Curriculum vitae

Education

• 2016-2019: Baccalaureate, Le Quy Don High school for the gifted students.
• 2019-2024: B.S. in Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city.

Work experience

• 2019 - now: Research internship - Organic Chemistry Department
  • Methodology development
    • MolUtil: molecular standardization, featurization, medicinal chemistry filtration, and chemical space visualization (incorporate with RDKit)
    • mlqsar: QSAR-machine learning pipeline development incorporate with post hoc Wilcoxon for decision making
    • MolAD: applicability domains detection with convex hull
    • MoleculeClustering: molecules clustering with Butina algorithms and diverse subsets selection
    • Mol2DSimi: molecular similarity searching, validation, and comparison between different fingerprints
  • Application of AI methods in drug discovery
    • HIV-1 integrase (Master thesis): QSAR pipeline for data type selection and model building, pharmacophore modeling with ensemble methods, alphafold2 for protein curation and benchmarking molecular docking packages (Vina, Smina, Qvina2, Vina GPU, Autodock GPU)
    • ALK: ANN model development, 3D-Image-QSAR using CNN with 6 times rotation, GNN with pytorch geometric
  • Duties included:
    • Experienced in silico techniques by collaborating in lab seminars and academic projects.
    • Collaborated with labmates to conduct 2D-QSAR utilizing MOE software to screen anticancer bioactivities of some isothiocyanate derivate.–>
• Supervisor:
  • Assoc.Prof.Truong Ngoc Tuyen, PhD
  • MS. in Pharmacy. Phan Tieu Long

Skills

• Programming: Python
• Cheminformatics: RDKit, MOE, Pymol
• Data science
  • Data analysis: visualization (seaborn, matplotlib, plotly), linear algebra, calculus, probability and statistics (numpy, pandas)
  • Data mining: data pipeline development including handle low variance features, missing values, univariate and multivariate outliers; conduct statistical test for decision making in model selection using cross-validation
  • Machine learning: scikit-learn, imblearn, XGBoost, CatBoost, optimization (grid search and bayesian search)
  • Deep Learning: Pytorch, Tensorflow, Keras, CNNs, RNNs, GNN.
• Process Automation
• Personal skill: Problem solving, crictical thinking, communication

Language

• English: Full Professional Proficiency
• Vietnamese: Native

Course

1. Python for developers - VTC Academy
2. AI specialist and machine enygineer - VTC Academy

Publications

Study on the effect of molecular fingerprints on the performance of machine learning model predicting hiv integrase bioactivty

Tieu Long Phan, Thanh An Pham, Van Thinh To, Bao Vy Doan Ngoc, Hoang Son Le Lai, Ngoc Tuyen Truong (2023). Study on the effect of molecular fingerprints on the performance of machine learning model predicting HIV integrase bioactivty. Vietnamese Pharmacy Journal (Accepted).

Honours

• 2019 - Second prize of Chemistry for excellent national students
• 2018 - First prize of Chemistry in the Northern region
• 2018 - Second prize of Chemistry for excellent national students
• 2017 - First prize of Chemistry in the Southern region

References

• Assoc.Prof.Truong Ngoc Tuyen, PhD
  • Position: Head of Department of Organic Chemistry, Pharmacy Faculty, University of Medicine and pharmacy at Ho Chi Minh city
  • Email: truongngoctuyen@ump.edu.vn
• MS. in Pharmacy. Phan Tieu Long
  • Position: Pursing Ph.D position in cheminformatics/machine learning
  • Email: ptlong.chcndpbc20@ump.edu.vn