Alejandro Flores Lamas

At CICESE, I acquired essential skills that have contributed significantly to my professional development, including time management, communication, and teamwork. My experience as a PhD student at CICESE was immensely gratifying and played a pivotal role in shaping my career.

• Supervisor: Dr. José Alberto Fernández-Zepeda.

While at the Autonomous University of Zacatecas, I gained proficiency in various programming languages, ranging from low-level machine language to high-level languages such as Java. Also, during my time at the University, I cultivated a keen interest in the analysis and design of algorithms.

At the University of Manitoba, I enriched my technical skills while acquiring valuable soft skills. I had the opportunity to immerse myself in diverse social settings, gaining insights into professional ethics and work culture. This experience helped me explore different career paths, making it a crucial milestone in my professional development journey.

The University of Belize allowed me to experience, for the first time, an international and multicultural environment with a rich cultural exchange. This exposure broadened my understanding of the world and equipped me with skills to navigate and overcome language and communication barriers.

This research involves developing and applying graph algorithms to accurately reconstruct the evolutionary histories of gene families, enabling a deeper understanding of their origins, diversification, and the genetic relationships among different species.

• Line of research: Algorithms for reconstructing evolutionary histories of gene families.
• Supported by: The Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav).

The focus of this project was on the handling of strings in software systems. Existing research relying on regular expressions to study strings often overlooks important features in modern programming languages. This project bridges such a gap by enhancing theoretical understanding and practical implementation.

• Line manager: Prof. Matthew Hague.
• Project: String Constraint Solving with Real-World Regular Expressions.
• Supported by: The Engineering and Physical Sciences Research Council, EPSRC [EP/T00021X/1].

The primary objective of the CONACYT Public Centers’ Artificial Intelligence Consortium is to foster the development of highly skilled professionals in the field of Artificial Intelligence through applied research. The Consortium emphasises key areas such as urban mobility, healthcare, environmental risks, and mathematics for advancing Artificial Intelligence.

• Project: Algorithms for Artificial Intelligence
• Supported by: The Artificial Intelligence Consortium of CONACYT Public Centers, Mexico

This project addresses the problem of finding a $2$-packing set in some planar graphs in polynomial time, in both centralized and distributed environments. The main result is a parameterized algorithm that computes a maximum $2$-packing set on a 1-outerplanar graph in linear time.

• Project: Feasibility study to solve the maximum $2$-packing set problem in polynomial time in outerplanar graphs (translated from Spanish)
• Supported by: CONACYT, National Scholarship for doctoral studies, Mexico

This work presents an approach to find a maximum $2$-packing set in a cactus graph. The main result is an algorithm that decomposes the input graph into biconnected components to form a tree, then it solves each component individually and merges partial solutions to find such a set.

• Project: An algorithm to find a maximum $2$-packing set in a cactus graph (translated from Spanish)
• Supported by: CONACYT, National Scholarship for master’s studies, Mexico

Taolue Chen, Riccardo De Masellis, Alejandro Flores-Lamas, Matthew Hague, Zhilei Han, Denghang Hu, Anthony W. Lin, Oliver Markgraf, Philipp Rümmer and Zhilin Wu. “The OSTRICH String Solver”. 2023. Available at: The 18th International Satisfiability Modulo Theories Competition.

Ignacio Garcia Labari, Alejandro Flores Lamas, Flavio E. Spetale, Pilar Bulacio and Elizabeth Tapia. “Transformer-Based Refinement of Pseudoknot Predictions in RNA Secondary Structures”. 2024. Available at: IEEE Biennial Congress of Argentina (ARGENCON).

Alitzel López Sánchez, José Antonio Ramírez-Rafael, Alejandro Flores-Lamas, Maribel Hernández-Rosales and Manuel Lafond. “The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees”. 2024. Available at: 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Also available at: arXiv.

Joel Antonio Trejo-Sánchez, Francisco A. Madera-Ramírez, José Alberto Fernández-Zepeda, José Luis López-Martínez and Alejandro Flores-Lamas . “A fast approximation algorithm for the maximum $2$-packing set problem on planar graphs”. 2022. Available at: Optimization Letters

Taolue Chen, Alejandro Flores-Lamas, Matthew Hague, Zhilei Han, Denghang Hu, Shuanglong Kan, Anthony W. Lin, Philipp Rümmer and Zhilin Wu. “Solving string constraints with Regex-dependent functions through transducers with priorities and variables”. 2022. Available at: Proceedings of the ACM on Programming Languages Vol. 6, Issue. POPL

Alejandro Flores-Lamas, José Alberto Fernández-Zepeda and Joel Antonio Trejo-Sánchez. “A distributed algorithm for a maximal $2$-packing set on Halin graphs”. 2020. Available at: Journal of Parallel and Distributed Computing

Joel Antonio Trejo-Sánchez, Andrés Vela-Navarro, Alejandro Flores-Lamas, José Luis López-Martínez, Carlos Bermejo-Sabbagh and Nora Leticia Cuevas-Cuevas. “Fast random cactus generation”. 2018. Available at: International Conference on Supercomputing in Mexico, ISUM 2018

Alejandro Flores-Lamas, José Alberto Fernández-Zepeda and Joel Antonio Trejo-Sánchez. “Algorithm to find a maximum $2$-packing set in a cactus”. 2018. Available at: Theoretical Computer Science

José Alberto Fernández-Zepeda, Alejandro Flores-Lamas, Matthew Hague and Joel Antonio Trejo-Sánchez. “A dynamic programming algorithm for a maximum $s$-club set on trees. 2024. Submitted to: Discrete Applied Mathematics, transferred to: The European Journal of Operational Research (EJOR).

Alitzel López Sánchez, José Antonio Ramírez-Rafael, Alejandro Flores-Lamas, Maribel Hernández-Rosales and Manuel Lafond. “The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees”. 2024. Submitted to: Algorithms for Molecular Biology.

Garcia Labari Ignacio, Flores-Lamas Alejandro, Spetale Flavio, Bulacio Pilar and Tapia Elizabeth. “ClaraFold: Prediction of RNA secondary structures including pseudoknots using Transformers”. 2025. Submitted to: Scientific Reports - Springer Nature.

José Alberto Fernández-Zepeda, Alejandro Flores-Lamas, Tadeo Alán Gutiérrez-Medina and Joel Antonio Trejo-Sánchez. “A simple algorithm for decomposing geometric Halin graphs”. 2025. In preparation, to be submitted to: Journal of Parallel and Distributed Computing.

Ignacio Garcia Labari, Alejandro Flores Lamas, Flavio E. Spetale, Pilar Bulacio and Elizabeth Tapia. “Transformer-Based Refinement of Pseudoknot Predictions in RNA Secondary Structures”. 2024. Presented at: RECOMB-CG 2024.

Ignacio Garcia Labari, Alejandro Flores Lamas, Flavio E. Spetale, Pilar Bulacio and Elizabeth Tapia. “Transformer-Based Refinement of Pseudoknot Predictions in RNA Secondary Structures”. 2024. Presented at: 20º Congresso Brasileiro de Bioinformática: X-Meeting 2024.