CURRICULUM VITAE

Education

• Sep 2023 - Aug 2024: Msc. BioHealth Engineering
  • Faculty of Medicine and Pharmacy – Grenoble Alpes University, France
  • GPA (1^st semester): 17.19/20 - top 2 of ranking - Very good classification
• Aug 2018- Aug 2023: Pharmacy Degree
  • Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, Vietnam
  • GPA: 3.30/4.0 - top 3% of ranking - Very good classification
• 2015-2018: Nguyen Binh Khiem High school for the gifted
  • Mathematics class

Research Experience

• Master Internship
  • Supervisor: Prof. Achène Boumendjel, PhD, RadioPharmaceutiques Bioclinique Laboratory (LRB), UGA, Inserm U1039.
  • Co-supervisor: Asst. Prof. Viet-Khoa Tran-Nguyen, PhD, Université Paris Cité, CNRS UMR8251, INSERM U1133, F-75013 Paris, France
  • Jan 2024 - July 2024: Master thesis
    • Exploring cutting-edge molecular modeling and deep learning models to develop novel drug candidates antifungal therapies, targeting the Cdr1 transporter.
    • Harnessing the power of 3D-Graph Neural Networks (3D-GNN) trained on multiple conformations, specifically utilizing advanced techniques like Message Passing Neural Network (MPNN) or Graph Attention Network (GAT). This enables the encoding of complex molecular structures, and extraction of local chemistry information, contributing to a comprehensive understanding of the compounds under investigation.
    • Integrating multiple ligand-based structural representation conjugating multi-instance 3D-GNN to create a robust ensemble classification model.
    • Identifying the most promising candidates through computational analyses, which will be synthesized and rigorously tested using bioassays.
    • HuggingFace demo: EMCIP: An Ensemble Model for Cdr1 Inhibitor Prediction
• Visiting Researcher
  • Aug 2024 - Present: Visiting researcher at the Bioinformatics Laboratory, University of Leipzig, Germany
    • Collaborating with PhD(c). Tieu-Long Phan on topics related to the ITN project entitled Training Alliance for Computational systems chemistry – TACsy.
• Lab assistant - Core member of MedAI laboratory, Department of Organic Chemistry, Faculty of Pharmacy, UMP
  • Supervisor: Assoc. Prof. Truong Ngoc Tuyen, PhD, Head of Department of Organic Chemistry, Faculty of Pharmacy.
  • Jan 2023 - Aug 2023: Graduation thesis (Mark: 9.9/10.0).
    • Development and integration of advanced Artificial Intelligence (AI) including Machine Learning, Artificial Neural Network (ANN), GNN in conjunction with consensus molecular docking for the prediction of potent Anaplastic Lymphoma Kinase (ALK) inhibitors.
    • Employing data-centric machine learning methodologies to ascertain the most effective molecular representation.
    • Executing an ANN model that leverages the identified optimal molecular representation.
    • Conducting an Ensemble-GNN utilizing the Pytorch Geometric and DeepChem library. This ad- vanced model harnesses the power of graph-based data structures.
    • Integrating consensus docking models, including Autodock-GPU 1.5.3, Vina-GPU-2.0, GNINA 1.0, and XGBoost algorithm.
    • Combining the aforementioned AI models to formulate a comprehensive and meticulous funnel. This integrated system is designed to efficiently filter and identify potential ALK inhibitors, showcasing the synergy of diverse AI techniques in drug discovery.
  • Jan 2021 - Aug 2023: Cheminformatics tools development
    • MolUtil is an automated pipeline for molecular standardization, featurization into molecular descriptors and fingerprints, medicinal chemistry filtration, and chemical space visualization.
    • Mlqsar is a comprehensive automated QSAR workflow facilitating benchmark analysis and data category selection via rigorous statistical evaluation.
    • MolAD helps identify the applicability domain of QSAR models using Principal Components Analysis (PCA) and Multi Dimensional Scaling (MDS) for dimension reduction with the convex hull.
    • Statistical_test improves decision-making in comparing machine learning models’ performance by implementing statistical tests, including Bayesian estimation and the Wilcoxon signed-rank test.
  • Jan 2021 - Aug 2023: Implementation of AI in Drug Discovery projects
    • HIV-1 integrase*: QSAR pipeline for data type selection and model building.
    • SGLT2i: Comparison between MACCs and ECFP4 in QSAR model, pharmacophore optimization by query threshold.
    • PD-1/PD-L1 immune checkpoint: Similarity comparison among MACCs, ECFP4 and RDK5; similarity searching.
    • VEGFR-2: QSAR model development integrated into Junction Tree Variational Autoencoder (JT-VAE) network for molecules optimization.
    • Tubulin: Leveraging multiple molecular docking tools to study the Colchicine Binding Site.
  • 2018-2019: Organic Synthesis projects
    • Synthesis of curcumin analogs containing 1H-pyrazoles heterocycle from 3-nitrophenylhydrazine
    • Synthesis, biological activity evaluations of some 6-methyl-1H-benzimidazole derivatives.

Publications and Conferences

• Publications
  1. The-Chuong Trinh, Tieu-Long Phan, Tuyen Ngoc Truong et al. A Graph Neural Network Model Enables Accurate Prediction of Anaplastic Lymphoma Kinase Inhibitors Compared to Other Machine Learning Models. In 2023 15th International Conference on Knowledge and Systems Engineering (KSE), Proceedings of KSE 2023, October 18-20, 2023; IEEE Xplore, 2023; pp 1-6. DOI: 10.1109/KSE59128.2023.10299477.
  2. Tieu-Long Phan, The-Chuong Trinh, Tuyen Ngoc Truong et al. Novel machine learning approach toward classification model of HIV-1 integrase inhibitors. RSC Advances 14, 14506-14513, DOI: 10.1039/D4RA02231A
  3. Van-Thinh To, The-Chuong Trinh, Tuyen Ngoc Truong et al. Innovative virtual screening of PD-L1 inhibitors: the synergy of molecular similarity, neural networks and GNINA docking. Future Medicinal Chemistry, 1–12, DOI: https://doi.org/10.1080/17568919.2024.2389773
  4. The-Chuong Trinh, Tieu-Long Phan, Tuyen Ngoc Truong et al. Synergy of advanced machine learning and deep neural networks with consensus molecular docking for enhanced potency prediction of alk inhibitors. ChemRxiv. 2024; Preprint at doi:10.26434/chemrxiv-2024-xpfm1
  5. Gia-Bao Truong, The-Chuong Trinh, Tuyen Ngoc Truong, et al. Discovery of VEGFR-2 Inhibitors employing Junction Tree Variational Encoder with Local Latent Space Bayesian Optimization and Gradient Ascent Exploration. ChemRxiv. 2024; Preprint at doi:10.26434/chemrxiv-2024-18mqh
  6. Tieu-Long Phan, Xuan-Truc Tran Dinh, The-Chuong Trinh, Qui-Hien Nguyen, Tuyen Ngoc Truong, et al. Application of machine learning in virtual screening of HIV integrase inhibitors. Vietnam Journal of Medicine and Pharmacy, 2022, 52, 26-35.
• Conferences
  1. Tuyet-Minh Phan, Thao-Linh Song-Nguyen, The-Chuong Trinh, Tieu-Long Phan, Tuyen Ngoc Truong, et al. Development of a Machine Learning Model for the Synthesis and Molecular Docking Study of HIV Integrase Inhibitors. In Asian Federation for Pharmaceutical Conference 2023, AFPS Conference 2023 Program Book, Hanoi, Vietnam, Novemver 8-10, 2023; The Asian Federation for Pharmaceutical Sciences, 2023; pp 158-159.
  2. Gia-Bao Truong, Tieu-Long Phan, The-Chuong Trinh, Hoang-Son Lai-Le, Tuyen Ngoc Truong, et al. Innovative Exploration of VEGFR-2 Inhibitors in Chemical Space with Gradient Ascent and Junction Tree Variational Autoencoder. In Asian Federation for Pharmaceutical Conference 2023, AFPS Conference 2023 Program Book, Hanoi, Vietnam, Novemver 8-10, 2023; The Asian Federation for Pharmaceutical Sciences, 2023; pp 326-327.
  3. Hoang-Son Lai-Le, Tieu-Long Phan, Gia-Bao Truong, The-Chuong Trinh, Tuyen Ngoc Truong, et al. New Thorough Molecular Docking Approach: A Virtual Screening Study Targeting the Colchicine Binding Site. In Asian Federation for Pharmaceutical Conference 2023, AFPS Conference 2023 Program Book, Hanoi, Vietnam, Novemver 8-10, 2023; The Asian Federation for Pharmaceutical Sciences, 2023; pp 367-368.
  4. Van-Thinh To, Bao-Vy Doan Ngoc, The-Chuong Trinh, Tieu-Long Phan, Tuyen Ngoc Truong, et al. Application of Molecular Similarity and Artificial Neural Networks for PD-L1 inhibitors Virtual Screening. In the 9th International Electronic Conference on Medicinal Chemistry, November 1-30, 2023; MDPI: Basel, Switzerland.

Selected Honors and Awards

• Chemistry, Biology, and Health (CBH) Graduate School Grenoble Alpes University Scholarship.
• Certificate of outstanding contribution to Activities of The Vietnamese Student Association and the Youth Union.
• Student of 5 merits of University of Medicine and Pharmacy at Ho Chi Minh City.
• The trophy “White Blouse follows Uncle Ho’s orders”.
• Academic scholarship in University of top 10%: 8/10 terms.
• HOTAMIN scholarship for excellent student.
• Vietnam Institute for Advanced Study in Mathematics scholarship for Mathematics Entrance Valedic- torian.
• Certificate of class excellent in Australian National Chemistry Quiz
• Entrance Valedictorian of Nguyen Binh Khiem High School for the gifted.

Skills

• Programming Languages: Python, R.
• Code management tools: Git, Linux, OOP, Automated pipeline for HealthCare Projects.
• Cheminformatics: RDKit 2023.09.03, DeepChem 2.7.1, Pymol 2.5, MOE 2015.10, Autodock-GPU 1.5.3, Vina-GPU 2.0, GNINA 1.0, ChemDraw.
• Bioinformatics: Multi-Omics analysis.
• Machine learning/Deep learning: Scikit-learn 1.2.2, Imblearn 0.11.0, XGBoost 2.0.3, CatBoost 1.2.2, Pytorch 2.0, Pytorch Geometry 2.4.0, TensorFlow 2.0, Optuna 3.2.0.
• Data analysis: Statistic, Causal inference, Propensity score, Data visualization (Seaborn, Mat- plotlib).
• Organic synthesis: Basic organic synthesis, TLC, Columns chromatography.
• Personal skill: Problem solving, crictical thinking, communication

Languages

• Vietnamese: Native language
• English: Advanced level
• French: Basic level

Courses

1. Python for developers - VTC Academy
2. AI specialist and machine enygineer - VTC Academy
3. Computational medicine summer school - European Scientific Institute, Archamps, France
4. Cheminformatics summer school - University of Strasbourg, Strasbourg, France

Extracurricular Activities

• Sep 2020 - Dec 2020: Vice President of the Organizing Committee of the Sports Festival.
• Jun 2019 - Sep 2019: The Organizing Committee of the Connection Ceremony.
• 2019 - 2021: Head of Human Resources department of Pharmacy English Club.

References

• Prof. Achène Boumendjel, PhD
  • Position: RadioPharmaceutiques Bioclinique Laboratory (LRB), UGA, Inserm U1039.
  • Email: Ahcene.Boumendjel@univ-grenoble-alpes.fr
• Assoc. Prof. Truong Ngoc Tuyen, PhD
  • Position: Head of the Department of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city.
  • Emal: truongtuyen@ump.edu.vn
• Assoc. Prof. Viet-Khoa Tran-Nguyen, PhD
  • Position:Assistant Professor about Cheminformatics and Bioinformatics, Université Paris Cité.
  • Email: viet-khoa.tran-Nguyen@u-paris.fr