
    This program was used in the international, indexed, journal paper
    2017, Coelho e Neto, "A method for regularization of evolutionary polynomial regression", DOI:10.1016/j.asoc.2017.05.047
    This is my most cited work, some of which two in 2023, six years after publishing.

Activity "Perception Correction" and results

    Implemented "Galaxity", a Java system to assess the correction of perceptions of AgentSpeak(L) agents using probabilistic methods, and "jpgm", a small Java library to support simple probabilistic graphical models (pgm) computations used in Galaxity. These are available in the public repositories <https://bitbucket.org/mangon/galaxity> and <https://github.com/fmgc/jpgm>.
    "Galaxity" (and "jpgm") where used in the conference paper 
        2015, Coelho e Nogueira, "Probabilistic perception revision in AgentSpeak(L)", DOI:10.1007/978-3-319-25524-8_44

Activity "Stochastic Answer Set Programs" and results

Started in 2023 and is currently my main research activity, a continuation of "Perception Correction" towards the combination of statistical ans logic AI. At this moment the outcomes of this activity are
    
    BII scholarship, supported by "Financiamento Plurianual da unidade de I&D UIDP/04516/2020", co-supported by FCT, Portugal.
    Draft programs, available in a public repository.
    A paper, "An Algebraic Approach to Stochastic ASP", in co-authorship, recently submitted to a international conference.

### Why would this grant be timely for me at this point in my career path and/or in my research? (3000)

> explain the timeliness of this project in the context of the current stage of his/her career, and/or the impact on his/her future research lines and development. Career and research development potential may include scientific production, activities and dissemination, team and project leadership, establishment of national or international collaborations/networks, and the ability to enable future research and to attract funding or other resources.

Given my background and this project research area there are several aspects to consider regarding the timeliness and potential impact of this project on my future research lines and development:

Alignment with Current Expertise. My expertise in logic and statistical AI, as evidenced by contributions to papers covering these subjects, aligns well with the objectives of the proposed project, which aims to overcome constraints in logical representations with probabilistic elements. My previous work in these areas provides a solid foundation for tackling the challenges outlined in the project.

Interdisciplinary Collaboration. The project emphasizes interdisciplinary collaboration, crucial in addressing complex research problems. My involvement in this interdisciplinary effort showcases my ability to collaborate across domains, enhancing my network and potentially leading to future collaborations and research opportunities.

Contribution to the Field. The proposed research addresses critical limitations in probabilistic logic programming, an area of increasing importance in AI and machine learning. By expanding Answer Set Programming with Stochastic Answer Set Programs, this project seeks to advance the field through innovative methodologies, such as assigning probability to general events and integration of evolutionary algorithms for model induction. My involvement can improve my profile within the academic community and position me as a competent expert in this specialized area.

Career Development Potential. Engaging in this project not only enhances my research credentials but also provides opportunities for career development. As a researcher, my involvement in cutting-edge research projects can strengthen my position within the academic community, attract funding for future research endeavors, and potentially lead to leadership roles within research teams or initiatives.

Establishment of Collaborations. This project emphasis on interdisciplinary collaboration and the integration of diverse perspectives ensures that I will have the opportunity to establish national and potential international collaborations/networks. These can lead to joint publications, participation in conferences, and access to resources that further enrich my research carrear.

Potential for Future Funding. Successful completion of the project and the generation of impactful results can significantly enhance my ability to attract funding for future research projects. My involvement in this research can strengthen my competitiveness in securing research grants.

This project aligns well with my expertise and offers significant potential for advancing my career and research development. Through interdisciplinary collaboration, contributions to the field, and the establishment of collaborations, I can leverage this project to make substantial strides in my research trajectory and position myself as a competent authority in the field of probabilistic logic programming.


<!-- 
2006, PhD thesis about deliberation.

Deliberation, selecting an action from perceptions and internal state, embodies the key challenges of AI, from computer vision to planning, learning, complexity or the frame problem. Each can be stated as a statistical problem (eg POMDP) or as a logical one (eg "plans" as formal expressions processed by symbolic rules).

Each has strengths and weaknesses. Statistical models require large amounts of data to train while inductive logic programs often result from background knowledge and small sets of examples but the former are robust to noise while the latter are fragile.

By then my research main interest become how to combine the strengths of statistical and logic AI.

2015, author of Galaxity, a system to play with correction of perceptions of logic agents using probabilistic methods; Described in DOI:10.1007/978-3-319-25524-8_44, a initial study on combining logic and statistical AI.

BDI agents often win planning competitions where, unlike real scenarios, perception is perfect. The Galaxity system introduces noise in the agent's perception and uses a HMM to estimate the probability of the real state. This is then tested in simulations, outperforming other agents also subject to probabilistic phenomena.

Despite the positive result, this is a shallow approach with no substantial theoretical base to support further work.

By then I have learned about probabilistic logic programming, the Sato semantics and Markov logic.

Also, my participation in the NOVALINCS research unit opened new opportunities.

Since 2023, mentor of a BII Scholarship about Stochastic Answer Set Programs (SASP), financed by national funds through FCT/MCTES: UIDP/04516/2020; NOVALINCS (UIDB/04516/2020).

Answer Set Programming (ASP) is a pure declarative logic language with excellent tool support and theoretical foundations (Gelfond and Lifschitz stable models). Semantics for probabilistic versions of ASP have been proposed but the problem is still very much open.

My, Bruno Dinis and Salvador Abreu approach is described in "An Algebraic Approach to Stochastic ASP", recently submitted to an international conference.

We address the problem of extending probability from total choices to stable models, and from there to general events. Possible applications include assigning a score to a logic program with respect to the empiric distribution of a dataset, which can be used by evolutionary algorithms searching optimal models of that dataset. From there we have induction of stochastic ASP.

This paper is the root to the research proposed with this project:

Investigate the structure and composition of SASP and transformation rules to support program space search by evolutionary algorithms.
Implement a library to support SASP evaluation using existing ASP systems.
Explore how distributed HPC systems can be used to scale-up and speed-up the evaluation of SASP.
Investigate the application of SASP to theoretical and real-world problems. -->