Ngoc-Quang Nguyen

About

I am currently a Research Scientist on the AI team at AIgensciences Inc. Previously, I was a full-time researcher at DMIS, where I had the privilege of working under the guidance of Professor Jaewoo Kang at Korea University.

Prior to this, I obtained my B.Eng. degree from Vietnam National University, Hanoi. I also completed my M.S. in Computer Science and Engineering at Gachon University, under the supervision of Professor Sangwoong Lee.

My research primarily focuses on integrating data science, artificial intelligence, machine learning, and formal reasoning to accelerate bio/medical science in the service of human health.

My recent research interests include:

• Generative AI (Diffusion, Flow-matching models) for peptide/cyclic-peptide and antibody design tasks
• 3D geometric information learning
• Molecular Dynamics
• Addressing workplace boreout

News

• [Apr(21~27). 2026]   We presented our PepTri work in Rio de Janeiro .
• [Jan(26). 2025]   PepTri: Tri-Guided All-Atom Diffusion for Peptide Design via Physics, Evolution, and Mutual Information was accepted to ICLR 2026!
• [Jun(23). 2025]   EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions was accepted by the Journal of Chemical Information and Modeling!
• [Feb(6). 2025]   I joined the AI team at AIgensciences Inc.!
• [Aug(23). 2024]   I received my Ph.D. degree from the CSE department at Korea University!
• [May(23). 2024]   I successfully defended my dissertation entitled "Multimodal Deep Learning Approaches for Compound-Protein Interaction Prediction Tasks in Drug Discovery."
• [Jun(28). 2024]   MolPLA: A Molecular Pretraining Framework was published in Bioinformatics!
• [Feb. 2024]   I received a BK21 Graduate Innovation Project Scholarship .
• [Dec. 2023]   The MulinforCPI paper was accepted to Briefings in Bioinformatics.
• [Nov. 2023]   I gave an invited talk at the Mogam Institute for Biomedical Research.
• [Feb. 2023]   I received an Excellent Paper Scholarship.
• [Nov(23). 2022]   Perceiver CPI was published in Bioinformatics!

Research Experience

AIgen Sciences Seoul, Korea

AI Research Scientist Feb. 2025 - Present

Team Leader: Sunkyu Kim, Ph.D.

DMIS Lab Seoul, Korea

Postdoc Sep. 2024 - Jan. 2025

Ph.D. Student Sep. 2020 - Sep. 2024

Advisor: Jaewoo Kang, Ph.D.

Colleague: Mujeen Sung, Ph.D. Letter of recommendation

AI Lab, Voronoi Inc. Incheon, Korea

Machine Learning and AI Researcher Aug. 2019 - Jul. 2020

Manager: Hyunseok Kim

Colleague: Tran Le Anh Tuan, Ph.D. Letter of recommendation

PRML LabGyeonggi, Korea

M.S. Student Sep. 2017 - Jul. 2019

Advisor: Sangwoong Lee, Ph.D. Letter of recommendation

Publications

Most recent publications are available on Google Scholar.

• Selected
• All

PepTri: Tri-Guided All-Atom Diffusion for Peptide Design via Physics, Evolution, and Mutual Information

Ngoc-Quang Nguyen; Jaeyoon Jung; Seijung Kim; Sunkyu Kim; Jaewoo Kang

The Fourteenth International Conference on Learning Representations (ICLR), 2026

Paper Code

EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions

Ngoc-Quang Nguyen; Jaewoo Kang

Journal of Chemical Information and Modeling(JCIM), 2025

Paper Code

MulinforCPI: enhancing precision of compound-protein interaction prediction through novel perspectives on multi-level information integration

Ngoc-Quang Nguyen; Sejeong Park; Mogan Gim; Jaewoo Kang

Briefings in Bioinformatics, 2023

Paper Slides Code

PerceiverCPI: A nested cross-attention network for compound-protein interaction prediction

Ngoc-Quang Nguyen; Gwanghoon Jang; Hajung Kim; Jaewoo Kang

Bioinformatics, 2022

Paper Slides Code

PepTri: Tri-Guided All-Atom Diffusion for Peptide Design via Physics, Evolution, and Mutual Information

Ngoc-Quang Nguyen; Jaeyoon Jung; Seijung Kim; Sunkyu Kim; Jaewoo Kang

The Fourteenth International Conference on Learning Representations (ICLR), 2026

Paper Code

EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions

Ngoc-Quang Nguyen; Jaewoo Kang

Journal of Chemical Information and Modeling(JCIM), 2025

Paper Code

MolPLA: A Molecular Pretraining Framework for Learning Cores, R-Groups and their Linker Joints

Mogan Gim; Jueon Park; Soyon Park; Sanghoon Lee; Seungheun Baek; Junhyun Lee;Ngoc-Quang Nguyen; Jaewoo Kang

ISMB (Intelligent Systems for Molecular Biology), 2024

Paper

MulinforCPI: enhancing precision of compound-protein interaction prediction through novel perspectives on multi-level information integration

Ngoc-Quang Nguyen; Sejeong Park; Mogan Gim; Jaewoo Kang

Briefings in Bioinformatics, 2023

Paper Slides Code

PerceiverCPI: A nested cross-attention network for compound-protein interaction prediction

Ngoc-Quang Nguyen; Gwanghoon Jang; Hajung Kim; Jaewoo Kang

Bioinformatics, 2022

Paper Slides Code

Contour-aware Polyp Segmentation in Colonoscopy Images using Detailed Upsampling Encoder-Decoder Networks

Ngoc-Quang Nguyen; Duc My Vo; Sang-Woong Lee

IEEE Access, 2020

Paper

Robust Boundary Segmentation in Medical Images Using a Consecutive Deep Encoder-Decoder Network

Ngoc-Quang Nguyen; Sang-Woong Lee

IEEE Access, 2019

Paper Slides Code

Classification of breast cancer histology images using incremental boosting convolution networks

Duc My Vo; Ngoc-Quang Nguyen; Sang-Woong Lee

Information Sciences, 2018

Paper

Colorectal segmentation using multiple encoder-decoder networks in colonoscopy images

Ngoc-Quang Nguyen; Sang-Woong Lee

AIKE, Laguna Hills, 2018

Paper

ISIC 2017 skin lesion segmentation using deep encoder-decoder network

Ngoc-Quang Nguyen

Preprint ISIC 2017 challenge, 2018

Paper

Academic Services

• Reviewer for: NeurIPS, Bioinformatics, IEEE Journal of Biomedical and Health Informatics, IEEE-ACM Transactions on Computational Biology and Bioinformatics, Sensors.

Vitæ

Full CV: PDF.

Boreout Reads

• Vận động tạo sáng tạo (Vietnamese) || Does Physical Activity Foster Creativity? (English)
• Điều gì dẫn đến ngán việc? (Vietnamese) || What Causes Boreout? (English)
• Ngán Việc (Vietnamese) || What is Boreout? (English)

• AIGEN Sciences Feb 2025 – Present

  AI research scientist
  AI team, AIGEN Sciences (https://www.aigensciences.com/)
• Korea University Sep 2020 – Jan 2025

  Ph.D, Postdoc(Sep 2024-Jan 2025), Computer Science and Engineering
  Advisor: Jaewoo Kang, DMIS Lab (https://dmis.korea.ac.kr/)
• Voronoi Inc. Aug. 2019 - Jul. 2020

  Machine learning and AI researcher
  AI team (https://voronoi.io/)
• Gachon University Sep. 2017 - Jul. 2019

  MSc, Computer Science and Engineering
  Advisor: Sangwoong Lee, PRML lab (http://pr.gachon.ac.kr/)
• NTQ Solution Jun 2015 - Sep 2015

  Robotic engineering intern
  R&D lab
• Vietnam National University Sep. 2012 - Mar. 2017

  BEng, Mechanical Engineering
  Hanoi, Vietnam