Van-Giang Trinh

I am a postdoctoral researcher at Polytech Marseille within Aix-Marseille University. I am a member of the LIRICA team, at the LIS laboratory. I defended my PhD at the Japan Advanced Institute of Science and Technology in November 2021. My research mainly focuses on theoretical computer science, artificial intelligence, and computational systems biology. You can take a look at my complete curriculum vitae.

Research links: Google Scholar, DBLP, Orcid
Keywords: Boolean network, attractor, Petri net, answer set programming, logical modeling, control theory
Contact: trinh.van-giang[at]lis-lab.fr

Research

My PhD has been supervised by Prof. Kunihiko Hiraishi. It has been conducted at the Japan Advanced Institute of Science and Technology (Nomi, Ishikawa, Japan). I worked on attractor detection and optimal control of Boolean networks. The manuscript can be found here and the defense slides here. Currently, I focus on Boolean networks, Petri nets, answer set programming, and their applications to modeling, analysis, and control of biological systems.

Submitted

  • Static analysis of logic programs via Boolean networks
    Van-Giang Trinh and Belaid Benhamou.
    International Joint Conference on Artificial Intelligence, 2024, submitted

  • mpbn: a simple tool for efficient edition and analysis of elementary properties of Boolean networks.
    Van-Giang Trinh, Belaid Benhamou, and Loïc Paulevé.
    Bioinformatics, 2023, under revision

  • Computing attractors of large-scale asynchronous Boolean networks using minimal trap spaces.
    Van-Giang Trinh, Belaid Benhamou, Tarek Khaled, and Kunihiko Hiraishi.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023, under review

International Journals

2023

  • Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding.
    Van-Giang Trinh, Belaid Benhamou, and Sylvain Soliman.
    Theoretical Computer Science (TCS), 2023 [TCS - paper]

  • Using answer set programming to deal with Boolean networks and attractor computation: Application to gene regulatory networks of cells.
    Tarek Khaled, Belaid Benhamou, and Van-Giang Trinh.
    Annals of Mathematics and Artificial Intelligence (AMAI), 2023 [AMAI]

  • Trap spaces of multi-valued networks: Definition, computation, and applications.
    Van-Giang Trinh, Belaid Benhamou, Thomas Henzinger, and Samuel Pastva.
    Bioinformatics, 2023 [Bioinformatics - paper - supplement]

2020

  • On attractor detection and optimal control of deterministic generalized asynchronous random Boolean networks.
    Van-Giang Trinh, and Kunihiko Hiraishi.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2020 [TCBB - paper - supplement]

  • An FVS-based approach to attractor detection in asynchronous random Boolean networks.
    Van-Giang Trinh, Tatsuya Akutsu, and Kunihiko Hiraishi.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2020 [TCBB - paper]

  • A study on attractors of generalized asynchronous random Boolean networks.
    Van-Giang Trinh, and Kunihiko Hiraishi.
    IEICE TRANSACTIONS on Fundamentals of Electronics, Communications and Computer Sciences, 2020 [IEICE]

2016

  • Modelling and congestion detection of wireless sensor networks: A concurrent-based approach using coloured Petri nets.
    Van-Giang Trinh, Le Ngoc Kim Khanh, Bang Ngoc Bao Tam, Tram Loi Quan, Bui Hoai Thang, and Quan Thanh Tho.
    International Journal of Applied Information Systems (IJAIS), 2016 [IJAIS]

2014

  • Assisting students in finding bugs and their locations in programming solutions.
    Pham Hong Long, Van-Giang Trinh, Dinh Hoang Mai, Mai Phuong Nam, Quan Thanh Tho, and Ngo Quang Hung.
    International Journal of Quality Assurance in Engineering and Technology Education (IJQAETE), 2014 [IJQAETE]

International Conferences

2024

  • Scalable enumeration of trap spaces in Boolean networks via answer set programming
    Van-Giang Trinh, Belaid Benhamou, Samuel Pastva, and Sylvain Soliman.
    Annual AAAI Conference on Artificial Intelligence, 2024, to appear, oral presentation [paper - supplement]

2023

  • Efficient enumeration of fixed points in complex Boolean networks using answer set programming
    Van-Giang Trinh, Belaid Benhamou, and Sylvain Soliman.
    In CP 2023 (LIPIcs, volume 280, pages 35:1–35:19) [LIPIcs - paper] [slides]

  • Trap spaces of multi-valued networks: Definition, computation, and applications
    Van-Giang Trinh, Belaid Benhamou, Thomas Henzinger, and Samuel Pastva.
    In ISMB/ECCB 2023 (OUP, 39(Supplement_1), i513–i522) [OUP - paper - supplement] 

2022

  • Computing attractors of large-scale asynchronous Boolean networks using minimal trap spaces
    Van-Giang Trinh, Kunihiko Hiraishi, and Belaid Benhamou.
    In ACM-BCB 2022 (ACM, pages 1–10) [ACM - paper] [slides]

  • Minimal trap spaces of logical models are maximal siphons of their Petri net encoding
    Van-Giang Trinh, Belaid Benhamou, and Sylvain Soliman.
    In CMSB 2022 (Springer, pages 158–176) [Springer] [slides]

2021

  • An improved method for finding attractors of large-scale asynchronous Boolean networks
    Van-Giang Trinh, and Kunihiko Hiraishi.
    In CIBCB 2021 (IEEE, pages 1–9) [IEEE] [slides]

2019

  • Algorithms for finding attractors of generalized asynchronous random Boolean networks
    Van-Giang Trinh, and Kunihiko Hiraishi.
    In ASCC 2019 (IEEE, pages 67–72) [IEEE] [slides]

2017

  • Probabilistic modelling for congestion detection on wireless sensor networks
    Le Ngoc Kim Khanh, Van-Giang Trinh, Bui Hoai Thang, and Quan Thanh Tho.
    In CoDIT 2017 (IEEE, pages 0190–0195) [IEEE]

2016

  • Fast-and-Fit: An intelligent auto-pricing system for airlines travel agencies
    Van-Giang Trinh, Nguyen Duc Khoan, Nguyen Duy Khuong, Vu Phu Thuc, and Quan Thanh Tho.
    In SAI 2016 (Springer, pages 853–865) [Springer]

  • Modeling and analysing Boolean networks by coloured Petri nets
    Van-Giang Trinh, Kunihiko Hiraishi, and Quan Thanh Tho.
    In IEICE Proceedings Series 2016 (IEICE, 61(4447)) [IEICE]

2015

  • Reusing symbolic observation graph for efficient model checking
    Bao Trung Pham Duy, Van-Giang Trinh, Le Dinh Thuan, and Quan Thanh Tho.
    In KSE 2015 (IEEE, pages 250–255) [IEEE]

International Workshops

2020

Talks & Seminars

  • Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding
    Lifeware Seminar, 30 November 2023.
    INRIA, Saclay. [slides]

  • Efficient enumeration of fixed points in complex Boolean networks using answer set programming
    IRISA Seminar, 30 November 2023.
    IRISA, Rennes. [slides]

  • Efficient enumeration of fixed points in complex Boolean networks using answer set programming
    LIRICA Seminar, 20 November 2023.
    LIS, Marseille. [slides]

  • Efficient enumeration of fixed points in complex Boolean networks using answer set programming
    Demi Journées du Pôle Calcul on Artificial Intelligence, 15 June 2023.
    LIS, Marseille. [slides]

  • Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding
    CANA Seminar, 30 May 2023.
    LIS, Marseille. [slides]

  • An approach based on ASP and Petri nets for the calculation of attractors in Boolean networks
    Journées BioLogique BIOSS/CAVIAR, 25 May 2023.
    LIP6, Paris. [slides]

  • Efficient enumeration of minimal trap spaces in large-scale Boolean networks of gene networks
    Journées Scientifiques du LIS, 23 May 2023.
    Carry le Rouet. [slides]

  • Minimal trap spaces of Boolean models are maximal siphons of their Petri net encoding
    LIRICA Seminar, 17 October 2022.
    LIS, Marseille. [slides]

  • An FVS-based approach to attractor detection in asynchronous Boolean networks
    LIRICA Seminar, 28 June 2021.
    Virtual. [slides]

Miscellaneous

Friends and Collaborators

Useful links