Curriculum

Oct 29, 2023 min read
Curriculum

This is a longer Curriculum, including things that are only relevant in an Academic context.

Professional Career

Netherlands eScience Center | Sep/2021 - Current

Senior Research Software Engineer

  • Helped maintain, developed and consulted on research software, focusing on best practices, such as licensing, testing, automated documentation, testing, CI, and other workflows.
  • Worked on and maintained cffinit, a web application for creating CITATION.cff files. I learned Typescript, Vue and Quasar for this project.
  • Co-organized and talked at a Julia for High-Performance Computing webinar with external speakers and over 50 attendants.

Federal University of Paraná | Nov/2014 - Aug/2021

Professor Adjunto (equivalent to Assistant Professor)

  • Taught around 5 courses a year.
  • Advised over 15 students.
  • 10 talks, 5 at international conferences.
  • Industrial Mathematics curriculum planning committee.

Data Science specialization program

  • Taught optimization and machine learning.
  • Advised students in various topics.

Researcher in optimization

  • Co-creator of several packages related to nonlinear optimization and numerical linear algebra inside the JuliaSmoothOptimizers organization.
  • Advised students in nonlinear optimization, operations research, and machine learning.
  • Co-creator of the CiDAMO study and research group.
  • 3 published papers.
  • Referee in various journals.

Education and courses

Udemy

Machine Learning A-Z, 2019

https://ude.my/UC-BZ056X6A

State University of Campinas

PhD in Applied Mathematics, 2009-2013

  • Title: Dynamic Control of Infeasibility for Nonlinear Programming
  • Advisor: Francisco de Assis Magalhães Gomes Neto

Bachelor’s degree in Computational and Applied Mathematics, 2005-2008

  • Scientific initiation project on quadratic optimization. Wrote a C++ code.

Professional Skills

Technical

  • Programming since 2005, having used multiple programming languages, including C, C++, Python, MatLab, Fortran, Javascript, Typescript, and Bash.
  • 8 years experience with the Julia language for research software.
  • My PhD and scientific initiation projects were in C++, accruing 5 years of experience.
  • I have supervised students on machine learning topics, using Python’s scikit-learn stack.
  • I have consulted and supervised on optimization modeling topics, include Julia’s JuMP modeling language.
  • I manage several GitHub repositories, setting continuous integration for automated testing, building documentation, code coverage, and various other workflows. I have used GitHub Actions, Travis, Codecov, and Coveralls.
  • I have experience building a Single Page Application in Typescript, Vue 3 and Quasar.

Social and community

  • I am a native Portuguese speaker and a fluent English speaker.
  • I have basic knowledge of Spanish and French, and I know a few words of Dutch and Russian.
  • I have solid written and verbal skills.
  • I am organized, proactive, and I am a team worker.
  • I can produce documentation in various formats, such as written tutorials and APIA reference documents, as well as videos and live coding on specific topics.
  • I managed a team translating the Think Julia book.

Open science and research software

  • I taught Shell, Git, LaTeX, and Julia in many workshops.
  • I helped organize 2 workshops related to Software Carpentry, 1 related to Hacktoberfest, and other local tutorial sessions.
  • I taught at the 2017 CODATA-RDA School of Research Data Science.
  • I have reviewed for the Journal of Open Source Software and the Journal of Open Research Software.

Projects

cffinit - Citation File Format initializer

https://citation-file-format.github.io/cff-initializer-javascript/

  • Web application to generate valid CITATION.cff files.
  • I joined the project during the implementation of v2.
  • Uses Typescript, Vue 3, and Quasar, which I learned on the job.

CiDAMO

https://cidamo.com.br

  • Study and research group on data science, machine learning, and optimization.
  • Co-creator of the group and supervisor of several students.
  • Organized a week-long data science event with over 300 participants and 8 companies, named CiDWeek.

JuliaSmoothOptimizers

https://JuliaSmoothOptimizers.github.io

  • GitHub organization with over 60 packages related to Linear Algebra and Nonlinear Optimization in Julia.
  • Co-creator of around 20 of those packages. My contributions span over 700 commits and tens of thousands of lines of code.
  • My involvement included software programming, reviewing, planning, theoretical research, advising, and publicizing the work through papers, talks, posts, and videos.

Jill

https://github.com/abelsiqueira/jill

  • Bash script to install various versions of Julia on Linux and MacOS

Intro a Julia BR (Think Julia book translation)

https://juliaintro.github.io/JuliaIntroBR.jl

  • Open source translation of Think Julia
  • I managed the translation team and reviewed each chapter

perprof-py

https://github.com/abelsiqueira/perprof-py

  • Python package for producing performance profiles.
  • One paper was published with occasional citations.

DCICPP

https://github.com/abelsiqueira/dcicpp

  • C++ implementation of a Trust Cylinder method for equality-constrained optimization
  • Main part of the code produced in my doctorate

Events

JuliaCon Local Eindhoven 2023. December 1st, 2023, Eindhoven/Netherlands. Title: Nonlinear Optimization with the Julia Smooth Optimizers packages.

Colombia Data Summit 2023. November 10th, 2023, Colombia/Online. Title: Optimization vs AI and the Julia Programming Language.

Julia Optimization Days Paris 2023. October 6th, 2023, Paris. Title: Julia Smooth Optimizers: JSO-compliant solvers, news, and current challenges.

JuliaLang Eindhoven Meetup. January 19th, 2023, Eindhoven. Title: Maintaining large ecosystems of packages. Tips and challenges.

Julia for High-Performance Computing Webinar June 23rd, 2022, Online. Organization.

II CiDWeek - Semana de Ciência de dados. 24 a 30 de Abril de 2021, Online, Brazil. Organização

I CiDWeek - Semana de Ciência de dados. 3 a 7 de Fevereiro de 2020, Curitiba/PR, Brazil. Organização

Congresso Internacional de Biomassa - 4° Expo Biomassa 26 de Junho de 2019, Curitiba/PR, Brazil. Título: Otimização na Linguagem Julia

Talk at PPGM - UFPR May 31st, 2019, Curitiba/PR, Brazil. Title: JuliaSmoothOptimizers

Invited talk at Université de Sherbrooke February 15th, 2019, Sherbrooke/QC, Canada. Title: Developing optimization software with JuliaSmoothOptimizers

Modeling and optimization tools in Julia - An introduction to JuMP and JSO. February 7th, 2019, Montreal, Canada. Title: JuliaSmoothOptimizers

XII Brazilian Workshop on Continuous Optimization. July 23rd, 2018, Foz do Iguaçu/PR, Brasil. Title: A Regularized Interior-Point Method for Constrained Nonlinear Least Squares

Second Annual JuMP-dev Workshop June 28th, 2018, Université de Bordeaux, Bordeaux, France. Title: Developing new optimization methods with packages from the JuliaSmoothOptimzers organization

CODATA-RDA School of Research Data Science. December 4th, 2017, ICPT-SAIFR/NCC-UNESP, São Paulo/SP, Brasil. Tutorial: The Unix Shell

Seminars on Convex Analysis and Optimization. December 1st, 2017, UFSC, Florianópolis/SC, Brazil. Title: Otimização Não-Linear na Linguagem Julia

15th EUROPT Workshop on Advances in Continuous Optimization. July 12th, 2017, Montréal, Canada. Title: Parameter Optimization in the Nonlinear Stepsize Control Framework for Trust-Region Methods

IX Simpósio de Análise Numérica e Otimização. February 20th to 22nd, 2017, UFPR, Curitiba, Brazil. Tutorial: Introdução à linguagem Julia

I Simpósio de Métodos Numéricos em Engenharia. November 30th to December 1st, 2016, UFPR, Curitiba, Brazil. Tutorial: Introdução à linguagem Julia

XI Brazilian Workshop on Continuous Optimization. May 23rd, 2016, UFAM, Manaus, Brazil. Title: Numerical Experience with a Class of Trust-Region Algorithms for Unconstrained Smooth Optimization

2016 Optimization Days. May 4th, 2016, HEC Montréal, Montreal, Canada. Title: A Workflow for Designing Optimization Methods in the Julia Language

VIII Simpósio de Análise Numérica e Otimização. 2016, UFPR, Curitiba, PR, Brazil. Tutorial: Otimização Não-Linear na Linguagem Julia

Oficina de Ferramentas Computacionais. Maio de 2015, UFPR, Curitiba, PR, Brazil. Member of the organization

VII Simpósio de Análise Numérica e Otimização. 2015, UFPR, Curitiba, PR, Brazil. Title: Ferramentas computacionais para pesquisadores

X Brazilian Workshop on Continuous Optimization. 2014, Florianópolis, SC, Brazil. Title: Dynamic Control of Infeasibility for Nonlinear Programming

26th European Conference on Operational Research. 2013, Rome, Italy. Title: Dynamic Control of Infeasibility for Nonlinear Programming

11th EUROPT Workshop on Advances in Continuous Optimization. 2013, Florence, Italy. Participation

Publications

Diego A. Tejada-Arango, Germán Morales-España, Lauren Clisby, Ni Wang, Abel S. Siqueira, Ali Subayu, Laurent Soucasse, and Zhi Gao, (2023). Tulipa Energy Model: Mathematical Formulation. arXiv, 10.48550/arXiv.2309.07711.

Tangi Migot, Dominique Orban, and Abel Soares Siqueira, (2022). PDENLPModels.jl: An NLPModel API for Optimization Problems with PDE-Constraints. Journal of Open Source Software, 7(80). 4736. 10.21105/joss.04736.

Tangi Migot, Dominique Orban, and Abel Soares Siqueira, (2022). DCISolver.jl: A Julia Solver for Nonlinear Optimization using Dynamic Control of Infeasibility. Journal of Open Source Software, 7(70). 3991. 10.21105/joss.03991.

Amanda Pereira Santos, Henrique Soares Koehler, Carlos Roberto Sanquetta, Sylvio Péllico Netto, Abel Soares Siqueira, and Alexandre Behling, (2022). Calibração de Equações de Volume em Nível de Povoamento e Parcela para Acácia Negra. BIOFIX Scientific Journal, 7(2). 104. 10.5380/biofix.v7i2.83574.

Dominique Orban, and Abel Soares Siqueira, (2020). A regularization method for constrained nonlinear least squares. Computational Optimization and Applications, 10.1007/s10589-020-00201-2.

Hugo José Lara, Abel Soares Siqueira, and Jinyun Yuan, (2018). A Reduced Semidefinite Programming Formulation for HA Assignment Problems in Sport Scheduling. TEMA (São Carlos), 19(3). 471-488. 10.5540/tema.2018.019.03.471.

Hugo Lara Urdaneta, Jinyun Yuan, and Abel Soares Siqueira, (2018). Alternative Integer linear and Quadratic Programming Formulations for HA-Assignment Problems. In XXXVII CNMAC, S. J. dos Campos/SP, Brasil. 10.5540/03.2018.006.01.0311.

Abel S. Siqueira, and Francisco de Assis Magalhães Gomes, (2016). Dynamic Control of Infeasibility for Nonlinear Programming. Technical Report rp11-16 Campinas/SP, Brazil, Universidade Estadual de Campinas. link.

Abel S. Siqueira, Raniere G. C. da Silva, and Luiz-Rafael Santos, (2016). Perprof-py: A Python Package for Performance Profile of Mathematical Optimization Software. Journal of Open Research Software, 4(1). e12. 10.5334/jors.81.

W. L. da Silva, R. R. V. Goncalves, A. S. Siqueira, J. Zullo, and F. A. M. Gomes Neto, (2011). Feature extraction for NDVI AVHRR/NOAA time series classification. In 2011 6th International Workshop on the Analysis of Multi-temporal Remote Sensing Images (Multi-Temp), Trento. 10.1109/multi-temp.2011.6005091.

Supervision

Rogério Otavio Mainardes da Silva, March/2021. Método do Gradiente Estocástico para otimização de funções separáveis em Aprendizagem de Máquina. Program Conclusion Project. Universidade Federal do Paraná.

Egmara Antunes dos Santos, August/2020. Aspectos Teóricos e Computacionais de um Método de Lagrangiano Aumentado com Subproblemas de Caixa Resolvidos por Região de Confiança. Master’s. Universidade Federal do Paraná.

Thaiza Rafaele dos Santos Rievrs, Dec/2018. Problema de Estoque e Roteirização com Transbordo. Program Conclusion Project. Universidade Federal do Paraná.

Francine Luise Milian Ribas, Jul/2017. Métodos de Região de Confiança para Minimização Irrestrita. Program Conclusion Project. Universidade Federal do Paraná.

Oksana Heringer da Silva, Jul/2017. Métodos de Penalidade e o Lagrangiano Aumentado. Program Conclusion Project. Universidade Federal do Paraná.

Adrean Cebola, Jun/2017. Resolução de Programas Lineares com Método de Pontos Interiores. Program Conclusion Project. Universidade Federal do Paraná.

Carlos Henrique Venturi Ronchi, May/2017. Estudo Matemático de Reconhecimento de Caracteres. Program Conclusion Project. Universidade Federal do Paraná.